ACROSS THE NIH, 19 INSTITUTES OF 27 TOTAL THAT NOW FUND MICROBIOME RESEARCH. I FORMED THIS FIVE YEARS AGO BECAUSE I SAW THE RESEARCH OCCURRING, WE FELT WE NEEDED TO COORDINATE. THE LAST FOUR OR FIVE YEARS, BUT THIS ONE IS PROBABLY GOING TO TOP EVERYTHING. WE WANT THIS THREE-DAY WORKSHOP, BEING WEBCAST, SO THERE'S AN OFF-SITE AUDIENCE AS WELL, WE WANT THIS WORKSHOP TO ACCOMPLISH TWO MAJOR THINGS. IT IS THE END OF THE HUMAN MICROBIOME PROJECT, SO WE REALLY WANT TO ASSESS WHAT HAVE WE ACCOMPLISHED, WHAT ARE THE LEGACY RESOURCES AND SO ON, HOW ARE THE DATA BEING USED, TOOLS BEING USED, PROBABLY MORE IMPORTANTLY WE WANT TO ASK THE QUESTION BECAUSE THIS IS A GROWING FIELD, WHAT ELSE DO WE NEED TO DO, SO THE OVERALL THEME FOR ALL THREE DAYS, THE WAY THE TALKS ARE STRUCTURED, THE WAY THE ROUNDTABLES ARE STRUCTURED, EVEN THE WAY THE JOINT QA SESSIONS ARE STRUCTURED TO HAVE US REVISIT OVER AND OVER AGAIN FROM THE COMMUNITY GAPS AND CHALLENGES FOR THIS FIELD. OKAY. BECAUSE WE HAVE 19 INSTITUTES REPRESENTED HERE, WE'RE ALL GOING TO TAKE THIS INFORMATION BACK TO OUR OWN HOME INSTITUTION AND HOPEFULLY UTILIZE IT TO FORM POSSIBLY NEW FOAs OR SIMPLY TO DIRECT THE DIALOGUE WITHIN OUR OWN INSTITUTE. OKAY. SO I JUST WANT TO TAKE A COUPLE MINUTES TO DESCRIBE IN MORE DETAIL WHAT I JUST QUICKLY OUTLINED. I SEE THAT ALL THE SEATS ARE NOT FILLED BUT I THINK SOME PEOPLE ARE FILTERING IN. SO JUST COME IN AT ANY POINT IN TIME. I WANT TO COVER THE GOALS AND PURPOSES OF THE WORKSHOP AND WHAT THE CHARGE IS TO YOU AS PARTICIPANTS. LET ME TAKE A MOMENT. DO YOU SEE THE WATERMARK IN THE BACK? TALK ABOUT COMMITTEE ENGAGEMENT. THIS IS A SCIENTIST AT JANELIA FARMS, MARRIED TO A COMMITTEE MEMBER, AN ARTIST BY HOBBY, INSPIRED TO CREATE THIS GRAPHIC OF THE MICROBIOME FAMILY, EVERY OUTLINE OF ALL THREE PEOPLE IN THE GRAPHIC IS MADE UP OF MICROBES. ISN'T THAT COOL? SO I MENTION THE TRANS-NIH MICROBIOME WORKING GROUP. WE'VE BEEN IN BUSINESS FOR ABOUT FOUR YEARS. NOW IT REPRESENTS 19 INSTITUTES, CENTERS AND OFFICES WHICH SUPPORT HUMAN MICROBIOME RESEARCH IN THE EXTRAMURAL PROGRAMS. EVEN THOUGH WE HAVE A LOT OF INTRAMURAL PEOPLE HERE AND CALLING INTO THE WEBCAST, BECAUSE WE'RE PROGRAM DIRECTORS, WE ACTUALLY DEDICATED MOST OF OUR ATTENTION TO TRYING TO HELP SUPPORT HUMAN MICROBIOME RESEARCH WITH THE EXTRAMURAL COMMUNITY. WE'VE BEEN VERY BUSY THIS PAST YEAR, NOT ONLY HAS IT TAKEN US A YEAR-AND-A-HALF, A YEAR-AND-A-HALF TO ORGANIZE THIS WORKSHOP, BUT AT THE SAME TIME WE'RE CONDUCTING AN IN-DEPTH PORTFOLIO ANALYSIS OVER FIVE YEARS OF HUMAN MICROBIOME RESEARCH AT THE NIH IN THE EXTRAMURAL PROGRAM, AND ARE WORKING TO GET IT PUBLISHED. IF ALL GOES WELL, WE'RE GOING TO SUBMIT IT TO CELL HOST AND MICROBE FOR CONSIDERATION. LET ME TRACE QUICKLY THE KIND OF LIKE MOMENTUM OR IMPETUS FOR THE WORKSHOP. YOU KNOW ABOUT THE HUMAN MICROBIOME PROJECT. IT'S BEEN A 10-YEAR COMMUNITY RESOURCE ACTIVITY. RESOURCES LIKE BUILDING AN ENTIRE RESEARCH COMMITTEE IS ONE EXAMPLE OF RESOURCE, RESOURCES LIKE REFERENCE DATASETS, COMPUTATIONAL TOOLS, COMMON FUND AT THE NIH TO CATALYZE AND KICK START THE FIELD. YOU CAN SEE INSTITUTES AND MEDICAL CENTERS THAT HAVE BEEN INVOLVED. AT THE SAME TIME, I SAW -- WE SAW -- GROWTH OF HUMAN MICROBIOME RESEARCH SUPPORT ACROSS THE NIH. FROM ABOUT 2012 TO PRESENT, WE'RE NOW SEEING OF THOSE 27 INSTITUTES, CENTERS AND OFFICES ALL OF THESE DIFFERENT INSTITUTES FUNDING THE AREA. NOW BECAUSE THEY EACH HAVE THEIR OWN MISSION, SOMETIMES THIS WORK CAN GET SILOED, UNINTENTIONALLY PERHAPS. AND IN OTHER CASES A GAP MIGHT BE IDENTIFIED BY ONE INSTITUTE CLEARLY GAP FOR ANOTHER, SO WE WANT TO HAVE THIS WORKSHOP BE A PLACE WHERE WE CAN REALLY COMPARE NOTES ABOUT WHAT WE THINK AS AN AGENCY IS NEEDED FOR THE FIELD, NOT ONLY EACH INSTITUTE. THE OTHER THING, YOU KNOW THIS IN 2015, IN THE OBAMA ADMINISTRATION, WHICH NOW FEELS LIKE A LIFETIME AGO, HE COMMISSIONED THE WHITE HOUSE'S OFFICE OF SCIENCE TECHNOLOGY COMMITTEE, THE FASTTRACK COMMITTEE, THIS IS THE LOGO OF LOGOS, COMMISSIONED TO DO AN ASSESSMENT OF PORTFOLIO ANALYSIS OF MICROBIOME RESEARCH ACROSS THOSE AGENCIES. NOW OBVIOUSLY NOT JUST HUMAN MICROBIOME RESEARCH, INCLUDED IN MICROBIOME RESEARCH WRIT LARGE, SO THE STUDY OF MICROBIAL COMMUNITIES USING MODERN 21ST CENTURY APPROACHES. WE PUBLISHED A PAPER IN THE INAUGURAL ISSUE OF THE JOURNAL NATURE AND MICROBIOLOGY AND SUMMARIZED WHAT WE CAME UP WITH, IDENTIFYING $900 MILLION ACROSS THE FEDERAL GOVERNMENT, OVER THREE FISCAL YEARS, ACROSS ALL OF THESE DIFFERENT AGENCIES. NIH HAD THE LION'S SHARE BUT WE'RE NOT THE ONLY GAME IN TOWN. SO THAT WAS A VERY IMPORTANT REALIZATION WHEN WE DID THIS DATA CALL, THIS ASSESSMENT. THAT BIRTHED THE NATIONAL MICROBIOME INITIATIVE AND WORKING GROUP, THE COMMITTEE THAT TALKS TO THE AGENCIES TO FIBBING OUT WHAT ARE WE DOING IN DIFFERENT AGENCIES AROUND A PARTICULAR TOPIC, HUMAN MICROBIOME RESEARCH. MANY MEMBERS ARE REPRESENTATIVES ON THE COMMITTEE AND AGREED TO PARTICIPATE IN ON THE PANEL TO TALK ABOUT WHAT THEY PERCEIVE AS GAPS, NEEDS AND CHALLENGES FOR THEIR AGENCIES AND ACROSS THE FEDERAL GOVERNMENT FOR HUMAN MICROBIOME RESEARCH. WE'RE IN 2017, MOMENTUM FROM 2012. TO REPEAT, THE PURPOSE IS TO TAKE STOCK OF NIH INVESTMENT IN THE HUMAN MICROBIOME PROJECT, VERY IMPORTANT ACTIVITY FOR THIS AGENCY, AND TO EVALUATE WHAT'S REALLY NEEDED TO ADVANCE THIS FIELD OVER THE NEXT DECADE. WE WANT ALL OF THE AUDIENCE MEMBERS, THE SPEAKERS, THE POSTER PRESENTERS, ROUND TABLE, AGENCY PANEL MEMBERS TO HELP US IDENTIFY AND DEVELOP THIS PRIORITY LIST OF KNOWLEDGE GAPS, TECHNICAL HURDLES, NEW APPROACHES AND RESEARCH OPPORTUNITIES. WE MIGHT SEE A THOUSAND DIFFERENT IDEAS OVER THESE NEXT THREE DAYS, OR WE MIGHT START TO SEE EMERGENT THINGS COMING UP AS WE TALK ABOUT GAPS, NEEDS AND CHALLENGES. LET'S SEE HOW IT GOES AT THE END OF THREE DAYS. FOR US AS AN AGENCY WE WANT TO USE THIS TO HELP INFORM DEVELOPMENT OF NOVEL PREVENTION AND TREATMENT STRATEGY BASED ON HOST MICROBIOME INTERACTION OVER THE NEXT DECADE. THIS IS A UBER WORKSHOP, I'LL CALL IT. IF YOU LOOK AT THE THEMES AND THE SESSIONS WITHIN EACH THEME, YOU CAN SEE THAT EACH OF THEM COULD BE A WORKSHOP ALONE, A STAND-ALONE WORKSHOP. THREE THEMES TODAY IS OVERVIEW AND APPROACHES. TWO IS INTERACTION OF MOST-MICROBIOME SYSTEM, AND THREE IS MICROBIOME INTERVENTION FOR MAINTAINING HEALTH AND DISEASE AND JOINT AGENCY PANEL. I WON'T READ THEM BUT THEY ARE STRUCTURED AROUND THE OVERALL THEME. DAY ONE, DAY TWO, DAY THREE. AND THEN FOR THE JOINT AGENCY THESE ARE THE AGENCIES, CDC, FDA, DoD, NIST, USDA, VA, CURRENTLY FUNDING HUMAN MICROBIOME RESEARCH ACTIVITIES OR PLANNING TO MOUNT THEM AND THAT'S WHY WE BROUGHT THEM TOGETHER. I BROUGHT TOGETHER A FEW OFFICES UNDER THE OFFICES OF DIRECTOR LIKE THE NATIONAL INSTITUTE FOR MINORITY HEALTH DISPARITIES, OFFICE OF RESEARCH ON WOMEN'S HEALTH, OFFICE ON AGE RESEARCH, THOSE OFFICES AND INSTITUTES HAVE PARTICULAR INTEREST IN THE MICROBIOME. IT'S SPEAKERS AND THE PARTICIPANTS WERE SELECTED FROM THIS POOL OF APPROXIMATELY 3500 INVESTIGATORS THAT THE TMWG IDENTIFIED WHEN WE WERE DOING THE PORTFOLIO ANALYSIS. WE SPENT MANY MONTHS DEBATING AND DISCUSSING WHO IS GOING TO BE A GOOD REPRESENTATIVE FOR THAT AREA OF THE MICROBIOME, AND WHO IS GOING TO BE GOOD ABOUT TALKING ABOUT WHAT'S NEEDED FOR THE FIELD. WE DIDN'T WANT SOMEONE, EXCUSE ME, TO STAND UP HERE AND TALK ABOUT THEIR OWN RESEARCH. WE WANTED THEM TO BE A REPRESENTATIVE OF THAT AREA IN THE LARGER MICROBIOME DISCIPLINE. SO A LOT OF EFFORT WENT INTO PICKING THE SPEAKERS AND PARTICIPANTS. THIS THING IS GOING TO GET PUBLISHED. WE HAD A CORE WRITING TEAM WITH THE EDITOR FOR CELL HOST AND MICROBE, GREG BUCK, CURTIS HUTTENHOWER, MIKE SNYDER AND OWEN WHITE. WE HAVE 16 DIFFERENT TMWG COMMITTEE MEMBERS TAKING NOTES ON GOOGLE DOCS AND OTHERWISE FOR THIS MEETING. AND ALL SPEAKERS WILL CONTRIBUTE TO THE REPORT. SO NO ONE IS GOING TO SPEAK FOR YOU. YOU'LL BE ABLE TO CONTRIBUTE AND EDIT THE FINAL REPORT. IT WILL INCLUDE A SUMMARY OF THE PRESENTATIONS, MAYBE MORE IMPORTANTLY IT WILL INCLUDE AN ASSESSMENT OF WHAT WAS IDENTIFIED AS THE CRITICAL GAPS, NEEDS AND CHALLENGES. IF ALL GOES WELL IT GETS SUBMITTED TO "CELL HOST AND MICROBE." THANK YOU, LAKSHMI, WHEREVER YOU'RE SITTING. THERE'S A LOT OF MOVING PARTS. SPEAKERS, PLEASE, PLEASE, PLEASE LOAD YOUR TALKS ON A FLASH DRIVE AND USE THE LAPTOPS THAT ARE ON THE PODIUM. WE HAVE A MAC AND P.C. THAT WILL SAVE US A LOT OF TIME. PLEASE MAKE SURE EVEN IF YOU DON'T HAVE A SLIDE CLOSE YOUR TALK BY ADDRESSING ONE, CRITICAL GAP, NEED OR CHALLENGE. WE'LL HAVE A ROUNDTABLE AT THE END OF EACH DAY. THOSE WHO TALK TODAY, PLEASE SIT IN THE FRONT SO IT MAKES IT EASIER FOR US TO ENTERTAIN QUESTIONS FROM THE AUDIENCE. AND THE OFF-SITE AUDIENCE. MODERATORS, YOU HAVE A BIG JOB. THIS IS A REALLY PACKED PROGRAM. PLEASE, PLEASE PLEASE KEEP YOUR SPEAKERS ON TIME. EACH OF YOU HAVE -- EXCEPT FOR KEYNOTES, EACH OF YOU HAVE 15 MINUTES. EACH SESSION HAS A JOINT Q-A SAYS, WE WON'T ENTERTAIN QUESTIONS AT THE END OF EACH TALK. WE'LL HAVE A JOINT Q-A SESSION AT THE END OF EACH SESSION. MODERATORS, YOU HAVE A BIG JOB OF KEEPING PEOPLE ON TIME, TIMERS HERE AND TIMERS ON THE TABLE. POSTER PRESENTERS PUT UP YOUR POSTERS. I SEE SOME UP ALREADY. UP BEFORE THE KEYNOTE TALK. YOU HAVE ALL DAY LONG. WE HAVE THREE DIFFERENT POSTER SESSIONS. PUT YOUR POSTER UP BEFORE THE KEYNOTE TALK, AND ADDRESS A GAP, NEED OR CHALLENGE AT THE ROUNDTABLE, IF YOU HAVEN'T ADDRESSED IN THE POSTER, BUT BE SURE TO TAKE YOUR POSTER DOWN AT THE END OF THE DAY, THE NEXT ROUND OF POSTERS HAVE TO GO UP. MORE HOUSEKEEPING, YOU ALREADY RECEIVED INFORMATION ABOUT THE PRE-ORDER INFORMATION FOR BOX LUNCHES. I THINK IT'S TOO LATE FOR TODAY, IF YOU DIDN'T PRE-ORDER FOR TODAY. BUT WE HAVE A CAFETERIA, AND A CAFE UP ON THE UPPER LEVEL, ON THIS END OF THE BUILDING. WE HAVE A TENT, A 250-PERSON TENT. THE IDEA BEHIND THAT, I KNEW IT WAS GOING TO BE OVERWHELMED, THIS BUILDING, IF WE TRIED TO GET EVERYBODY TO THE CAFETERIA. THERE'S NO GOOD SEATING EXCEPT IN THE CAFETERIA. SO WE HAVE A TENT ON THE LAWN. THAT'S FOR US. OKAY? 250 PEOPLE. AND YOUR BREAKS, YOUR LUNCHES, IT'S UP ALL THREE DAYS. EVEN AFTER THE WORKSHOP IN THE AFTERNOON IF YOU WANT TO KEEP TALKING GO TO THE TENT. ALL RIGHT? USE THIS AS A NETWORKING OPPORTUNITY TOO. DINNER OPTIONS, I DON'T KNOW IF YOU NOTICED BUT REGISTRATION TABLE IS ON THIS SIDE OF THE HALLWAY. ON THE OTHER SIDE IS A TABLE THAT SAYS MICROBIOME-RELATED MATERIALS. BUT ALSO ON THERE IS INFORMATION ABOUT LOCAL RESTAURANTS AND SO ON FOR THOSE WHO ARE FROM OUT OF TOWN. OH, I SHOULD SAY THIS. RESTROOMS, ANOTHER HOUSEKEEPING, ARE AT EITHER END, RIGHT? EITHER END OF THIS HALLWAY, THERE'S A SET OF RESTROOMS AT THE TOP. AND WE'RE WEBCASTING THIS ENTIRE THING LIVE. EACH DAY HAS ITS OWN URL. WE ALSO HAVE A TWITTER HASHTAG, HASHTAG #ETMICROBIOME. WE HAVE A G MAIL ACCOUNT, ETMICROBIOME@GMAIL.COM. AARON FROM THE COMMON FUND WHO DID A GREAT JOB OF ORGANIZING AND COORDINATING THE TWITTER ACCOUNT AND G MAIL, THE REASON WE'RE DOING THIS, WE WANT TO ALLOW PEOPLE TO LIVE TWEET THE WORKSHOP BUT ALSO WE WANT QUESTIONS FROM THE OFF-SITE AUDIENCE TO BE SENT TO US SO WE CAN ENTERTAIN THEM AT THE DAILY ROUND TABLES AND AGENCY PANELS. CUTOFFS ARE 4:30 FOR WEDNESDAY AND THURSDAY, 12 NOON FOR FRIDAY. PLEASE MAKE USE OF THIS TWITTER AND GMAIL. HOWEVER, HOWEVER, WE ALSO WANT TO MAKE SURE THAT EVERY SPEAKER WAS COMFORTABLE WITH HAVING STUFF TWEETED, WEBCAST, PHOTOGRAPHED AND SO ON. THAT'S TRUE FOR SPEAKERS AND POSTER PRESENTERS. OKAY? SO PLEASE, PLEASE, I'M TRYING TO -- WE'RE ALL TRYING TO ASK EVERY SPEAKER WHAT THEIR PREFERENCE IS. PLEASE ASK THE PRESENTER WHETHER THE POSTER PRESENTER OR SPEAKER IN THE SESSION, IF THEY DO OR DON'T WANT THEIR TALKS -- POSTER LIVE TWEETED, AND PRESENTERS, PLEASE ALSO SHARE THAT RESPONSIBILITY. LET THE AUDIENCE KNOW WHAT YOUR PREFERENCE IS. OKAY. PHOTOGRAPHING, ESPECIALLY WITH POSTERS, ALSO WITH SLIDES, PLEASE ASK THE PRESENTER IF THEY MIND IF THEY HAVE THEIR TALK OR POSTER PHOTOGRAPHED. PRESENTERS, SHARE THE RESPONSIBILITY. LET THE AUDIENCE KNOW WHAT YOU DO OR DON'T WANT. OKAY? AND ESPECIALLY BECAUS WE'RE WEBCASTING PLEASE LET YOUR MODERATOR KNOW IF YOU DON'T WANT YOUR TALK WEBCAST. OKAY. IT COULD BE SIMPLY A HEAD SHOT, BUT IF YOU DON'T WANT YOUR SLIDES SHOWN OR IF YOU DON'T WANT A HEAD SHOT, WHATEVER IT IS, LET YOUR MODERATOR KNOW SEE WE CAN ACCOMMODATE. WE HAVE A CREW OF I.T. AND VIDEOCAST PEOPLE IN THE BACK THAT WILL ACCOMMODATE US. I'D LIKE TO INTRODUCE HOWARD OCHMAN, I'VE KNOWN HIM FOR A LONG TIME. I THOUGHT IT WAS IMPORTANT TO PROVIDE EVOLUTIONARY PERSPECTIVE TO THE MICROBIOME. WE DON'T OFTEN TALK ABOUT THE EVOLUTIONARY PERSPECTIVE HERE AT NIH BUT CLEARLY THE MICROBIOME AND HOST IS A CO-EVOLVED SYSTEM. LET'S HEAR FROM HOWARD. HOWARD IS OUR -- WALTER, CAN YOU HELP HOWARD? AND THE TITLE OF HOWARD'S TALK IS "WHAT THE GREAT APE MICROBIOME CAN TELL US ABOUT THE HUMAN MICROBIOME." THANK YOU, HOWARD. HOWARD IS ONE WHO CHOOSES NOT TO HAVE HIS TALK WEBCAST, AUDIO WILL BE ACROSS THE WEBCAST BUT NO HEAD SHOTS, NO DATA. THANKS, HOWARD. >> THANKS SO MUCH. SO THANKS SO MUCH FOR THE INVITATION TO SPEAK WITH YOU. I'D LIKE TO TALK A LITTLE BIT, THE FIRST HALF OF MY TALK IS AN OVERVIEW OF WHERE WE'VE COME FROM IN THE LAST TEN YEARS, AND THEN I'LL BASICALLY SHIFT TO TELL YOU WHERE WE THINK WE'RE GOING IN THE FUTURE OF OUR WORK. AND SO WHAT WE'VE BEEN WORKING ON, THE GREAT APE MICROBIOME, THE REASON IS ACTUALLY REALLY SIMPLE. AT THE TIME, IN 2007, WHEN THE HUMAN MICROBIOME PROJECT WAS STARTED, WE HAD A LOT OF INFORMATION ABOUT WHAT WAS GOING ON IN THE HUMANS BUT WE DECIDED AS EVOLUTIONARY BIOLOGISTS TO LOOK AT WHAT WAS GOING ON IN GREAT APES, OUR CLOSEST RELATIVES. WHAT I SHOW HERE IS THE FIGURE OF THE RELATIONSHIPS OF GREAT APE, WE HAVE HUMANS HERE, MOST CLOSE RELATIVES ARE CHIMPANZEESES, THE BENOBA, THE COMMON CHIMPANZEE, AT LEAST THREE SUBSPECIES. WE'RE MORE CLOSELY RELATED TO ONE ANOTHER THAN TO GORILLAS. & THEN THE GREAT APE SPECIES, ASIAN GREAT APES, ORANGUTANS, AND HUMANS AND CHIMPANZEES AT THE DNA LEVEL ARE 99% IDENTICAL TO ONE ANOTHER. OUR QUESTIONS WERE REALLY SIMPLE WHEN WE STARTED OUT ABOUT THE GUT MICROBIOME. WE WANTED TO KNOW WHETHER THE GUT MICROBIOME EVER CHIMPANZEES WAS SIMILAR TO THAT OF HUMANS, BECAUSE OF THE GENETIC RELATEDsNESS, RECENT ANCESTRY, DIFFERENT DUE TO DIET, GEOGRAPHY, AFRICANATES AND MOST OF US ARE IN THE STATES, SOCIAL STRUCTURE, AND THEN MOST IMPORTANTLY IS WHAT MIGHT THE APE MICROBIOME INFORM US ABOUT HUMAN MICROBIOMES. SO WHEN WE DID THIS WORK, THE ONLY WORK THAT HAD BEEN DONE AND SAMPLES THAT WERE AVAILABLE WERE PRINCIPALLY FROM ANIMALS FROM ZOOS. WE WANTED TO FIND SAMPLES FROM NATURAL HABITATS OF APE, FROM THAT I WORKED WITH A COLLEAGUE OF MINE, MIKE WORABY, WHO GOES TO AFRICA OFTEN LOOKING FOR THE ORIGINS OF HIV. AND SO HE'S TAKING CHIMPANZEE FECAL SAMPLES. I CALLED MIKE, MANY SAMPLES. HE GOT ME IN TOUCH WITH BEATRICE HAHN, UNIVERSITY OF ALABAMA, A LARGE REPOSITORY OF FECAL SAMPLES OF AFRICAN APES, WE LOOKED AT EASTERN AND WESTERN LOWLAND GORILLA, SPECIES OF CHIMPANZEES, SHOWN ON THE UPPER LEFT. THAT'S PANTROGLADITES, SUBSPECIES BY BLUE DOTS, GREEN DOTS ARE PANTONISCUS,BANOBAS, FROM AFRICA AND UNITED STATES. WE USED THE TECHNIQUE, ALL OF YOU KNOW ABOUT THIS UNLESS YOU'VE BEEN ASLEEP TEN YEARS, IT'S BASED ON WORK DONE BY NORM PACE, CULTURE INDEPENDENT TECHNIQUES FOR LOOKING AT MICROBES, AND THEN MADE A HIGH THROUGHPUT APPROACH, BASED ON THE WORK OF MITCH SOGEN IN 2005. IT'S A VERY SIMPLE METHODOLOGY WHICH IS WHY IT'S SO WIDELY APPLIED. COLLECT SAMPLES, EXTRACT DNA, AMPLIFY THE 16 RIBOSOMAL RNA, UBIQUITOUSLY PRESENTS, HIGHLY CONSERVED REGIONS AND SOMEWHAT VARIABLE. YOU SEQUENCE, GET MANY, MANY SEQUENCE AMPLIPODS, OTUs, THIS IS A TERMINOLOGY DEVELOPED IN THE 1960s BY BOB SOAKEL, THE GROUP OF WHATEVER ORGANISMS YOU'RE LOOKING AT. IT'S NOT ASSIGNING TAXONOMIC RANK. IT'S INTENTIONALLY A VAGUE TERM. WE'RE LOOKING AT THE OTUs, BIDDING THE SEQUENCES BASED ON OVERALL SIMILARITIES, WE GET SEVERAL OTUs, TAXONOMICALLY ASSIGN, DATABASES ARE AVAILABLE, MANY STUDIES STOP AT THIS POINT. ACTUALLY IT'S AFTER THIS POINT THAT ALL THE FUN BEGINS, ONCE YOU HAVE EVERYTHING TAXONOMICALLY ASSIGNED. WHEN WE FIRST DEVELOPED THESE DATA, THERE WERE VERY FEW TOOLS IN WHICH TO ANALYZE THEM. WE PRODUCED THESE HEAT MAPS, THIS IS JUST SHOWING YOU A HEAT MAP OF WHAT'S PRESENT, AND THE RELATIVE ABUNDANCE OF THESE THINGS, THESE OTUs, AMONG THESE APE SPECIES, HUMANS AT THE TOP, CHIMPANZEES THE BLUE DOTS, BENOBOS AND GORILLAS. IF YOU SQUINT YOU SEE THE DIFFERENCE, 9,000 OTUs WE GOT OUT OF THIS, OTUs PRESENT IN TWO OR MORE INDIVIDUALS, AND THE REASON THEY ARE IN TWO OR MORE INDIVIDUALS, WE THOUGHT IF SOMETHING WAS UNIQUE TO AN INDIVIDUAL IT COULD HAVE BEEN AN ARTIFACT SO WE WOULD THROW IT OUT FOR THE TIME BEING. AND WE FIND OUT THE THREE DOMINANT SAMPLES, AND A COUPLE OTHER PHYLA PRESENT IN THE SAMPLES. WHEN WE FIRST STARTED TO LOOK WE WANTED TO KNOW RELATIONSHIPS OF THE MICROBIOMES TO ONE ANOTHER. WE KNEW THE RELATIONSHIPS OF THE HOST, HERE IS AN UNROOTED PHYLOGENY, THE BENOBOS AND CHIMPANZEES ARE THE MOST CLOSELY RELATED, THE HUMANS ARE MOST CLOSELY RELATED TO THEM, OUTSIDE OF THAT ARE THE GORILLAS. THIS IS A TREE BASED ON MITOCHONDRIAL DNA, CLOSE RELATIVES CHIMPANZEES AND GORILLAS. LOOKING AT THE ABUNDANCE OF OTUs, IT LOOKED LIKE THIS, TERMINAL BRANCHES ARE LONG, SHOWING A LOT OF VARIATION BETWEEN INDIVIDUALS IN THE SPECIES. IF YOU LOOKED AT THIS CLOSELY, THE INTERSPECIES BRANCHING ORDER, THAT'S WHAT'S COMING UP IN THE NUMBERS HERE, HAPPENED TO MATCH THE TREE. SO THIS SHOWED US THAT HOST PHYLOGONY WAS A DRIVING FORCE OF MICROBIOMES. YOU CAN SEE THE SPECIES CLUSTERED TOGETHER BASED ON MICROBIOME. IF YOU GAVE ME A SAMPLE, I COULD TELL YOU WHAT SPEECHES IT WAS BASED ON THE MICROBIOME, BUT ALSO THE MICROBIOMES OF HUMANS MORE CLOSELY RELATED TO THAT OF CHIMPANZEES AND TWO CHIMPANZEES SPECIES MOST CLOSELY RELATED LIKE GENETIC RELATEDNESS. IT STARTED TO BOTHER US WHY ARE TERMINAL BRANCHES SO LONG, WHAT ARE THE FORCES DRIVING THE INDIVIDUAL VARIATION WITHIN THE SPECIES? SO WE LOOKED TO A VERY LARGE DATASET AVAILABLE AT THE TIME, THE DATASETS AVAILABLE FOR HUMANS WERE NOT AS EXTENSIVE WHEN WE FIRST DID THIS ANALYSIS. WE TURNED TO LOOK IN A CHIMPANZEE MICROBIOMES, LOTS OF SAMPLES AVAILABLE FOR GAMBI CHIMPANZEES, THE SAME JANE GOODSALL HAS BEEN LOOKING AT SINCE THE 1960s. WE TALK CHIMPANZEES FROM TWO COLONIES, TWO GEOGRAPHIC REGIONS TO SEE WHETHER GEOGRAPHY PLAYED A ROLE IN THE SEPARATION OF MICROBIOME. WE ALSO AS YOU CAN SEE HERE KNOW GENETIC RELATEDNESS OF INDIVIDUALS, THAT IS THE PARENTS AND OFFSPRING HAVE ALL BEEN WATCHED, SO WE COULD TELL BY FECAL SAMPLES WHICH INDIVIDUALS THEY CAME FROM. SO WE HAD THAT. WE HAD CASE WHERE IS WE HAD PARENTS AND OFFSPRING, WHERE THE PARENTS OF THE OFFSPRING AND OFFSPRING WENT INTO TWO COLONIES. CASES ALSO, MOST OF THE SAMPLES CAME FROM 2008, THE SAME SEASON, TRYING TO CORRECT, ALSO SAMPLES FROM SEVEN INDIVIDUALS COLLECTED IN THE YEAR 2000, 2001, 2008, CROSS-HATCHED ON HERE. WE HAD A TOTALS OF 35 OR 40 SAMPLES, WE DID THE SAME EXACT PROCEDURE ON THAT. WE SAW WHAT ASSORTED -- HOW WE COULD ASSORT THE MICROBIOME. WE HAD TO FIND OUT THE GAMBI, DO THEY LIKE GHAMBIESQUE? ALL THE GHAMBI WERE MORE CLOSELY RELATED TO ONE ANOTHER BASED ON MICROBIOMES AND GENETICS THAN TO OTHER SPECIES OF PAN TROGLODITES, ONE GROUP, GUT MICROBIOME LOOKED LIKE CHIMPANZEES, HERE IS PHYLOGENETIC ANALYSIS, HERE IS COORDINATES PLOT SHOWING ALL THE GHAMBI CHIMPANZEES CLUSTERED TOGETHER. SEPARATING FACTORS WE SAW GEOGRAPHIC STRUCTURING IN THE POPULATION, MICROBIOME. SO LOOK AT THE DIFFERENT MICROBIOMES, PLOTTING WHERE THEY ARE, YOU CAN SEE THE COMMUNITIES CAN BE SEPARATED MOST OF THE TIME, THERE ARE SOME INDIVIDUALS INTERMEDIATE, THE INDIVIDUALS BORN IN ONE COMMUNITY AND MOVED TO ANOTHER, TOLD US THERE WAS A LOT OF SHARING BETWEEN MEMBERS. ALSO SOME SORT OF TEMPORAL STRUCTURING, SAMPLES COLLECTED IN 2008 JUST ON THIS PLOT STARTED TO CLUSTER TOGETHER. THERE WAS ALMOST NO GENETIC STRUCTURING TO THE POPULATION. OVERALL RELATEDNESS OF HOST, HAMILTONIAN, RELATED TO CHILDREN BY ONE HALF, NIECES AND NEPHEWS BY ONE-QUARTER, SHOWN BY BLUE DOTS, DARKER BLUE TELLS YOU MORE CLOSELY RELATED. MORE CLOSELY RELATED HOSTS HERE DON'T REALLY HAVE MORE CLOSELY RELATED MICROBIOMES. JUST TO PUT THIS IN ORDER TO SHOW YOU STATISTICS, GUT MICROBIOTA CAN DIFFER BY COMMUNITIES AND BY COMMUNITY AFFILIATION AND BY GENDER, BUT COULDN'T DIFFERENTIATE BY OVERALL GENETIC RELATEDNESS. WHILE WE WERE DOING THIS WORK A LOT OF INFORMATION CAME OUT ABOUT THE HUMAN MICROBIOME. WE HAD A DIRECT LOOK AT THE CONTENTS OF THE MICROBIOME OF HUMANS, GREAT APE, CHIMPANZEES. YOU CAN SEE AT THE ORDER OF PHYLUM, THE ORDER OF HUMANS AVAILABLE AT THE TIME VERSUS CHIMPANZEES, WE CAN SHOW WITHOUT LABELS THE PROFILES LOOK ABOUT THE SAME. THIS IS THE SAME THING WE FOUND, THREE MAJOR PHYLA, LOOKING AT THE LEVEL OF BACTERIA CLASS, THEY LOOK SIMILAR, AT THE LEVEL OF ORDER THEY LOOK SIMILAR. ONCE YOU GET DOWN TO THE GENERIC LEVEL FOR THE BACTERIAL GENE THERE'S SHARING, COLORS TELL YOU SPECIFIC -- DENOTE SPECIFIC TAXA, THERE ARE SOME DIFFERENCES. AT THE TIME A PAPER CAME OUT THAT LOOKED AT WHAT THEY CALLED ENTEROTYPES IN THE HUMAN BIOME, LOOKING AT 30-SOME INDIVIDUALS MAINLY FROM EUROPE AND THE UNITED STATES THEY FOUND OUT THEY SHOWED THAT THE MICROBIOTA ASSORT INTO THREE GROUPS, WHICH THEY CALLED ENTEROTYPES, NOT NATION OR CONTENT SPECIFIC, NOT RELATED TO AGE, SEX, WHAT YOU HAVE TO REALIZE ABOUT ENTEROTYPES, BASED ON RELATIVE ABUNDANCE OF DIFFERENT TAXA. ENTEROTYPE 1, BACTEROIDES, THERE'S THE PREVOTELLA ENTEROTYPE, THAT HAS PROPORTION OF -- HIGH PROPORTION OF PREVOTELLA, BASED ON ABUNDANCE OF GENERA IN THE MICROBIOMES. TRYING TO FIGURE OUT WHAT THE PURPOSE OF THESE ENTEROTYPES ARE, IF THEY REALLY EXIST, I LIKE THIS PAPER BY GARY WU LOOKING AT EFFECT OF LONG TERM DIETARY PATTERNS, IN THIS PAPER SOME AUTHORS ON THIS ARE IN THE AUDIENCE HERE. TWO ENTEROTYPES IN THE PREVOTELLA, DIFFERENT ABUNDANCE OF EACH ONE IN THAT. OF COURSE THEY FAVORED TWO ENTEROTYPES, NOT THREE, LONG-TERM DIET WAS ASSOCIATED WITH ENTEROTYPE. IF YOU HAD HIGH FAT, LOW FIBER LIKE MOST OF US HAVE, WE HAD BACTEROIDES. THEY DID A NICE EXPERIMENT TO SHIFT FROM ONE TO ANOTHER. SO WHEN WE STARTED TO LOOK AT THAT, WE WERE LOOKING, ARE THESE THINGS REAL? ENTEROTYPES? WE STARTED TO THINK ABOUT THIS. HOW COULD WE COMPARE THIS TO CHIMPANZEES? HUMAN-SPECIFIC FEATURES OR PRESENT IN GREAT APES? WHAT AROSE FROM THE SWITCH TO HIGH FAT DIET, WE SHOULDN'T SEE IT IN NON-HUMAN PRIMATES. MAYBE IT'S A REAL ADAPTATION IF PRESENT IN OTHER SPECIES. WE LOOKED IN GHAMBI CHIMPANZEES, THE SAME STUDY, AND FOCUSED ON THESE BECAUSE THEY ARE ABOUT THE SAME AGE AS HUMAN POPULATIONS, GHAMBI CHIMPANZEE POPULATION PROBABLY AROSE ABOUT 100,000 YEARS AGO BASED ON GENETIC DATA. HUMAN POPULATIONS DIVERSIFIED OUT OF AFRICA APPROXIMATELY 100,000 YEARS AGO. SO WE DID THE SAME SORT OF ANALYSIS AND FOUND THE DATA PARTITIONS INTO THREE GROUPS, AS WE DID, AS WE SAW IN HUMAN POPULATIONS. AND IN FACT, WE HAD THE SAME SPECIES DRIVING THE ENTEROTYPES IN CHIMPANZEES AND IN HUMANS. SO WE CAN SEE HERE THERE'S THE BACTEROIDES HERE, BACTEROIDES IN THE CHIMPANZEE AS WELL. HAVE YOU THE SAME ENTEROTYPES HAVING THE SAME COMPOSITIONAL FEATURES IN CHIMPANZEES AND IN HUMANS. ALSO AS I MENTIONED, WE ALSO HAD SAMPLES THAT WE COULD FOLLOW LONGITUDINALLY. AFTER A YEAR-LONG PERIOD EVERY CHIMPANZEE SWITCHED ITS ENTEROTYPE. HERE ARE THE SEVEN SAMPLES FOR WHICH WE HAD MULTIPLE SAMPLES FROM MULTIPLE YEARS. IN EVERY CASE THERE WAS A SWITCH FROM ENTEROTYPE 2 TO 1, THERE WAS NO CONSISTENT PATTERN EVEN AMONG RELATIVES. TWO CHIMPANZEES THAT HAPPEN TO BE SIBLINGS, THEY STARTED WITH DIFFERENT ENTEROTYPES AND ENDED WITH DIFFERENT ENTEROTYPES IN THAT. NOW YOU MIGHT RECALL AS I'VE MENTIONED A SAMPLE FROM CHIMPANZEES AND GIVE ME ONE FROM HUMANS I CAN ALWAYS DIFFERENTIATE THESE SAMPLE AND TELL YOU WHETHER IT'S A CHIMPANZEE FECAL SAMPLE OR HUMAN BASED ON CONTENT OF MICROBIOME. I CAN SEPARATE THEM. IF YOU THINK ABOUT THIS, WHAT DOES THIS TELL YOU ABOUT THE ORIGIN OF ENTEROTYPES? WELL, THAT MEANS THEY WERE PROBABLY ANCESTRAL, THAT IS BEFORE, THAT IS CHIMPANZEES AND HUMANS, WE HAVE FOUND SOME ENTEROTYPE FEATURES IN GORILLAS AS WELL. IT SHOWS ANCESTRAL, PRESENT IN COMMON ANCESTOR, MAINTAINED FOR MILLIONS OF YEARS AND DID NOT RESULT -- ARISE AS A RESULT OF MODERN DIET. SO IF YOU THINK ABOUT THIS IN EVOLUTIONARY TERMS, YOU CAN SAY THERE'S AN ANCESTRAL STRAIN HERE OF SOME GENUS HERE, FOLLOWING THE LINEAGES OF CHIMPANZEES IN HUMANS, BEING SEPARATED FOR MILLIONS OF YEARS JUST AS THE GENETICS OF THESE ORGANISMS, IT'S VERY REMINISCENTS OF THINGS THAT ARE SYMBIONS THAT CO-DIVERSE IF I WITH DIVERSIFY WITH HOSTS. LOOKING AT CO-DIVERSIFICATION, MAYBE MICROBES ARE CO-DIVERSIFYING WITH THE HOST. WE ASKED THE QUESTION, DID THE BACTERIA CO-DIVERSIFY WITH THE HOST IN GREAT APE EVOLUTION? THIS IS A CARTOON TAKEN FROM A PAPER BY NANCY MORAN AND DAN SLOAN, COMMUNITY ASSORTMENT OF MICROBES AND HOST, THESE ARE EXTREME, YOU CAN HAVE INTERMEDIATE AS WELL, ENVIRONMENT WITH LOTS OF MICROBES IN IT. AND THEN THE COMMUNITIES AGAIN ASSORT, THEY SELECT FROM THE ENVIRONMENT SO YOU GET DIFFERENT ONES, OR PURE CO-DIVERSIFICATION, CERTAIN BACTERIA THAT ARE ANCESTRAL AND THEY HAVE BEEN CO-DIVERSIFYING WITH LINEAGE OF EVOLUTIONARY TIME. SO OUR PREDICTION OF COURSE IS THAT BECAUSE HUMANS AND OTHER ORGANISMS UPTAKE THEIR GUT MICROBIOTA, EVE GENERATION ANEW, AND THERE ARE CHANGES AT THE INDIVIDUAL LIFETIME, TAKEN FROM THE ENVIRONMENT, IT SUGGESTS THE FIGURE ON THE LEFT IS CORRECT, THAT HOSTS SELECT FROM THE ENVIRONMENT. WE WANTED TO TEST FOR CO-DIVERSIFICATION BETWEEN GUT BACK YEAH, THE BACTERIA. DIFFICULT TO DO. I'VE BEEN TELLING YOU ABOUT COMMUNITY COMPOSITION, RELATIVE COMPOSITION OF ONE TAXA AND ANOTHER, RELATIVE ABUNDANCE OF THESE. TO FIND EVIDENCE OF CO-DIVERSIFICATION OR SO SPECIESATION, MOST PEOPLE LOOK FOR CONCORDANCE OF PHYLOGENY. HERE YOU HAVE APHIDS, AND YOU CAN SEE THE TWO TREES, ONE ON THE LEFT AND THE ONE ON THE RIGHT OF THE APHID HOST, ALMOST COMPLETELY CONCORDANT, THAT IS THEY MATCH, GOOD INFORMATION THEY HAVE CO-DIVERSIFIED OVER MILLIONS OF YEARS. THEY HAD TO TAKE AN INDIVIDUAL GENE AND FOLLOW ITS PHYLOGENY, BUILD A PHYLOGENETIC TREE. THE SEQUENCES WE'VE BEEN USING, 16S SEQUENCES TO LOOK AT MICROBIAL, EVOLVE TOO SLOWLY. ONE MAY CONTAIN SEQUENCES DIVERGE ON THE ORDER OF 10 TO 20 MILLION YEARS AGO, THE ENTIRE TIME OF THE GREAT APE DIVERSIFICATION. SO WE HAVE TO START LOOKING AT FEATURES THAT LOOKED FASTER. SO THIS TELLS YOU WHY -- THIS EXPLAINS IN A CARTOON, AN OTU, WITHIN EACH OTU WE MIGHT HAVE MANY, MANY BACTERIAL SPECIES OR EVEN GENERA, EACH COULD DIVERSIFY WITH THE HOST, THEY CAN NOT TELL YOU MUCH ABOUT CO-DIVERSIFICATION, IT COULD HAVE DIVERGENT. WE NEEDED A METHOD WITH HIGH LEVELS OF RESOLUTION TO THAT. AND SO TO DO THAT WHAT WE DID WAS THE SAME THING EVERYONE HAS DONE WITH 16S GENES, FOR PROTEIN CODING GENES, YOU DON'T HAVE TO READ THIS BECAUSE IT TELLS YOU EVERYTHING I'VE ALREADY SAID. ALL YOU HAVE TO KNOW FROM THIS IS THAT WE'VE TURNED THIS TECHNIQUE CALLED PHYLO TAGS. IF WE GET 16S TAGS, SOMETIMES THEY ARE CALLED I-TAGS OR PYRO TAGS, IF IT'S MADE ON A LUMINA OR MACHINE. WE CAN FOLLOW THE PHYLOGENY OF INDIVIDUAL GENE IN THE MICROBIOME. WE FOCUSED ON GYRASE B, BACTERIAL FAMILIES, THESE ARE FROM MY GORILLA SAMPLES. WE LOOKED AT A COUPLE FAMILIES, IF YOU LOOK WITHIN A SAMPLE OF GORILLAS, IN THAT WE TAKE ALL THE SAMPLES TOGETHER, HAVE APPROXIMATELY 100,000 READS. IF YOU LOOK IN THAT WE HAVE A TOTAL OF 425 OF THOSE READS WERE ASSIGNED TO LACTOSPORACIA, OVER ALL 73 AT THE 99% LEVEL. ALL OF THESE TARGETED TO THE FAMILIES, SO 8,000 READS, ALL OF THAT, WE GET 3,000 TAGS NOW OF SEQUENCES OR OTUs THAT DENOTE SPECIES. MORE IMPRESSIVELY IF WE LOOK AT ACA, SAME NUMBER OF READS, NO READS ASSIGNED TO THIS FAMILY. WHEN YOU LOOK AT 16S GENES. BUT IF YOU TARGET GYRASE B WE HAVE UP TO 300. WE HAVE LOTS OF VARIATION IN THAT. THEN WE STARTED TO DO THE SAME STUDY THAT WE DID BEFORE, TAKING THE SAME SAMPLES, CHIMPANZEES, TWO SPECIES OF CHIMPANZEES, GORILLAS AND HUMANS WHICH ALL CAME FROM NEW HAVEN, CONNECTICUT, I WAS AT YALE AT THE TIME. WE SEQUENCED THEM AND HAVE THIS NUMBER OF OTUs FOR EACH OF THESE CASES. WE HAVE BACTEROIDES, THESE ASSORTED INTO MANY SPECIES. THE STRAIN PHYLOGENY OF SPECIES IN THERE MATCHED IN MANY CASES THE PHYLOGENY OF THE STRAINS. THIS TOLD US THESE WERE STRAINS OR SPECIES OF BACTEROIDES AND BIFIDO BACTERIA THAT MATCHED, CO-DIVERSIFIED, SO SPECIESATION WITH THE GREAT APE HOSTS. PEOPLE ASK THE ONE AT THE TOP, SPECIES 1, WHAT IS IT? YOU DON'T HAVE A NAME FOR THIS. OKAY? HERE IS A SPECIES THAT'S BEEN CO-DIVERSIFYING WITH GREAT APE HOSTS FOR MILLIONS OF YEARS. JUST FOR THIS MEETING I'VE GIVEN NAMES. IF YOU WANT TO KNOW WHAT SPECIES, CO-DIVERSIFYING, WE HAVE NAMES FOR IT HERE. THIS ISN'T ALWAYS THE CASE WITH BACTERIA WE LOOK AT. WE FIND MANY OTUs, THIS HAS BEEN TRANSFERRED MANY TIMES WITHIN ALL THESE LINEAGES. SO AS A RESULT OF THIS, AND THIS IS -- BY TESTING FOR CO-DIVERSIFICATION WE SEE HUMANS AND AFRICAN APE MICRO BIOMES, COMPOSITE OF STRAINS CO-DIVERSIFYING AND THOSE TRANSFERRED BETWEEN LINEAGE FOR A MILLION YEARS, FOR MILLIONS OF YEARS, IF WE LOOK AT THE DIVERGENCE TIMES, CO-LINEAR WITH THE HUMAN HOST, DIVERSIFICATION DURING EVOLUTION. NOW THAT IS BY WAY OF BACKGROUND INFORMATION. WHAT ABOUT MICROBIOMES OF MOST CURRENT CONCERN? ONE THING THAT WE'RE LOOKING AT, WHAT ARE THE PHYLOGENETIC DEPTHS, DO DIFFERENT HUMAN SUBPOPULATIONS HAVE THEIR OWN STRAINS? MUCH LIKE WHAT WE'VE SEEN WITH HELICOBACTER, HUMAN POPULATIONS WILL HAVE THEIR OWN STRAINS. HAS CO-DIVERSIFICATION OCCURRED IN HUMAN POPULATION OR TRANSFER OF STRAINS AMONG HUMANS? ALSO HOW FAR BACK DOES IT GO? MAMMALS HAVE BACTERIAL LINEAGE CO-DIVERSIFYING WITH ALL MAMMALS? WE WANT TO KNOW WHETHER CO-DIVERSIFICATION DENOTES CO-EVOLUTION. EVOLUTIONARY BIOLOGIESISTS ARE LOOKING FOR FUNCTION, IS THERE FUNCTIONAL RELEVANCE? CHIMPANZEES HAVE A STRAIN, YOU HAVE ONE, IS IT BETTER TO HAVE THE ONE NORMALLY IN HUMANS OR DOESN'T IT MATTER AT ALL? IT'S JUST BY CHANCE, THESE THINGS ARE CO-DIVERSIFYING. ALSO, WE'VE DEVELOPED THIS PHYLO TYPE METHOD, WE'RE STARTING TO LOOK AT METAGENOMIC DATA, COULD WE GET CO-DIVERSIFYING? ANOTHER ISSUE WE LOOKED AT RELATED TO ANOTHER PROJECT, ABSOLUTE ABUNDANCES OF BACTERIA MORE RELEVANT THAN RELATIVE ABUNDANCE? TECHNIQUES WE'VE BEEN DOING SO FAR USING THIS 16S TAGGING METHOD AND EVEN THE PHYLO TAG GIVES YOU RELATIVE ABUNDANCE BUT IT COULD BE SOME ORGANISMS HAVE VERY (INDISCERNIBLE) MICROBIOTA, A COUPLE PAPERS ON INSECTS CAME OUT SAYING PEOPLE HAVE BEEN DOING A LOT OF TAGGING, LOOKING AT MICROBIOTA, THEY HAVE VERY LOW -- THERE'S A PAUCITY OF MICROBES IN THE GUT MICROBIOTA, HOW DO WE CLASSIFY MICROBES? I MADE UP NAMES OF COURSE. HOW DO WE CLASSIFY MICROBES TO SPECIES OR TAXOMOMMIC LEVELS AND WHAT ARE CLASS FINAL BACTERIAS? TO LOOK AT ONE ISSUE, WE'VE LOOKED AT HOW MUCH STRAIN CO-DIVERSIFICATION, METAGENOMIC DATASETS, ALREADY AVAILABLE FOR MALAWIAN SETS TO SEE IF WE COULD FIND CO-DIVERSIFYING STRAINS, THAT IS WE SEARCHED DATASETS FOR GYRASE B SEQUENCES, FOR BIFIDO BACTERIA CASES WITH MALAWIANS, WE FOUND A FEW SEQUENCES, MALAWIAN ARE OUTGROUPS TO OTHER HUMAN POPULATIONS WHICH IS EXACTLY WHAT YOU EXPECT FOR GENETIC DATA BECAUSE AFRICANS ARE THE MOST ANCIENT HUMAN POPULATIONS. WE'VE DONE THIS WITH BACTERIAOIDES, MALAWIAN IS AN OUTGROWTH, THERE'S MY SPECIES NAME. HERE IS A CO-DIVERSIFYING STRAIN NOT FOUND IN GORILLAS BUT IN HUMAN, AT LEAST OF AFRICAN ORIGIN, AND CHIMPANZEES. WE'RE FINDING OF THE DEPTHS OF MOST METAGENOMIC SEQUENCES WE DON'T FIND MANY CO-DIVERSIFYING LINEAGE BECAUSE WE'RE LOOKING FOR HOMOLOGS, THINGS LOOK BETTER WHEN WE GET A METAGENOMIC ON THE ORDERS OF A 100 MILLION READS SHOULD BE ABLE TO DETECT THEM. ANOTHER PROBLEM THAT WE'VE HAD IS HOW DO WE CLASSIFY MICROBES TO SPECIES OR HIGHER TOXONOMY ORDER, THIS WAS PUBLISHED LAST YEAR IN NATURE MICROBIOLOGY, THEY CLAIM A CATANASE PHYLUM, AND THEY GAVE THESE NAMES. THEY GAVE THEM DIFFERENT NAMES. ARE THESE NEW PHYLA? EVERY TIME WE LOOK AT MICROBIOME DATASET IT HAS A LOT OF UNCLASSIFIABLE BACTERIA. HOW DO WE KNOW WHETHER IT'S A NEW PHYLUM IN THE LAB. A STUDENT WAS TRYING TO FIGURE OUT, TAKING SMALL SEQUENCES, TAKING NOVEL PRIMERS TO THAT. MAKING FULL LENGTH 16S SEQUENCES OUT OF THAT. AND THEN TRYING TO CLASSIFY THESE LATER ON. AND MOST OF THE CLASSIFIED ONES ALREADY DO GET ASSIGNED TO KNOWN GROUPS ONCE WE DO THIS. SO A LOT OF THINGS PEOPLE CALL UNCLASSIFIABLE ARE KNOWN BACTERIA. A FEW WERE ARTIFACTS WE DIDN'T PICK UP BY CHIMERIC CHECKER OR OTHER TESTING BUT SOME SEEMED TO REPRESENTATIVE NEW PHYLA. I SAW A PAPER IN BIOARCHIVE BY STEVE QUAKE'S GROUP, OTHER PEOPLE ARE STARTING TO LOOK AT UNIDENTIFIED BACTERIA. THESE ARE FROM BLOOD SAMPLES, YOU CAN SEE FROM THE TITLE, HIGHLY DIVERGENT MICROBES IN THAT. WE HAVE ALL THESE THINGS THAT CANNOT BE CLASSIFIED. HOW DO WE CLASSIFY TO A NEW PHYLUM OR SPECIES? I WANT TO BECOME AN EVOLUTIONARY BIOLOGIST, WHAT CONSTITUTES A SPECIES. THERE'S THIS THING DEVELOPED IN 1942, BIOLOGICAL SPECIES CONCEPT. HE DEFINES SPECIES AS ACTUALLY OR POTENTIALLY INTERBREEDING NATURAL POPULATIONS REPRODUCTIVELY ISOLATED FROM OTHER SUCH GROUPS. THIS IS NOT ARBITRARY. I DON'T LOOK AT SEQUENCE CUTOFFS. IT'S NOT BASED ON ATTRIBUTES OF INDIVIDUALS BUT OF A POPULATION. THAT IS, THEY CAN INTERBREED WITH ONE ANOTHER. BIOLOGICAL SPECIES CONCEPT, THE SPECIES ITSELF IS THE ONLY TAXONOMIC CATEGORY, BASED ON GENE EXCHANGES, ABILITY TO HAVE SEX. INTERBREEDING, REPRODUCTIVE, HOW DO YOU APPLY SOMETHING LIKE THIS TO BACTERIA OR ANY ASEXUAL LIFE FORM? THEY REPRODUCE BY BINARY FIGURES AND ARE CLONAL, THEY REPRODUCE AS CLONES. EACH CELL IS REPRODUCTIVELY ISOLATED FROM OTHER CELLS. WHAT CONSTITUTES BACTERIAL SPECIES IN MAYBE IT'S A SINGLE CELL, SINCE IT DOESN'T REPRODUCE. SO IN LIGHT OF THE BIOLOGICAL SPECIES CONCEPT HOW CAN YOU CLASSIFY BACTERIA, ASEXUAL BACTERIA INTO SPECIES? THE ANSWER IS YOU CAN'T DO IT. LOTS OF PEOPLE HAVE TRIED. YOU'LL FIND PAPER AFTER PAPER, TRYING TO DEFINE PROKARYOTIC SPECIES OR ASEXUAL SPECIES. HERE IS A SLIDE FROM A TALK GIVEN IN 2004 AT AN ASN MEETING, I THROWS UP HIS ARMS, IT'S A LOVE/HATE RELATIONSHIP, PROKARYOTIC SPECIES, ARBITRARY, ARTIFICIAL BECAUSE IT'S MAN-MADE AND PRAGMATIC. PEOPLE DEFINE SPECIES HOW THEY WANT TO DO IT. NOW, WE KNOW THOUGH THAT EVEN THOUGH BACTERIA ARE ASEXUAL, THERE IS RECOMBINATION AMONG BACTERIA. THERE'S SEX AND RECOMBINATION, MAYBE WE CAN START TO APPLY THE BIOLOGICAL SPECIES CONCEPT. SO HOW DO I DETECT BACTERIA RECOMBINATION? WELL, THIS HAS BEEN DONE SINCE THE 1970s AND 80s WORK PIONEERED BY ROGER MILKMEN, A PICTURE FROM AN OLD PAPER. FIVE MINUTES? OH. NO PROBLEM. WHAT HE'S DONE BASICALLY ASSIGNS SEQUENCES AND SAYS HOW MUCH RECOMBINATION IS THERE. WE LOOK FOR TRACKS WHERE THERE ARE A LOT OF CHANGES VERSUS INDIVIDUAL CHANGES, IF THERE ARE A LOT OF CHANGES WHAT ARE CHANCES MUTATIONS WILL HAPPEN NEXT TO EACH OTHER, HE THINKS LOW, HE COUNTS UP, IN THIS CASE IF YOU COUNT THIS UP, YOU WOULD FIND OUT THAT THERE ARE TEN BLOCKS THAT ARE DARK COLORED AND 50 INDIVIDUAL POINT MUTATIONS, SO HE HAS AN ESTIMATE FOR E. COLI WHICH HE CALLS POLYMORPHISM INTRODUCED BY RECOMBINATION, AND INTRODUCED BY MUTATION M, AND HE SAID THERE ARE TEN BLOCKS HERE, 50 HERE, R OVER M EQUALS .2, PRODUCING VARIATION. SO THIS HAS BEEN DONE WITH MANY, MANY SPECIES NOW THAT THERE'S BEEN A LOT OF SEQUENCING IN PLACE, AND HERE IS A QUOTE FROM BRIAN SPRAT, POPULATION IN WHICH RECOMBINATION IS ABSENT OR EXTREMELY RARE PROBABLY REPRESENTS MINORITY OF SITUATION, A BACKWARDS WAY OF SAYING ALMOST ALL BACTERIA RECOMBINE AT SOME LEVEL. IF WE SHOW YOU THIS, HERE IS A COMPENDIUM TABLE TAKEN BY A PAPER THAT SHOWS FOR ALL THE SPECIES THAT WERE SURVEYED AT THE TIME, HERE ARE THE CLONAL SPECIES, THAT IS THEY HAVE VERY LITTLE RECOMBINATION, HERE AT THE TOP ARE FREELY RECOMBINING POPULATIONS. YOU CAN SEE THE R OVER M VALUES, THERE ARE NONE THAT ARE ZEROES, SOMETIMES THERE'S VERY LOW SOMETIMES HIGH LEVELS OF RECOMBINATION. SINCE THERE'S RECOMBINATION IN ALL OF THESE, PERHAPS IT'S POSSIBLE TO APPLY BIOLOGICAL SPECIES CONCEPT. SO THIS IS WHAT WE TRIED TO DO TO DEFINE SPECIES AS GROUPS THAT EXCHANGE GENES, LIKE WE DO WITH ANIMALS. SO HOW DID WE DO THIS? WE TRIED TO DETECT RECOMBINATION, LOOKING AT HOMOPLASIES, NOT SHARED BY COMMON ANCESTRY. IF YOU ALIGN SEQUENCES YOU CAN SEE THERE ARE VERY DIFFERENT PARTS OF THE TREE, HAVE THE SAME BASE, SO BASICALLY THIS COULD BE TRANSFERRED FROM HERE TO HERE, THIS LOOKS LIKE A RECOMBINATION EVENT AS OPPOSED TO ANCESTRAL AND LOST OR ALL THESE INDIVIDUAL MUTATIONS. WE GO THROUGH ALL THESE PHYLOGENETIC TREES AND COUNT UP HOMOPLASIES AND SEE THESE AS A ROBUST SIGNAL OF COMBINATION, LOOK AT INDIVIDUAL POLY MORPHIC SITES OVER THE ENTIRE GENOME. TECHNIQUE WAS SIMPLE IN DOING THIS STUFF. APPROACHES, WE DOWNLOADED SEQUENCES FROM A SPECIES, FROM GENBANK, OF THAT WE TOOK CLOSELY RELATED GENOMES, DEFINE CORE SET OF GENES, THOSE ARE GENES SHARED BY ALL THE TAXA IN THERE. COMPUTE GENOMIC DISTANCES, IDENTIFY THE NUMBER OF HOMOPLASIC SITES AND HAVE A DEFINITION OF APPLIES HOMOPLASY, H OVER M, HOMOPLASY VERSUS MUTATION FOR EVERY TREE. THIS IS THE ONLY CONFUSING SLIDE I'LL SHOW TODAY, BASICALLY HOW WE TABULATE THIS, AND SO HERE IS A CARTOON SHOWING IF WE HAD A LOT OF STRAINS, GENOME SEQUENCESES, SAMPLED FOUR STRAINS AT RANDOM, MADE THE TREE, COUNT THE HOMOPLASY OVER MUTATION, UP TO N MINUS 2 SUBSAMPLE STRAINS. YOU WOULD SEE A CURVE LIKE THIS, THAT HAS H OVER N VALUE USUALLY LESS THAN 1, A LOT OF HOMOPLASY GOING ON VERSUS MUTATION. IF THERE'S A SECOND SPECIES IN THERE, FOR EXAMPLE I'M SHOWING BY THE RED DOT, SAMPLE FOUR STRAINS YOU'RE NOT GOING TO GET IT. CURVES WILL BE IDENTICAL FOR THE TWO. ONCE YOU START GETTING THAT ONE STRAIN THAT DOESN'T RECOMBINE, YOU'LL SEE THIS PRECIPITOUS DROP IN THE DISTRIBUTION. SO WE LOOK FOR THESE DISCONTINUEY WHICH TELLS US THERE'S PROBABLY MORE THAN ONE SPECIES IN THERE. WE DID THIS FOR THE 93 STRAINS, I HOPE EVERYONE MEMORIZES THIS. I WON'T SHOW IT LOOK. SPECIES FALL INTO THREE MAIN CATEGORIES, TRUE BIOLOGICAL WHICH FOLLOW WHAT I'VE SHOWN YOU. WE HAVE CASES THAT ARE CLONAL, THAT IS THINGS DON'TS RECOMBINE AT ALL SO H OVER N IS LOW, WE CAN'T CLASSIFY AS BIOLOGIC SPECIES. AND THERE'S CASES WHERE THE NAMED SPECIES THAT'S IN GENBANK HAS DISCONTINUITY, WE TAKE THEM OUT, RERUN ANALYSIS, WE'RE A HAPPY FAMILY AGAIN. IT'S NOW ONE SPECIES. AND WE HAVE SOME STRAINS IN ANOTHER GROUP. BY DOING THIS WE'RE ABLE TO CLASSIFY 85% OF ALL NAMED BACTERIA INTO SPECIES BASED ON THE BIOLOGICAL SPECIES CONCEPT. EVEN THOUGH BACK TEARA ARE -- BACTERIA ARE ASEXUAL, YOU CAN APPLY. WE DID IT WITH DROSOPHILA, SEQUENCES, WE GET DISCONTINUITY. WE PUT THE SEQUENCES OF TROLIDITES AND HOMO SAPIENS, FIND CONTINUITY, TAKE OUT THE CHIMPANZEES, WE DON'T INTERBREED, WE'RE SEPARATE SPECIES. MOST PEOPLE LOOK AT 16S, 97% IDENTITY CONSTITUTES A SPECIES. HOWEVER, WE SEE CASES WHERE THERE'S A BIOLOGICAL SPECIES, WHERE THE STRAINS DIFFER BY 30% IN THE GENOME. USING THAT ONE STRICT CUTOFF IS NOT USEFUL AT ALL AND DOESN'T REALLY APPLY. HERE IS DROSOPHILA AND HOMO SAPIENS, SHOWING YOU WE'RE ALL CLOSELY RELATED TO ONE ANOTHER. YOU DIFFER FROM THE PERSON NEXT TO YOU BY ONE BASE PAIR OUT OF EVERY FEW THOUSAND. NOW WE CAN DEFINE BIOLOGICAL SPECIES OF BACTERIA, COMBINED WITH WORK BY PHIL'S GROUP, THE GENOME TAXONOMY DATABASE, TRYING TO CLASSIFY AT EVERY OTHER TAXONOMY LEVEL. ARE THEY NEW PHYLUM, ORDER, CLASS, AND NOW WE'LL BE ABLE TO DEFINE AND CLASSIFY MICROBES AT EVERY TAXONOMY LEVEL. IF YOU HAVE A GENOMIC SEQUENCE, WE'LL BE ABLE TO FIGURE OUT IF IT'S A NEW SPECIES, NEW PHYLUM ORDER. IS IT PRIMARY FACTOR OVER TIME& SCALES, WE KNOW LOTS OF OTHER FACTORS ARE GOING TO BE INTRODUCED, DIET, GEOGRAPHY, BUT THERE'S A LARGE PHYLOGENETIC SIGNAL TO MICROBIOME. WILL THIS LIMIT OUR ABILITY TO ALTER MICRO BIOMES KNOWING THERE HAS TO BE A PARTICULAR SET OF MICROBES IN THERE. CHIMPANZEES HARBOR THESE ENTEROTYPES ANALOGOUS TO THOSE IN HUMANS. ARE ENTEROTYPES STABLE, DO THEY AFFECT HOST, DO THEY HAVE SOME FUNCTION AT ALL? BACTERIAL GROUPS CO-DIVERSIFY WITH GREAT APES, DID BACTERIA CO-EVOLVE WITH HUMAN POPULATIONS, AND HOW LONG AND WHICH STRAINS PERSIST, WHAT TAXA ARE CO-DIVERSIFYING, ARE THEY CO-EVOLVING, IS THERE A FUNCTION TO THEM? BACTERIA REPRODUCE CLONALLY, DIFFER IN PROPENSITY FOR RECOMBINATION, WE CAN DEFINE SPECIES ON BARRIERS TO GENE FLOW, SO THERE IS A UNIFORM AND RATIONAL APPROACH TO DELINEATE ORGANISMS ACROSS ALL DOMAINS OF LIFE? AND FINALLY, DON'T TOSS OUT, IGNORE OR UNDERREPORT UNCLASS FINAL SEQUENCES, THE MOST INTERESTING BACTERIA IN MICRO BIOME SAMPLES, PEOPLE DON'T REPORT THEM. I'M ASKING SOURCE, ORIGINS AND ROLE OF CRYPTIC LINEAGES. FINALLY I'D LIKE TO GIVE ACKNOWLEDGMENTS, THE MAIN SHOUT OUT IN THE FIRST STUDY TO MIKE WARABY, I'M GRATEFUL TO BEATRICE HAHN, THE COLLABORATOR THROUGH MOST STUDIES. A COUPLE TERRIFIC POSTDOCS AND GRADUATE STUDENTS, PARTICULARLY PATRICK DEDMAN AND ANDREW CORNELL, AND FINALLY I'D LIKE TO THANK THE GENEROUS SUPPORTS FROM THE NATIONAL INSTITUTES OF HEALTH. THANK YOU VERY MUCH FOR YOUR ATTENTION. [APPLAUSE] TIME FOR A QUESTION OR NOT? ONE MINUTE? OWEN? >> WE HAVE AT BEST KIND OF AN OPERATIONAL DEFINITION OF WHAT SPECIES IS, COULD I JUST ASK YOU TO SPECULATE OR AMPLIFY ON WHAT ARE THE CONSEQUENCES OF THAT FOR HUMAN MICROBIOME RESEARCH? NEGATIVE OR POSITIVE? >> WELL, THE MAIN THING IN KNOWING WHETHER SOMETHING IS A SPECIES, WHETHER IT CAN RECOMBINE AND TAKE NEW GENES, WE'RE FINDING ALL THESE TAXA, AS FAR AS WE'RE CONCERNED, THAT ARE CO-DIVERSIFYING, CO-EVOLVED, WE DON'T KNOW WHETHER THEY ARE NEW SPECIES, PART OF A GENUS OR WHATEVER. SOME ARE PROBABLY FUNCTIONALLY IMPORTANT. WE TALK ABOUT DIFFERENT TAXONOMIC GROUPS. THEY ARE TELLING YOU WHETHER GENES HAVE BEEN EXCHANGED BETWEEN A GROUP OR NOT. >> IT'S INTERESTING -- CAN YOU HEAR ME? >> NOW, I CAN, YEAH. >> IT'S INTERESTING TO OBSERVE DIFFERENTIALS IN COMPOSITION OF MICROBIOME BY DIFFERENT SPECIES. HAVE YOU GIVEN CONSIDERATION HOW THIS MIGHT AFFECT TRANSLATIONAL RELEVANCE OF MOUSE MODEL RESEARCH? >> THE HONEST ANSWER IS I'VE NEVER GIVEN IT A THOUGHT. IF YOU GIVE ME A SECOND ... I HAVEN'T THOUGHT ABOUT IT AT ALL, I'M SORRY TO SAY. OKAY. YEAH, MIKE? >> SOME OF THE DIFFERENCES, I LIKE WHAT YOU'RE DOING ABOUT THE SPECIES CLASSIFICATION AND RECOMBINATION CONCEPT IS A GOOD ONE TO ME. BUT GEOGRAPHICALLY THEY ARE NOT IN THE SAME AREA, THAT IS THEY ARE CAPABLE OF RECOMBINING, ALTHOUGH THEY ARE NOT, YOU COULD ENVISION SOME THINGS ISOLATED BECAUSE THEY ARE ISOLATED BUT THEY MIGHT COMBINE AGAIN, WHAT ARE YOUR THOUGHTS ABOUT THAT? >> RIGHT. SO BASICALLY THIS IS THE SAME QUESTION YOU ALWAYS HAVE. WE HAVE SQUIRRELS ON BOTH SIDES OF THE GRAND CANYON, NO IDEA WHETHER THEY WILL EVER REPRODUCE. THIS IS OUR DEFINITION OF HOW WE WOULD DEFINE SPECIES. WE CAN'T SET UP EVERY POTENTIAL MATING IN THAT. THERE AREGEOGRAPHIC FACTORS. WE TEND TO THINK THINGS ACCUMULATE ENOUGH GENETIC DIFFERENCES THROUGH TIME THAT EVENTUALLY THESE THINGS WHICH ARE SIBLING OR SISTERS SPECIES WILL BECOME SEPARATE SPECIES BUT IT'S A PROBLEM CLASS CLASSIFYING IF THEY ARE SEPARATED GROUPS PART OF THE SAME OR DIFFERENT SPECIES. WE'RE HOPING BACTERIA ARE WIDESPREAD ENOUGH THAT ACTUALLY, YOU KNOW, THEY CAN GET WORLDWIDE, WE CAN SEE WHETHER THERE'S RECOMBINATION WITHIN EACH GROUP, AND THESE WE JUST TAKE ALL THE SEQUENCES THAT ARE NAMED OF THAT GROUP SO IT'S BASED ON METABOLIC CHARACTER, THERE ARE NAMES IN GENBANK, SOME FROM LARGE GEOGRAPHIC AREAS, SOME FROM RESTRICTED PLACES, THAT WILL ALWAYS BE A PROBLEM IN CLASSIFICATION OF SPECIES. >> WE BETTER CUT IT OFF THERE. >> I'LL TALK TO YOU LATER. >> WILL YOU BE AROUND ALL DAY? >> OF COURSE, AND TOMORROW. >> ROUND TABLE TOMORROW? >> SURE. >> THANKS HOWARD. >> THANKS A LOT. [APPLAUSE] >> I'M GOING TO ASK ALL THE SPEAKERS FOR SESSION 1 TO JOIN US TO SAVE TIME. COULD YOU SIT HERE? I'LL INTRODUCE YOU ALL AT ONCE. YEAH, COME ON UP HERE. AND I'M HAVING A PROBLEM, WALTER. NO ONE TAUGHT US ABOUT THE TIMER ON THE PODIUM OR HERE AT THE TABLE. IF WALTER OR ANYBODY ON THE I.T. TEAM IS LISTENING TO THIS, YEAH. WE WEREN'T SHOWN ABOUT THE TIMER SO I WAS USING MY CELL PHONE. THANKS FOR DOING THIS. OUR FIRST FORMAL SESSION IS CATALYST FOR EMERGING FIELD. TO SAVE TIME I ASKED THE SPEAKERS TO COME TO THE TABLE. THE SESSION PURPOSE HERE IN EACH SESSION WITH A SPECIFIC PURPOSE IS TO REALLY REFLECT ON THE RESOURCES, OUTCOMES AND LEGACY OF YOUR INVESTMENT IN THIS FIELD, WE HAVE THE CURRENT INVESTIGATORS FOR PHASE 2 OF THE PROGRAM, WE ALSO HAVE MARY PERRY FUND, THE OFFICE THAT FUNDED THIS ACTIVITY. I'LL READ TITLES AND CALL THEM UP. THE FIRST TITLE IS THE NIH MICROBIOME PROJECT OVERVIEW OF HUMAN MICROBIOME GOALS AND ACCOMPLISHMENTS, ARE WE OKAY? THAT TALK WILL BE DELIVERED BY DR. MARY ELLEN PERRY, THE SECOND WILL BE GREG BUCK AT VIRGINIA COMMONWEALTH UNIVERSITY, HIS TALK IS IMPACT OF THE MICROBIOME OF THE FEMALE REPRODUCTIVE TRACT ON HEALTH AND PREGNANCY FOLLOWED BY A TALK BY MIKE SNYDER, AT STANFORD UNIVERSITY, DISCUSSING HIS PROJECT, INTEGRATIVE PERSONAL OMICS PROFILING DURING PERIODS OF ENVIRONMENTAL STRESS, AND FINALLY WE'LL CLOSE WITH CURTIS HUTTENHOWER FROM THE BROAD INSTITUTE, CHARACTERIZING GUT MICROBIAL ECOSYSTEM FOR DIAGNOSIS AND THERAPY IN INFLAMMATORY BOWEL DISEASE. THERE'S A JOINT Q&A SESSION, EACH SPEAKER WILL CALL OUT ONE CRITICAL GAP TO ADDRESS DURING THE Q&A. I'M SORRY, I DIDN'T TURN THE PAGE. I'M SORRY. THE LAST PERSON IS OWEN WHITE AT THE UNIVERSITY OF MARYLAND, WHO WILL TALK ABOUT MANAGEMENT AND INTEGRATION OF iHMP DATA. THANK YOU. >> IT'S A PRIVILEGE TO BE HERE TODAY TO TELL YOU ABOUT GOALS AND ACCOMPLISHMENT OF THIS WONDERFUL MICROBIOME PROGRAM, A 10-YEAR INVESTMENT BY THE COMMON FUND. AND THE GOALS TO CHARACTERIZE AND CATALOG THE MICROBES ON AND IN OUR HEALTHY HUMAN BODIES, AND ALSO TO ENABLE OTHERS TO INVESTIGATE THE ROLE OF THE MICROBIOME IN HEALTH AND DISEASE. ONE VERY INDIRECT INDICATION OF THE SUCCESS AND IMPACT OF THIS PROGRAM, NIH FUNDING, INSTITUTES HAVE GONE UP 40-FOLD SINCE THE BEGINNING OF THE PROGRAM. THIS IS PART OF THE PORTFOLIO ANALYSIS LITA INTRODUCED, THANKS FOR THAT. COMMON FUND PROGRAMS ARE INTENDED TO BE SHORT TERM CATALYTIC PROGRAMS WITH BROAD AND TRANSFORMATIVE IMPACT. WHAT WAS IT ABOUT THE MICROBIOME THAT CONVINCED NIH LEADERSHIP THERE SHOULD BE A MICROBIOME PROGRAM IN 2007? WE KNEW THERE WERE VERY MANY HUMAN PATHOGENS, OUTNUMBERED ON EARTH BY MORE BENEFICIAL BACTERIA. ON OUR BODIES THERE ARE MORE MICROBIAL AND HUMAN CELLS, AND THOSE CONTAIN ABOUT 100 TIMES AS MANY GENES AS OUR BODIES DO. AND WE KNEW THERE WERE INDICATIONS THAT THESE INFLUENCE OUR HEALTH SOMEHOW BUT DIDN'T KNOW WHAT THE MICROBES WERE THAT MADE UP A HEALTHY MICROBIOME AND DIDN'T KNOW HOW CHANGES IN THE MICROBIOME INFLUENCED OUR HEALTH, WHETHER THEY DIRECTLY INFLUENCED OUR HEALTH. BY 2007 WE HAD ADVANCES IN TECHNOLOGIES THAT WILL HELP US ANSWER THESE QUESTIONS. MAINLY THERE WERE FASTER AND CHEAPER DNA SEQUENCING TECHNIQUES, ALLOWING VERY HIGH DEPTH SEQUENCING OF MANY DIFFERENT SAMPLES THAT COULD BE DONE AND FASTER AND CHEAPER BIOINFORMIC TOOLS TO ANALYZE THE COMPLEX MIXTURES OF GENOMES, OR META GENOMES FROM THE BODY SITES. SO NIH APPROVED THROUGH THE COMMON FUND THE HMP, 2007 TO 2012. THE FIRST PHASE IS HMP1. GOALS WERE TO CATALOG MICROBES THAT INHABIT THE HEALTHY HUMAN BODY, EXAMINE WHETHER CHANGES IN THE MICROBIOME CAN BE RELATED TO CHANGES IN HEALTH AND DISEASE, AND TO PROVIDE A STANDARDIZED DATA RESOURCE TO ENABLE THE COMMUNITY TO STUDY THE HUMAN MICROBIOME. IT ALSO ALONG THE WAY DEVELOPED TECHNICAL APPROACHES, COMPUTATIONAL TOOLS TO HELP GENERATE THE DATA AND ANALYZE THE DATA. THE DATA WERE RELEASED AS SOON AS THEY WERE QUALITY CONTROLLED TO THE COMMUNITY FOR ANALYSIS, AND TOTAL BUDGET FOR THE FIRST PHASE WAS AROUND $180 MILLION WITH CO-FUNDING FROM INSTITUTES AND CENTERS AND OTHER SOURCES OF ABOUT $30 MILLION, COMMON FUND CONTRIBUTING ABOUT $150. THE PROGRAM WAS RUN AS LARGE CONSORTIUM OF HUNDREDS OF MEMBERS ON SIX INITIATIVES INCLUDING TECHNOLOGY DEVELOPMENT AND COMPUTATIONAL TOOL DEVELOPMENT, AND THEY WERE COORDINATED A LOT BY THE DATA ANALYSIS COORDINATING CENTER, URL HERE YOU MIGHT WANT TO CHECK OUT, WE'LL TALK ABOUT THIS LATER TODAY. AND THE TWO MAJOR INVESTMENTS OF TIME, ENERGY AND BUDGET FOR THIS FIRST PHASE WERE ON A HEALTHY COHORT STUDY WHICH WAS TO ANSWER THAT QUESTION ABOUT IS THERE A CORE HUMAN MICROBIOME WE ALL SHARE, AND THE SECOND EMPHASIS WAS DEMONSTRATION PROJECTS THERE WERE ABOUT 15 OF THESE WHOSE JOB IT WAS TO INVESTIGATE CHANGES IN THE MICROBIOME AND THAT RELATION TO HEALTH STATUS, A BROAD ARRAY OF DIFFERENT CONDITIONS THAT WERE ADDRESSED. IN 2012 THE CONSORTIUM PUBLISHED A PAPER COLLECTION, IN "NATURE" AND "PLOS." AT THE TIME THIS WAS THE WORLD'S LARGEST COLLECTION OF METAGENOMES FROM A HUMAN, AND THIS RECORD WILL BE MAINTAINED AS YOU'LL HEAR. A SERIES OF PAPERS HAD A LARGE IMPACT, ONE OF THE INDICATIONS OF THAT IS OVER 2,000 CITATIONS FOR THE COLLECTIONS IN 2012, A COMMUNITY RESOURCE FOR DISCOVERY BY OTHERS. THE OBSERVATION FROM THE GROUP AT THAT TIME WAS 360 MICROBIAL GENES, AND FOR TOTAL OF ABOUT 800 MILLION UNIQUE MICROBIAL GENES, SOME OF WHICH HAVE UNKNOWN FUNCTIONS. TOGETHER, IF WE POOLED ALL OUR MICROBES, WE WOULD HAVE 10,000 SPECIES. WE DON'T EACH CARRY THESE, BUT TOGETHER WE HAVE THIS COLLECTION. THESE DATA THAT WERE DEPOSITED, FROM 2012, YOU CAN SEE YOU CAN GET THE DATA AND YOU COULD GET THE TOOLS. THIS PORTAL IS STILL VERY POPULAR, IN THE LAST YEAR IT HAD OVER 82,000 VISITORS FROM OVER 175 COUNTRIES. AND THOSE PEOPLE ARE USING THE HMP DATA TO DO TWO THINGS, TWO BIG CATEGORIES OF INVESTIGATIONS. ONE IS REPRESENTED HERE WHERE THEY TAKE THE DATA AND USE IT TO DEVELOP NEW ANALYTICAL TOOLS TO MINE DATA FOR INFORMATION. IN THIS CASE, THEY ASSIGNED SOME UNKNOWN GENES TO SPECIFIC ENZYME TYPES. AND IN THIS CASE, HYPOTHESIS-DRIVEN RESEARCH AIDED BY HMP DATA, THIS GROUP DISCOVERED NEW ANTIBIOTICS. THE HMP PAPERS DEMONSTRATED A NUMBER OF IMPORTANT FINDINGS,& AND THE ONE SHOWN HERE IS IMPORTANT TO YOU TODAY BECAUSE IT HELPS INTRODUCE THE NEXT PHASE OF THE PROGRAM WHICH IS THE ONE YOU'RE GOING TO HEAR ABOUT IN THE TOP OF THE SESSION. YOU FOCUS ON THE FIRST PANEL, THIS IS A REPRESENTATION OF THE TAXONOMIC ASSIGNMENT OR PHYLA IN BODY, THE NOSE, THE SKIN, UROGENITAL, THE VAGINA, YOU CAN SEE THE PHYLA ARE VERY DIFFERENT FROM ONE SITE TO ANOTHER. SO ON OUR OWN BODIES WE DON'T HAVE ONE MICROBIOME, ALL OVER, IT DIFFERS FROM PLACE TO PLACE. IF YOU LOOK ACROSS INDIVIDUALS WE DIFFER EVEN WITHIN OUR BODY SITES, NOSES AREN'T ALL THE SAME IN THE MICROBIOME. THERE ISN'T A PARTICULAR CORE HEALTHY MICROBIOME WE ALL SHARE. BUT IF WE LOOK -- ASSIGN METABOLIC PATHWAYS TO THOSE GENES ENCODED BY THOSE BACTERIA WE SEE MUCH MORE CONSERVATION, METABOLIC PATHWAYS LOOK QUITE SIMILAR ACROSS SITES EXCEPT FOR VERY SPECIALIZED VAGINA, AND THEY LOOK MUCH MORE CONSTANT ACROSS INDIVIDUALS. SO THIS INDICATED THAT PERHAPS A FUNCTION OF THE MICROBES WE NEED TO BE THINKING ABOUT MORE THAN JUST AN INVENTORY OR CATALOGING OF WHO IS THERE, PART OF THE IMPETUS FOR THE SECOND PHASE, HMP2 OR iHMP, BECAUSE THEY ARE INTEGRATING DATA AND WE'LL TELL YOU ABOUT THIS IN A LITTLE BIT. OWEN WILL TELL YOU ABOUT IT A LOT. THE GOAL OF THIS PART OF THE PROGRAM WAS TO CHARACTERIZE THE MICROBE'S FUNCTION FOR DOING MULTI OMIC ANALYSES OF BOTH HOST AND MICROBE FUNCTION. SO GENOMICS, METABOLOMICS, TRANSCRIPT OMICS, PHENOTYPIC DATA, EACH GROUP HAS DATA THEY ARE ACCUMULATING. IMPORTANTLY EACH OF THE STUDIES FOR THE SECOND PHASE IS A LONGITUDINAL STUDY TO HELP US MAKE LINKS BETWEEN CHANGES THAT COULD BE CAUSAL IN THE MICROBIOME, SORRY, CAUSAL TO CHANGES IN THE DISEASE. AGAIN, THE DATASETS ARE BEING DISSEMINATED FOR ANALYSIS TO THE COMMUNITY. THE COMMON FUND BUDGET FOR THIS PHASE WAS $26 MILLION, AIDED VERY MUCH BY CO-FUNDING FROM INSTITUTES, CENTERS AND OFFICE AT THE NIH. IN 2014, THIS HMP2 OR iHMP CONSORTIUM PUBLISHED A MARKER PAPER INDICATING WHERE THEY ARE GENERATED AND BEING DEPOSITED. THEY ARE DEPOSITING DATA AT THE DAK SO YOU CAN FIND THE HMP1 OR 2 DATA. AS LITA INTRODUCED, THE HMP2 PROJECT WILL BE PRESENTED BY GREG BUCK, INFLAMMATORY BOWEL DISEASE PROJECT, AND MIKE WILL TELL YOU ABOUT STRESS AND DIABETES. THE CONSORTIUM HAS BEEN ACTIVE, ESPECIALLY IN THE RESEARCH COMMUNITY. VERY EARLY ON ONE OF THE CHARGES WAS TO PROVIDE A CATALOG OF REFERENCE GENOMES, THEY PUT OUT A MOST WANTED POSTER ASKING THE COMMUNITY WHICH MICROBES DO YOU WANT US TO SEQUENCE AND PUT IN THIS REFERENCE CATALOG SO YOU CAN REFER BACK TO IT LATER WHEN YOU DO AN ANALYSIS. THEY REALIZED THEY WERE GENERATING TOO MUCH DATA FOR THE HUNDREDS OF THEM TO ANALYZE, SO REACHED OUT TO THE COMMUNITY AND SAID WHO WANTS TO BE PART OF DATA ANALYSIS WORKING GROUP CALLED THE DOG, AND THAT GROUP GENERATED A LOT OF COMPUTATIONAL TOOLS THAT HELPED TO REVEAL SOME OF THE FINDINGS THAT WERE LATER PUBLISHED IN THE PAPER COLLECTION IN 2012. THIS BLUE LINE SHOWS GOOGLE SEARCHES FOR THE MICROBIOME OVER TIME. WE'D LIKE TO TAKE CREDIT FOR THE BUMP, MAYBE FROM THE "NATURE" PAPER. IN-- OOPS, IN 2013 AND 2014 -- HI GUYS. IN 2013 AND 14 OWEN WHITE AT THE DAK COLLABORATED WITH FOLKS AT NIH GRI AND NIAID HERE AT THE NIH TO MOVE THE MICROBIOME DATA ON TO THE AMAZON CLOUD TO MAKE IT AVAILABLE FOR PEOPLE WITHOUT HAVING TO DOWNLOAD THE VAST AMOUNTS OF DATA, THEY COULD ANALYZE IT ON THE CLOUD. AND THAT IS STILL PRESENT FOR PEOPLE. IMPACT RECENTLY, OWEN'S GROUP AT THE UNIVERSITY OF MARYLAND CARRIED OUT A TRAINING WORKSHOP TO HELP PEOPLE LEARN HOW TO ANALYZE DATA IN THE CLOUD. ALSO I HAD MENTIONED, THE CONSORTIUM PUBLISHED A MARKER PAPER IN 2014, TO LET THE COMMUNITY KNOW WHAT THEY WERE DOING AND WHERE TO FIND THE DATA. I DON'T KNOW. THIS IS KIND OF WEIRD. IF YOU EVER WANT DO COME UP HERE -- WE TURN THAT THING AROUND. [LAUGHTER] SO ANOTHER INDICATION OF THE IMPACT ON POPULARITY OF THIS PROGRAM IS THE PAGE VIEWS ON THE NIH COMMON FUND WEBSITE, WHERE WE HAVE ABOUT 30 PROGRAMS AT ANY ONE TIME. IN 2016 WE HAD 30. YOU CAN SEE THE HMP GOT A QUARTER OF HITS, IT'S 1 OUT OF 30 PROGRAMS, THAT'S ABOUT 190,000 PAGE VIEWS, SO VERY HIGH INTEREST IN THIS PROGRAM. ANOTHER INDICATION OF THE IMPACT IS THE RELATIVE CITATION RATIO OF THE PROGRAM, WHICH IS THE MEDIAN WOULD BE ONE, NORMALIZED TO ONE, THAT ONE WOULD BE THE RELATIVE CITATION RATIO PER PAPER, MICROBIOME PAPER, IN WHATEVER FISCAL YEAR YOU'RE TALKING ABOUT. OVERALL THE PROGRAM HAS A MEAN RCR OF 7.5, BUT WHAT'S REALLY INTERESTING, VERY POWERFUL ABOUT THIS ANALYSIS, IT SHOWS THAT THERE ARE MANY PAPERS, MAYBE ABOUT 50 OR 60, THAT HAVE AN RCR GREATER THAN 14. VERY HIGHLY CITED. AND THESE INCLUDE OF COURSE THE "NATURE" PAPER THAT I TALKED ABOUT WHICH HAVE AN RCR OF 136 IN THIS ANALYSIS, BUT ALSO SEVERAL PAPERS ON COMPUTATIONAL TOOLS AND TECHNOLOGY DEVELOPMENT, VERY HIGHLY IMPACTED, INCLUDING ONE THAT HAS AN RCR OF 285. THE HMP PUBLICATIONS ADDRESS MANY DISEASE AREAS, INCLUDIG SOME OF THE ONES YOU'LL HEAR MORE ABOUT AFTER THIS TALK, AND THERE'S YET MORE TO COME. THIS FALL AND WINTER THERE WILL BE AN UPDATE TO THE HMP ONE HEALTHY COHORT STUDIES, THERE WILL BE MORE AND MORE iHMP DATA FOR DOWNLOAD FROM THE DACC, AND A PAPER COLLECTION FROM THE HMP2 CONSORTIUM. MY CRITICAL GAP WOULD BE TO INTEGRATE THE HMP DATASETS, ESPECIALLY PHENOTYPIC DATA YOU'LL SEE THERE'S A LOT OF COMING OUT OF ESPECIALLY THE SECOND PHASE OF THE PROGRAM, WITH OTHER HUMAN PHENOTYPIC DATA. THANK YOU TO THE PRODUCTIVE AND HAPPY GROUP, THIS IS THE SHOT FROM YESTERDAY'S FINAL STEERING COMMITTEE MEETING FOR THE HMP PROGRAM. NOT ALL OF US WERE HAPPY. I MENTIONED EARLIER THE CO-FUNDING FROM THE I.C.s, YOU CAN SEE MANY INSTITUTES, CENTERS AND OFFICES THAT CONTRIBUTE TO THIS PROGRAM. I WANT TO ACKNOWLEDGE THE iHMP EXTERNAL SCIENTIFIC, FRANCIS IS NOW ACTING AS CHAIR, AND EUGENE CHANG AND RICK STEVENS, AND P. P.I.s, CARRYING OUT ASSIGNMENTS WE KEEP PILING ON. AND LITA PROSECUTOR, THE COORDINATOR, WHOSE ENERGY AND POSITIVE ATTITUDE ARE ESSENTIAL. WITHOUT LITA'S PUSH AND DRIVE THE SECOND PHASE OF THE PROGRAM I CAN SAY WITH CONFIDENCE WOULD NOT HAVE HAPPENED. THANK YOU. [APPLAUSE] >> BECAUSE OUR TIMER ISN'T WORKING APPARENTLY, IT'S NOT HOOKED UP, I'M GOING TO USE MY CELL PHONE. SO WHAT I'LL DO IS THROW MY HAND AS FIVE, FIVE MINUTES LEFT. THANKS, MARY. UP NEXT IS GREG BUCK, TALKING ABOUT THE IMPACT OF THE FEMALE REPRODUCTIVE TRACT ON HEALTH AND PREGNANCY. >> I WANT TO ADD MY THANKS TO TO MARY AND COMMON FUND FOR FUNDING OUR RESEARCH OVER THE PAST COUPLE YEARS. AND NIAID AND NICHD, NHGRI, ORWH AND OTHER INSTITUTES THAT PROVIDED FUNDING FOR OUR RESEARCH. A SHOUT OUT TO LITA PROCTOR, HMP 1 AND 2 PROJECTS, HELPED US GET OUR WHOLE PROJECT ORGANIZED AND WORKING TOGETHER. SO WHAT I'M GOING TO DO IS TALK TODAY ABOUT WHAT WE'VE BEEN DOING IN THE HMP2 STUDY, A CONTINUATION AT SOME LEVEL OF OUR HMP1 STUDY ON VAGINAL MICROBIOME, NOW TAKING A MULTI-OMIC APPROACH TO LOOK AT THE IMPACT OF THE MICROBIOME ON PREGNANCY, MOMS PI. OBJECTIVE, WE'RE TAKING LONGITUDINAL MULTI OMIC STRATEGIES TO ELUCIDATE MECHANISMS BY WITH THE MICROBIOME IMPACTS OUTCOMES IN PREGNANCY WITH A FOCUS ON PRE-TERM BIRTH. WHY PRE-TERM BIRTH? WELL, APPROXIMATELY 1 IN 10 BIRTHS IN THE WORLD ARE PRE-TERM, PRE-TERM IS LESS THAN 30 WEEKS, 37 WEEKS OF GESTATION. THIS CAN BE HIGHER IN OTHER POPULATIONS, UP TO 1 IN 6 AFRICAN-AMERICANS HAVE HIGHER RATES OF PRE-TERM BIRTH. AND OVER 12 MILLION BIRTHS ANNUALLY IN THE WORLD ARE PRE-TERM. MORTALITY RATE CAN BE FAIRLY HIGH IN SOME CASES. THE SURVIVORS AS YOU'RE PROBABLY AWARE HAVE LONG AND VERY SHORT-TERM HEALTH ISSUES THAT CAN BE DEVASTATING TO THE FAMILIES. OVER $26 BILLION PER YEAR IS SPENT IN THIS -- IN THE UNITED STATES FOR PREMATURITY-ASSOCIATED HEALTH CARE. AT SOME LEVEL WE KNOW THIS IS CAUSED BY POORLY DEFINED BACTERIAL AGENTS. WE REALLY DON'T KNOW EXACTLY HOW THE IT IMPACTS ON PRE-TERM BIRTHS AND OUTCOMES OF PREGNANCY. WE KNOW COMPLEX MICROBEIUMS HAVE A NEGATIVE RISK FOR ADVERSE OUTCOMES AND WE'RE GETTING MORE DATA ABOUT THAT EVERY DAY. SO DEFINES OUR STUDY, LONGITUDINAL STUDY. WE EVENTUALLY RECRUITED 1594 MOTHERS AND THEIR BABIES SO WE HAD OVER 3,000 TOTAL SUBJECTS. IT WAS A LONGITUDINAL STUDY, AND WE'RE FOLLOWING PEOPLE FROM FIRST TRIMESTER THROUGH THIRD TRIMESTER AND LABOR AND DELIVERY. WE'RE TAKING A VERY COMPREHENSIVE SET OF SAMPLES, CERVICAL, VAGINAL, RECTAL, NARIES, BUCCAL, URINE AS WELL, FOLLOWED BABIES AT BIRTH AND DISCHARGE, IF THEY STAY IN THE NICU WE FOLLOWED THEM AS WELL. THERE'S IN OUR PROJECT WE'VE HAD 10+ CLINICAL COORDINATORS, OVER THREE-YEAR PERIOD COLLECTING IN ALL OF THE CLINICS AT OUR MEDICAL CENTER, AS WELL AS GLOBAL ALLIANCE TO PREVENT PREMATURITY AND PRE-TERM BIRTH IN SEATTLES, SAMPLES FROM UNIVERSITY OF WASHINGTON, YAKIMA AND OTHER HOSPITALS IN THE SEATTLE AREA. IT WAS A FAIRLY COMPREHENSIVE COLLECTION PROGRAM, WE WERE COLLECTING SAMPLES 24/7 FOR OVER 3 1/2 YEARS. THIS IS THE RESULT OF THAT PROCESS. WE COLLECTED ALMOST A QUARTER OF A MILLION SAMPLES OVER THE 3 1/2-YEAR PERIOD. THE SAMPLES WE COLLECTED WERE FOR DIFFERENT MULTI-OMIC APPROACHES DESCRIBED HERE BRIEFLY. TOTAL OF 231,000, I THINK THIS IS AN UNDERESTIMATE IN THE NUMBER OF SAMPLES COLLECTED, STORED IN FREEZERS AT UCU FOR YOUTH USE AND WE LOOK AT IT AS A GOLD MINE OF OPPORTUNITIES FOR THE FUTURE. THESE ARE THE SAMPLES WE'VE ANALYZED, 15,000 FOR THE MULTI-OMIC APPROACHES. THESE SAMPLES, THE DATA FROM THESE SAMPLES ARE GOING TO BE STORED AS MARY POINTED OUT AT THE DCC IN UNIVERSITY OF MARYLAND. SOME WILL GO IN OPEN ACCESS WHICH MEANS ANYBODY CAN HAVE ACCESS TO IT. THERE'S NO CONTROL AT ALL. THIS WILL BE HOSTED AT THE DCC. SOME OF OUR DATA HAS TO GO INTO A CONTROLLED ACCESS BECAUSE OF TE SENSITIVITY. THIS IS A PRE-TERM BIRTH STUDY, YOU CAN IMAGINE METADATA WOULD BE EXTENSIVE, IRB REQUIRES IT GOES IN A CONTROLLED ACCESS DATABASE. CONTROLLED ACCESS DATABASE IS THE dbGAP, AS YOU'RE PROBABLY AWARE TO GET ACCESS TO dbGAP YOU HAVE TO GO THROUGH A PROCESS TO HAVE THE ACCESS. THAT'S THE DIFFERENCE BETWEEN OPEN ACCESS AND CONTROLLED ACCESS. MOST OF OUR DATA WILL BE LINKED AT THE DCC, EVEN IF IT'S GOING TO CONTROLLED ACCESS, THERE WILL BE POINTERS AT THE DCC THAT WILL POINT TO WHERE THAT DATA IS AND COORDINATED IN SOME WAY, SHAPE OR FORM. EITHER DATA WILL GO IN METABOLOMICS WORKBENCH, METABOLOMICS DATA. THESE ARE THE DATA SETS THAT ARE AVAILABLE. THERE ARE THREE FOCUSED DATASETS, DESCRIBED HERE. EARLY PREGNANCY, TERM PREGNANCY, PRE-TERM BIRTH, THE WAY THE PROJECT PROGRESSED. WE STARTED WITH CROSS-SECTIONAL EARLY PRE-TERM AND LOOKED AT LONGITUDINAL TERM BIRTH AND NOW LOOKING AT THE PRE-TERM BIRTHS. THESE ARE THE NUMBERS OF SAMPLES IN EACH ONE OF THE DATA, OR THE SAMPLING TYPES WE HAVE HERE. AND THE OMICS TYPE OF ANALYSIS THAT WE'RE DOING. WE ALSO HAVE AROUND 15 OR 16,000 SAMPLES THAT HAVE BEEN PROCESSED IN KIND OF A GENERAL APPROACH TO DOING THE ANALYSIS. WE DO HAVE A SUBTEXT ON THE RACIAL DISPARITIES HERE. WE'RE VERY INTERESTED IN RACIAL DISPARITIES, AND THERE ARE RACIAL DISPARITIES, ASSOCIATED WITH PRE-TERM BIRTH AND ADVERSE OUTCOMES OF PREGNANCY. SO ALL OF OUR STUDIES HAVE ABOUT 50% OR MORE AFRICAN-AMERICANS THAT WE'RE LOOKING AT FOR THIS RACIAL DISPARITIES. WE PROBABLY WON'T -- I PROBABLY WON'T TALK MUCH ABOUT RACIAL DISPARITIES TODAY BUT THERE'S TWO POSTERS, POSTER 7 ON FRIDAY AND I DIDN'T MARK THE POSTER DOWN TODAY BUT THERE'S ANOTHER POSTER TODAY WITH JEN, A GENERAL PRESENTATION OF SOME OF THE DATA THAT WE'RE COLLECTING IN OUR ANALYSIS HERE. SO THERE WILL BE SOME WAY THAT YOU CAN GET ACCESS TO WHAT'S GOING ON IN OUR RACIAL DISPARITIES. WHAT HAVE WE LEARNED SO FAR? THIS IS A GENERAL SLIDE THAT COVERS MOST OF THE MULTI-OMIC DATA WE'VE BEEN LOOKING AT. 16S PROFILE, DNA PROFILES, RNA PROFILES, AND METABOLIC POTENTIAL AND PROGRESSION HERE. THE TAKEHOME MESSAGE IF YOU LOOK AT 16S, THIS IS DATA COMING FROM VAGINAL SAMPLES COLLECTED IN THE SECOND TRIMESTER IN OUR STUDY HERE SO IT'S NOT -- IT'S BASICALLY ALL IN THE SECOND TRIMESTER. 16S DATA AND METAGENOMIC DATA ACTUALLY ARE CLOSELY REFLECTING EACH OTHER, DIFFERENCE SUGGESTS OUR 16S ANALYSIS IS PRETTY ROBUST. INTERESTING THING ABOUT THE TRANSCRIPTOMIC ANALYSIS, IT DOESN'T EXACTLY REFLECT THE GENETIC POTENTIAL THAT ONE SEES IN THE METAGENOMIC DATA. ONE CAN SEE DIFFERENCES PARTICULARLY IN THIS, WE'RE VERY INTERESTED IN THIS DYNAMIC HERE. THIS LIGHT BROWN IS A BACTERIA ASSOCIATED WITH BACTERIAL VAGINOSIS, ASSOCIATED WITH HIGHER RISK OF PRE-TERM BIRTH, ADVERSE OUTCOMES IN PREGNANCY. G VAGINALIS IS RED, THIS IS ASSOCIATED WITH ADVERSE OUTCOMES AND PRE-TERM BIRTH. YOU CAN SEE IT LOOKS LIKE THE TRANSCRIPTION OF GARDENERELLA VAGINAL IS, WE DON'T KNOW WHAT'S GOING ON BUT IT SUGGESTS RELATIVELY QUIESCENT OR THAT GARDENERELLA EXPRESSING GENES AT RELATIVELY HIGH RATE. THIS IS ALSO REFLECTED IN THE METABOLIC POTENTIAL. THIS METABOLIC POTENTIAL IS BASED ON GENOMIC SEQUENCING AND METABOLIC EXPRESSION BASED ON RNA SEQUENCE. YOU CAN SEE PATHWAYS OVEREXPRESSED, THEY ARE ASSOCIATED WITH THE WHAT'S CALLED THE PENTO PHOSPATE SHUNT MAKING APP AND ANAEROBIC ENVIRONMENT, INTERESTING BECAUSE GARDENERELLA VAGINALIS, PHOSPATE SHUNT, THERE'S SOME OTHER DIFFERENCES HERE AS WELL. FOR EXAMPLE THIS IS A COUPLE OF THESE METABOLIC PATHWAYS ASSOCIATED WITH SYNTHESIS, CAPSULAR MATERIALS, THERE ARE SOME INTERESTING OBSERVATIONS HERE ASSOCIATED WITH -- LACTOBACILLUS HERE OVEREXPRESS IT'S IN THESE CAPSULAR GLYCAN MATERIALS, AND WE THINK THIS IS REFLECTIVE OF WHAT'S GOING ON WHY LACTOBACILLUS IS DOMINATING THE TYPE. IF WE CAN USE INTEGRATED MULTI-OMICS DISCRIMINATE DATA THAT WILL DISCRIMINATE CLINICAL SYMPTOMS, SO WE LOOKED AT TWO CLINICAL SYMPTOMS, DIVERSE VAGINAL MICROBEIUM, LOW PH IS CONSIDERED HEALTHY, HIGH Ph UNHEALTHY. ANALYSIS SHOWN HERE LOOKING AT CYTOKINE PROFILES, THIS IS RELATIVELY SMALL N INCLUDED BUT WE CAN INTEGRATE MULTI-OMIC DATA, USE INTEGRATED DATA TO DISCRIMINATE SOME CLINICAL PARAMETERS WHICH SUGGESTS WE MAY BE ABLE TO USE THIS AT SOME POINT TO PREDICT OUTCOMES, THAT MIGHT BE HELPFUL FOR TREATMENT OR AT LEAST PREVENTION. WHAT HAPPENS TO THE VAGINAL MICROBIUM IN PREGNANCY? THIS CAME FROM EARLY WORK, PREGNANT WOMEN HAD A MUCH MORE EXPANDED LACTOBACILLUS PROFILE THAN NON-PREGNANT WOMEN, AND WE WANTED TO ASK THE QUESTION, DOES MULTI-OMIC DATA PROVIDE INSIGHT ON MECHANISMS ABOUT WHICH CHROMOSOME -- THE MICROBIUM CONTRIBUTES TO ADVERSE PREGNANCY OUTCOMES IDENTIFYING EARLY PREDICTORS OF EARLY PRE-TERM BIRTH. WHEN DOES DIVERSITY -- DECREASE IN DIVERSITY OCCUR, FIRST, SECOND, THIRD TRIMESTER SAMPLES. DIVERSITY DECREASES BY SECOND TRIMESTER, SO THIS IS HAPPENING VERY EARLY IN PREGNANCY, INVOLVES INCREASED DOMINANCE BY LACTOBACILLUS, DEPRESSED PRINCE OF COMPLEX MICROBEIUMSES. VAGINAL SAMPLES, DIVERSITY INDEX, IT'S LOOKING AT CHANGE IN DIVERSITY IN FIRST, SECOND, AND THIRD TRIMESTER IN VAGINAL, RECTAL AND BUCCAL SAMPLES. THERE'S CHANGE IN DIVERSITY IN SECOND TRIMESTER IN VAGINAL SAMPLES, NOT TRUE FOR RECTAL OR BUCCAL, LOCALIZED TO THE FEMALE REPRODUCER TRACT. WE WANTED TO KNOW IF MULTI-OMIC DATA PREDICTION OF CHANGES IN COMMUNITY STATES, THIS IS SHOWING DIFFERENT COMMUNITY STATES ASSOCIATED BY DOMINANT BACTERIA. TRACKING LONGITUDINALLY ACROSS PREGNANCY, FIRST, SECOND AND THIRD TRIMESTER, INITIAL COMMUNITY STATES ARE RELATIVELY STABLE. LACTOBACILLUS GASSERI, PLOTTED HERE, MORE STABLE AND PERSISTENT THAN THE RIGHT-HAND SIDE. BY LOOKING AT MULTI-OMIC DATA COULD WE PREDICT THE CHANGES? SO WE LOOKED AT CYTOKINE PROFILES, CYTOKINE PROFILES JUST IN BRIEF, IF YOU LOOK AT THE LESS HEALTHY COMMUNITY STATES, G VAGINALIS OR BVAB1, DOMINATED BY LESS HEALTHY BACTERIA, TENDS TO HAVE INCREASED CYTOKINE EXPRESSION. THERE'S A PATTERN HERE, I'M NOT GOING INTO THAT RIGHT NOW BUT THERE'S A PATTERN HERE THAT CAN BE USED IN ANALYSIS OF MULTI-OMIC DATA AND PAUL BROOKS IN OUR GROUP USED CONTINUOUS MARKED OFF CHAIN MODELING OF COMMUNITY STATE TYPES USING THIS MULTI-OMIC DATA TO SEE IF WE COULD PREDICT CHANGES IN THE MICROBIUM WITH ACCURACY. HIS ANALYSI SHOWED YOU CAN PREDICTING TRANSITION, DEPENDENT ON HOST FUNCTION. WE LOOK AT THE PREDICTIONS OF CHANGE AND LOW IL-5 OR HIGH IL-5 TO PULL OUT ONE OF THE CYTOKINES THAT WE LOOKED AT. YOU CAN SEE, YOU CAN PREDICT PROBABILITY OF TRANSITION, HIGH IL-5 TRANSITION FROM A HEALTHY STATE WITH LACTOBACILLUS TO NOT CHANGE, IT'S ALMOST 100% AT HIGH IL-5 THAT WILL STAY HEALTHY. IN LOW IL-5 IT'S DECREASED. G VAGINALIS, LESS HEALTHY TO ANOTHER -- ANOTHER LESS HEALTHY LACTOBACILLUS ENTERUS, IN LOW THAT CHANGES, IN HIGH IL-5 PROBABILITY IS HIGH. SO YOU CAN USE THESE MULTI-OMIC ANALYSES OF HOST FACTORS TO PREDICT PREGNANCY RISK AND IT'S POSSIBLE THAT AT SOME POINT THIS WILL HAVE CLINICAL APPLICATIONS. I'M GOING TO SKIP OVER THE CONCLUSION SLIDE BECAUSE I THINK WE'VE COVERED THAT ALREADY. I WANTED TO MENTION SOME POSTERS WE HAVE HERE TODAY, WE HAVE TWO GENERAL POSTERS FROM SERRANO AND FETWISE, FRIDAY POSTER 7 TALKING ABOUT THE MOM'S P.I., AND TODAY POSTER 24 TALKING ABOUT THE PRE-TERM BIRTH STUDY WHICH I WASN'T ABLE TO TALK ABOUT TODAY. TWO POSTERS TALKING ABOUT SPECIFIC SPECIES, SMOKING GUN ON WHAT'S GOING ON IN THE VAGINAL MICROBIUM AND TWO TOOL-BASED POSTERS, FROM TOM USING NETWORK DIFFERENTIAL EXPRESSION AND MACHINE LEARNING APPROACHES TO TRY TO DETERMINE -- DISCOVER DIFFERENCES BETWEEN TRANSCRIPTOMES WE'VE BEEN LOOKING AT. STEVE FONG IS USING METABOLIC& MODELING TO DEFINE WHAT'S GOING ON IN THE MICRO BIUM AS WELL, TODAY, FRIDAY, STEVE IS POSTER 32. THE CRITICAL GAP THAT I WANTED TO MENTION, I'LL MENTION IT BRIEFLY, THE HUMAN GENOME. I THINK ONE OF THE THINGS THAT I HAVEN'T BEEN ABLE TO TALK ABOUT IN THE SHORT TIME TODAY IS RACIAL DISPARITIES, RACIAL DIFFERENCES WE SEE IN THE IMPACT. MICROBIUM ON ADVERSE OUTCOMES IN PREGNANCY, SIGNIFICANT DIFFERENCES, AFRICAN-AMERICANS HAVE HIGHER PROBABILITY OR HIGHER RISK OF ADVERSE OUTCOMES. AND WE'VE SHOWN THIS IS -- CLEAR RACIAL DIFFERENCES, WE HAVE NOT BEEN ABLE TO DETERMINE WHETHER THIS IS ALL GENETIC OR ENVIRONMENTAL. IT'S OBVIOUSLY BOTH ENVIRONMENTAL AND GENETIC. WE WOULD LIKE TO LOOK IN DEPTH AT THE HUMAN GENOME, IN PARTICULAR EPIGENETICS TO DETERMINE WHAT THOSE DIFFERENCES ARE. SO I THINK THAT'S THE CRITICAL GAP I'D LIKE TO MENTION, AMONG OTHERS. AND THIS IS THE TEAM THAT'S WORKED ON THIS, VAGINAL MICROBIUM CONSORTIUM AND VCU, OUR NIH PARTNERS AND GAPPS TEAM IN SEATTLE. I'LL STOP THERE. THANK YOU. >> MIKE SNYDER FROM STANFORD TO TALK ABOUT INTEGRATE IRV PERSONAL OMICS PROFILING DURING PERIODS OF ENVIRONMENTAL STRESS. >> I WOULD ALSO LIKE TO EXTEND MY THANKS TO LITA. IT'S BEEN WONDERFUL BEING PART OF THIS PROGRAM. IT'S VERY EXCITING, WE'RE NOW AT THE VERY BEST TIME. SO OUR PROJECT IS TO ANALYZE A SET OF PRE-DIABETICS FOR THEIR PROFILES OVER TIME AND THROUGH VARIOUS PERTURBATIONS. UST BY WAY OF BACKGROUND, MOST OF YOU APPRECIATE THAT DIABETES IS A GROWING PROBLEM IN THE WORLD, AND THE IN THE U.S. ALONE 29 MILLION INDIVIDUALS ARE CURRENTLY DIAGNOSED AS DIABETIC, 86 MILLION THAT ARE PRE-DIABETIC, ANNUAL COST OF $245 BILLION EACH YEAR, ESTIMATED TO AFFECT THE ECONOMY. ALSO EQUALLY POWERFUL IF YOU THINK ABOUT IT, 90% OF INDIVIDUALS WHO ARE PRE-DIABETIC DON'T EVEN KNOW IT. THAT MEANS LOOKING AT THIS ROOM THERE'S A LOT OF YOU OUT THERE ACTUALLY SPIKING YOUR GLUCOSE, PRE-DIABETIC AND HAVE NEW IDEA. I GUARANTEE THAT'S TRUE. WHY IS THIS SIGNIFICANT? WELL, A LOT OF THESE PRE-DIABETICS WILL GO ON TO BECOME DIABETICS IN THEIR LIFETIME. OBVIOUSLY THERE'S A STRONG NEED FOR UNDERSTANDING ETIOLOGY, MANAGEMENT AND TREATMENT OF BOTH DIABETES AND CERTAINLY TO PREVENT PEOPLE FROM BECOMING DIABETIC. SO, AGAIN, OBJECTIVE MUCH OUR PROJECT LONGITUDINAL PROFILING, BOTH MICROBIAL AND HOST COMPONENTS FOR OVER THE NOW FOUR-YEAR PERIOD WE'VE BEEN FUNDED. WHAT WE'RE PARTICULARLY INTERESTED IS PROFILING PEOPLE WHILE HEALTHY AND DURING PERIODS OF TIME OF STRESS. THERE'S BEEN QUITE A FEW STUDIES, I DON'T HAVE TIME TO SHOW THE RELATIONSHIP BETWEEN DIABETES AND MICROBIAL COMPOSITION. AND SOME EVIDENCE SUGGESTING THAT STRESS IS ASSOCIATED WITH TYPE 2 DIABETES, SOME WORK FROM OUR GROUP, PERHAPS VIRAL INFECTIONS ARE CONTRIBUTING. WE'VE BEEN PROFILING SAMPLES FROM 116 INDIVIDUALS, 66 ARE PRE-DIABETIC OR INSULIN RESISTANT, RESISTANT TO THE FORM OF GLUCOSE MISREGULATION THAT'S OFTEN ASSOCIATED WITH ULTIMATELY BECOMING DIABETIC. SINCE WE PROFILED OVER TIME WE SAMPLED EVERY THREE MONTHS WHILE HEALTHY, WHEN ADVERSE EVENT COMES ALONG LIKE RESPIRATORY VIRAL INFECTION WE'LL TAKE FIVE MORE SAMPLES THROUGH THIS PERIOD. A NUMBER EVER FOLKS HAVE UNDERGONE DIET PERTURBATIONS SUCH AS WEIGHT GAIN, WEIGHT LOSS, OTHER DIETARY STUDIES. AT OTHER TIMES OF STRESS, FOR EXAMPLE SEVEN INDIVIDUALS I BELIEVE UNDERGONE A COLONOSCOPY, WE'LL DO MANY MORE SAMPLES THEN. BOTTOM LINE THERE'S ADVERSE THINGS GOING ON, WELL, WE'LL TRY AND GET DATA FROM THAT. THESE ARE ASSAYS WE'VE BEEN DOING ON HMP SAMPLES, 105 MADE IT INTO THE HMP ANALYSIS PIPELINE. WE'VE BEEN ANALYZING EIGHT FROM THESE, VERY EXTENSIVE MEDICAL TESTING AS WELL. BOTH TRADITIONAL SORTS AS WELL AS THOSE THAT ARE VERY GLUCOSE RELATED. WE ALSO HAVE COLLECTED OTHER KINDS OF DATA, I'LL MENTION A LITTLE BIT LATER. THE ONES IN BLUE ARE HOST DATA THAT WE'RE COLLECTING, THE FIRST NUMBER IS THE NUMBER OF ANAYLTES, MEASURED IN EACH OF THESE SAMPLES, THESE ARE THE SAMPLES, TOTAL MEASURE BEHIND THAT. WE'RE GENERATING LOTS OF DATA FROM EACH OF THE DATA TYPES. BLUE IS HOST. GREEN IS HOST AND MICROBE. AND THEN RED ONES OVER HERE ARE MICROBIAL ASSAYS WE'VE BEEN RUNNING. SO THIS IS A SUMMARY OF THE SAMPLING OVER THIS FOUR-YEAR PERIOD. WE'VE COLLECTED ROUGHLY 1800 TIME POINTS, MULTIPLE SAMPLES AT EACH TIME POINT, OVER 8,000 SAMPLES COLLECTED AND STORED IN THE FREEZER. WE'VE PROFILED UNDER THE HMP ABOUT 990, SO CLOSE TO 1,000 TIME POINTS, GENERATED ROUGHLY 7,000 DATASETS FROM NINE OMES NOW, OVER 13 MILLION MEASUREMENTS HAVE BEEN MADE. WHAT'S VERY SPECIAL ABOUT THIS PROJECT AND WHY IT WILL BE A POWERFUL REFERENCE IS THAT NEARLY ALL OF THE INDIVIDUALS, NOT ALL BUT NEARLY ALL AGREED TO MAKE DATA OPEN ACCESS IN THE PUBLIC DATABASE, INCLUDING GENOME SEQUENCES. THAT MEANS YOU DON'T NEED RESTRICTED ACCESS TO GET ACCESS TO DATA, ALL OF YOU CAN LET YOU LOOK AT IT. WHAT'S SPECIAL ABOUT THE MICROBIOME DATA, I SHOULD SAY HERE IS A SUMMARY. MOSTLY DOING 16S SEQUENCING FOR BUDGETARY REASONS, BUT WE DO HAVE METAGENOMIC DATA FROM CRITICAL SAMPLES AND META TRANSCRIPTOMIC DATA AS WELL. WHAT HAVE WE LEARNED? ALL RIGHT. I'M GOING TO GO THROUGH FIVE THINGS WE LEARNED. EVERYONE IS UNIQUE. WE'RE ALL SPECIAL AND NOT JUST TO OUR MOTHERS. THIS IS THE EXAMPLE FROM THE MICROBIOME. MARY HAS TOLD YOU WE ALL HAVE INDIVIDUAL AND PERSONAL MICROBIOMES, BUT IF YOU THINK ABOUT IT WE'VE BEEN PROFILING PEOPLE NOW FOR THREE OR FOUR YEARS, SO WE CAN SEE HOW THE& MICROBIOME IS STABLE OR BOUNCING AROUND. TURNS OUT PERSONAL MICROBIOMES FOR THE MOST PART ARE QUITE STABLE. EVEN OVER LONG PERIODS. IN BLUE IS ACTUALLY DIVERSITY OF SAMPLES WITHIN AN INDIVIDUAL. IN RED IS THEIR COMPARISON TO OTHER INDIVIDUALS IN THE COHORT. FOR THE MOST PART PERSONAL MICROBIOMES ARE PERSONAL AND STABLE. IT IS INTERESTING AS YOU GET TOWARDS THIS END OF THE CURVE THERE ARE PEOPLE WHO ARE AS DIFFERENT AMONGST THEIR SAMPLES AS WITH OTHERS, SO THAT WILL BE A VERY INTERESTING COHORT SET OF FOLKS TO LOOK AT IN MORE DETAIL. WE THINK THIS IS TRUE FOR VIRTUALLY EVERY OME, WHEN WE LOOK AT HEALTHY TIME POINTS, WE SEE IN GENERAL PEOPLE'S PROFILES WILL CLUSTER ACCORDING TO THEMSELVES, NOT ACCORDING TO TIME OR THINGS LIKE THAT. FOR EXAMPLE, THIS IS LOOKING AT ONE PARTICIPANT, SPACE OF METABOLOME, HEALTHY SAMPLES CLUSTER TOGETHER DOWN HERE. THIS OTHER INDIVIDUAL'S SAMPLES WILL CLUSTER HERE, SO A AND SO FORTH. WE'LL SEE THIS FOR CYTOKINES AND SUCH AS WELL. AGAIN, WE ALL HAVE PERSONAL MOLECULAR COMPOSITIONS, AND THEY ARE FAIRLY STABLE OVER TIME. ONE THING IMPORTANT FROM A CLINICAL STANDPOINT, INSULIN RESISTANCE FOLKS ARE DIFFERENT FROM THE INSULIN SENSITIVE FOLKS NO MATTER WHICH ASSAY WE USE. TO RUN YOU THROUGH A LITTLE OF THIS, THIS IS THE MICROBIOME, SENSITIVE FOLKS WILL HAVE DIFFERENT STRAINS AND SUBSPECIES DIFFERENT FROM RESISTANT FOLKS. THIS IS THE METABOLOMICS PROFILE, SAME THING TRUE HERE. THIS IS INSULIN SENSITIVE FOLKS, TENDS TO HAVE THESE, RESISTANTS HAVE THOSE. WE CAN GET INDIVIDUAL REGRESSION ANALYSIS, INDIVIDUAL METABOLITES THAT WILL DISTINGUISH THESE, THIS ONE IS QUITE INTERESTING BECAUSE WE FOUND IT'S DIFFERENT IN INSULIN RESISTANT PEOPLE. METABOLITE COMES FROM THE MICROBIOME SO A LOT OF METABOLITES ARE FROM THE MICROBIOME, SOME FROM THE MOST, SOME MAY BE FROM THE FOOD. THE POINT IS WE CAN DISTINGUISH THIS. I SHOULD SAY TO DO THESE INSULIN RESISTANT ASSAYS THE WAY WE DO IT, 6-HOUR TESTS THAT COST THOUSANDS OF DOLLARS. WE CAN NOW WE BELIEVE START SETTING UP WHAT SHOULD BE MORE PREDICTIVE TESTS FOR PROBABLY SOMETHING ON THE ORDER OF $50 THAT WILL ONLY TAKE A BLOOD DRAW AS OPPOSED TO ALL-DAY VISIT FROM FOLKS. ONE OF THE INTERESTING THINGS IS BY INTEGRATING DIFFERENT DATA WE CAN SEE HOW SYSTEMS, IF YOU WILL, BIOLOGY AND CHEMISTRY WILL CHANGE AMONGST DIFFERENT CLASSES OF INDIVIDUALS. THAT IS TO SAY HERE IS COMPARING METABOLITES AND THE MICROBIOME IN BOTH SENSITIVE AND RESISTANT FOLKS, AND THEY BEHAVE DIFFERENTLY IN THOSE TWO CONTEXTS. SO THIS METABOLITE, FOR EXAMPLE, WILL ACTUALLY SHOW A DIFFERENT CORRELATION WITH THIS MICRO IN INSULIN SENSITIVE VERSUS INSULIN RESISTANT. DEPENDING ON THE ENVIRONMENT, THE POWER OF MATCHING CLINICAL PHENOTYPES WE THINK IS WHAT'S GOING ON IN MORE COMPLEX SYSTEMS LEVEL. LIKEWISE WE KNOW INSULIN SENSITIVE AND INSULIN RESISTANT FOLKS RESPOND DIFFERENTLY TO INFECTION. THIS IS TRANSCRIPTOME, RNA-SEQ DATA, WE BELIEVE TRUE FOR OTHER ASSAYS AS WELL. IN GREEN HERE ARE THE INSULIN SENSITIVE FOLKS. HERE ARE RESISTANT. FIRST THREE TIME POINTS, IF YOU WILL, THIS IS EARLY, MIDDLE, LATE IN THE VIRAL INFECTION TIMES. THIS IS RESISTANT ONES EARLY, MIDDLE, LATE. THOSE ARE MOLECULAR PATHWAYS, IF YOU WILL. WHAT YOU'RE SUPPOSED TO APPRECIATE, LOOK AT THE PATH THE GREEN PATTERNS ARE DIFFERENT FROM PURPLE. PATHWAYS CHANGING IN SENSITIVE FOLKS ARE DIFFERENT FROM RESISTANTS FOLKS, NOT ACTUALLY RESPONDING TO INFECTIONS EXACTLY THE SAME WAY. MAYBE TECHNICAL REASONS FOR SOME OF THIS. WE'LL POINT OUT THAT TAKE NEITHER LOOKED AT IMMUNIZATION, REAL AND VIRAL INFECTION IS NOT SURPRISING. REAL VIRAL INFECTION HAS A DIFFERENT RESPONSE, WE WOULD ARGUE THAN SIMPLE IMMUNIZATION, WHICH IS WHAT MOST PEOPLE STUDY. WE ARGUE IT'S POWERFUL TO BE STUDYING DISEASE AS IT'S ACTUALLY OCCURRING. A SUBSET OF OUR FOLKS HAS DONE A WEIGHT GAIN-WEIGHT LOSS STUDY MEANING THEY HAVE OVER EATEN FOR 30 DAYS AND GO ON A DIET FOR 60 DAYS AND SAMPLE BEGINNING, MIDDLE, HALF INSULIN RESISTANT, HALF BMI MATCHED HEALTHY CONTROLS. AND WHAT WE FOUND BY DOING MULTI-OMICS ANALYSIS WE CAN ACTUALLY SEE THE DIFFERENT PATTERNS OF MOLECULES AND HOW THEY WILL CHANGE AS PEOPLE GAIN AND LOSE WEIGHT, WE'LL ALSO BE ABLE TO DRILL INTO SOME OF THESE AND SEE SPECIFICALLY SOME OF THE PATTERNS. EXAMPLE, IF YOU LOOK DOWN HERE AT THIS ONE, CASE FOR MOLECULES GO UP, DIFFERENT MOLECULES INCREASE IN WEIGHT GAIN, RETURN DURING WEIGHT LOSS, TOP PATHWAY IS INFLAMMATION. SECOND HIGHEST PATHWAY, CHANGES ARE EQUALLY HIGH, HYPERTROPHIC CARDIOMYOPATHY PATHWAY, AS YOU GAIN WEIGHT YOU'RE MORE SENSITIVE TO HEART ATTACKS, WE ARGUE THIS IS A POSSIBLE MOLECULAR EXPLANATION FOR THAT SORT OF OBSERVATION, THAT THESE PATHWAYS ARE MISREGULATED. WE DO KNOW THAT PEOPLE WILL SHIFT MICROBIOME, THIS IS WORK FROM GEORGE'S LAB, LOOKING AT MICROBIOME SHIFT, AS PEOPLE GAIN, SORRY, GO THROUGH A VIRAL INFECTION. MICROBIOME WILL SHIFT. ONE OF THE THINGS WE FOUND FROM THE WEIGHT GAIN AND WE BELIEVE THE MICROBIOME CASE AS WELL, YOUR MICROBIOME WILL SHIFT DURING THESE ADVERSE TIMES, BUT IT ACTUALLY TURNS OUT YOU STILL LOOK MORE LIKE YOURSELF THAN THE PERSON SITTING NEXT TO YOU. PERSONAL MICROBIOMES ARE ROBUST, WE WOULD ARGUE, TO SHORT-TERM PERTURBATION. EACH COLOR IS A DIFFERENT PERSON, WEIGHT GAIN-WEIGHT LOSS, THEY CLUSTER BY PERSON, NOT BY WHETHER THEY HAVE GAINED WEIGHT OR LOST WEIGHT. SO, AGAIN, YOUR PERSONAL MICROBIOME WE WOULD ARGUE IS FAIRLY ROBUST, THE SHORT-TERM PERTURBATIONS, I DOUBT THAT'S TRUE FROM LONG TERM FROM THINGS MENTIONED ALREADY BUT WE BELIEVE IT'S TRUE FOR SHORT TERM. ONE NICE THING WE DID DURING THIS PROJECT, WE INTRODUCED THE IDEA OF BRINGING WEARABLES, COMMON WEARABLES, FOR RESEARCH. THIS HAS BEEN DONE FOR TRACKING ACTIVITY AND SUCH. OKAY. WE GET TO SEE OUR ILLUSTRIOUS PANEL HERE. THEY LOOK BEAUTIFUL. IF WE CAN BRING THEM BACK TO REALITY, AS MUCH AS I ENJOY SEEING THEM. [LAUGHTER] LET ME TELL YOU ABOUT THIS. DID I DO SOMETHING WRONG HERE? OKAY. WELL ANYWAY, WE STARTED BRINGING WEARABLES, I'M WEARING ABOUT EIGHT OF THESE THINGS RIGHT NOW. THESE WE THINK ARE POWERFUL FOR THIS KIND OF RESEARCH, LONGITUDINAL RESEARCH. WE'RE ALMOST THERE. BECAUSE THEY COLLECT MEASUREMENTS CONTINUOUSLY, 250,000 MEASUREMENTS A DAY. WE HAVE DONE MANY THINGS WITH THEM BUT I CAN TELL YOU ONE THING THAT STOOD OUT IS THAT WE CAN PICK UP WHEN PEOPLE ARE PICKING UP INFECTIOUS DISEASES, VERY EARLY IN THE PROCESS. FOR EXAMPLE, THIS IS SHOWING THE ACQUISITION OF LYME DISEASE FROM ONE PERSON YOU'RE STARING AT RIGHT NOW, WHICH IS YOU CAN ACTUALLY PICK THIS UP BY OUTLYING HEART RATE MEASUREMENTS AND OUTLYING SKIN TEMP MEASUREMENTS, THEY WILL SHOW UP VERY EARLY IN THE PROCESS. THIS IS A DAILY MEASUREMENT SCHEME. AND IT TURNS OUT EVERY TIME FOR THIS PARTICULAR INDIVIDUAL HE'S GOTTEN SICK HE GETS THESE OUTLYING HEART RATE AND SKIN TEMPERATURE MEASUREMENTS. WE'VE LOOKED AT OTHER SUBJECTS, THEY ARE WELL MEDICALLY PHENOFIND. WE CAN PICK THIS DELTA HEART RATE, IF YOU WILL, VERY EARLY WE THINK BEFORE IT'S OBVIOUSLY -- BEFORE IT'S SHOWING STRONG SYMPTOMS, IF ANY SYMPTOMS, WE THINK WE CAN PICK THIS UP AT THE EARLIEST TIMES OF INFECTION, THIS CAME OUT OF THE COURSE OF OUR STUDY FROM THIS PROJECT. WE ALSO THINK THERE ARE PHYSIOLOGICAL DIFFERENCES BETWEEN SENSITIVE AND INSULIN RESISTANT FOLKS. I WON'T HAVE TIME TO GET INTO THIS. PUBLISHED SO YOU CAN TAKE A LOOK. WE THINK THIS TYPE OF PROJECT IS A PRECURSOR FOR PRECISION MEDICINE INITIATIVE AS WELL AS OTHER INITIATIVES THAT HAVE STARTED. BECAUSE AS YOU DO THESE DEEP PROFILES ON PEOPLE, YOU WILL LEARN THINGS THAT ARE VERY, VERY IMPORTANT FOR THEIR HEALTH. AND I'LL GIVE YOU ONE EXAMPLE. THERE ARE MANY EXAMPLES BUT FROM THE FIRST 70 FOLKS WE'VE ANALYZED WE'VE GONE OVER DETAIL -- GENOME IN INCREDIBLE DETAIL, AND 12 OF THEM HAVE INFORMATION IN THEIR GENOME THEY SHOULD KNOW ABOUT. IT AFFECTS WHEN THEY GO TO A DOCTOR'S OFFICE, THAT WILL BE A TEST RELATED TO THIS. ONE GOOD EXAMPLE THAT MANY ARE FAMILIAR WITH, ONE INDIVIDUAL HAS A BRCA MUTATION, PUTTING THEM AT HIGH RISK FOR BREAST CANCER. ANOTHER HAS MUTATION IN HEART FUNCTIONING GENE, SURE ENOUGH THIS PERSON HAS A HEART ISSUE THAT GOT EXPOSED IN FOLLOW-UP TESTS AND HE'S NOW ON DRUGS BECAUSE OF THIS. THIS IS THE SORT OF THING YOU CAN LEARN. IT'S FUN TO REFLECT WHERE WE'VE GONE THROUGH THE HUMAN MICROBIOME PROJECT OVER THE YEARS. IT WAS SANGER, THEN 454, ALGORITHMS DEVELOPED, CURTIS WILL MENTION, HAVE GOTTEN BETTER. IN THE LAST PHASE WE'VE BROUGHT IN MULTI-OMIC ANALYSIS AND LONG REACH SEQUENCING. THIS IS A SUMMARY OF SOME OF THE ALGORITHMS THAT HAVE BEEN GENERATED FROM OUR GROUP, I WON'T HAVE TIME TO DO THIS BUT YOU CAN VISIT SOME FOLKS' POSTERS AND LEARN ABOUT ALGORITHMS THEY HAVE DONE. I WOULD ARGUE LONG REACH SEQUENCES, WE'VE BEEN INVOLVED AS WELL AS OTHERS, FRUITFUL FOR PULLING OUT SUBSPECIES INFORMATION AND ASSEMBLING FROM COMPLEX META GENOMES, IF YOU GET LONG ENOUGH LONG READS. WHAT ARE SOME CHALLENGES? I THINK A BIG CHALLENGE OUT THERE IS WHAT'S CAUSE AND EFFECT, YOU SEE THE ASSOCIATIONS WITH BIOLOGICAL PHENOTYPES, BUT DON'T KNOW WHAT'S CAUSING WHAT, WHAT'S COMING ALONG FOR THE RIDE. WE NEED METHODS FOR BEING ABLE TO UNRAVEL THAT. I WOULD ARGUE RELATED CHALLENGE, SETTING UP PREDICTIVE MODELS FOR USING OMIC INFORMATION, FOR PREDICTING HEALTH STATES AND SUCH, AND I THINK THAT CAN EASILY BE GENERATED FROM THIS. THESE ARE THE POSTERS FROM OUR GROUP. AGAIN A JOINT PROJECT WITH GEORGE'S GROUP AND OUR GROUP, ONE POSTER TODAY, AND FOUR ON FRIDAY IN THIS AREA. AGAIN, THESE ARE THE FOLKS WHO DID THE WORK, LISTED HERE. WONDERFUL COLLABORATION WAS TRACY McLAUGHLIN AND GEORGE WINESTOCK HAS BEEN AN IMPORTANT PART OF THIS. AGAIN, THANKS TO NIH FOR SUPPORTING THIS. THANKS. >> NEXT UP WE HAVE CURTIS HUTTENHOWER FROM THE BROAD INSTITUTE AND HARVARD SCHOOL OF PUBLIC HEALTH, CHARACTERIZING THE GUT MICROBIAL ECOSYSTEM FOR DIAGNOSIS AND THERAPY IN INFLAMMATORY BOWEL DISEASE. >> MANY THANKS, LITA, FOR ORGANIZING, EVERYONE FOR ATTENDING, I ESPECIALLY WANT TO THANK MY CO-P.I., RAMNIK XAVIER, AND THE ENTIRE TEAM, MANY ARE HERE AND WE'LL SEE POSTERS ON PARTS OF THE WORK. OUR HUMAN MICROBIOME PROJECT IS ON INFLAMMATORY BOWEL DISEASE, AS MANY PEOPLE KNOW BOTH A CRITICAL HEALTH CONDITION IN AND OF ITSELF AND AN INTERESTING MODEL FOR THE COMPLEX INVOLVEMENT OF THE GUT MICROBIOME, SPECIFICALLY IN CHRONIC DISEASES. SPECIALLY 5 TO 10 YEARS KNOW BETTER STUDIES OF THE MICROBIOME HAVE HELPED TO QUICKLY REFINE OUR UNDERSTANDING OF THIS INVOLVEMENT FROM A HIGH LEVEL OBSERVATION EVER ECOLOGICAL DISRUPTION IN INFLAMMATORY BOWEL DISEASE TO A BETTER UNDERSTANDING OF SPECIFIC TAXA AND THEIR COMMON METABOLIC AND OTHER MOLECULAR FUNCTION DISRUPTED IN SUBSETS OF INFLAMMATORY BOWEL DISEASE, INCLUDING TWO MAIN SUBSETS, CROHN'S DISEASE AND ULCERATIVE COLITIS AND HETEROGENEITY IN THE TWO SUBTYPES. WE WERE INTERESTED IN BETTER UNDERSTANDING MECHANISMS DERIVING DISRUPTION, WHAT'S CAUSAL VERSUS RESPONSIVE IN THE MICROBIOME, DURING INFLAMMATORY BOWEL DISEASE, CHANGES IN DISEASE ACTIVITY AND SPECIFICALLY HELPING TO TRANSLATE SOME OF THE EMERGING ECOLOGICAL UNDERSTANDING INTO ACTIVITIES THAT WOULD HELP IN THE CLINIC. SOME MIGHT INVOLVE FOR EXAMPLE UNDERSTANDING HETEROGENEITY OF THE DISEASE. AGAIN, EVEN WITHIN THE TWO MAIN SUBTYPES IS A GREAT DEAL OF CLINICAL DIFFERENCE IN DISEASE PROGRESSION, AND IN PHENOTYPES LIKE RESPONSE TO TREATMENT. WE CAN TAKE A LOOK AT LINKING THOSE TWO CHANGES IN THE MICROBIOME, HELPING TO PREDICT RESPONSE TO TREATMENT OVER TIME, PREDICTING EITHER ONSET OR REMISSION OF DISEASE ACTIVITY, CROHN'S AND COLITIS, BOUTS OF GREATER OR LESSER DISEASE ACTIVITY. AND THEN IDENTIFYING EITHER IN THE HOST OR MICROBIAL SIDE PATHWAYS MOLECULAR TARGETS THAT MIGHT BE EITHER CAUSAL OR POINTS OF INTERVENTION FOR NEW TREATMENT. SO OVER THE COURSE OF THE PAST THREE TO FOUR YEARS NOW WE'VE FOLLOWED A COHORT THAT ENDED UP BEING JUST OVER 100 INDIVIDUALS DRAWN FROM CROHN'S, COLITIS AND CONTROLLED POPULATIONS OVER IN TOTAL A SET OF FIVE COHORTS AT FOUR PHYSICAL LOCATIONS. AND THIS REPRESENTS A MIXTURE OF ADULT AND PEDIATRIC IBD PATIENTS AND CONTROLS, RECENT ONSET AND ESTABLISHED DISEASE PATIENTS. THEN WE ULTIMATELY COLLECTED 4,000 TOTAL SPECIMENS FROM WHICH WE GENERATED DATA FOR JUST OVER 2,000, DRAWN MAINLY FROM STOOL SAMPLES CONTRIBUTED BY PARTICIPANTS BIWEEKLY FOR THE COURSE OF ONE YEAR EACH GIVING DATA ABOUT THE GUT MICROBIOME, TARGETING MICROBIAL INFORMATION PRIMARILY THROUGH SEQUENCING BUT THEN IN ADDITION TO METABOLOMICS, PROTEOMICS, BIOPSYS AND BLOOD DRAWS AT BASELINE TELLING ABOUT HOST MOLECULAR INFORMATION, INCLUDING GENOME SEQUENCING, EPIGENETICS AND SEROLOGICAL PROFILES FROM A SMALL NUMBER OF BLOOD DRAWS, ROUGHLY QUARTERLY IN ADDITION TO BASELINE FOR BIOPSY. YOU CAN SEE A PROFILE FOR THESE SAMPLES OF ROUGHLY WHAT WE TARGETED OVER THE COURSE OF ONE YEAR EACH PER INDIVIDUAL, AS FAR AS TIME POINTS AND DATA TYPES, AND WHEN WE COMPARE TARGETED LONGITUDINAL PROFILE TO THE DATA THAT WE'VE ULTIMATELY GENERATED FOR THE SAMPLE SETS, IT WAS CLOSE, A COLLECTION ACROSS THE THREE TARGETED PHENOTYPES OF A COMBINATION OF SUBJECTS WITH LONG DENSE TIME COURSES OVER ONE YEAR EACH, IN ADDITION TO MOST DATA TYPES DRAWN FROM MOST SUBJECTS, AT THE SERIES OF SIX OR SEVEN TARGETED ANCHOR TIME POINTS FROM ACROSS THE YEAR, PARTICULARLY DENSE DURING BASELINE WHEN WE'RE GETTING THE BULK OF INFORMATION ABOUT EACH PATIENT. SO WE'VE BEEN MAKING THE FULL DATASET AVAILABLE AS IT BECOMES GENERATED THROUGH IBD MULTI-OMIC DATABASE OR SITE IN ADDITION FOR REPOSITORIES, NOW INCLUDING PILOT DATASETS GENERATED OVER THE COURSE OF THE PROJECT, OF SEVERAL, NOT QUITE ALL BUT SEVERAL LARGE DATASETS FOR THE WHOLE COHORT AND THEN OTHER DOCUMENTS WHEN WE'VE BEEN ABLE TO PROVIDE INCLUDING SAMPLE COLLECTION PROTOCOL, TIPS TO COLLECT FROM MULTI-OMICS ANALYSIS, SOME DATA GENERATION THAT HELPED TO DERIVE THESE DIFFERENT TYPES OF DATA FROM SEVERAL SAMPLE TYPES. PARTICULARLY TAKING A LOOK AT SEVERAL PILOT DATASETS THAT WE'VE GENERATED OVER THE COURSE OF THE PROJECT, WE'VE HAD A LITTLE BIT OF TIME TO START LOOKING INTO THE BIOLOGY OF DIFFERENT TIMES OF MULTI-OMICS. ANYTIME YOU SEE A FACE ON THE SLIDES SUCH AS MELANIE, THE POSTDOC WHO WORKED ON THIS PROJECT, STARTING WITH PILOT DATASET THAT SPECIFICALLY COMPARED GUT META TRANSCRIPTOME TO METAGENOME OVER TIME IN INFLAMMATORY BOWEL DISEASE. ONE OF THE THINGS THAT MELANIE LOOKED AT WAS IDENTIFYING CASES IN WHICH THE META TRANSCRIPTOME WAS PARTICULARLY INFORMATIVE WITH RESPECT TO DISEASE PROGRESSION. ONE EXAMPLE HERE, MUCOUS DEGRADATION PATHWAY THAT ACROSS THE COHORT THIS PATHWAY IS EXPRESSED, META TRANSCRIPTOME EXAMPLES, PARTICULARLY BY ONE SPECIES BACTEROIDES. THIS IS MOSTLY CROSS-SECTIONAL DATA AT BASELINE. WHEN WE PULL OUT TIME COURSES FOR INDIVIDUAL PATIENTS SOMETIMES YOU CAN SEE THE UNIQUE CONTRIBUTOR OF THIS PATHWAY IN THIS PARTICULAR INDIVIDUAL, GUT MICROBIOME, OVER TIME BOTH IN THE METAGENOME AND META TRANSCRIPTOME. THIS BUG IS CARRYING MOST OF THIS PARTICULAR SUBSET OF MUCOUS DEGRADATION FOR THIS INDIVIDUAL IN CONTRAST TO INDIVIDUALS WHERE EVEN WHEN AT THE METAGENOMIC LEVEL, IT'S THE MAIN CONTRIBUTOR FOR LOW LEVELS OF OTHER ORGANISMS THAT OVER TIME CAN SWEEP IN TO TRANSCRIBING, NOT ALWAYS CORRESPONDS TO CHANGES IN DISEASE ACTIVITY AS WELL. YOU CAN SEE EVERY TWO-WEEK TIME POINTS, MOSTLY DIFFERENT BACTEROIDES IN ADDITION TO UNCLASSIFIED ORGANISMS COMING IN AND OUT OF TRANSCRIBING PATHWAY EVEN WHEN DNA LEVELS DON'T CHANGE, GUT PATHWAYS, SOME STABLE OVER TIME, OTHERS CAN SWITCH BETWEEN MICROBES, PARTICULARLY DURING DISEASE ACTIVITY. IN GENERAL, WE ZOOM AND ASK ABOUT GENERAL PRINCIPLES, ONE OF THE THINGS I THOUGHT WAS INTERESTING WAS A TRADEOFF BETWEEN HOW MANY ORGANISMS CAN CONTRIBUTE A PATHWAY VERSUS HOW HARD THEY WORK TO DO IT OR OVERTRANSCRIBED PROCESSES ARE. IF WE SUMMARIZE DIVERSITY OF ORGANISMS VERSUS THOSE THAT CAN TRANSCRIBE YOU'LL SEE FIRST MORE ORGANISMS TEND TO CARRY PATHWAYS METAGENOMICALLY THAN TRANSCRIBING THEM, WHAT YOU WOULD EXPECT, BUT ALSO FOR PATHWAYS PARTICULARLY UNIQUE TO ONE OR A FEW ORGANISMS THESE TEND TO BE OVEREXPRESSED. SO IF YOU AS OCCUPY TRANSCRIPTIONAL OR METABOLIC NICHE, YOU'RE WORKING AT THAT PROCESS. COMPARING META TRANSCRIPTOMES, GUT METABOLOME TO METAGENOME, ALLOWING US TO PICK OUT FOR EXAMPLE SPECIFIC SMALL MOLECULE COMPOUNDS, PARALLELLING EACH OTHER IN CROHN'S AND ULCERATIVE COLITIS BUT START RELATING TO SPECIFIC MICROBES. YOU CAN SEE A LIST OF INDIVIDUAL ORGANISMS DEPLETED IN THE GUT, INDIVIDUAL SMALL MOLECULE COMPOUNDS, AND THEN SIGNIFICANT CO-VARIATION BETWEEN THOSE THAT STARTS TO SUGGEST POTENTIAL MECHANISM, CO-VARIATIONS ABOVE AND BEYOND WHAT YOU WOULD EXPECT JUST FROM THE DISEASE ITSELF, SUCH THAT EACH OF THESE MICROBES MIGHT BE GENERATING COMPOUND THAT THEY CO-VARY WITH, MIGHT BE DEPENDENT ON THAT COMPOUND OR MIGHT INTERACT ECOLOGICALLY WITH ANOTHER. MANY HAVE DRIVEN US TO DIVE INTO META GENOMES AND GENOMES OF THESE BUGS IN A LITTLE MORE DETAIL SO DUE TO GENOME GAZING, FIGURE OUT WHAT MIGHT BE MECHANISTIC. I WANT TO SPEND A FEW SLIDES ON OTHER HMP2 OR HMP1-II. I DON'T NEED TO DESCRIBE THE POPULATION TOO MUCH. MARY INTRODUCED THE BACKGROUND OF HMP1. WE'VE FOCUSED ON SEVERAL THOUSAND METAGENOMES, FROM ACROSS THE BODY FOR THE HMP1 HEALTHY POPULATION OVER THREE TIME POINTS. ALONG WITH OWEN AND OTHERS, JASON AND A GROUP IN MY LAB, ANALYZING THESE ADDITIONAL META GENOMES, TO GET ADDITIONAL INSIGHT INTO MICROBIAL FUNCTION ACROSS THE BODY IN THE ABSENCE OF PERTURBATIONS FROM DISEASE. THIS HAS LED TO NOT JUST MORE DATA BUT SERIES OF MORE RECENT TOOLS, ANALYSIS TECHNIQUES, STRAIN PROFILING, OWEN WILL DESCRIBE THESE LATER, MARY MENTIONED DCC SPECIFICALLY LOADED THESE ON THE CLOUD FOR USER ANALYSIS, A HUGE BOON DURING HMP 1-II AND HMP DATA AS WELL. FROM THE HMP1-II, OUR ABILITY TO LOOK CLOSELY AT MARY INTRODUCED AS POTENTIAL FUNCTIONAL CORE OF THE HUMAN MICROBIOME. BY PROVIDING MORE SPECIFIC TAXON-SPECIFIC FUNCTIONAL PROFILING ACROSS THE BODY, WE'VE BEEN ABLE TO PULL OUT A SERIES OF TASK WAYS, POST-ASSOCIATED MICROBIAL COMMUNITY ENRICHED PATHWAYS. EXAMPLES SUCH AS VITAMIN D METABOLISM PRESENT ACROSS THE BODY, NOT JUST THE GUT OR ONE BODY AREA, BUT IN SEVERAL BODY AREAS TYPICALLY CARRIED BY MANY ORGANISMS BOTH ACROSS BODY SITES AND WITHIN BODY SITES BETWEEN INDIVIDUALS THAT ARE ENRICHED IN THE HMP1-II AND SPECIFICALLY NOT PRESENT IN ENVIRONMENTAL GENOMES, SEEM TO BE CONTRIBUTING FUNCTIONALITIES WITH MICROBIAL ECOLOGY, REGARDLESS OF EXACT MICROBIOME. SITE SPECIFIC PROCESSES GENERATED IN HUMAN MICROBIOME PROJECT HMP1-II, SUCH AS THIS IN THE ORAL COMMUNITY, THIS OCCURS THROUGHOUT THREE ORAL BODY SITES METAGENOMICALLY SEQUENCED HERE, DIFFERENT MICROBES PROVIDING THIS PROCESS ACROSS SPECIFIC ORAL SITES, AND ACROSS INDIVIDUALS IN THE SITE BUT THIS PATHWAY SEEMS TO BE UNIVERSALLY PRESENT IN MICROBIOME COMMUNITIES. WE FOUND IT USEFUL TO THINK OF THIS TYPE OF FUNCTIONAL DIVERSITY IN ECOLOGICAL TERMS SPECIFICALLY FOR CONTRIBUTIONAL ALPHA AND BETA DIVERSITY, WHICH MICROBES CAN PROVIDE AT THE METAGENOMIC LEVEL OR DO PROVIDE AT THE META TRANSCRIPTOMIC LEVEL A PARTICULAR PROCESS AND PARTICULAR ENVIRONMENT. SOMETIMES YOU'LL FIND PROCESS, METAGENOMIC EXAMPLES, PROVIDED ACROSS A PARTICULAR BODY SIDE UNIQUELY BY INDIVIDUAL ORGANISM DEMONSTRATING LOW CONTRIBUTIONAL ALPHA DIVERSITY AND LOW BETA DIVERSITY, THE SAME ORGANISM PROVIDING THIS PARTICULAR PATHWAY ACROSS MANY DIFFERENT ENVIRONMENTS. WE CAN FIND PATHWAYS WITH LOW CONTRIBUTIONAL ALPHA DIVERSITY, HIGH CONTRIBUTIONAL BETA DIVERSITY, ONLY A FEW BUGS PER INDIVIDUAL BUT DIFFERENT BUGS BETWEEN INDIVIDUALS. BOTH COMBINATIONS ARE COMMON AS WELL, WITH HIGH ALPHA AND LOW CONTRIBUTIONAL BETA DIVERSITY, A GROUP OF DIFFERENT BUGS CAN DO THIS, ROUGHLY THE CAME GROUP OF BUGS BETWEEN INDIVIDUALS AND THEN PERHAPS THE MOST COMMON CASE FOR META GENOMES IN PARTICULAR IS HIGH CONTRIBUTIONAL ALPHA AND BETA DIVERSITY, A BUNCH OF DIFFERENT BUGS CAN CARRY OUT A PARTICULAR PROCESS AND DIFFERENT BUGS SHOW UP IN DIFFERENT PEOPLE. I'M ABOUT TO GET ELECTROCUTED. I CAN SEE THE RED LIGHT GETTING CLOSE. I'LL WRAP UP WITH THE EXAMPLE I PROMISED LINKING TOGETHER A FEW OF THE FUNCTIONAL ANALYSES AND METABOLIC ANALYSES, SPECIFICALLY A STUDY IN A SUBSET OF PARTICULARLY LONG DENSE LONGITUDINAL TIME COURSES FROM ANOTHER PILOT DATASET FROM THE HMP2, A SMALL SET OF COLITIS PATIENTS, CONTROL INDIVIDUALS, IN WHICH TWO POSTDOCS BRANTLY AND MORAN LOOKED AT GROUPING TAXONOMIC, COMBINING FUNCTIONAL ENRICHMENTS IN INFLAMMATORY BOWEL DISEASES, AND SOMETHING THEY NOTICED ONE OF THE MOST ENRICHED FUNCTIONAL TREES AMONG MICROBES, WIDELY DISTRIBUTE IN IBD, TURNED OUT TO BE FASTER AND -- TURNED OUT TO BE FACULTATIVE, ANY MICROBE CAN BE LABELED USING CONTROLS FROM HMP1 POPULATION OR ANOTHER IBD STUDY FROM A COUPLE YEARS AGO NOW. THIS REPRESENTS A GROUP OF SPECIFIC ORGANISMS, ONE OF MANY -- MOST OF WHICH, SORRY, MOST OF WHICH ARE NOT INDIVIDUALLY STATISTICALLY SIGNIFICANT, ONE IS THE PNEUMOCOCCUS I CALLED OUT EARLIER, SOMEWHAT ENRICHED IN IBD, WE CAN PIN THIS DOWN TO A GROUP OF GROUPS ASSOCIATED WITH A GROUP OF SPECIFIC STRAINS ONLY EVER PRESENT IN SUBSETS OF OUR INFLAMMATORY BOWEL DISEASE PATIENTS, RUMINOCOCCUS, BASED ON PROFILING TOOLS CALLING OUT WHICH GENES ARE UNIQUE TO THIS. YOU'LL SEE MOST OF THESE ARE NOT CHARACTERIZED. IN PROCESSES LIKE IRON ACQUISITION OR OXIDATIVE STRESS. THIS LEADS ME TO MY LAST SLIDE, ONE OF THE BIGGEST GAPS IN SOME OF WHAT WE'RE INTERESTED IN ANALYZING, THE LACK OF FUNCTIONAL CHARACTERIZATION IN UNDERLYING MICROBIAL GENES. THERE ARE MANY CASES IN WHICH ASSUME THIS IS TRUE FOR MOST OF THE AUDIENCE, TRACED DOWN A PHENOTYPE OF INTEREST TO A PARTICULAR SET OF MICROBES OR MICROBIAL GENES. WE DON'T KNOW ANYTHING ABOUT WHAT THEY DO. THERE'S A BIG OPPORTUNITY IN TERMS OF PROVIDING BOTH BIOCHEMICAL AND COMPUTATIONAL SUPPORT TO BETTER CHARACTERIZE SUBSETS OF INTERESTING LOOKING MICROBIOME-ASSOCIATED GENES. THE OTHER GAP I'LL CALL OUT IS TECHNICAL. WE COMPLETED THE FIRST STEP IN THE MICROBIOME QUALITY CONTROL PROJECT AT MBQC TO PIN DOWN TECHNICAL VARIATION IN LARGE POPULATION STUDIES OF THE MICROBIOME. I DON'T HAVE TIME TO GET INTO THAT TODAY. ONE OF THE THINGS THAT THEY FOUND, THERE REALLY IS A SURPRISING AMOUNTS OF PROTOCOL VARIATION AMONG LABS THAT CAN CONTRIBUTE TO DIFFERENCE IN DATA GENERATION AT THE VERY LARGE SCALE END OF MICROBIOME EPIDEMIOLOGY, IF WE THINK OF THIS AS AN OPPORTUNITY, THIS PROVIDES AN OPPORTUNITY TO GENERATE A BETTER CHARACTERIZED MENU OF EXPERIMENTAL DESIGN CHOICES THAT INVESTIGATORS CAN USE TO MINIMIZE TECHNICAL DIFFERENCES. I'LL WRAP UP WITH THAT. I WANT TO THANK THE TEAM, ALONG WITH EVERYONE FROM THE HMP1, AND CALL OUT POSTERS FOLKS FROM THE GROUP HAVE HERE, FROM THE HMP PROJECT AND OTHER PROJECTS IN THE LAB. THANKS AGAIN. [APPLAUSE] >> THE LAST SPEAKER FOR THE SEX, OWEN -- THE LAST SPEAKER FOR THE SESSION, OWEN WHITE FROM UNIVERSITY OF MARYLAND, MANAGEMENT AND INTEGRATION OF THE iHMP DATA. >> I'M OWEN WHITE, UNIVERSITY OF MARYLAND. THE MAYOR HIRED A WORK CREW LAST NIGHT AND TOOK DOWN ALL OUR STATUES. SOMEBODY WHO LIVES REALLY CLOSE TO THE STATUES, I'M DELIGHTED. SO CURTIS INTRODUCED THE HEALTHY HUMAN SUBJECT STUDY, AND I WON'T TALK TOO MUCH ABOUT THE RESULTS OF THIS STUDY AS MUCH AS TO TRY TO JUST IMPRESS ON PEOPLE THAT IT'S A LOT OF DATA. IN THIS FIGURE HERE, THERE'S SHADED IN DIFFERENT LEVELS OF GRAY AN INDICATOR FOR ALL THESE HISTOGRAMS, IF IT'S DARK WE HAVE THAT MANY SAMPLES IN TERMS OF TIME POINTS. IF IT'S THIS COLOR, BLUISH OR REDDISH, THAT'S AN INDICATOR OF WHAT WAS PUBLISHED IN 2012, IN THE FIRST WAVE FOR THE HEALTHY HUMAN SUBJECTS, AND WHAT WILL BE PUBLISHED VERY SOON IN "NATURE." WE HAVE BASICALLY A LOT MORE SAMPLES AS WELL AS A WHOLE LOT MORE TECHNICAL REPLICATES OF THE DATA THAT ESSENTIALLY REPRESENTS A TRIPLING OF THAT INFORMATION. JUST AS A QUALITY CONTROL POINT OF VIEW, WE PERFORMED A LOT OF DIFFERENT TYPES OF ANALYSIS, CURTIS INTRODUCED THAT VERY WELL. BUT IF THERE WERE CONCERNS ABOUT HOW THAT DATA BEHAVED DURING THE COURSE OF THE PROJECT, THERE SHOULDN'T BE, YOU CAN'T REALLY SEE IT, THESE ARE COLOR CODED BY BODY SITES AND SHAPE, ASSOCIATED WITH CIRCLE OR SQUARE, DEPENDING ON WHAT PART OF THE PROJECT IT CAME FROM. YOU CAN SEE A VERY NICE INTERMINGLING OF CIRCLES AND SQUARES. ESSENTIALLY ALL THE DATA ACROSS THE ENTIRE PROJECT IS BEHAVING VERY NICELY. I DO WANT TO CALL YOUR ATTENTION TO JASON'S POSTER THAT WILL PRESENT A LOT OF RESULTS THAT CURTIS SHOWED AS WELL AS SOME OTHERS, WHICH IS VERY EXCITING PROJECT THAT WAS A COLLABORATION WITH CURTIS AND MY GROUP AS WELL AS ROB KNIGHT AND REPRESENTED AN ENORMOUS AMOUNT OF COMPUTING TIME IN TERMS OF AMOUNT OF ASSEMBLIES AND ANNOTATION WE HAD TO DO, SO WE'RE QUITE PROUD OF THAT DATA. YOU'VE ALREADY SEEN THESE PRESENTATIONS FROM THROUGH iHMP STUDIES. I WANT TO MOTIVATE YOU TO THINK A LITTLE BIT ABOUT THE VERY RICH CLINICAL DATA THAT WAS ASSOCIATED WITH THIS. EVERYTHING INCLUDING THE SUBJECTS THAT WE HAD, THE TIME POINTS, THERE'S LOTS OF PRIMARY DATA. THERE'S LOTS OF DERIVED DATA. AND THERE'S A PROBLEM WITH THIS THAT I JUST WANT TO MAKE PEOPLE AWARE OF, AND I THINK IT'S IMPORTANT TO HIGHLIGHT. SO THE BEST WAY TO DO THAT IS TO SHOW YOU AN OLD SPREADSHEET THAT WAS GENERATED BY STEVE SHERRY AT dbGAP, AND EACH ONE OF THESE COLUMNS IS REPRESENTATIVE OF AN EARLY HMP DEMONSTRATION PROJECT, DIFFERENT INVESTIGATORS WERE FUNDED TO DEMONSTRATE THAT THERE MAY BE SOME CAUSAL RELATIONSHIP BETWEEN MICROBIOME AND DISEASE, AND SO FOR EACH OF THESE STUDIES THEY COLLECTED LOTS OF DIFFERENT TYPES OF CLINICAL INFORMATION, AND I KNOW IT'S HARD TO READ BUT THINGS LIKE DRUG, BLOOD PRESSURE, THE WEIGHT OF THE PATIENT, AND WHAT STEVE SHERRY DID WAS MARK USING DIFFERENT COLORS IF INFORMATION LIKE WEIGHT HAD BEEN COLLECTED, AND ALSO LOOKED AT IF THE VARIABLES FOR THOSE DIFFERENT STUDIES WERE COMPARABLE ACROSS THE STUDIES, AND IT WAS KIND OF MIND BLOWING TO DISCOVER TYPICALLY IN CLINICAL STUDIES, I MEAN MY BACKGROUND IS MUCH MORE IN GENOMICS, NOT WITH PROJECTS SUCH AS THIS, THAT THINGS AS SIMPLE AS BLOOD PRESSURE OR MEDICATION OR SMOKING HISTORY ARE ALL COLLECTED IN DIFFERENT WAYS. AND THAT MAKES FINDING ALL DATASETS THAT ARE ASSOCIATED WITH LET'S SAY A BLOOD PRESSURE RANGE FOR PATIENTS THAT ARE MALE NEARLY IMPOSSIBLE UNLESS YOU KIND OF SIT SOMEBODY DOWN TO SLOG THROUGH THE DATA AND HARMONIZE IT ACROSS TO PULL THAT INFORMATION TOGETHER. AND SO WHAT I'M GOING TO IDENTIFY AS A VERY SIGNIFICANT GAP IN THE FIELD, YOU START TO THINK ABOUT PRESENTATIONS THAT YOU'RE GOING TO HAVE, AND THAT YOU'VE ALREADY HAD, IS THAT WE'RE COLLECTING CLINICAL DATA AND IT'S VERY HARD TO SORT OF REPRODUCE WHAT THAT INFORMATION IS AND ALSO MORE IMPORTANTLY KIND OF RETRIEVE ROBUSTLY ACROSS ALL THOSE PROJECTS TO GET INFORMATION THAT YOU COULD THEN REUSE FOR YOUR OWN RESEARCH. SO I DON'T HAVE A SLIDE FOR THIS BUT RIGHT NOW THERE'S OVER 10, 000 SAMPLES AT SRA FOR HUMAN STOOL -- MICROBIOME STOOL SAMPLES, VIRTUALLY NO WAY TO ROBUSTLY PULL THAT DATA DOWN, VIRTUALLY NO WAY TO IDENTIFY WHICH OF THOSE SAMPLES CAME FROM, FOR EXAMPLE, DISEASE PATIENTS THAT WERE PART OF CURTIS' STUDY. THAT'S NOT A DEFECT OF SRA. THEY ARE DOING THE BEST JOB THEY CAN TO BE COLLECTING THAT INFORMATION. BUT THERE'S JUST NOT ONE UNIFORM WAY THAT DATA IS DEPOSITED INTO A DATABASE. SO LET ME JUST SHOW YOU HOW WE APPROACHED THIS STUDY, AND LET'S HOPE OR IMAGINE THAT AS MICROBIOME RESEARCH KIND OF METASTASIZES INTO ALL THE DIFFERENT NIH INSTITUTES, THAT THEY START THINKING ABOUT ISSUES LIKE THIS. SO THE WAY WE DID THIS WAS TO STAND UP A DATA MANAGEMENT WORKING GROUP, ALL THE iHMP PROJECTS, THIS REPRESENTED SOME PEOPLE WHO WERE DATA MANAGERS THAT WERE EMBEDDED AT THE LABS AS WELL AS PARTNERING WITH THE DATA COORDINATING CENTER, AND WE DID SOMETHING AS FACILITY OR ADMINISTRATIVELY SIMPLE AS THIS. THIS IS A GOOGLE SPREADSHEET THAT REPRESENTS LOTS OF DIFFERENT BROAD DATA TYPES LIKE SOMETHING LIKE A PROJECT OR STUDY OR SUBJECT, AND YOU CAN IMAGINE FOR SUBJECTS THERE'S LOTS OF PHENOTYPIC INFORMATION THAT YOU COLLECT. AND EACH ONE OF THESE PROJECTS, THESE COLUMNS REPRESENT THREE PROJECTS PRESENTED, AND I'LL CALL EACH ONE OF THOSE DATA TYPES A NODE, AND WHAT YOU COULD DO FOR OUR PURPOSES, WAS TO JUST CLICK ON A NODE AND GENERATE A DOCUMENT THAT LISTS ALL THE SPECIFIC FIELDS THAT WERE ASSOCIATED WITH SOMETHING LIKE THE SUBJECT. WE IDENTIFIED THE COMMON DATA ELEMENTS, EXAMPLE COULD BE BLOOD PRESSURE OR GENDER OR THINGS OF THAT TYPE. AND IDENTIFY EITHER BY CREATING OUR OWN CONTROL VOCABULARIES TO DESCRIBE THAT INFORMATION OR INTERNATIONALLY TO DESCRIBE THE INFORMATION ACROSS THE PROJECT. THIS IS A SIMPLE ADMINISTRATIVE TOOL FOR BEING ABLE TO DO THAT, BUT IT'S ESSENTIALLY KIND OF A BREAKTHROUGH IDEA WITH RESPECT TO BEING ABLE TO INTEROPERATE AND SHARE DATA ROBUSTLY ACROSS PROJECTS. THE LANDSCAPE FOR NIH DATA IS GOING TO KIND OF EXPLODE EVEN LARGER THAN IT IS NOW, I HOPE AS THIS.NGAGE IN PROJECTS SUCH- THIS IS NOT A NOVEL IDEA, BUT IT'S A VERY IMPORTANT ONE. THEN WHAT WE ENDED UP WITH WERE THESE DIFFERENT SUBMITTERS, AND WE HAVE ONE CENTRAL DATABASE THAT CAN RECEIVE DOCUMENTS KNOWN AS J-SON OBJECTS, ONCE YOU'VE GOT A REASONABLE WAY OF DESCRIBING DATA AND ATTACHING KEY WORDS TO THAT INFORMATION IT'S PRETTY STRAIGHTFORWARD TO WRITE SOFTWARE THAT HANDLES SUBMITTING THAT INFORMATION INTO A COMMON DATABASE. IF YOU'RE INTERESTED IN THAT, COME TAKE A LOOK AT POSTER 28 WHICH I BELIEVE IS ON FRIDAY, FOR OUR SYSTEM, OPEN SCIENCE DATA FRAMEWORK. YOU CAN DEPOSIT MACHINE READABLE DOCUMENTS TO CAPTURE THAT INFORMATION AND WE HAVE VALIDATORS THAT REVIEW -- ELECTRONIC VALIDATORS TO REVIEW THAT ITERATIVE PROCESS, NO DAY WE PULLED THE TRIGGER AND SAID THIS IS THE WAY WE'RE GOING TO DO IT. IT WAS HIGHLY ITERATIVE OVER THE COURSE OF THE PROJECT. THAT'S THE WAY THE DATA WAS DEPOSITED INTO THE SYSTEM. CURTIS' GROUP WAS RESPONSIBLE FOR MAKING SOMETHING CALLED ANADAMA, A DATA ANALYSIS MANAGEMENT SYSTEM, AND THIS HAS LOTS OF DIFFERENT FEATURES, IN ADDITION TO WHAT I'M GOING TO DESCRIBE, ALLOWS YOU TO MAKE REPRODUCIBLE WORK FLOWS, HANDLE DEPENDENCIES, IF A DATASET CHANGES IN TERMS OF DATA YOU'RE SEARCHING AGAINST IT UPDATES THE INFORMATION AS PART OF THAT CHAIN, YOU CAN PARALLELIZE INFORMATION, BUT WE ADOPTED IT MOSTLY FOR ITS ABILITY TO USE AS A SUBMISSION TOOL. SO WHAT I JUST DESCRIBED TO YOU IS THE DATA HARMONIZATION PROCESS, ONE HAPPENED ACROSS THREE iHMP PROJECTS, YOU CAN IMAGINE EXPANDING THE NUMBER OF PEOPLE PARTICIPATING AND HAVING A GROUP OF PEOPLE IN A SMOKE-FILLED ROOM HANDLING AGREEMENT TO FINDING A COMMON DATA ELEMENT, COMMON DATABASE. USING ANADAMA, ACCESS TO SOFTWARE THAT HANDLES SUBMISSION OF REGULARIZED DATABASE INTO EXTERNAL ARCHIVES. THE ADVANTAGE, THE ARCHIVES, I LOVE THEM, NOT A CRITICISM, BUT THEY ARE OVERLY FLEXIBLE IN THE WAY THEY CAN RECEIVE INFORMATION AS SIMPLE AS, YOU KNOW, LET'S DESCRIBE THE FORWARD AND REVERSE PRIMERS USED FOR 16S EXPERIMENT. SO AT LEAST ACROSS OUR PROJECT, THERE WAS A LOT OF UNIFORMITY IN TERMS OF THE WAY DATA WAS BEING SUBMITTED, WHICH IS A GOOD THING. THINK ABOUT THE OMIC DATA, HOW WOULD YOU FIND PROTEOMIC DATA, METABOLOMIC DATA, AND 16S DATA THAT CAME FROM THE SAME PROJECT? YOU WOULD ONLY BE ABLE TO DO THAT IF THEY CONTAINED THE SAME PROJECT I.D WHAT WE TRY TO DO IS MAKE SURE THAT THAT SAME PROJECT I.D. TRAVELED WITH ALL THE INFORMATION. OKAY. WE HAVE CREATED A NEW WEBSITE, AND IF YOU'RE INTERESTED IN THE DETAILS PLEASE GO TO POSTER 30, IT CONTAINS ALL THE INFORMATION FOR THE HEALTHY HUMAN SUBJECTS AS WELL AS iHMP. ONE OF THE THINGS THAT WE ARE PROUD OF, WE'VE BEEN CAPTURING PROTOCOL INFORMATION AND WE'LL CONTINUE TO HAVE THE PROTOCOLS FROM HEALTHY HUMAN SUBJECTS AS WELL AS iHMP. WE'RE ALSO VERY PROUD OF AN INTERFACE, A VERY RESPONSIVE PORTAL THAT ALLOWS YOU TO CLICK ON LOTS OF ELEMENTS, JUST AS I DESCRIBED THINGS LIKE THE GENDER OF THE PATIENT, ET CETERA, AND SEE REALLY RAPIDLY DISPLAYED PIECHARTS FOR ALL THAT INFORMATION, AND SELECT ON THE PIECHARTS THEMSELVES, IT WOULD PASS YOU TO A LISTING OF EACH OF THE FILES AND YOU COULD PASS FILES TO A MANIFEST, AND THAT MANIFEST WE HAVE TOOLS THAT ALLOW YOU TO THEN DOWNLOAD THAT DATA DIRECTLY TO YOUR OWN COMPUTER OR USE IT IN OTHER CONTEXTS. IF YOU'RE INTERESTED IN SOME OF THOSE THAT WORK FLOW, HOW COULD YOU DO THAT, HOW TO LOOK AT JONATHAN'S POSTER 31. ALL RIGHT. LET ME IDENTIFY ONE LAST GAP THAT I THINK IS GOING TO BE A SERIOUS CONCERN, OUR ABILITY TO ANALYZE DATA IN REASONABLE TIME. WHEN YOU START THINKING ABOUT THE VOLUME OF THIS DATA, SOMETHING'S GOT TO HAPPEN IN TERMS OF ENABLING PEOPLE TO DO THIS. WE HAD A PILOT STUDY, I'M GRATEFUL TO THE COMMON FUND AND OTHER NIH INSTITUTES FOR HELPING TO SUPPORT THIS, WHERE WE RECENTLY HELD A TRAINING WORKSHOP TO ANALYZE ALL THE DATA THAT I JUST SHOWED YOU ON AMAZON. WE INVITED A NUMBER OF LUMINARIES IN THE FIELD TO PRESENT THEIR ANALYSIS TOOLS, AND WE BUNDLED ALL THE ANALYSIS TOOLS INTO ONE COMMON SYSTEM THAT COULD BE LAUNCHED ON AMAZON, AND THEN FOR A DAY AND A HALF WE WALKED USERS THROUGH THE PROCESS OF DOING THIS ANALYSIS. THIS WAS REALLY EXCITING FOR A NUMBER OF DIFFERENT REASONS. THE DEVELOPERS GOT TO HAVE DIRECT INTERACTIONS WITH THE USERS, THE USERS GOT A CHANCE TO HAVE THE DEVELOPER RIGHT OVER THEIR SHOULDER, TOOLS PLACED INTO AN EXECUTABLE IMAGE, REFERRED TO NOW AS DOCKER, WHICH IS AVAILABLE TO PEOPLE. HERE IS ALL THE ANALYSIS TOOLS. AND THIS WAS JUST VERY EXCITING WAY OF SORT OF DEMONSTRATING THIS BOLD NEW FUTURE FOR HOW YOU COULD DO ANALYSIS ON THE CLOUD. THAT WAS VERY NICE. I'M GOING TO WRAP IT UP. I REALLY STRONGLY WANT TO THANK TWO SENIOR PERSONNEL, MICHELE AND ANUTE, THE PEOPLE THAT LED TACTICAL AND STRATEGIC DEVELOPMENT OF ALL ASPECTS OF OUR PROJECT. HERE IS THE PEOPLE WHO DID THE WORK. AND THEIR POSTERS ARE HERE AND REPRESENT DIFFERENT DIMENSIONS OF THE WHOLE OVERALL PROJECT. AND I'M VERY GRATEFUL TO ALL OF THEM. WE'RE REALLY WRAPPING UP ALMOST NINE YEARS OF THE HMP PROJECT OVERALL, THIS IS AN EXCITING TIME FOR US, BUT THESE PEOPLE REALLY MADE IT HAPPEN IN VERY EXCITING WAYS. AND I ALSO WANT TO THANK THE DATA MANAGEMENT WORKING GROUP FOR REALLY MAKING A ROBUST SET OF DATA, AND STRONGLY ENCOURAGE PEOPLE TO THINK ABOUT SOME OF THE STUFF I'M THINKING ABOUT, REPRESENTED WITH RESPECT TO METADATA MANAGEMENT. I THINK IT WILL BE A BIG DEAL IN THE FUTURE. HERE IS MY SUMMARY SLIDE. ROB IS HERE, I'M GRATEFUL TO HIM AS WELL AS THE ORIGINAL SEQUENCING CENTERS, GENERATED HMP DATA AND OUR SOURCES OF FUNDING. THANK YOU. [APPLAUSE] >> NOW WE'RE GOING TO TRY A JOINT Q&A SESSION. JUST AS A POINT OF INTEREST HERE, WALTER AND OTHERS WHO ARE RUNNING IN THE BACKGROUND, I GUESS THE WEBCAST IS EITHER NOT WORKING OR ONLY WORKING ON CERTAIN BROWSERS. SO IF YOU FOLKS WHOEVER IS HERE TRYING TO RUN THE WEBCAST IF YOU COULD SOMEHOW DOUBLE CHECK THAT OVER OUR LUNCH BREAK, IT WOULD BE VERY GOOD. THANKS. I'M GOING TO ASK A SOFTBALL AND ONE OF YOU OR ANY OF YOU CAN ANSWER. THE REAL MOTIVATION BEHIND PHASE 2 AS MARY SAID WAS TO ASK THE QUESTION, WHAT OTHER OMIC BIOLOGICAL PROJECTS OF THE MICROBIOME DO WE NEED TO COLLECT TO GET INSIGHT INTO THE HUMAN SYSTEM. WE WORKED ON PRE-TERM BIRTH AND IBD AND DIABETES, THERE COULD BE LESSONS FOR THE LARGER COMMUNITY. COULD SOME OF YOU SPEAK TO WHAT YOU THOUGHT WAS THE BIGGEST INSIGHT YOU GOT WHEN YOU STARTED TO COLLECT THESE OTHER OMIC PROPERTIES? AND HOW THAT MIGHT BE IMPORTANT TO THIS AUDIENCE? >> GO AHEAD. >> LET ME PASS THE MIC. >> MY FIRST IMPRESSION, HOST PROPERTIES, ONE OF THE BIG QUESTIONS, SEVERAL PEOPLE ALLUDED TO TODAY, TAKING THE ASSOCIATIONS THAT WERE IDENTIFIED IN THE INITIAL MICROBEIUM STUDIES, OPERATIONALLY UNDERSTOOD, MECHANISMS, CAUSES, ETIOLOGY OF DISEASE OR HEALTH CONDITIONS WE'RE LOOKING AT. STARTING TO LOOK AT THE HOST, FOR EXAMPLE, THE METABOLOME, THE CYTOKINE PROFILE, IMMUNOPROTEOME PROFILE, HOW THAT CORRELATES WITH THE MICROBIUM COMMUNITY STATES OR WHAT BACTERIA ARE PRESENT STARTS TO GIVE YOU SOME KIND OF IDEA WHAT'S GOING ON IN THE INTERACTION BETWEEN THE HOST AND THE MICROBIUM AND START TO UNDERSTAND HOW THAT MICROBIUM IS AFFECTING THE HOST. AND POSSIBLY AFFECTING DISEASES THAT LEADS TO HYPOTHESES THAT ONE CAN TEST BY LOOKING AT INDIVIDUAL BACTERIAL STRAINS OR SPECIES, TO ASK THE QUESTION ARE THOSE IMPACTS REALLY BEING CAUSED BY THAT BACTERIAL STRAIN OR GROUP OF BACTERIA. THE HOST-PARASITE INTERACTION OR INTERSECTION IS IMPORTANT AND BY GETTING A MULTI-OMIC APPROACH WE CAN START ASKING QUESTIONS ABOUT THE HOST. >> THERE WE GO. I MEAN, I WOULD CONCUR. YOU DO NEED THE HOST INFORMATION TO GET THE COMPLETE PICTURE. MANY OF THE OBSERVATIONS WE OBSERVE ARE CONTEXTUAL. IN OUR CASE, HOW THE METABOLITES AND MICROBIOME BEHAVE DEPENDS WHETHER YOU'RE INSULIN SENSITIVE OR RESISTANTS IN CERTAIN CASES, YOU WOULD LACK THAT UNDERSTANDING IF YOU WERE COLLECTING THAT INFORMATION. SO I THINK THAT'S GOING TO BE ABSOLUTELY CRITICAL FOR UNDERSTANDING HOW DISEASE COMES TO BE AND ALSO HOW TO MANAGE DISEASE. I THINK WE'RE GOING TO NEED THAT KIND OF INFORMATION TO BE ABLE TO IMPLEMENT ULTIMATELY IN THE CLINIC. >> SO I'LL DEFINITELY ECHO BOTH WHAT MIKE AND GREG SAID WITH RESPECT TO HOST PROPERTIES. IT'S A PLACE THAT WE HAVEN'T GOTTEN AN OPPORTUNITY TO LOOK CLOSELY AT YET. AND WHAT OWEN SAID DURING THIS IS TALK REGARDING METADATA. IT'S EASY TO THINK OF HOST PHENOTYPE AND ENVIRONMENT AS AN AFTERTHOUGHT BUT HAVING THAT IN AN ORGANIZED WAY HELPS YOU UNDERSTAND DISEASE. FROM THE HMP2 IN PARTICULAR I THINK ONE OF THE BIGGEST LESSONS THAT WE'VE GOTTEN HAS BEEN THERE'S NO ONE OMIC SILVER BULL IT. HMP2 HAS BEEN AN OPPORTUNITY TO SLICE IT IN MANY WAYS. WHAT WE'RE SEEING HERE AND I THINK IN OTHER PHENOTYPES VERY MUCH LIKE WHAT YOU WOULD EXPECT IN A SINGLE ORGANISM YOU'RE NEVER GOING TO SEE THE MECHANISM FOR PHENOTYPE USING ONE TOOL, NOT 16S, NOT SEQUENCING, AND WE'VE HAD AN OPPORTUNITY TO USE MOLECULAR TOOLS FROM THE HOST AND IBD AND THEY HAVE ALL SHOWN INTERESTING PROPERTIES UNDER DIFFERENT CONDITIONS OVER DIFFERENT QUESTIONS. >> I'M GOING TO KEEP ON ASKING QUESTIONS BUT IF THERE ARE QUESTIONS IN THE AUDIENCE, YES, PLEASE, GO AHEAD. >> HI. THE QUESTION IS ABOUT METABOLITE DATA. >> IT MIGHT BE VALUABLE, PEOPLE ARE LISTENING, ANNOUNCE YOUR NAME. >> KATIE POLLARD. MY QUESTION IS ABOUT METABOLITE DATA FOR CURTIS AND MIKE I GUESS BUT ANYONE IS WELCOME TO CHIP IN. IT'S COOL TO SEE METABOLTES SORT OF GOING UP AND DOWN AND TO SEE TAXONOMIC GROUPS GOING UP AND DOWN. THIS IS A QUESTION ABOUT THE FUTURE, BEYOND THE DATA YOU'VE COLLECTED, WHAT ARE PROSPECTS FOR RESOLVING METABOLITE CHANGES TO SPECIFIC MICROBES, HOST, ET CETERA. >> WHAT DO YOU MEAN RESOLVING? >> UNDERSTAND THE MECHANISM, TO KNOW FOR EXAMPLE, TO BE SPECIFIC, IF THERE'S A METABOLITE THAT'S HEALTHY OR UNHEALTHY, CAN I FIGURE OUT WHAT MICROBE IS CONTRIBUTING, ONE OR A COLLECTION OF MICROBES, IF A MICROBE AND HOST ENZYME, TRYING TO UNDERSTAND PATHWAYS AND MECHANISMS. >> I'M GOING TO SELFISHLY START WITH THE RESPONSE, TIED BACK TO ONE OF MY GAPS. ONE OF THE BIGGEST CHALLENGES THERE IS JUST LACKING A LOT OF MOLECULAR LEVEL ANNOTATIONS AND INFORMATION FOR TYPICAL BUGS WE SEE IN THE GUT OR HUMAN MICROBIOME, EVEN SOMEPLACE WELL STUDIED LIKE THE GUT, THE MAJORITY OF GENE FAMILIES ASSOCIATED WITH META GENOMES, AS YOU KNOW, ARE NOT BIOCHEMICALLY OR FUNCTIONALLY CHARACTERIZED. SO WE CAN LOOK AT THINGS LIKE CO-VARIATION AND FIND STRONG CO-VARIATION SPECIFICALLY BETWEEN SMALL MOLECULES AND GENE FAMILIES AND RIGHT NOW THAT'S ABOUT AS FAR AS IT GOES, UNTIL THERE'S NOR INFRASTRUCTURE FOR ISOLATING MICROBES, DOING TOUGH BIOCHEMISTRY TO CHARACTERIZE WHAT SPECIFIC GENES FAMILIES YOU'RE DOING AND CATALOGING IN A SYSTEMATIC WAY AND INFRASTRUCTURE FOR CHARACTERIZATION AS WELL. >> I THINK I WOULD AMPLIFY, EVEN IF YOU TAKE A SIMPLER SYSTEM, JUST THE HUMAN GENOME, THERE'S NOT A RELATIONSHIP BETWEEN DISCOVERY THAT METABOLITE IS GOING UP OR DOWN, AND KNOWING SPECIFICALLY WHAT PATHWAY THAT'S ASSOCIATED WITH, EVEN THAT IS A NON-SIMPLE PROBLEM, MAP TO BACTERIA WHERE THERE'S, YOU KNOW, AND ENORMOUS NUMBER OF UNCHARACTERIZESSED OR DUPLICATED GENES, MAKE IT A COMPLEX PROBLEM. >> I TOTALLY AGREE. I WAS WONDER FIGURE WE COULD THINK BEYOND SEQUENCING TO IMAGING OR OTHER THINGS WITH MASS SPEC. MIKE, DO YOU HAVE ANY THOUGHTS? >> TO ADD, I THINK WE'LL BE NOT FAR FROM MAKING ASSOCIATIONS, POWER OF HMP WE'LL HAVE THESE DATA. IT WILL BE MASSIVE, TO SEE ASSOCIATIONS ACROSS DATA TYPES WILL BE POWERFUL. WHAT WILL BE EXTREMELY POWERFUL WILL BE THE PERTURBATIONS YOU DO ON TOP OF THAT, PROBIOTICS PEOPLE TAKE, TO SEE HOW THAT AFFECTS THINGS AS WELL AS DRUGS PEOPLE TAKE THAT WILL, YOU KNOW, PERTURB ONE PARTICULAR PATHWAY OR ASPECT AND YOU'LL SEE HOW THE ASSOCIATIONS CHANGE. I THINK THAT WILL BE VERY -- THESE ARE HUMANS, WE CAN LOOK AT NATURAL GENETIC VARIANTS BUT WE'RE NOT MICE, WE'RE NOT GOING TO GO AND CRISPR OUR CELLS. PERTURBATIONS WILL BE POWERFUL FOR GETTING AT MECHANISTIC ASPECTS YOU RAISE. OTHER TECHNOLOGIES, I THINK THEY ARE POWERFUL. I HAVEN'T DONE MUCH IMAGING WITH MICROS, A LITTLE BIT WITH SCAN E M. I DO BELIEVE DISEASE TISSUE IMAGING IS POWERFUL. WE'RE DOING A LOT OF THIS NOW WITH CANCER AND OTHER DISEASES, TAKE IMAGE INFORMATION AND CO-ASSOCIATE WITH DIFFERENT OMICS PATTERNS, QUITE INTERESTING AND REVEALING FOR SOME MECHANISTIC UNDERSTANDING AS WELL AS PROGNOSTIC VALUE. I DO THINK IMAGING WILL BE EXTREMELY POWERFUL. I DO THINK THE LONGITUDINAL AND AGAIN PERTURBATION EXPERIMENTS WILL BE THE MOST COMPELLING FOR UNRAVELING THESE ASSOCIATIONS. >> A QUICK FOLLOW-UP COMMENT, ONE OF THE GOALS OF THE HMP2 WAS TO DEVELOP TOOLS TO ADDRESS EXACT QUESTIONS YOU'RE ASKING. IT'S NOT SIMPLY NEW KINDS OF BIOLOGICAL TOOLS BUT SOME EFFORTS GOING INTO DEVELOPING COMPUTATIONAL TOOLS, AND I KNOW MIKE AND CURTIS AND OWEN'S GROUPS HAVE DONE THAT. WE'VE DONE A LITTLE BIT TOO. THERE'S A COUPLE POSTERS I MENTIONED TODAY WHERE SOME COMPUTATIONAL BIOLOGISTS IN OUR TEAM ARE TRYING TO DEVELOP NEW WAYS TO USE MACHINE LEARNING AND NETWORK ANALYSIS TO LOOK AT THESE ASSOCIATIONS AND STILL YOU MAY GET A HYPOTHESIS, BUT IT BRINGS US TO TRY TO BRING US CLOSER TO GETTING HYPOTHESIS THAT WE CAN JUST BIOLOGICALLY MORE EFFICIENTLY RATHER THAN TRYING TO DO WILD GOOSE CHASES. >> HI. UC SAN DIEGO. THE THING I STRUGGLE WITH WHEN I'M INVESTIGATING OR THINKING ABOUT HUMAN TRIALS, INVESTIGATING MICROBIOME IN HUMANS, IS THAT WE'RE TRYING TO UNDERSTAND WHAT'S GOING ON IN DIFFERENT PARTS OF THE GUT BY JUST LOOKING AT THE STOOL OR LOOKING AT METABOLITES IN THE STOOL. HOW CAN WE REALLY UNDERSTAND THAT PHYSIOLOGY WHEN, FOR EXAMPLE, WE LOOK AT MICE, WE KNOW THE STOOL IS QUITE DIFFERENT THAN WHAT WE SEE IN THE TERMINAL ILIUM OR CECUM OR PART OF THE LUMEN. CAN WE REALLY UNDERSTAND PHYSIOLOGY BY LOOKING AT THE STOOL OR SHOULD WE USE IT AS A BIOMARKER AS OPPOSED TO SOMETHING ELSE? >> I'LL START, SINCE WE'VE LOOKED AT THAT A LITTLE BIT. MOSTLY IN NON-HUMAN SYSTEMS. BOTH COMPARING STOOL IN A HUMAN POPULATION WE WORKED WITH TO BIOPSY 16S PROFILES FROM DIFFERENT LOCATIONS. THAT'S TYPICALLY CROSS-SECTIONAL. IN PRIMATE MODELS DOING MORE LONGITUDINAL WITHIN SUBJECTS, BIOPSIES ACROSS THE SMALL BOWEL AND STOOL. I DON'T KNOW ABOUT RODENTS. IN THE PRIMATE MODEL DIFFERENCES BETWEEN STOOL AND OTHER SITES WERE MOSTLY DUE TO SMALL NUMBER OF TAXA. SO THAT FOR THE MAJORITY OF TAXA, THERE'S A DIRECT LINEAR QUANTITATIVE RELATIONSHIP BETWEEN WHAT YOU SEE IN STOOL AND WHAT YOU SEE AT THE MUCOSAL SURFACE, WITH A SMALL NUMBER OF EXCEPTIONS THAT WERE VERY DIFFERENT, THUS LEADING TO AN APPARENTLY LARGE OVERALL DIFFERENCE. THAT BEING SAID, THERE ARE CLEARLY BIOLOGICAL DIFFERENCES SUCH THAT I THINK THE ANSWER TO YOURS BIOMARKER VERSUS MECHANISM QUESTION IS BOTH. THAT THERE'S SOME EXCEPTIONS WHERE YOU CAN'T NECESSARILY THINK ABOUT DETAILED MECHANISMS AT THE MUCOSAL SURFACE FROM THE STOOL BECAUSE YOU'RE LOSING OR GAINING BUGS BUT A BULK OF THE COMMUNITY IS REPRESENTED THERE, STOOL REPRESENTS A USEFUL BIOMARKER SUCH THAT IN SOMETHING LIKE PREDICTING COLORECTAL CANCER, GOOD WORK ON THAT, THAT'S WHERE THE STOOL MICROBIOME IS LITERALLY A BIOMARKER REGARDLESS OF WHAT THE UNDERLYING MECHANISM WOULD BE. >> THANKS. >> HI. BRANDON ANCHOR, I WORK FOR NUTRILITE. A PERSONAL CONCERN, MANY WESTERN POPULATIONS HAVE SIGNIFICANT DIETARY DEFICIENCIES, SO WE'RE RUNNING CLINICAL TRIALS AND THINGS, ESPECIALLY IN THE WEST, I IMAGINE THIS GOES TO MOST DEVELOPED NATIONS, THE CONSUMPTION OF DIETARY FIBER IS AROUND 15, 20 GRAMS TOPS. WE LOOK AT EASTERN POPULATIONS, MAYBE, FORGIVE ME, WILD HUMANS, THEIR CONSUMPTION IS 80, 90, 100 GRAMS, SOME REPORTS. I FEAR MANY INFERENCES WE'RE MAKING ABOUT A HEALTHY CONTROL MIGHT BE A LITTLE OFF, BECAUSE WE'RE GOING TO DO A BLOOD PANEL AND SAY MODERN MEDICINE SAYS THAT INDIVIDUAL IS HEALTHY. I THINK I SIGNIFICANTLY DISAGREE WITH THAT POINT OF YOU. I WAS WONDERING WHAT YOU MIGHT BE DOING IN FUTURE STUDIES TO FIND BETTER CONTROLS SO WHEN WE CONTROL A DISEASED INDIVIDUAL VERSUS A WESTERNER, THESE ARE SUBTLE DIFFERENCES VERSUS WHEN YOU GO FIND SOMEBODY WHO LIVES IN A MORE RURAL ENVIRONMENT AND DIET HIGHER LEVELS OF DIETARY FIBER, GUTS MY BE SIGNIFICANT AND EASIER TO PROVED DISEASED VERSUS HEALTHY INDIVIDUALS. THANK YOU. >> I'LL TAKE A CRACK. YOUR POINT IS WELL TAKEN. WHAT IS THE DEFINITION OF HEALTHY? THAT'S ALWAYS RELATIVE. IT'S POSSIBLE NONE OF US ARE TRULY HEALTHY AT SOME LEVEL OF DEFINITION. I THINK ONE THING WE ARE DOING, YOUR POINT IS WELL TAKEN, WESTERN DIETARY GENERALLY, AND WE'LL TALK ABOUT THIS, ONE OF HIS BIG MANTRAS, WESTERN DIET IS POOR IN FIBER COMPARED TO OTHER GROUPS. AND ONE THING WE ARE DOING WITH JUSTIN AS PART OF OUR PROJECT WE HAVE PEOPLE DOING A NUMBER OF FIBER PERTURBATIONS. THOSE DATA CAME LATE IN THE STUDY, THEY ARE SITTING THERE AND WE HOPE TO ANALYZE THEM. THEY ARE GETTING MORE ANALYZED IN A MORE SUPERFICIAL FASHION. I HOPE TO DIG DEEPER. WE NEED TO TEAR THAT APART LIKE ANALYTICAL CHEMIST. PEOPLE THROW IN COMPLEX MIXTURES, IT WOULD BE NICE TO KNOW WHAT EACH FIBER IS DOING TO EACH INDIVIDUAL, SO WE CAN PERSONALIZE THIS, AND THAT IS NOT BEING DONE AS FAR AS WE CAN TELL AT LEAST IN A SYSTEMATIC FASHION, AND IF YOU THINK ABOUT THE COMBINING, PEOPLE ARE DIFFERENT MICRO BIOMES, SHORT CHAIN, LONG CHAIN, HYDROPHILIC, STUDIES NEED TO BE DONE TO KNOW WHAT AN INDIVIDUAL FIBER OR SUPPLEMENT DOES TO A PERSON AND CUSTOMIZE, THAT'S MY OWN BELIEF. >> YES, (INDISCERNIBLE) FROM RUTGERS. IT'S EXCITING TO SAY WE HAVE LONGITUDINAL MULTI-OMICS OF DATASETS, AND SO THERE'S GOING TO BE A HUGE OPPORTUNITY FOR KNOWLEDGE AND DISCOVERY. BUT IF YOU LOOK AT THE DATASETS, THEY ARE STILL SO-CALLED BIG SMALL DATA, HUGE NUMBER OF VARIABLES, WILL YOU LIMITED NUMBER OF SAMPLES. ALSO THE DATA DATASETS, A LOT OF ZEROES BECAUSE OF INDIVIDUAL DIFFERENCE. IT'S VERY IMPORTANT TO HAVE BIOLOGICALLY MEANINGFUL WAY TO REDUCE THE DIMENSION, SO THE FIRST ATTEMPT OUGHT TO BE TAXON-BASED ANALYSIS BUT WE KNOW IT'S ACTUALLY NOT RIGHT TO ANALYZE DATA AT DIFFERENT TAXON LEVEL BECAUSE WE'RE LUMPING ALL DIFFERENT THINGS IN ONE, YOU KNOW, IN A NEW DATASET. SO WHAT WOULD BE BIOLOGICALLY OR ECOLOGICALLY MEANINGFUL WAY TO REDUCE THE DIMENSIONALITY OF THE DATA SO THAT WE CAN REALLY GO AFTER SUCH KIND OF, YOU KNOW, DATASET? >> I THINK WE ALL HAVE AN OPINION ON THIS ONE SO PROBABLY LOTS OF RESPONSES HERE. I THINK DON'T UNDERSTATEMENT POWER OF LONGITUDINAL DATA. YES, SMALL NUMBER OF HAVE INDIVIDUALS BUT WE'RE LOOKING FOR DELTAS, SITUATIONS ACROSS, IBD, PREGNANCY OR IN OUR CASE WHAT'S HAPPENING IN VIRAL INFECTION FOR PRE-DIABETICS VERSUS NOT. AND THAT REALLY EMPOWERS YOU IN A WAY THAT YOU MAY NOT APPRECIATE AND YOU CAN BE VERY ROBUST FOR INDIVIDUALS AND YOU DON'T NECESSARILY NEED LARGE N IF YOU'RE FOLLOWING PERTURBATIONS. IT GIVES EMPOWERMENT, YOU HAVE TO SHAKE THE GWAS 100,000 CONTROL MENTALITY TO APPRECIATE THE POWER OF WHAT WE'RE DOING, I BELIEVE. >> I CAN'T ADD MUCH EXCEPT TO THINK ON THE CONTINUUM FROM LARGE SCALE EPIDEMIOLOGY STYLE STUDIES WHERE YOU'RE TARGETING MANY, MANY INDIVIDUALS, USUALLY CROSS-SECTIONALLY, USUALLY RELATIVELY SHALLOW DATA, DOWN TO MODEL SYSTEM STUDIES IN GREAT DEPTH, HMP2, CORRECT ME IN I'M WRONG, WITH THE HOPE OF GETTING THE BEST OF BOTH WORLDS AS WE MOVE THE MICROBIOME TO DETAILED MECHANISTIC UNDERSTANDING. >> I WAS HOPING, CURTIS, YOU WOULD COMMENT EVEN IF THE DATA IS SPARSE, WHICH WE ALL AGREE ON, THERE'S STILL LOTS OF OPPORTUNITY TO BE STATISTICALLY ROBUST, RIGHTS? THAT'S FAIR, RIGHT? >> AND YOU ALSO GET IS A LOT OF INFORMATION AT THE PATHWAY LEVEL, EVEN IF YOU CAN'T GET IT DOWN TO THE INDIVIDUAL MOLECULE LEVEL, IF YOU'RE UNDERPOWERED THAT WAY AS WELL. >> THERE'S METHODS OF THE WRONG DIMENSION, SPARSE AND WHAT NOT STATISTICALLY AS WELL. >> PETER (INDISCERNIBLE) UCSF. I'M WONDERING IT SEEMS LIKE A LOT OF RESOURCES FINANCIALLY AND IN TERMS OF TIME, PART OF HMP1 AND 2, SAMPLE COLLECTION AND ESTABLISHING HUGE BIOBANKS, YOU GUYS ALL HAVE ACCESS TO, I'M WONDERING IS THERE SOME SORT OF PLAN MOVING FORWARD TO MAKE THE SAMPLES AVAILABLE EITHER TO PEOPLE THAT ARE PART OF THIS CONSORTIUM OR BROADER RESEARCH COMMUNITY THAT MIGHT BE DEVELOPING NEW TECHNOLOGIES TO ANALYZE INITIAL SAMPLES OR NUCLEIC ACIDS OR OTHER DEMONSTRATING MATERIALS? >> I CAN SPEAK FOR PHASE 1, BECAUSE THERE IS A CATALOG OF DNA EXTRACTS AVAILABLE, NOT FREELY OPENLY AVAILABLE. THEY ARE MEANT TO -- THEY ARE SET UP IN SUCH A WAY YOU WOULD HAVE TO COLLABORATE WITH ONE OF THE CLINICAL CENTERS THAT'S COLLECTED THE SAMPLE. SO IF YOU'RE INTERESTED IN DNA EXTRACT FROM HEALTHY COHORT STUDY, PHASE 1, NOT A LOT LEFT BUT THERE ARE SOME, I WOULD RECOMMEND YOU CONTACT ME DIRECTLY. >> I GUESS IDES LIKE TO GO META ON YOUR QUESTIO, IF WE THINK ABOUT EVERY PRESENTATION WE'RE GOING TO SEE TODAY, OR ANYTHING THAT'S FUNDED BY NIH, ONE OPPORTUNITY THAT'S OUT THERE, IT WOULD BE NICE TO HAVE ESSENTIALLY KIND OF A P.I. REGISTRY, WHERE YOU COULD ASK THE QUESTION, OKAY, YOU PUBLISHED THIS, BUT ARE THE SUBJECTS AVAILABLE FOR RECONSENT OR ARE THE SAMPLES AVAILABLE THAT YOU COULD PULL OUT OF THE REFRIGERATOR RESOURCES ASSOCIATED WITH IT. THERE'S TREMENDOUS LOSS BETWEEN ALL THAT REALLY -- THOSE INCREDIBLY RICH RESOURCES THE TAXPAYER PAID FOR AND MAY BE AVAILABLE AND WHEN YOU GO TO SRA, NOT TO BEAT UP ON THAT DATABASE, ANY PUBLIC REPOSITORY, IT'S NOT EXPLICITLY STATED. >> TO ECHO, WE HAVE THE BIGGEST BIOREPOSITORY OF DATA FROM THE HMP2 STUDY, ORDER OF A COUPLE HUNDRED THOUSAND SAMPLES IN OUR BIOBANK, WHAT'S CALLED THE RESEARCH ALLIANCE FOR MICROBEIUM SCIENCE REGISTRY, LEVERAGED IN OUR GROUP AND IN COLLABORATION WITH OTHERS. WE'RE WILLING TO DO THAT. THE ISSUE IS THE MAINTENANCE OF THIS FACILITY AND THE INTERACTION AND WE REALLY DON'T HAVE FINANCIAL RESOURCES FOR CURATING AND PROCESSING THESE SAMPLES SO WE CAN DISTRIBUTE THEM OR HAVE ANY WAY TO DO THAT YET. WE'RE TRYING TO WORK ON SOMETHING LIKE THAT. BUT AT THE MOMENT WE DON'T HAVE THAT. IF SOMEBODY DOESN'T WANT TO HAVE A COLLABORATION WITH US WE'RE HAPPY TO TALK ABOUT IT. >> TO WRAP IT UP, I DON'T WANT TO CUT INTO LUNCH HOUR OR ACTUALLY MORE IMPORTANTLY MAYBE THE POSTER SESSION. SO THE FIRST -- THERE'S THREE POSTER SESSIONS, ONE EACH DAY, 40 IN THE ATRIUM. VISIT THE POSTERS. IF YOU ORDERED LUNCH, YOU HAVE TO ASK THE REGISTRATION DESK WHERE YOU PICK THEM UP, I BELIEVE DOWN ON THE LOWER LOBBY. THAT TENT, THAT BIG WHITE TENT OUT THERE ON THE NATCHER LAWN, IS OURS. GO OUT THERE AND ENJOY YOURSELF. NETWORK WITH PEOPLE YOU HAVEN'T MET BEFORE. AND COME BACK AT 1:00. >> OKAY, EVERYONE. WELCOME BACK FROM LUNCH. I LIKE TO BE RIGHT ON TIME SO WE'RE ALREADY THREE MINUTES LATE, THAT'S CAUSING ME STRESS. WONDER WHAT THAT'S DOING TO MY MICROBIOME. SO THIS SESSION IS -- SORRY. I SHOULD INTRODUCE MYSELF. MY NAME IS LISA CHADWICK, I'M PROGRAM DIRECTOR AT THE NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES WHERE WE ARE INTERESTED IN HOW THE MICROBIOME INTERACTS WITH ENVIRONMENTAL CHEMICALS. IF YOU WOULD LIKE TO BE INTERESTED IN THAT TOO, FEEL FREE TO FIND ME AND TALK TO ME ABOUT IT. SO IN THIS SESSION WE'LL TALK ABOUT THE TOOLS, TECHNOLOGIES AND APPROACHES FOR MICROBIOME RESEARCH THAT GO BEYOND SEQUENCING AND TRY TO IDENTIFY BIG NEEDS GAPS AND CHALLENGES IN THAT AREA. WE'LL HAVE A SESSION JUST LIKE LAST ONE, FOUR TALKS IN A ROW THOUGH WE'LL HAVE ONE TALK, ONE SORT OF MEGA TAG TEAM TALK AND THEN ANOTHER TALK AND THEN WE'LL HAVE THAT JOINT Q&A SESSION AT THE END. OUR FIRST TALK IS FROM KATIE POLLARD, UNIVERSITY OF CALIFORNIA SAN FRANCISCO AND COME UP HERE. >> GREAT. HI, EVERYBODY. WELCOME BACK FROM LUNCH. I WANT TO START BY PUTTING UP A PICTURE THAT REPRESENTS WHAT I THINK A LOT OF THE WORK ON MICROSCIENCE HAS BEEN TO DATE ESPECIALLY SCIENCE RELATED TO THE HUMAN MICROBIOME AND HELPFUL TRANSLATIONAL WORK,. A PATIENT WITH SYMPTOMS. GATHER MOLECULES AND COUNT UP THE PERCENTAGE OF SEQUENCES THAT COME FROM EACH MICROBE OR EACH GENE, MAKE THESE STACKS BAR PLOTS OR PIE CHARTS AND THEN TRY TO ASSOCIATE THAT WITH WHAT'S GOING ON WITH THE PATIENT AND ADS WE KNOW MANY INTERESTING ASSOCIATIONS ARE DETECTED. WHAT I'M INTERESTED IN IS MOVING BEYOND THESE ASSOCIATIONS TOWARDS MECHANISMS. AND TRYING TO UNDERSTAND WHAT'S GOING ON IN A GENETIC LEVEL IN THE MICROBES EXPLAINING THOSE ASSOCIATIONS AND WHAT ASSOCIATIONS MIGHT WE BE MISSING WITH THE STACK BAR CHARTS AND PIE CHARTS. THE REASON I'M WORRIED ABOUT THIS IS IF WE CAN CHARACTERIZE MICROBES AT THE LEVEL OF INDIVIDUAL SPECIES WE KNOW DIFFERENT EXAMPLES OF THAT SPECIES, DIFFERENT POPULATIONS OF CELLS HAVE DIFFERENT GENES. THIS TOUCHES ON WHAT HOWARD SPOKE ABOUT IN THE KEYNOTE, WHAT IS A SPECIES ANYWAY. WE ARE INTERESTED IN THE SAME QUESTION AND WE KNOW ALL OF US FROM LOOKING AT GENOME SEQUENCES THE GENE CONTENT IS DIFFERENT ACROSS DIFFERENT STRAINS OF THE SAME SPECIES. MY LAB DEVELOPED A TOOL TO QUANTIFY USING SHOTGUN META GENOMICS DATA SO WE TOOK TWO PEOPLE FROM A VARIETY OF STUDIES THAT WERE AVAILABLE IN THE PUBLIC DOMAIN AND ASKED FOR SEQUENCES THAT THAT REPRESENT A GIVEN SPECIES WHAT PERCENTAGE OF GENES ARE THEY SHARING. HERE IS AN OVERVIEW OF THE RESULTS. THE HORIZONTAL ACCESS IS WHAT PERCENTAGE OF GENES ARE SHARED ACROSS PEOPLE SO EACH DOT IS A PAIR OF PEOPLE. AND THEY ARE ORGANIZED BY THE DIFFERENT SPECIES. YOU CAN SEE A LOT OF VARIATION. WITH SOME HAVING 10% GENE CONTENT DIFFERENCE BUT SOME HAVING UP TO 40, 45, EVEN 50% OF THEIR GENES DIFFERENT BETWEEN TWO PEOPLE WHO HARBOR THE EXACT SAME SPECIES. IF YOU GO TO GENUS OR HIGHER TAX NOMIC LEVEL THAT'S EVEN MORE TRUE. THEN WE LOOKED TO SEE WHETHER THE GENE CONTENT WAS ORGANIZED TO WHERE PEOPLE WHERE FROM AND THE ANSWER IS IT DEPENDS ON THE BUG. FOR SOME BUGS THERE'S HUGE DIFFERENCES BETWEEN GENE CONTENT THAT HAS NOTHING TO DO WITH WHERE SOMEONE IS FROM. THERE'S BASICALLY A STAR PHYLOGENY AND THE STRAINS GET EVERYWHERE. AND HOWARD'S TALK THERE WAS A QUESTION ABOUT WE GOT INTO TALKING ABOUT DISPERSAL LIMITATIONS AND WHETHER THERE'S BARRIERS TO GENE FLOW. FOR SOME SPECIES THERE SEEM NOT TO BE. WHEREAS OTHERS LIKE ERECTILE HERE THERE'S STRUCTURE WITH CLADES BASED ON EITHER THE SNPS, THE NUCLEOTIDE DIFFERENCES IN THEIR GENOME OR IN THEIR GENE CONTENT ORGANIZING BY CONTINENTS. HOWEVER, BUT WITH SHARING OF THESE CLADES HERE BETWEEN NORTH AMERICA AND EUROPE. THE OR REASON I'M WORRIED ABOUT GETTING DOWN TO GENETIC LEVEL RATHER THAN A TOX NOMIC OR GENE -- TAX NOMIC OR GENE DESCRIPTION LEVEL OF THE MICROBIOME, EVEN WHEN YOU HAVE THE SAME SPECIES IN TWO PEOPLE AND YOU LOOK AT GENES IN THE CORE GENOME THAT ARE SHARED SO THEY HAVE THE SAME SPECIES AND THE SPECIES HAS THE SAME GENE, THOSE GENES HARBOR GENETIC MUTATIONS. SOME OF THEM MAKE FUNCTIONAL DIFFERENCES IN WHAT THAT GENE IS DOING. SO THESE ARE DIFFERENT SPECIES. THIS IS HUMAN MICROBIOME PROJECT DATA. IN RED ARE BETWEEN HOST DIFFERENCES, ACROSS THE MICROBES ON AVERAGE T ABOUT ONE IN HUNDRED BASE BARES, SO TEN TO THE MINUS 2, ONE EVERY TEN TO MINUS 2 BASE PAIR THERE'S A GENETIC MUTATION BETWEEN PEOPLE AND EVEN WITHIN HOSTS WE SEE GENETIC VARIATION MAYBE EVERY THOUSAND OR 10,000 BASE BARES. IT DIFFERS ACROSS THE DIFFERENT PATHWAYS AND SPECIES BUT THERE'S FREQUENTLY 25% OF THOSE MUTATIONS, THAT I'M DESCRIBING HERE, CHANGE THE PROTEIN SEQUENCE OF A GENE. SO THEY HAVE POTENTIAL TO BE FUNCTIONAL. HIGH POTENTIAL TO BE FUNCTIONAL. SO THE IDEA THAT I WANT TO PUT FORWARD FOR FUTURE VIEW OF THE MICROBIOME IS STUDY MICROBES IN THE HUMAN BODY AT THE LEVEL OF GENETIC MUTATIONS JUST LIKE WE DO IN HUMAN BASED PRECISION MEDICINE. IF WE SEQUENCE PEOPLE AND GIVE TREATMENTS AND DIAGNOSTICS, AND PROGNOSTICS BASED ON GENETICS, WHY NOT DO THAT ALSO FOR THE MICROBES. S. THIS EXTENDS TO OTHER OMICS NOT JUST GENETICS BUT THE SAME OF PROTEOMICS AND METABALOMICS AS WELL. WE DEVELOPED META GENOTYPING AND THE IDEA IS TO IDENTIFY GENE LOSS GAIN AND MUTATION EVENT I WAS SHOWING YOU PICTURES OF TO CONFIDENTLY BE ABLE TO CALL THOSE WITHIN THE POPULATIONS OF CELLS FOR EACH SPECIES PRESENT IN A META GENOME. THE REASON BESIDES TWO I PRESENTED OR THE REASON MAYBE THE REASON I'M THE ONE DOING THIS AND IN THE SOMEONE ELSE IS THAT I COME AT MICROMYBIOLOGY RESEARCH FROM EVOLUTIONARY PERSPECTIVE. I SPENT MY CAREER STUDYING EVOLUTION AND GENETICS OF THE HUMAN GENOME AND OF COURSE THEREFORE THINK HOW FORM AND FUNCTION CHANGE THROUGH GENETIC MODIFICATIONS. ALSO AT UCF ON BIOMEDICAL CAMPUS I'M THINKING WHAT DOES THE HOST CARE ABOUT, WHICH IS THE CHEMICALS AND BIOMOLECULES PRESENTED BY THE MICROBIOME AND HOW THE CELLS ARE INTERACTING WITH HOST CELLS. SO THOSE REASONS MAKE ME VERY INTERESTED IN UNDERSTANDING THIS STRAIN LEVEL SUBSPECIES LEVEL GENETIC VARIATION AND DOING THIS METAGENOTYPING. SO WHY IS THIS NOT MORE PREVALENT? IT'S HARD. FIRST OF ALL, THERE'S A LOT OF CHALLENGES IN ANY ANALYSIS OF META GENOMIC DATA AND THESE APPLY TO TRYING TO GENOTYPE THE MICROBIOME AS WELL. I'M NOT GOING TO GO INTO THEM IN THE TALK TODAY BUT AS CURTIS MENTIONED ALSO THIS MORNING THERE ARE OTHER GROUPS LOOK AT THIS, THE DIFFERENT SOURCES OF ERROR, WE WROTE A REVIEW LAST YEAR THAT GOES OVER SOME OF THEM. MANY ARE COMMON IN ANY GENOMICS OR MULTI-OMICS STUDY WHEREAS OTHER ONES WE AS A FIELD HAD TO WORK OUT THAT ARE SPECIFIC TO STUDYING POOLED SAMPLES OF COMMUNITIES. HOW FAST ARE CELLS DIVIDING, SIZE OF THE GENOME, SIZE OF THE TARGET YOU'RE TRYING TO SEQUENCE. AND UNKNOWN SPECIES AND GENES IN A SAMPLE, ALL LEAD TO SYSTEMATIC DIFFERENCES IN THE RELATIVE MEASUREMENTS OF OTHER THINGS THAT ARE THERE. SO THE KNOWNS. SO THIS IS SOMETHING WE HAVE SPENT A DECADE THINKING ABOUT AND THAT I LITERALLY THOUGHT WE MAYBE SPEND SIX MONTHS OR A YEAR ON TEN YEARS AGO. BUT I FEEL LIKE AS A FIELD COLLECTIVELY WE HAVE DISCOVERED A LOT OF THESE GOTIAS AND MANY CASE VERSUS THE TOOLS IN THE LAB OR BIOINFORMATICALLY TO HANDLE THEM NOW. DOING THIS IS CRITICAL TO TYPE OF DATA SHARING META ANALYSIS WE HEARD ABOUT THIS MORNING. SO THAT'S GENERAL. WHEN YOU GET DOWN TO DOING THIS METAGENOTYPING THERE'S ADDITIONAL CHALLENGESES. ONE OF THE BIGGEST IS MOST OF THE SPECIESES THAT ARE PRESENT IN MOST MICROBIOMES HAVE NO GENOME. SO IF YOU WANT TO IDENTIFY POLYMORPHISMS AND SAY THEY'RE OCCURING IN A SPECIFIC SPECIES, IT'S VERY HELPFUL TO HAVE THIS GENOME LEVEL REFERENCE DATA. WE AND OTHERS ARE THINKING ABOUT WAYS TO DO GENOTYPING WITHOUT MAPPING TO A REFERENCE GENOME BUT THAT IS A BIG CHALLENGE COMPUTATIONALLY AND JUST IN TERMS OF HOW YOU WOULD THINK ABOUT APPROACHING THAT PROBLEM. SO AS A FIRST PASS MY LAB IS FOCUSED ON REFERENCE BASED GENOTYPING BUT IT'S INCREDIBLY LIMITED BY THE AVAILABILITY OF REFERENCE GENOMES SO WHAT I'M SHOWING HERE ARE ESTIMATES THAT WE MADE USING UNIVERSAL SINGLE COP P GENES TO UNDERSTAND HOW WELL DATABASES OF TENS OF THOUSANDS OF GENOMES SEQUENCED SO FAR COVER THE SPY SPECIES LEVEL DIVERSITY AND DIFFERENT TYPES OF MICROBIOMES. FOR THE HUMAN MICROBIOME IT'S BETTER THAN OTHER ENVIRONMENTS BUT IT DEPENDS WHERE YOU'RE FROM SO OUR DATABASES ARE BIASED TOWARDS INDUSTRIALIZED MICROBIOMES AND IT ALSO I'LL POINT OUT THE MOUSE MICROBIOME IS DOWN HERE BELOW 10% OF WHAT'S THERE AT SPECIES LEVEL SEQUENCED SO THAT IS A CHALLENGE FOR USING THE MOUSE AS A MODEL. EVEN THOUGH IT'S HARD, THE METAGENOTYPING APPROACH IS VERY IMPORTANT SO I WANT TO GIVE YOU COUPLE OF EXAMPLES, THIS IS -- I WILL SAY TOTALLY SCRATCHING THE SURFACE OF WHAT I THINK IS POSSIBLE WITH META GENOTYPES. SHOW YOU A COUPLE OF TWO EXAMPLES OF WHAT WE HAVE BEEN ABLE TO DO SO FAR. THE FIRST ONE IS WE CAN NOW DISENTANGLE TAX NOMIC SIGNAL AND SUNKSAL SIGNAL IN META GENOMICS DATA BECAUSE GENE PRESENCE, ABSENCE PER SPECIES. THIS IS THE WORK OF PATRICK BRADLEY. AND WHAT I'M SHOWING HERE IS AN EXAMPLE OUTPUT, I WON'T TELL YOU FOR SAKE OF TIME ABOUT THE METHOD BUT HAPPY TO TALK TO YOU ABOUT IT. THIS IS A PARTICULAR GENE FAMILY. WHOSE PRESENCE IS ASSOCIATED WITH KROHN'S DISEASE, NOT OVERALL, NOT THE OVERALL ABUNDANCE BUT IT'S PRESENCE IN SPECIFIC SPECIES SO ON THIS SIDE WE'RE SEEING THE ASSOCIATION OF THIS GENE WITH KROHN'S DISEASE AND HERE IS THE PRESENCE OF IT IN THESE ORGANISMS. THESE TREES MIRROR EACH OTHER BEAUTIFULLY AND YOU CAN SEE FOR EXAMPLE HERE THERE'S A GROUP THAT HAS THE GENE AND IN GRAY ONE THAT DOESN'T. HERE THOSE SPECIFIC STRAINS ARE FOUNDING CROHN'S INDIVIDUALS AND THIS ONE THAT DOESN'T HAVE THE GENE IS NOT FOUND IN CROHN'S INDIVIDUALS. I'M EXPLAINING THAT AS A BINARY BUT IT'S A QUANTITATIVE VARIABLE SO WE CAN ASSOCIATE SPECIFIC GENES IN SPECIFIC TAXERA WITH DISEASE, BODY SITES AND WE CAN ALSO LOOK AT THE NATURAL VARIATION OF THAT ACROSS PEOPLE. THIS IS DIFFERENT TO GET BACK TO WHAT I STARTED WITH, THIS IS VERY DIFFERENT THAN LOOKING HOW ABUNDANT ARE THE TAX NOMIC GROUPS OR HOW ABUNDANT ARE THE GENES. THIS WOULD HAVE BEEN MIXED WITH EITHER APPROACH. I WILL SAY THE PROTEOBACTERIA ARE CONTRIBUTING TO THE SIGNAL YET ARE A TINY PIECE OF THE STACKED BAR CHART THAT MIGHT BE OVERLOOKED IN A TAX NOMIC ANALYSIS. SORRY MY NECKLACE IS SCRATCHING THIS. I'M GOING TO TRY TO STOP THAT. SORRY. WE HAVE BEEN ABLE ALSO IN CASES WHERE THE GENES WE IDENTIFY AS HAVING INTERESTING PATTERNS OF BEING VARIABLE ACROSS PEOPLE, BODY TYPES AND ASSOCIATED WITH DISEASES. WE HAVE BEEN ABLE WHEN ANNOTATED TO LOOK AT HOW THE INDIVIDUAL COMPONENTS OF THE PATHWAY MAP OUT. SO WE FOUND THAT IN PARTICULAR ACROSS HMP AND CONTROLS FROM PUBLICLY AVAILABLE CONTROL STUDIES HEALTHY INDIVIDUALS TYPE 3 AND 6 SECRETION VARY ACROSS PEOPLE. IT'S NOT THE WHOLE PATHWAY, IT'S SPECIFIC GENES SO THE COMPONENTS THAT SIT HERE IN THE MEMBRANE AND THESE P PARTS OF SECRETION ARE FAIRLY NOT VARIABLE ACROSS PEOPLE AS SHOWN BY THEIR GENES BEING SHOWN BY THESE BLUE BLOCKS. WHEREAS PIECES OF MACHINERY THAT ARE SENSING SIGNALS IN SIDE THE CELL, DOING SECESSION HOST OR ANOTHER MICROBE CELL THESE INJECTORS ARE HIGHLY VARIABLE. SO IT'S SPECIFIC COMPONENTS OF THE PATHWAY THAT WE CAN DISENTANGLE AND TRY TO MOVE TOWARDS MECHANISM. THIS IS IMPOSSIBLE IN MOST CASES WHERE WE FIND AN INTERESTING SIGNAL, BUT WE HAVE NO IDEA WHAT THE GENES DO OR SPECIFIC MUTATIONS, EVEN IF THE GENE IS THERE WITH THE MUTATIONS SAY A NON-CODING MUTATION AND GENE, WHAT IS THE AFFECT OF THAT HAVE GOING TO HAVE. THIS IS ONE OF MY GAPS AND CHALLENGES FOR KNOWLEDGE IN THE FUTURE TO TRY TO UNDERSTAND THAT. AND THE CHALLENGE IS EXEMPLIFIED BY THIS NUMBER. WE HAVE A SHORT LITTLE PAPER WE'RE PUTTING TOGETHER EVALUATED ALL AVAILABLE GENE FAMILIES WE CAN FIND IN DATABASES AND FOUND THAT 53% NOT ONLY DO WE NOT KNOW WHAT IT DOES, THEY HAVE NOT EVEN A SINGLE PROTEIN DOMAIN ANNOTATED. SO THERE'S NOTHING TO EVEN GO ON. SOR A LOT OF THEM THAT HAVE A DOMAIN, WE DON'T KNOW WHAT THEY DO. THAT'S A HUGE GAP. THE LAST THING I WANT TO SAY IS THAT EVEN WITHOUT KNOWING WHAT GENES DO, WE CAN USE THIS GENERAL TAKE VARIATION FOR TRACKING STRAINS. THIS WILL BE USEFUL IN A NUMBER OF SETTINGS INCLUDING CLINICAL SETTINGS. HERE WE REANALYZE PUBLICLY AVAILABLE DATA ON THE INFANT MICROBIOME WE AND THEY SHOWED THE INFANTS TAX NOMIC COMPOSITION LOOKS MORE LIKE THE MOM OVER THE FIRST YEAR OF LIFE. HOWEVER, WE SWAPPED THE KIDS ON THE COMPUTER AND MATCHED THEM TO A MOM THAT WASN'T THEIR MOM AND THEY ALSO START TO LOOK MORE LIKE THAT PERSON OVER THE COURSE OF THE FIRST YEAR OF LIFE IN TERMS OF TAX NOMIC COMPOSITION REFLECTING A GENERAL MATURITY OF THE MICROBIOME, NOT WHAT'S INFERRED BY US AND OTHER PEOPLE FROM THIS THAT THERE WAS DIRECT TRANSFER OF THE MICROBES. TO ZEST THAT WE FOUND GENETIC MUTATIONS IN SPECIFIC MICROBES IN THE MOM THAT WERE NOT FOUND IN ANY OTHER MOTHER IN THE STUDY, NOT IN THE HMP, NOT ANY PUBLIC DATABASE SO PRIVATE MUTATIONS, WE TRACKED HER STRAINS TO SEE WHETHER WHEN THE INFANT ACQUIRE IT IS SAME SPECIES THAT THE MOM HAS, IS IT THE SAME STRAIN OR NOT. THERE ARE SOME DIRECT TRANSMISSIONS ESPECIALLY AT BIRTH BUT THE OVERALL SIGNAL IS THE OPPOSITE, OVER THE COURSE OF THE FIRST YEAR OF LIFE THE INFANT IS GETTING STRAINS FROM SOMEWHERE OTHER THAN THE MOM'S STOOL. SO TO WRAP UP, WE QUANTIFIED MASSIVE DIVERSITY AT THIS GENETIC LEVEL. SOME VERTICAL TRANSMISSION BUT NOT A LOT. WHAT I WANTED TO GO ON TOWARDS THAT WE'RE GOING TO ACHIEVE THIS MICROBIOME PRECISION MEDICINE IS ONE OTHER JUST TO CONCLUDE ONE OTHER TECHNOLOGICAL GAP. THIS ECHOS WHAT WAS SAID THIS MORNING BUT I WANT TO MAKE A SPECIFIC PITCH FOR REFERENCE DATA IN THE CLOUD. NOT JUST MICROBIOME SAMPLES IN THE CLOUD BUT CURATIVE REFERENCE DATA. NOT JUST SITTING IN THE CLOUD FOR SOMEONE TO DOWNLOAD. AND NOT NECESSARILY WORKING WITH THE SAME VERSION AS SOMEONE ELSE AND NOT BEING ABLE TO NECESSARILY HANDLE THE SIZE OF THAT DATA ON THEIR OWN COMPUTER. BUT SITTING WITH HIGH SPEED COMPUTE YOU CAN SIT UP AND LOTS OF USERS LOOKING AT THE SAME DATA AND RUNNING ANALYSES IN THE CLOUD. CREATING ANNOTATIONS ESPECIALLY THROUGH MULTI-OMIC STUDIES THROUGH FUNCTION, CUR RATION OF THAT DATA AND ADDING CURE RATION BACK UP INTO THE CLOUD FOR OTHERS TO SEE. SO THIS IS NOW A PIPE DREAM BUT WE HEARD GREAT STEPS IN THAT DIRECTION FROM O WEB AND OTHER THIS IS MORNING -- OWEN AND OTHERS THIS MORNING AND IT'S SOMETHING NIH CAN TACKLE AND I WANT TO MAKE A PITCH FOR IT TODAY. SO THANKS A LOT. HERE ARE THE FOLKS WHO DID THE WORKND I WILL TAKE QUESTIONS AT THE END. [APPLAUSE] >> THANK YOU FOR THAT TALK. THE NEXT TALK IS GOING TO BE A TWO PERSON SHOW. BY ROB KNIGHT AND PIETER DORRESTEIN FROM UCSD. >> ALL RIGHT. >> I WANT TO BEGIN BY THANKINGLY IS A FOR ORGANIZING THIS AND I'LL SAY TO LISA AND BOB HAVE BEEN GREAT. AND WHAT WE'RE GOING TO TELL YOU ABOUT IS INTEGRATED MODEL OMICS FOR DISEASE AND ORIGINALLY WE WERE GOING TO DO LISA'S ONE TALK IN THE MICROBIOME AND ONE TALK ME TABLOID BUT WE DECIDED THESE TOPICS WERE INSEPARABLE (INDISCERNIBLE) TALKS. THERE'S VERY RAPID ADVANCES IN THE FIELDS AND CHANGING WHAT WE THINK IT MEANS TO BE HUMAN. I WOULD TO TAKE A MOMENT TO CONSIDER WHAT YOU SAW WHEN YOU LOOKED IN THE MIRROR THIS MORNING. WE SORT OF (INDISCERNIBLE) 43% HUMAN AND THEN WE GOT HERE AND FOUND NO COFFEE AND IT DROPPED TO 33%. WITH THAT 43% NUMBER COMES FROM, WHEN WE THINK WHAT MAKES US HUMAN, WE HAVE ABOUT 30 TRILLION HUMAN CELLS AND 39 TRILLION MICROBIAL CELLS ACCORDING TO LATEST ESTIMATES, THEREABOUTS SO THAT'S WHERE THAT 43% NUMBER COMES FROM. AS YOU HEARD THIS MORNING WHEN WE THINK ABOUT LEVEL OF DNA WE HAVE ABOUT 20,000 HUMAN GENES TO 20 MICROBIAL GENES THE PHASE 2 WE HAVE ADDITIONAL GENES SO (INDISCERNIBLE) SO BY THAT MEASURE WE'RE AT BEST 1% HUMAN AND THERE'S EXCITEMENT ABOUT SYSTEMS BIOLOGY AND SYSTEMS BUT HARD TO DO THAT WHEN NEE COLLECTING # 9% OF THE -- 99 -- NEGLECTING 99% OF THE SYSTEM. YOU HEARD ABOUT AMP AND THE TREMENDOUS ACHIEVEMENT AND PRODUCING (INDISCERNIBLE) BASICALLY THIS PROJECT COLLECTED A TOTAL OF 4 1/2 TRILLION A, T, D, AND Cs SO THE GREAT THING ABOUT THIS IS WE HAD A LOT OF DATA BUT THAT WAS ALSO TERRIBLE THICK ABOUT IT SO WHEN I SHOW YOU FIRST FILE DATA FROM HMP DESPITE THE FACT WHAT WE'RE FUNDAMENTALLY DOING IS ECOLOGY, IT'S HARD TO TELL WHO LIVES WHERE IN THE ENVIRONMENT FROM THIS. RIGHT? THIS IS JUST THE FIRST FILE OF THE DATA, THERE'S ANOTHER 17,000 LIKE IT AND THUS 0.1% OF THE CONTENTS OF THAT FILE SO WE HAVE OUR WORK CUT OUT FOR US, MOSTLY PROBLEMATIC NOW THAT THIS THING IS IN THE HANDS OF ORDINARY MEMBER OF THE PUBLIC BECAUSE THROUGH PROJECTS LIKE AMERICAN GUT AND THROUGH VARIOUS COMPANIES YOU CAN GET YOUR MICROBIOME PROFILE DONE, SAFE PEOPLE COMING TO THE COKETORS SAYING HEY I HAVE GREAT NEWS FOR YOU WHICH IS I HAD MY MICROBIOME DONE, NOW I HAVE A LIST OF A THOUSAND MICROBES IN MY GUT OR EVEN BETTER I HAVE THEM WITH SHOTGUN, I HAVE THIS LIST OF A MILLION GENES IN MY GUT. WITH ALL THIS DATA YOU CAN TELL ME WHAT'S WRONG WITH ME, RIGHT? AND WHAT ARE YOU GOING TO DO? REFER TO COLLEAGUES IN PSYCHIATRY FOR BEING CRAZY TO BRING THAT STUFF TO YOU AND INTERPRET IT IN THE 15 MINUTES YOU HAVE. BUT OUR GOAL AS A COMMUNITY IS TO MAKE IT NOT CREE SY ANY MORE AND FIGURE HOW TO GET SOMETHING OUT OF THAT PROFILE WITH OTHER DATA FROM THE SAME PERSON OVER TIME OR WHAT THE REFERENCE DATA SO YOU HEARD BRIEFLY THIS MORNING ABOUT CHIME THIS MORNING, MY LAB DEVELOPED HMP DATA YOU TAKE ALL THE SEQUENCES AND YOU GET MUCH MORE INTERPRETABLE. SO WHAT'S GOING ON IS EACH REPRESENTS THE COMPLEXITY OF THE MICROBIOME, DNA, TYPICALLY YOU CAN USE TECHNIQUES IN SHOTGUN META TRANSCRIPT OMICS OR SOME EXTENT METABALOMICS AS WELL. ACCORDING TO MAIN VARIABLE THAT AFFECTS VARIATION IN SAMPLES YOU CAN SEE IMMEDIATELY THAT THE MAIN THING GOING ON IN THE HMP SAMPLES THE DIFFERENT PARTS OF THE BODY DIFFERENT FROM ONE ANOTHER. I HIGHLIGHT THE FIRST YOU CAN SEE IN THE MOUTH THE GUT TOTALLY DIFFERENT REGIONS, ALMOST LIKE DIFFERENT CON INNOCENTS, IT WAS ONLY WHEN WE DID THE MICROBIOME PROJECT LOOKING AT TENS OF THOUSANDS OF SAMPLES, THAT WE UNDERSTOOD HOW PROFOUND THESE DIFFERENCES ARE ON THE HUMAN BODY WERE BECAUSE IF YOU -- WHAT WE CAN DO IS GO OUT AND ASK WHAT TWO POINTS ADJUSTS DIFFERENCE IN THE GAP (INAUDIBLE) YOU THINK ABOUT YOUR MOUTH AS A CORAL REEF WITH STRUCTURES AND THE AMAZING FACTORS IN YOUR MOUTH IS AS FAR FROM FROM YOUR GUT THE MICROBIOME, THERE'S WATER FROM THE DIRT AND SO THERE'S ESSENTIALLY NON-(INDISCERNIBLE) COMMUNITIES. WHEN DO THESE HUGHLEY DIFFERENTIATED COMMUNITIES AS ADULTS COME FROM IN THE FIRST PLACE. IF YOU HAVE DOGS OR KIDS YOU LIKELY HAVE QUESTIONS ABOUT THAT. ALL TRUE SO I CAN MATCH YOU UP TO YOUR DOG WITH FAIRLY HIGH PRECISION BASED ON YOUR MICROBIOME AND EVEN YOUR DOG'S MICROBES AFFECT HOW YOU DEVELOP. HOW WE'RE BORN HAS A TREMENDOUS IMPACT ON MICROBES AND THEN HOW WE SUBSEQUENTLY DEVELOP. SO I'M NOT GOING TO SHOW YOU THAT BUT I WILL SHOW YOU THE VALUE OF LONGITUDINAL DATA, THIS IS WHAT WE DID LOOKING AT THE DEVELOPMENT AND THE GUT MICROBIOME, ONE CHILD, FIRST TWO AND A HALF YEARS OF LIFE, YOU CAN SEE FROM THE FECAL SAMPLE LOOKS NOTHING LIKE A HEALTHY ADULT GUT SAMPLE SO IT'S UP THERE IN THE VAGINAL REGION WHICH WE EXPECT FROM THE SALIVARY MODE. I'M GOING TO MAKE A COUPLE OF POINTS, ONE TO THE NEXT TO THE NEXT SO YOU CAN SEE THE TWO AND A HALF YEARS OF DEVELOPMENT, AT ONE WEEK INTERVALS. IN CASE YOU WONDER WHY TWO AND A HALF YEARS THAT'S WHEN THE KID WAS TOILET TRAINED AND EASIER TO GET IT OUT OF THE DIAPER THANKED TO FIND SOMEONE WHO HAS LEARNED HOW TO FLUSH. SO WHAT YOU CAN SEE IS SOMETIMES THERE'S TREMENDOUS VARIATION ONE WEEK TO THE NEXT. OTHER TIMES LITTLE VARIATION. SOMETIMES DISTANCE TRAVELED IN A WEEK IS GREATER THATTEN THE DIFFERENCE BETWEEN ANY TWO HEALTHY ADULT SAMPLES IN THE HMP. SO THINK A CHILD LOOK LIKE A DIFFERENT PERSON ONE WEEK TO THE NEXT THAT CAN LITERALLY BE TRUE IN TERMS OF MICROBIOME WHERE THE GENES ARE IN THE FIRST PLACE. BY COMING UP HERE WITH SOMETHING FASCINATING, WHAT YOU'RE GOING TO SEE IS ANTIBIOTICS FOR EAR INFECTION YOU CAN SEE REGRESSION OF MICROBIOME FOLLOWED BY RAPID RECOVERY. THAT WENT BY FAST SO I'M GOING TO REWIND AND PLAY IT AGAIN. YOU'LL SEE ORAL ADMINISTRATION OF AMOXICILLIN. YOU CAN SEE THE MICROBIOME DOING MONTHS OF NORMAL DEVELOPMENT FOLLOWED BY A RELATIVELY RAPID REBOUND IN A FEW WEEKS. BY TWO AND A HALF YEARS YOU CAN SEE HE'S BASICALLY IN HEALTHY REGION OF THE PLOT. SO WHAT WE'RE TRYING TO FIGURE OUT AT THE MOMENT AND EVERYTHING I HAVE SHOWN YOU IS TAXONOMY, WHY ARE SOME RESILIENT AND OTHERS FRAGILE TO THIS MICROBIOME CHANGE? WE STARTED TO ADDRESS THIS DETERMINING CHEMISTRY ASSOCIATED WITH MICROBIOTA. WE STARTED TO ADDRESS THIS BY ASKING A FUNDAMENTAL QUESTION, WHAT MOLECULES DOES YOUR MICROBIOTA PRODUCE THAT CAN CONTROL COLONIZATION OF VARIETY OF PATHOGENS. SO THE FIRST THING WE DID IS WE MADE EVERYBODY WORK OUT IN THE LAB AND THEN WE HAD THE MICE BASICALLY SWABS TO ISOLATE MICROBES FROM THEM AND IF YOU WERE TO DO THIS EXERCISE ON YOURSELF, ORGANISMS THAT LOOK LIKE THIS, THIS IS ABSOLUTELY BEAUTIFUL, BASICALLY ANYBODY WILL BE ABLE TO SEE THESE MICROBES THAN PLAY FOOTBALL AS IT LOOKS LIKE, REALLY UNUSUAL FEATURES, SO ON. WE THEN TAKE THESE MICROBES AND CO-CULTURE WITH PATHOGENS AN DEVELOP SOMETHING CALLED MASS SPECTROMETRY TO ALLOW US TO LOOK AT THE CHEMISTRY ASSOCIATED WITH MICROBES FROM PETRI DISHES. WHAT YOU SEE HERE IS THE BACILLUS CAME FROM A INDIVIDUALS IN THE SAMPLE FROM THAT PRODUCES A MOLECULE, GRADIANT OF A MOLECULE, BUT THEN YOU SEE THE BLUE MOLECULES, DELTA TOXINS, PRODUCED BY STAPH AUREUS. THERE'S A LOT OF STAPH AUREUS INVADE HEALTHY INDIVIDUALS SO BASED ON THIS IMAGE WE PROPOSE IF THE RED MOLECULE IS PRESENT ON THE SKIN, MAYBE SUPPRESSES REDUCTION IN VIRULENCE FACTORS DECREASIBILITY TO HAVE STAPH AUREUS TO COLONIZE THE SKIN ENVIRONMENTS, THAT'S A TESTABLE HYPOTHESES SO WE ISOLATED THESE PARTICULAR MOLECULES, WE THEN ADD STAPH AUREUS TO IT AND WE SIMPLY ASK THE QUESTION, HOW MANY COLONY FORMING UNITS OF SALVE AUREUS CAN YOU ISOLATE? WHAT YOU WILL SEE IS UPON TREATMENT WITH THIS PARTICULAR MOLECULE, WE SEE ABOUT 75% REDUCTION OF COLONY FORMING UNITS THAT YOU CAN OBSERVE FROM OF STAPH AUREUS. SO IT SUPPORTS THE HYPOTHESIS ORGANISMS LIVE ON US THAT THEY PRODUCE MOLECULES THAT CONTROL RELEASE COLONIZATION PROLIFERATION OF PATHOGENS. WE PUSH THIS FURTHER AND YOU CAN SEE IF THESE ORGANISMS PRODUCE THESE MOLECULES WHAT IMPACT THAT HAS ON HEALTH AND DISEASE AND ENDED UP BEING PUBLISHED IN THIS PAPER, RICH GAL LOW AND CARSON WHO IS HERE AS WELL WE TOOK HEALTHY MICROBES ADDED DERMATITIS PATIENTS AND WHAT YOU WILL SEE IS DECREASE IN ATOPIC DERMATITIS SYMPTOMS RELATED TO SUPPRESSION OF STAPH AUREUS SO IT'S AN IMPORTANT RELATIONSHIP THERE. THIS IS AN ARTIFICIAL SYSTEM. WE'RE OVERWHELMING THE SYSTEM WITH THESE HEALTHY MICROBES. SO THE QUESTION I HAVE IS REALLY A NORMAL CONDITION THAT MIGHT BE PRESENT ON THE SKIN. THE REASON I ASK THAT IS BECAUSE THESE MOLECULES HAVE NEVER BEEN DIRECTLY DETECTED FROM THE SKIN. SO WE WANTED TO COME TECHNOLOGIES THAT ALLOW US TO SEE THE CHEMISTRY ASSOCIATED WITH IT. AND THAT LED TO OUR FIRST RESEARCH PAPER ROB KNIGHT WE STARTED TO MAP IN THREE DIMENSION ON THE HUMAN SURFACE. THE IDEA IS SIMPLE. IF YOU SPATIALLY COLLECT MOLECULE INFORMATION AS WELL AS MICROBIAL INFORMATION YOU SHOULD WITH ABLE TO DETERMINE WHAT MOLECULES ARE ASSOCIATED WITH THESE MICROBIAL COMMUNITIES BECAUSE THE CHEMISTRY DECK AT A TIMES THE GROWTH OF THESE IMMUNITIES OR IT COULD BE THAT THE MICROBES PRODUCE MOLECULES OR THEY MODIFY MOLECULES THAT ARE PRESENT ON THESE DIFFERENT REGIONS OF THE SKIN. VERY FIRST DATA SET FOR METABALOMIC DATA, THAT'S THIS MOVIE HERE, BUT WHAT YOU WILL SEE IN THE UPPER RIGHT HAND CORNER ARE THE MOLECULES THAT WE'RE ABLE TO DETECT BY MASS SPECTROMETRY, ITS LOW CONCENTRATION AND HIGH CONCENTRATIONS OF THESE MOLECULES. THIS IS HOW MUCH YOU CAN SEE AS WE'RE SCANNING THE MOLECULES, YOU CAN START TO SEE IT FLICKERING. WHAT THIS ESSENTIALLY IS TELLING US, THERE ARE DIFFERENT CHEMICAL DISTRIBUTIONS THAT EXIST ON THE SKIN SURFACE. WHEN WE STOP THESE IN TIME YOU GET MOLECULES ASSOCIATED WITH THE BELLY BUTTON, MOLECULES WITH THE HANDS, MOLECULES IN THE GROIN REGION, SHOULDER REGION THAT UNIFORMLY DISTRIBUTE THROUGHOUT THE SURFACE BUT SOME MOLECULES LOW IN CONCENTRATION, IT INCREASES IN CONCENTRATION. SO IF YOU'RE A MICROBE AND WANT TO FIND YOUR ECOLOGICAL NICHE WHERE IN THAT GRADIANT DOES IT FIT. WE HAVE LITTLE UNDERSTANDING FOR THIS. WHAT THIS ALLOWS US TO DO, WE GOT CREATE THE CORRESPONDING MICROBIAL MAPS. HERE WE LOOK AT ON THE CHEST BACK AND HEAD AREA, AND THERE'S ABOUT 850 GENRE WE DETECTED IN THESE PARTICULAR STUDIES. SO NOW WHAT WE CAN DO IS TAKE ADVANTAGE OF THE SPATIAL INFORMATION AND SAY WHAT MICROBES ARE CO-CORRELATED WITH THE DIFFERENT MOLECULES THAT ARE PRESENT, THEY CAN BE USED TO UNDERSTAND WHY THOSE MOLECULES ARE THERE, WHAT THE MOLECULES ARE DOING. BENIGN A SERIES OF MOLECULES ASSOCIATED WITH THE DEGRADATION OF TRIGLYCERIDES. U YOU CAN RECAPITULATE IN VITRO WHEN YOU TAKE TRIGLYCERIDES YOU CAN SEE THE DEGRADATION OF ACID OR OXIDIZED VERSION. SO WHAT THIS BASICALLY MEANT IS MICROBES DON'T ONLY JUST CONTRIBUTE MOLECULES THAT ARE PRESENT ON THE SURFACE OF THE SKIN BUT ALSO MODIFY EXISTING MOLECULES THAT ARE PRESENT THERE AS WELL. THE DATA SET LIKE THIS, REALLY, IT GENERATES MANY -- HAS CAPACITY GENERATING MANY HYPOTHESES. THIS WAS RECOGNIZED BY FRANCIS COLLINS WHEN HE BLOGGED ABOUT THIS PARTICULAR PAPER. THIS DATA ESSENTIALLY CAN GENERATE LOSS OF HYPOTHESES, HOW WE CONTINUE TO LEARN ABOUT KNOWLEDGE FROM DATA SET LIKE THIS? FOR METABALOMICS SIDE WE BUILT THIS CROWD SOURCE ANALYSIS INFRASTRUCTURE, THIS IS A WORLDWIDE EFFORT BASICALLY WITH 127 AUTHORS PUBLISHED. WHAT THIS IS A PLACE TO DEPOSIT YOUR DAYTIME, THE LARGEST REPOSITORY AT THE MOMENT, HAS ABOUT 3 BILLION SPY TRAY IN IT. -- SPECTRA IN IT YOU CAN MAKE ANNOTATIONS TO YOUR DATA OR ANYBODY ELSE IN THE WORLD CAN MAKE ANNOTATIONS TO YOUR DATA AND IF THEY MATCH TO OTHER PEOPLE'S DATA THEY WILL GET THAT INFORMATION RELAYEDED TO THEM SO YOU BUILT THIS COMMUNITY KNOWLEDGE. ASSOCIATED WITH METABALOMIC DATA AND IT'S A WAY TO CAPTURE THAT KNOWLEDGE. KNOWLEDGE IS GROWS FAST, AND YOU CAN SEE INDIVIDUAL CONTRIBUTIONS AND SOMETIMES YOU HAVE LARGE CONTRIBUTIONS SUCH AS ONE FROM PNAL, -- I HIT THE WRONG BUTTON. BUT THE SKIN DATA SETS IT WAS CLEAR THAT THE KNOWLEDGE ABOUT THIS PARTICULAR SKIN DATA SET HAS GROWN FAST AS WELL. WHEN WE DEPOSIT THE DATA WE HAD 98 ANNOTATIONS AND BY NOW WE'RE 772 ANNOTATIONS SO IT'S GROWN QUICKLY. T A ONE POINT WE GOT AN EMAIL SAYING HEY, YOU HAVE THESE DEGRADATION PRODUCTS RIGHT HERE THAT COME FROM HEMODEGRADATION. SOMEBODY IN THE WORLD WAS STUDYING AN ORGANISM, DEGRADING HEME AND THEY MADE ANNOTATIONS WE FOUND THEM IN HUMAN MAPS. WHERE DID WE FIND THOSE? THEY WERE IN THE GROIN REGION OF THE FEMALE. WE HAD ALREADY SEEN IN THE PAPER WHEN WE PUBLISH IT THAT HEME WAS PRESENT AND THAT WAS CONSISTENT WITH THE FACT THAT LATE STAGE MENSTRUAL CYCLE. BUT WHAT THIS SHOWS IS THERE'S NOW A POSSIBILITY THAT THERE IS SOME PROCESS THERE THAT IS INVOLVED IN HEME DEGRADATION. ONE THING WE CAN LOOK FOR MICROBES IN A PARTICULAR REGION, YOU CAN LOOK IF ANY OF THESE ORGANISMS HAVE THIS HEME OXGENASE, PEP TA STREP TACOCCUS HAS ONE OF THOSE PRESENT, NOW YOU CAN BUILD HYPOTHESIS THESE MICROBIAL COMMUNIQUES ARE INVOLVED IN NORMAL PHYSIOLOGICAL PROCESS THAT AFFECTS 50% OF THE POPULATION. IF YOU WANT TO DETERMINE WHICH ORGANISM IS TRULY RESPONSIBLE LONG TUESDAY ANALYST STUDIES WOULD BE -- LONGITUDINAL STUDIES ARE IDEAL TO DO THAT. >> ABSOLUTELY. SO WE HAVE BEEN GETTING MORE INTO LONGITUDINAL STUDIES OF THE KIND YOU SAW THIS MORNING HMPT WHICH IS CRITICAL FOR UNDERSTANDING THERAPEUTIC RESPONSE. THIS IS SNAP SHOT DATA FOR EXAMPLE IN THE AMERICAN GUT WE HAD 10,000 PEOPLE SIGN UP TO GET THEM ANALYZED. NOT EVERYONE WANTS TO KNOW WHAT'S IN THERE. AT LEAST THE MIDDLE SCHOOL IS -- LITERALLY USING ROBOTS TO STUDY THE BACTERIA. YOU CAN GET SO MUCH MORE, ESPECIALLY WHEN YOU INTEGRATE FOR DATA LIKE HMP DATA. SO THIS, TIME SERIES, SHOWS YOU WHAT YOU CAN GET INTEGRATING WITH THE HMP, IN THOSE CASES WE WILL LOOK AT C DIFF INFECTION, IN COLLABORATION WITH MIKE AT THE UNIVERSITY OF MINNESOTA. BUT WHEN WE LOOK AT THE FECAL SAMPLES FROM THE PATIENTS YOU SEE THE SPIKING SYMBOLS ARE TOTALLY DIFFERENT FROM THE HEALTHY STOOL AT THE BOTTOM. WHAT'S GOING TO HAPPEN IS FOUR OF THESE PATIENTS BEGIN TO GET FECAL TRANSPLANT FROM ONE DONOR TO REPLACE MICROBIOME. C DIFF INFECTIONS ARE ONE OF THE MOST INFECTIONS IN THE UNITED STATES, KILLS ABOUT 14,000 PEOPLE A YEAR. SO ANYWAY, THE QUESTIONS ARE VERY MUCH LIKE THE QUESTIONS I SHOWED YOU WITH THE INFANT TIME SERIES NOW INSTEAD OF TAKING A WEEK EACH FRAME IS ONE DAY IN THE LIVES OF PAINS WITH THE FECAL TRANSPLANT. GIVEN C DIFF PATHOGEN WILL YOU SEE ANY AFFECT OF THE COMMUNITY LEVEL WHEN YOU DO THIS. WHAT YOU CAN SEE IS ESSENTIALLY IMMEDIATELY IN JUST TWO OR THREE DAYS ALL FOUR PATIENTS MOVED MICROBIOMES COMPLETELY TO THE HEALTHY STATE AND THEY STAY DURING THE MONTHS OF FOLLOW-UP. THIS IS REMISSION OF ALL THE CLINICAL SYMPTOMS, IN FACT, LAST LARGE SCALE TRIAL DONE TO COMPARE FECAL TRANSPLANT HAD TO BE STOPPED EARLY BECAUSE TRANSPLANT WAS 90% EFFECTIVE. ANTIBIOTIC STANDARD OF CARE LESS THAN 40% EFFECTIVE. IT WAS CONSIDERED UNETHICAL TO CONTINUE TRANSPLANT FROM THOSE ON THE ANTIBIOTIC PART OF THE TRIAL. WHAT'S AMAZING ABOUT THIS IS IT SHOWS YOU HOW THE MICROBIOME AT THE TIME CAN SHOW YOU PROGRESSION THROUGH PARTICULAR THERAPY. SHORTLY AFTER I GOT TO UCSD LARRY SMART AT IDD WAS LOOKING AT THE HMP DATA WITH ME ON THE 64 PIXEL DISPLAY WALL. YOU KNOW, ROB, I HAVE A SPECIFIC MICROBIOME AS WELL BECAUSE I'M AN IBD PATIENT. YOU EXPECT A CERTAIN AMOUNT OF CRAP FROM COLLEAGUES. IN MY CASE -- LARRY IS FASCINATING AND STUDYING HIMSELF FOR THE LAST 17 YEARS WITH ONE DIMENSION OF HIS WEIGHT WEIGHT AND ADDING THOUSANDS OF DIMENSIONS WITH SNP PROFILING AND NOW MILLIONS OF DIMENSIONS WITH SHOTGUN META GENOMICS. AND STUDYING HIS MICROBIOME A FEW YEARS AND GOT THIS GREAT TAXONOMY CHART. IF U YOU DON'T SEE PATTERNS DON'T WORRY NEITHER DID LARRY BUT THINK ABOUT THE AMOUNT OF COMPUTER THAT WENT INTO MAKING THAT GRAPH. WHEN WE RETOUCH WITH (INDISCERNIBLE) WHAT WE SEE IS A CLEARER BLUE AND RED REGION. WHEN I ANIMATED OVER TIME WHAT WHAT YOU'LL SEE IS IT STARTS OFF THE EDGE WITH BLUE, MOVES THROUGH THE BLUE, CROSSES TO THE RED AND THEN BASICALLY BOUNCES AROUND AT RANDOM IN THE RED. SO YOU MIGHT BE WONDERING WHAT THIS HAS TO DO WITH HIS HEALTH, YOU CAN SEE THE INITIAL SHIFT IN THE MICROBIOME TREATED BY ANTIBIOTICS FOLLOWED BY THAT HE HAD FREQUENT IBD, HE WAS LOSING WEIGHT, HE SWITCHES HIS MEDS, FROM BLUE REGION TO THE RED AND SOON HE'S IN THE RED REGION HIS WEIGHT GOES BACK UP TO HEALTHY SET POINT FEELING BETTER AND MOST IBD SYMPTOMS ARE IN REMISSION. SO WHAT'S AMAZING IS HOW WE KNOW IN LARRY'S INDIVIDUAL CONFIGURATION SPACE WE TELL THEM AS SOON AS YOU'RE IN THE RED REGION YOU'RE GOING TO BE FINE FOR A FEW YEARS. HAVING THESE PROFILES ARE REALLY IMPORTANT. YOU'RE PROBABLY THINKING THIS IS JUST ONE GUY. CAN YOU GENERALIZE THIS. THIS IS WHAT WE DID WITH JENSONND OTHER COLLABORATORS LOOKING AT THE DYNAMICS OF MANY FRIENDS PATIENTS WITH DIFFERENT PERFORMANCE OF TRENDS. AND WHEN I START ANIMATIONS GOING YOU CAN SEEP THE YELLOW AND RED TRACES WHICH ARE WITH AND WITHOUT SURGERY, THERE'S MORE VARIATION THAN FOR EXAMPLE HEALTHY CONTROLS IN GREEN, COLITIS PATIENTS IN BLUE WHO OVERALL. YOU CAN SEE THE VISITATION TO THE HEALTHY REGION GIVEN THE PEOPLE WITH IBD MAKING IT DIFFICULT TO TELL WHAT'S GOING ON FROM A SINGLE TEMPLATE. WE FIGURED HOW TO MODEL IN A HEALTHY PLANE LOOK AT DISTANCE SO THE TOP ROW IS HOW WE FETCHED THE HEALTHY FRAME AND MEASURED THE DISTANCE FROM IT, THE BOTTOM IS THE ACTUAL DATA WITH TWO DISTANCE MATRIX. WHAT'S AMAZING IS WE GOT DISEASE CLASSIFICATION FROM THE MICROBIOME BASED ASSAY WHICH IS CURRENTLY THE GOLD STANDARD. SO LOOKING AT TIME CHANGES IS ONE OF THE WAYS WE CAN BEGIN TO UNDERSTAND CHANGES THAT HAPPEN WITHIN THE MICROBIOME BUT SPATIALLY YOU CAN ALSO DO THIS AND REALLY IT'S AN OPPORTUNITY TO INTEGRATE MULTI-OMICS INFORMATION. SO I WILL HIGHLIGHT THIS WITH THIS PARTICULAR HIGHLY INTERDISCIPLINARY STUDY. THAT IS LED BY MY FORMER POST-DOC FACULTY MEMBER AT GEORGIA TECH, SHE WAS FUNDAMENTALLY INTERESTED WHAT ARE THE CHEMICAL ENVIRONMENTS ASSOCIATED WITH THE MICROBIAL COMMUNITIES THAT EXIST WITHIN A CYSTIC FIBROSIS LUNG. SO ONE OF THE THINGS THAT HAPPENS IN CYSTIC FIBROSIS IS LUNG FUNCTION DIMINISHES SO WHEN YOUR LUNG FUNCTION DIMINISHES SO SIGNIFICANTLY YOU GET PUT OPT TRANSPLANT LIST SO WHAT THEY ARRANGED WAS THAT WE WOULD GET THESE EXPLANTED LUNGS FROM THE PATIENTS AND THEN SECTION THESE SEVERAL HUNDRED PIECES AND SUBJECT TO BOTH METABALOMICS ANALYSIS AS WELL AS SEEKING INVENTORIES SO WHAT YOU WOULD DO IS ESSENTIALLY MAP THIS DATA ON TO THE CLERKST SCAN OF INDIVIDUALS TO GAIN SPATIAL INSIGHT IN TERMS OF DISTRIBUTION OF THE MICROBES AS WELL AS MOLECULES THAT ARE PRESENT. USING THE CO-LOCALIZATION STRATEGIES AND REALLY CREATING NETWORKS OF CHLORO-- CO-LOCALIZATION OF MOLECULES AN MICROBES, FORM VERY INTERESTING ABLE TO OBSERVE SOMETHING INTERESTED IN THEY'RE ACTUALLY MICROBIAL INTERACTIONS THAT TAKE PLACE. THAT CHANGE METABOLISM OF THESE ORGANISMS WHEN THEY'RE INTERACTING. EXAMPLE WE SEE QUINOLONES, THEY ARE KNOWN TO INCREASE BIOFILM FORMATION IN PSEUDOMONAS RIG MOW IS A, WHEN YOU HAVE INCREASE OF THESE BIOFILMS THAT ARE CREATED. SO THIS IS ONE OBSERVATION THAT YOU HAD, THERE'S A LOT OF OTHER THINGS WE'RE ABLE TO OBSERVE, FOR EXAMPLE CAN SEE THE DISTRIBUTION OF ANTIBIOTICS IN THIS CASE SHOWING YOU FOUR OF THEM, BUT FOUND AT LEAST 20 BUT REALLY INTERESTED GRADIANTS HERE, IT LOOKS LIKE EITHER ONLY PAR PENETRATING, THIS IS AN INTERESTING OBSERVATION BECAUSE THAT SUGGESTS MAYBE THERE ARE MICROBIAL COMMUNITY GRADIANTS THAT EXIST WITHIN THE LUNGS AS WELL SO SHE WAS INDEED ABLE TO FIND MICROBIAL GRADIANTS LOOK AT THE GRADIANTS OF ANTIBIOTICS ON THE LEFT HERE AND ONE OF THE THINGS WE NOTICE IS THAT WE STARTED TO SEE OTHER MICROBES IN A TYPICALLY -- YOU WOULDN'T THINK OF A LUNG TO HAVE AN ROBES PRESENT BUT WHERE WE DON'T SEE THESE MICROBES ANTIBIOTICS PENETRATE WE SEE INCREASE IN AN AROBES. SO THE QUESTION THAT WE HAD IS WHAT'S REALLY HAPPENING TO ANTIBIOTICS HERE IN THESE TYPE OF GRADIANTS AND HOW CAN WE TEST THIS IN MORE IN VITRO MODEL? SO ROB QUINN IN MY LABORATORY CAME ONE A SYSTEM WHERE YOU HAVE BASICALLY CAPILLARY TUBE TEN MILLIMETER TUBE, BOTTOM SEALED AND HE ADDS SPUTUM TO THIS. SO WHAT YOU NOW HAVE IS A ZONE THAT IS OXYGENATED AND BOTTOM PART ESSENTIALLY BECOMES MINOXIC SO WE RECAPITULATE PHENOTYPE WITHIN THESE LUNGS WHERE YOU HAVE OXYGEN LOVING ORISM THOUGH PSEUDOMONAS CAN GROW INTO THE ZONE BUT WE CAN SEE SOME AN AROBES THAT ARE PRESENT IN THESE PARTICULAR SAMPLES AS WELL. NICE IN VITRO MODEL YOU CAN RECAPITULATE, IS YOU CAN ALTER THE CONDITIONS FOR EXAMPLE YOU CAN ADD ANTIBIOTICS TO IT. ONE OF THE STRIKING FEATURES THAT WE SAW IS WHEN WE ADDED ANTIBIOTIC TO AN INHALED ANTIBIOTIC USED IN CYSTIC FIBROSIS, WE COULD BARELY DETECT THE TOBOMYCIN ITSELF IN 16 OF 19 PATIENTS TESTED WHEREAS IN THREE OF THE PATIENTS THERE IS NO DEGRADATION OR DISAPPEARANCE OF THE TOBOMYCIN ANTIBIOTIC AT ALL. IF WE LOOK AT THE SEQUENCING OF THOSE PARTICULAR PATIENTS, THOSE THREE PATIENTS WE SAW SOMETHING VERY INTERESTING, USING REPLICATION WE SAW ABUNDANCE OF ASPERGILLUS MITOCHONDRIA THERE. THE ANNOTATION CHOOSING FEET FORWARD AMPLIFICATION MITOCHONDRIA IS NOT THAT STRONG TO CONFIRM THIS IS ASPERGILL LIS BUT THIS IS WHERE MULTI-OMICS COMES INTO PLACE WE SEE ASPERGILLUS IN THE SAME ZONES. THIS SUGGESTED THAN WITH ANTIBIOTIC TREATMENT WE WERE REMOVING MICROBES IN THE PATIENTS ALLOWING ASPERGILLUS TO THRIVE AND THIS IS A COMMON PROBLEM IN CYSTIC FIBROSIS WHERE YOU SEE ASPERGILL LIS FROM COMMON PARTS. ONE QUESTION I HAD IS WHAT'S HAPPENING TO THE TOBOMYCIN. WHY IS IT DISAPPEARING IN OTHER PATIENTS? WE USE MOLECULAR NETWORKING A UNIQUE ANALYSIS TOOL THAT WE HAVE INTRODUCED IN 2012 BUT NOW PART OF THE COMMUNITY RESOURCE THAT ALLOWS YOU TO MAKE RELATIONSHIPS BETWEEN THE MOLECULES THAT ARE VERY SIMILAR. AND ONE OF THE THINGS IS YOU CAN INCLUDE VERY QUICKLY SEE THAT THERE ARE A LOT OF DEGRADATION PRODUCTS ASSOCIATED WITH THIS TOBOMYCIN BUT THIS ONE PATIENT VERY INTERESTING, THE OTHER PATIENT THAT HAD MAJORITY OF THIS, WHAT WE ENDED UP FINDING OUT IS IT MODIFIES THIS HERE WITH A PROPYL GROUP BUT ONLY IN THE AKNOXIC ZONE AND NOT ANYWHERE ELSE. THIS IS A NEW MODIFICATION NOT DEMONSTRATED BEFORE BUT IT SHOWS THAT IF WE START TO LOOK IN THESE LUNG ENVIRONMENTS INTO THESE GRADIANTS WE MAY FIND NEW MECHANISMS OF ANTIBIOTIC RESISTANCE. >> SO WE'RE ASKED TO SPECULATE ABOUT WHERE THIS CAN ULTIMATELY LEAD. WHAT WE WOULD LIKE TO DO IS IS THE GET STUFF OUT OF THE LAB WHERE YOU NEED MILLIONINGS OF DOLLARS IN MASS SPECTROMETRY SEQUENCING EQUIPMENT INTO THEICALLY I CAN IN AND PERHAPS TO YOUR HOME AND THE CONCEPT IS MICROBIOME AND METAL LOAM ENVIRONMENT IS EASY AS LOOKING AT YOURSELF IN THE MIRROR, THE MOLECULES WHISK AWAY IN THE MASS SPEC BASED ASSAY AND BREATH TEST THINGS LIKE CYSTIC FIBROSIS EXACERBATION PLACEBO SO THAT'S -- THE INSTANT MOLECULAR READ OUT IS BETTER USER INTERFACE ON YOUR MIRROR AS YOU LOOK AT IT. WE CAN USE THE SAME TECHNOLOGY THAT'S IN GOOGLE TRANSLATE TO TURN INTO MICROBIOME PROFILE LIKE THE AMERICAN GUT OR ALTERNATIVETILY CONNECTS TO THE (INDISCERNIBLE) THE IDEA IS TO INTEGRATE WITH LARGE MULTI-OMICS RESOURCES HMP TO IDENTIFY WHEN AT RISK FOR A PARTICULAR DISEASE BASED ON CHANGES IN YOUR INDIVIDUAL MICROBIOME PROFILE AND IF THERE'S ANYTHING YOU CAN TRY AT HOME OR IF YOU CAN STAVE THERE'S SOMETHING YOU CAN TALK TO A PHYSICIAN ABOUT AND YOU CAN IMAGINE HAVING THAT COMMUNICATE BACK TO YOUR SMART PHONE SO WHEN FACED WITH A THOUSAND KINDS OF YOGURT IN A SUPERMARKET YOU CAN ZOOM IN ON THE ONE THAT YOU'RE TRYING TO FIND AND SCAN BAR CODE TO CONFIRM YOU GOT IT. AND WHAT THIS MIGHT SOUND LIKE IS A BIT OF SCIENCE FICTION THINK ABOUT SUPER COMPUTER FROM 30 YEARS AGO, THE IDEA THAT YOU WOULD HOLD IN YOUR HAND THIS THING THE SIZE OF THE ROOM REQUIRE A TEAM OF TECHNICIANS TO KEEP IT GOING AND NETWORKED TO A BILLION OTHERS WORLD WIDE AND YOU WOULDN'T NEED TRAINING TO GET STARTED WITH IT. THAT'S AMAZING. SO THE IDEA THAT WE COULD INTERFACES NOT JUST INSTRUMENTATION BUT ALSO MICROBIOME ITSELF IS INSPIRING. THAT'S THE KIND OF THING THAT WE'RE TRYING TO PUT TOGETHER AT UC SAN DIEGO. JUST TO FINISH TO MOTIVATE YOU WITH, IF YOU COULD DO THIS, WHAT KIND OF INSIGHT CAN YOU GET RIGHT NOW FROM CURRENT TECHNOLOGY AND THROUGH DISEASE PROCESS THROUGH MULTI-OMICS TECHNIQUES YOU MAY OTHERWISE MISS ENTIRELY. >> SO CASE STUDY ROB AND I IMPLEMENT AD PROGRAM TO GIVE FAIRLY EFFICIENT FEEDBACK IN FUNCTIONAL UNDERSTANDING WHAT'S HAPPENING TO THE MICROBIOME. SO THIS WAS AN ADULT FEMALE 39 YEARS OLD, LONG HISTORY OF HEART PROBLEMS OR FOUR-YEAR-OLD HISTORY OF HEART PROBLEMS AFFECTING IN 2012 HER HEART STOPPED BEATING AND SHE HAD TO BE RESCUED AND FORTUNATELY ABLE TO. THE CAUSE WAS NEVER ESTABLISHED SO THEN IN 2016 SHE AGAIN STARTED TO HAVE MANY MAJOR HEART PROBLEMS, IN FACT SHE WOULD HAVE A HEART BEAT OF 55, GOOD SHAPE ACTUALLY JUST BY STANDING UP IT WOULD JUMP TO 188. SO PRETTY SEVERE. ALSO STARTED TO HAVE LUNG PROBLEM, STARTED AFTER THREE MONTHS AFTER FLU BUT NONE OF THE TESTS COULD REVEAL A CAUSE. SO WE INITIATED AN EFFORT TO UNDERSTAND THIS. FORTUNATELY IN THIS PARTICULAR CASE WE HAD A SAMPLE FROM 2014. SO WE WERE ABLE TO COMPARE TO CURRENT STATE TO PREVIOUS STATE. ONE THING YOU CAN SEE LOOK AT SEQUENCING YOU DON'T HAVE TO SQUINT. YOU CAN SEE A BRIGHT GREEN BAR. THIS IS PNEUMONIA. THIS IS PAN INTERCELLULAR PATHOGEN THAT INVADE HEALTHY TISSUE, INVADE THE LUNG, THE BRAIN, THE HEART. AND WHEN THIS ORGANISM ACTIVATED IT PARALYZES ALL THE CELLS THAT IT'S IN. UPON SUBSEQUENT TREATMENT IN THIS CASE THEY DECIDED ON ANTIBIOTIC TREATMENT YOU CAN SEE THAT ORGANISM DISAPPEARED AND YOU CAN SEE HOW THIS PARTICULAR INDIVIDUAL RECOVERED. ALL THE HEART SYMPTOMS DISAPPEARED UPON TREATMENT. MEEK MONITOR METABALOMICS INFLAMMATORY STATEMENTS HE WAS REALLY SICK YOU CAN SEAL PROTEOLYSIS AS MARKER OF CREEL DEATH AND UPON TREATMENT YOU CAN SEE THE DRUGS DISAPPEARING. SO JUST TO REILLUSTRATE HERE PICTURE OF SEMIHEALTHY INDIVIDUAL, DISEASE STATE UPON TREATMENT STARTING TO RECOVER OVER 80 DAYS GETTING CLOSER TO THE HEALTHY STATE. AND RECAPITULATE BOTH MICROBIOME AS WELL AS METABALOME. WHAT I FIND REMARKABLE IS THAT THIS WAS PERSON THAT WAS HAVING HEART PROBLEM YET THE TREATMENT IS ANTIBIOTIC USE. SO OF COURSE ROB AND I BOTH RUN LARGE GROUPS, AND COLLABORATE EXTENSIVELY SO WE HAVE A LOT OF PEOPLE TO ACKNOWLEDGE CROWD SOURCE GROUP THAT STARTED IT, MY GROUP, COLLABORATORS. IF YOU HAVE ANY QUESTIONS SEND US AN EMAIL AND WE WOULD BE HAPPY TO ANSWER THEM. THESE ARE GAPS AND CHALLENGES. [APPLAUSE] >> THANK YOU. REALLY GLAD WE GOT TO SEE MY FAVORITE SLIDE, THE HORRIFIED MIDDLE SCHOOL PHOTO. SO THE FINAL TALK ON THIS SESSION IS ELHANAN BORENSTEIN WHO WILL TALK MORE ABOUT SYSTEMS BIOLOGY AND MODEL BASED ANALYSIS AND GAPS IN THIS AREA. >> IT'S A PLEASURE TO BE HERE. I WANT TO THANK THE ORGANIZERS FOR INVITING ME TO SPEAK ABOUT THE RESEARCH IN MY LAB. AFTER LISTENING TO THE OTHER TALK I HAVE TO SAY I REALIZE NOT ONLY MY TALK WILL BE IN SYNC WITH THE OTHER SPEARS IN THE SESSION BUT WILL BE A GOOD FOLLOW-UP TO SOME OF THE TALKS WE HEARD BECAUSE A LOT OF WHAT I'LL DESCRIBE ARE METHODS WE DEVELOP TO GENERATE THE OMICS GENERATED. IF U YOU SEE THE LAST POINT ON ROB AND PIETER'S SLIDE TRYING TO CREATE A SYSTEM LEVEL UNDERSTANDING, THIS IS EXACTLY WHAT MY LAB IS GOING TO DO. SO FIRST, WAY OF INTRODUCTION, IF NOT FAMILIAR WITH MY LAB, THE PREMISE WE HAVE BEEN PUSHING THE LAST SEVEN OR EIGHT YEARS IS WHEN YOU TRY TO STUDY A SYSTEM COMPLEX AS MICROBIOME IT IS NOT ENOUGH TO MAKE LONG LIST OF GENE AND SPECIES AND METABOLITES IN COMPARED ACROSS DIFFERENT SETTINGS BUT APPLY A SYSTEMS REALITY APPROACH AND MODEL BASED APPROACH IN ORDER TO UNDERSTAND HOW THOSE DIFFERENT ELEMENTS OF THE MICROBEAMBIOME COME TOGETHER TO CREATE THE PHENOMENON WE SEE. WE'RE DOING THIS PRIMARILY THROUGH TWO LINE OF WORKS. THE FIRST LINE OF WORK TRYING TO BUILD MODELS OF MICROBIOME, FOCUS ON METABOLISM TO PREDICT HOW THE MICROBIOME INTERACTS WITH THE HOST, HOW THE MICROENVIRONMENT RESPONDS TO DIE AND ULTIMATELY USE THE MODEL AS A WAY TO DESIGN MICROBIOME INTERVENTION. THIS IS PART OF THE LAB THAT WE'LL TALK ABOUT TODAY. IF YOU HAVE A QUESTION MORE DETAILS BE HAPPY TO TALK ABOUT THIS OFFLINE. THE SECOND PART OF THE LAB IS TAKING AGAIN MODEL BASED APPROACH AS PART OF ANALYSIS OF MICROBIOME DATA, SPECIFICALLY A WAY TO INTEGRATE MULTI-OMIC MICROBIOME DATA WE HEARD ABOUT AND I'LL TRY TO CONVINCE YOU THIS APPROACH IS MAYBE THE FIRST STEP TOWARD WHAT THE CHALLENGES WE'RE FACING SO JUST TO GIVE A BIT OF MOTIVATION AS WE HEARD NUMEROUS TIME THIS IS MORNING NOWADAYS WHEN YOU HAVE A MICROBIOME SAMPLE, WE'RE IN LONGER JUST CHARACTERIZING COMPOSITION OF SPECIES IN THE SAMPLE BUT ALSO CHARACTERIZING ADDITIONAL GENE AND COMPOSITION OF TRANSCRIPT AND PROTEIN AND METABALOMICS. IT IS CLEAR TO US THE POINT IS NOT TO ANALYZE EACH OF THESE OMIC INDEPENDENTLY AND SEVEN TRYING TO STUDY ELEPHANT FROM DIFFERENT PERSPECTIVE, AND TO INTEGRATE THOSE DIFFERENT OMICS. AND THE LAST FEW YEARS HAVE SEEN TREMENDOUS EFFORTS TO TRY TO UNDERSTAND HOW THE DIFFERENT OMICS THAT WE ASSAY FROM A GIVEN MICROBIOME SAMPLE LINK TO ONE ANOTHER AND ASSOCIATE. WE HAVE SEEN STUDIES TRYING TO UNDERSTAND ASSOCIATION BETWEEN THE GENE I FOUND IN THE META GENOMES AND THE SET OF GENES IN THE TRANSCRIPTOME. WE HAVE SEEN NUMEROUS STUDIES INCLUDING THE MORNING TRYING TO ASSAY SPECIES COMPOSITION AND FINDING CORRELATION IS A WAY TO GENERATE HYPOTHESIS AND IMPLICATE SPECIFIC TAXA IN THE GENERATION OF A SPECIFIC METABOLITE. THIS IS AN EXTREMELY LAWFUL APPROACH EXACTLY BUT WHAT I WANT TO ARGUE AT THE END OF THE DAY LIMITED. LIMITED BECAUSE TO SOME EXTENT, IGNORING THE KNOWLEDGE WE HAVE ABOUT THE SYSTEM AND WHAT I'M TRYING TO ARGUE IS THAT THERE ARE SPECIFIC OTHERRY IN GENOMICS TO TELL US HOW THEY RELATE TO ONE ANOTHER. WE MIGHT USE METABOLIC MODELING AND CONTROL THEORY TO TELL US HOW COMPOSITION OF GENE AND ENZYME IN A SPECIFIC ENVIRONMENT WOULD AFFECT THE DIFFERENT METABOLITES. WE CAN USE INFORMATION FROM ECOLOGY, TO TELL US HOW THE PRESENCE OF ONE SPECIES IN THE ENVIRONMENT MAY AFFECT THE BEHAVIOR OF ANOTHER SPECIES. SAME IS TRUE FOR EVERY THAT YOU THINK ABOUT SO WHAT MY LAB IS TRYING TO DO IS TAKE A DIFFERENT APPROACH AND RATHER THAN FINDING ASSOCIATION AND IN RETROSPECT FIGURE WHETHER THOSE ASSOCIATION FIT WHAT WE KNOW ABOUT THE SYSTEM, WHAT WE KNOW ABOUT THE BIOLOGY TRYING TO GENERATE HYPOTHESIS WHAT WE'RE TRYING TO DO IS START WITH THIS DATA, START WITH THIS INFORMATION ABOUT GENOMIC ECOLOGY BIOLOGY BUILDING MODELS ON HOW TWOOMICS SHOULD RELATE AND USE THESE MODELS AS PART OF THE ANALYSES ITSELF. THE REST OF THE TALK I'LL SHOW YOUMENT EXAMPLES OF THE FRAMEWORK AND HOW YOU CAN USE THAT TO GENERATE POTENTIALLY MORE INSIGHT FROM DATA YOU HAVE. MOST I WILL SHOW YOU TODAY FOCUSING ON INTEGRATING THE TWOOMICS PROBABLY THE MOST COMMON IN MICROBIOME DATA WHICH IS SPECIES COMPOSITION AND GENE COMPOSITION. SO FIRST JUST TO MAKE SURE WE'RE ON THE SAME PAGE, ASSUMING YOU HAVE MICROBIOME SAMPLE, WITH A MIX OF SPECIES EACH HAS A DIFFERENT COMBINATION OF GENES AS WE HAVE SEEN WE CAN APPLY ANALYSIS TO A MARKER BASED APPROACH TO CHARACTERIZE THE COMPOSITIONAL SPECIES AT THE MICROBIOME GENERATE A PIE CHART OR BAR PLOT AND UNDERSTAND THAT RELATIVE ABUNDANCE OF EACH TAXA. YOU CAN APPLY A SHOTGUN METHOD GENOMIC APPROACH, MAP THOSE TO GENE CATALOG AND GET A SENSE OF THE ABUNDANCE OF ENGINE FAMILIES -- GENE FAMILIES IN MODELS OF META GENOME. IT'S CLEAR TO ALL OF US THESE TWO FACETS ARE NOT INDEPENDENT. AND WHAT LINKS THE TWO IS GENOMICS. AND WE CAN REPRESENT VERY SIMPLE MODEL WHERE THE SET OF GENE AND ABUNDANCE IN THE GENOME IS NOTHING MORE THAN AGGREGATE GENOMIC CONTENT OF SPECIES IN YOUR COMMUNITY WEIGHTED BY THE RELATIVE ABUNDANCE. WE CAN REPRESENT AS A SIMPLE MATHEMATICAL SET OF EQUATIONS. WHAT WE HAVE HERE IS A SIMPLISTIC MODEL THAT LINK TAXONOMIC INFORMATION AND GENOMIC AND META GENOMIC INFORMATION. THIS MODEL IS NOT SURPRISING WHEN DOING META GENOMICS, USING THIS TO PREDICT META GENOME BASE SPECIES COMPOSITION. HOW RARELY WE USE THIS MODEL COME TO ANALYZE GENE COMPOSITION AND SPECIES COMPOSITION IN PARALLEL. THE SINGLE THING YOU CAN DO IS VISUALIZE THOSE THINGS SO THIS IS A SCREEN SHOT FROM WE HOPE TO RELEASE IN A COUPLE OF MONTHS CALLED BURRITO, IT WILL GIVE YOU META GENOMIC INFORMATION TO SHOW YOU TRADITIONAL BAR CHARTS OF ALL THE SPECIES THAT YOU HAVE AND ALL THE FUNCTION YOU CAN LOOK AT THAT DIFFERENT RESOLUTIONS. BUT IT WILL ALSO HIGHLIGHT ALL THE LINKS, IF YOU NOW CLICK OVER A SPECIFIC TAXA IT WILL SHOW YOU USING THE GRADIANTS HERE WHAT PART OF THE META GENOME IS BEING CONTRIBUTED BY THESE SET OF SPECIESES THAT YOU SELECTED. VICE VERSA. YOU CAN USE IT AS A WAY TO EXPLORE FUNCTIONAL VARIATION COMBINED WHILE ACCOUNTING FOR THE WAY THESE TWO ARE LINKED TO ONE ANOTHER. YOU CAN DO THINGS MORE SOPHISTICATED. SEVERAL YEARS AGO A POST DOC IN MY LAB SHOW IN CASES WHERE YOU DO NOT HAVE GENOMIC DATA, SAMPLE INCLUDES SPECIES YOU DO NOT HAVE GENOME BUT YOU HAVE TAX NOMIC INFORMATION AND INFORMATION YOU CAN USE THIS MODEL AS A WAY TO THE -- THE GENOME, WHICH GENE IN THE META GENOME MUST BE ASSOCIATED ORIGINATE IN THE META GENOME BY RESOLVING THIS SET OF EQUATION. A COUPLE OF YEARS AGO SHARON GREEN LOOM FOCUS ON THE CASES WHERE THIS MODEL FAILED IN WHAT WE EXPECT TO FIND IN THE META VOLUME BASED WHAT THE TAXON ME TELLS US IS NOT WHAT WE FIND IN THE META GENOME. THE REASON FOR THAT IS WAS OF STRAIN ELEVATIONS ABLE TO USE TO CHARACTERIZE EXTENSIVE STRAIN IN PRESENCE AND ABSENCE OF GENE IN THE META GENOME ACROSS NUMEROUS SAMPLES. ANOTHER POST-DOC IN THE LAB SHOW AGAIN THIS MODEL CAN BE USED TO CORRECT FUNCTIONAL DATA AND SPECIFICALLY TO ADDRESS PROBLEM WE FACE, HOW DO WE NORMALIZE FUNCTIONAL DATA SO WE TRY -- WE USE THIS IDEA OF COMPOSITION, WE LOOK AT RELATIVE ABUNDANCE WE KNOW THIS IS A PROBLEM BUT TAKING INTO ACCOUNT WE CAN USE GENOMIC DATA TO RENORMALIZE THE META GENOME AND WE HAVE SHOWN BY DOING THAT YOU CAN FIGURE OUT DISEASE ASSOCIATED SHIFT THAT ARE MORE PRONOUNCED. SOMETHING WE PUBLISHED EARLIER THIS YEAR, IF YOU HAVE A CONVERSATION MODEL I'M TRYING TO FIGURE OUT WHY DO WE SEE TREMENDOUS VARIOUS ON TAXA LEVEL AND LITTLE VARIATION ON FUNCTIONAL LEVEL YOU CAN SHOW UNIFORMITY PUZZLING CONONCAL RESEARCH IN MICROBIOME RESEARCH HAS TO DO WITH HOW TO ANALYZE THE DATA. IF YOU DO BETWEEN GENOMES AN ME GENOMES YOU CAN REVEAL DRAMATIC VARIATION IN THE FUNCTIONAL DATA. THE LAST ONE I WANT TO TALK ABOUT IN MORE DETAIL, ALL THESE ARE AVAILABLE ON THE WEBSITE, YOU CAN DOWNLOAD THEM, MOST HAVE EASY TO USE INTERFACE AND IF YOU HAVE ANY ISSUE DEFINITELY CONTACT US. THE LAST I'LL TALK ABOUT IS USING THE SAME MODEL LINKING GENE INFORMATION AND SPECIES INFORMATION IN A COMPARATIVE SETTING. AT THAT TIME FROM DISCUSSION WITH INITIAL CLINICAL COLLABORATOR THAT SAYS THIS IS GREAT YOU CAN EXPLAIN ABUNDANCE OF SAMPLE BASED ON THE SAMPLE BUT AT THE END OF THE DAY WE'RE INTERESTED IN CROSS SECTIONAL COMPARATIVE ANALYSIS. SPECIFICALLY THEY HAD A SET OF CASES AND CONTROL SAMPLES, CHARACTERIZE TAX NOMIC COMPOSITION AND FOUND SPECIES WHERE ENRICH DISEASE, THEY DID FUNCTIONAL ANALYSIS, META GENOMIC BASED ANALYSIS AND FOUND A SET OF GENE FAMILIES AND METABOLIC PATHWAY IN REACH IN DISEASE STATE AND WHAT THEY WANTED TO KNOW IS CAN YOU LINK THESE TWO? IN OTHER WORDS TELL ME WHAT IS THE CONTRIBUTION OF EACH TAXA, BUT FUNCTIONAL GENOME I HAVE SEEN IN SPECIFIC DISEASE. USE IT TO IDENTIFY PUNITIVE INERVENTION TARGET THAT I A DRESS SPECIFIC IMBALANCE. TURN OUT THIS IS A COMPLEX PROBLEM THEME@ICALLY TOOK US TWO YEARS TO SOLVE THIS. AND WITHOUT GOING INTO TOO MANY DETAILS THIS IS A TOOL WE PUBLISHED EARLIER THIS YEAR CALLED FIST TACO FOR REASON I CAN'T DISCUSS. WHAT FISH TA COIS DOING THAT IS THAT TAKING SAMPLES FROM GENOMIC PROFILE META GENOMIC PROFILE, IF YOU HAVE THE GENOME OF THE SPECIES IN YOUR SAMPLE WE CAN USE AS INPUT, NOT USE META GENOMIC DIMENSION BEFORE. WE USE MACHINE LEARNING, CONCEPTS FROM -- AT THE END OF THE DAY, WE'RE PROVIDING LINEARIZED TAX NOMIC CONTRIBUTION TO FUNCTIONAL SHIFT. WHATLY SHOW YOU IS A SLIVER OF HOW THOSE RESULTS LOOK LIKE. SO LET'S ASSUME YOU ANALYZE META GENOMIC GENE CONTENT FROM PATIENT AND COMPARE TO HEALTHY CONTROLS YOU CAN SEE THE THREE DIFFERENT TRANSPORT MORE ABUNDANT IN PATIENT WITH TYPE 2 DIABETES. IF YOU'RE DOING META ANALYSIS THIS IS WHERE ANALYSIS STOPS. IF YOU HAVE TAX NOMIC YOU FIND SPECIES MORE ENRICHED IN TYPE 2 BUT YOU DON'T HAVE A WAY TO LINK THEM. IF YOU'RE ON FISH TACO, IT WILL SHOW YOU THE ENRICHMENT IN TYPE 2 DIABETES IN THESE SPECIFIC SUGAR TRANSPORT IS 80% BECAUSE OF CERTAIN SPECIES AND 10% BECAUSE OF (INDISCERNIBLE) SPECIES. THERE ARE FEW TRYING TO PUSH THIS ENRICHMENT IN THE OTHER DIRECTION JUST NOT CONTRIBUTING STRONG N. WHAT GOT US EXCITED IS THAT WHEN YOU APPLY FISH TACO TO THE OTHER SUGAR TRANSPORT YOU CAN SEE COMPLETELY DIFFERENT CONTRIBUTION PROFILE. IN OTHER WORDS, IF YOU'RE TRYING TO HAVE VERSE A SPECIFIC IMBALANCE THERE IS A VERY SPECIFIC SET OF TAXONOMICAL TARGET YOU CAN ADDRESS IN ORDER TO REVERSE THIS SPECIFIC FUNCTIONAL SHIFT WITHOUT CHANGING OTHER FUNCTIONAL PROFILE OF THE MICROBIOME. THIS IS SPECIFICITY BETWEEN CONTRIBUTOR AND FUNCTIONAL SHIFT IS SOMETHING WE SAW IN EVERY DATABASE WE ANALYZE, THOSE ASIDE FUNCTION AND DISEASE SPECIFIC EFFECT THIS IS ANOTHER EXAMPLE THAT I THOUGHT WAS INTERESTING, LOOK AT THE META GENOME OF PATIENT WITH TYPE 2 DIABETES AND INFLAMMATORY BOWEL DISEASE AND COMPARE TO CONTROLS YOU CAN FIND IN THESE YOU HAVE ENRICHMENT OF GENE INVOLVING METABOLISM BUT IF YOU'RE ON FISH TACO, WHAT YOU WILL SEE IS THAT THE UNDERLYING STACKS NOMIC CONTRIBUTORS ARE DIFFERENT. SO AGAIN IF YOU TRY TO USE IT TO FIGURE OUT WHAT IS INTERVENTION TARGET IT WILL HAVE TO BE DISEASE SPECIFIC THOUGH WE'RE DEALING WITH THE SAME FUNCTIONAL IMPLANTS. FISH TACO IS AVAILABLE ONLINE, THERE'S SEVERAL LABS WORKING WITH THAT AND PUBLISHED WITH THAT AND WE HAVE A WEB INTERFACE THAT WILL GENERATE THOSE PLOTS THAT I HAVE SHOWN YOU BEFORE. LAST THING I WANT TO SAY IS THIS APPROACH USING THE MODEL TO LINK BETWEEN DIFFERENT OMICS IS NOT LIMITED JUST TO SPECIES INFORMATION AND GENE INFORMATION. THAT IS A PRODUCT BY ANOTHER LAB TO USE THE SAME APPROACH TO LINK SPECIES INFORMATION OF THE MICROBIOME ALL THE WAY TO THE METABOLITE. AGAIN, RATHER THAN TRYING TO FIND ASSOCIATION IN EXPLAINING RETROSPECT SHE WAS TRYING TO BUILD A MODEL USING GENOMIC INFORMATION, METABALOMIC INFORMATION, METADATA BASE AND TRYING TO BUILDING A SIMPLISTIC COMPUTATIONAL MODEL HOW THE COMPOSITION OF SPECIESES IN THE MICROBIOME LOOK LIKE TO THE CONCENTRATION OF DIFFERENT METABOLITE. THE BASIC QUESTION TO ASK, IS THIS MODEL SUFFICIENT TO EXPLAIN THE CONCENTRATION OR THE VARIATION IN CONCENTRATION OF METABOLITE ACROSS DIFFERENT SAMPLES. I'LL NOT GO INTO DETAIL BUT BASICALLY -- ANSWER IS THAT YES, WE CAN DO THAT, AT LEAST FOR SUBSTANTIAL FRACTION OF THE METABOLITE LOOKING INTO WHICH SPECIESES ARE THERE AND WHAT ARE THEIR METABOLIC POTENTIAL TO ALLOW US TO EXPLAIN THE VARIATION WE SEE BETWEEN CONCENTRATION METABOLITE ACROSS SAMPLES. THIS IS A TOOL THAT IS AVAILABLE ONLINE, WE'RE WORKING ON A SECOND VERSION THAT WILL HOPEFULLY BE MORE ACCURATE BUT YOU'RE WELCOME TO TALK TO ME IF THAT'S OF INTEREST. SO I THINK I'LL END WITH THAT, CONCLUDE WITH THIS SLIDE ABOUT CRITICAL GAPS AND CHALLENGES. I WANT TO ECHO EVERYTHING THAT WAS SAID IN THE MORNING ABOUT THE KNOWLEDGE GAP WHICH AS SOMEBODY THAT IS TRYING TO BUILD MODELS AND HOPING THIS WILL BE AS COMPLETE AND ACCURATE AS POSSIBLE, THE MAIN CHALLENGE WE HAVE IS THOSE MISSING FUNCTIONAL ANNOTATION, THIS IS SOMETHING IN THE LAB WE FONDLY CALL MICROBIAL GRAY MATTER. SO NOT THE DARK MATTER SEQUENCING THAT WE DON'T HAVE, SEQUENCES WE DON'T KNOW WHAT THEIR FUNCTION MIGHT BE. BUT I WANT TO EMPHASIZE AGAIN WHAT I THINK IS A BIGGER CHALLENGE HOW TO MOVE FROM KNOWING WHAT IS IN THE MICROBIOME TO UNDERSTANDING WHAT THE MICROBIOME IS DOING. AND THE THING IN ORDER TO DO THAT WE HAVE TO DEVELOP THOSE KIND OF FRAMEWORK TAKING THE DIFFERENT OMICS APPLYING INTO A MODEL BASED APPROACH THAT IS GOING BEYOND ASSOCIATION. AND I WANT TO EMPHASIZE EVERYTHING I SHOW YOU TODAY IS JUST TIP OF THE ICEBERG IN TERMS OF WHAT IS NEEDED. MANY INVOLVED WHEN YOU TRY TO BUILD A MOVE THAT SCALE AND RESOLUTION AND DYNAMIC AND TIME FRAME, ALL THOSE THINGS NOT RESOLVED AND A LOT OF CHALLENGES AND HOPING THAT COMMUNITY HELP US DO. SO WITH THAT I WILL END, WE'LL -- THAT'S WHAT'S EXCITING. BUT I GUESS WHAT'S WHAT WE HAVE NOW. THE PEOPLE THAT DID THE WORK OUR COLLABORATOR. THANK YOU. [APPLAUSE] >> HE DEFINITELY WINS THE GOLD STAR BECAUSE HE CAME IN 10 SECONDS UNDER 15 MINUTES. A PLUS. SO WE HEARD A LOT OF EXAMPLES IN THIS SESSION ABOUT HOW POWERFUL IT IS TO INTEGRATE ALL THESE MULTIOMIC DATA SETS. SO WE CAN TAKE QUESTIONS IN THIS PERIOD AND SEE -- PEOPLE ARE STARTING TO RUSH TO THE MICROPHONES PERHAPS. GREAT. >> I WANT TO ADDRESS THIS TO KATHERINE POLLARD. THIS IS MARTY WISER FROM NYU. KATHERINE, IN YOUR TERRIFIC TALK YOU MENTIONED COMPARISON OF SEQUENCES FROM THE MOMS AND THE BABIES. AND HOW WHEN YOU DIDN'T SEE THE SEQUENCE IN THE OLDER BABIES, YOU CONCLUDED THEY DIDN'T GET FROM IT THE MOM. BUT THE ALTERNATIVE IS THAT MOMS ARE UNDERSAMPLED TO SOME DEGREE BECAUSE ORGANISMS MAY BLOOM IN THE BABIES NOT IN THE MOM. SO WONDER IF YOU CAN COMMENT ON THAT. >> THANKS. GREAT POINT. THE MOMS ARE RELATIVELY STABLE OVER TIME BUT YOUR POINT WAS WHETHER THOSE ARE MINOR CONSTITUENTS OF THE MOM'S MICROBIOME. THAT'S DEFINITELY POSSIBLE. WE -- LET ME TELL YOU THE RESOLUTION WHAT WE CAN DETECT. THE ANALYSIS WAS BASED ON ORGANISMS WITH HIGH ENOUGH COVERAGE TO CALL SNPS FOR GENES PRESENCE ABSENCE YOU NEED #X COVERAGE OF GENOME FOR SINGLE NUCLEOTIDE POLYMORPHISMS WE NEED 10X. THAT'S HOW DEEPLY -- ANYTHING THAT WASN'T AN ORGANISM OR DIDN'T HAVE A GENOME OR NOT PREVALENT TO HAVE IT COVERED WAS NOT ANALYZED T ALL. THIS WAS JUST FOR THE ORGANISMS THAT WE CAN STUDY. AMONG THOSE WE CAN -- SO BECAUSE OF THOSE THRESHOLDS WE CAN SEE SNPS TO POLYMORPHISMS THAT WOULD BE IN THE MOM DOWN TO 10X COVERAGE IF THERE'S ONE OUT OF TEN SO ONE-TENTH OF HER CELLS BASICALLY AMONG SAMPLE CELLS HAVING THE LOW LESS PREVALENCE STRAIN SO SOMETHING BELOW THAT. WOULDN'T BE DETECTED IF THERE WAS ONLY 10X COVERAGE FOR SOME OF THE SPECIES I TALKED ABOUT WE HAVE HUNDREDS OFX COVERAGE SO THE RESOLUTION GOES LOWER. SO WE CAN REPORT A SENSITIVITY FOR EVERY SPECIES THAT WE ANALYZE AND IT'S GREAT FOR SOME OF THEM AND REALLY NOT AS GREAT FOR OTHERS UNLESS YOU DO MORE SEQUENCING. >> SO THEREFORE I MODIFY THE CONCLUSION BUT THE OTHER POSSIBILITY IS SAMPLING THE MOMS MORE DEEPLY SO YOU CAN HAVE A BETTER DENOMINATOR BASIS FOR THIS BASED ON LIMITATIONS THAT YOU MENTION. >> ABSOLUTELY. THIS WAS DATA MINING OF PUBLICLY AVAILABLE DATA SETS SO OUR HANDS WERE TIED IN TERMS OF MORE SEQUENCING BUT THAT'S AN IMPORTANT THING TO DO TO TEST THE HYPOTHESIS WE GENERATED. I WILL LEAVE IT THERE. >> I HAVE A QUESTION. A LOT OF OMIC DATA SETS ARE EASY TO THINK ABOUT OR EASIER TO THINK ABOUT CONCEPTUALLY HOW YOU INTEGRATE THEM BUT IN YOUR TALK YOU WERE ALSO INTEGRATING THAT WITH IMAGING, SPATIAL INFORMATION. WHAT ARE THE BIGGEST CHALLENGES THAT COME WITH TRYING TO INTEGRATE THE MULTI-OMICS DATA ITSELF AND WITH OTHER DATA TYPES THAT WERE NOT NECESSARILY USED TO THINKING ABOUT MOST CONTEXT. >> I WILL ANSWER FROM THE METABALOMICS STANDPOINT. IT'S 2% OF THE DATA SO IN TERMS OF MORE SAMPLING IN ORDER INCREASES SENSITIVITY ACTUALLY INCREASE THE NUMBER OF UNANNOTATED INFORMATION BY TWO FOLD. SO THAT WILL CONTINUE TO INCREASE. SO IF YOU DON'T KNOW WHAT THE MOLECULE IS, IT'S HARD TO THINK OF PATHWAYS TO INTEGRATE. THAT'S ONE OF THE REASONS WE STARTED THINKING ABOUT SPATIAL. SO FOR ME, ANNOTATIONS AND HAVING REFERENCE DATA SETS ARE REALLY KEY TO BE ABLE TO ANNOTATE. IT WOULD BE HELPFUL IF WE GET A MOLECULAR FEATURE MS FRACKMENT OVERFRAGMENTED MOLECULE TO SAY THAT'S IN THAT PHYLOGENETIC TREE, ONLY OBSERVED IN THAT PHYLOGENETIC TREE, WE CURRENTLY DON'T HAVE THOSE CAPABILITIES. >> (INDISCERNIBLE) CORRELATIONS IS HARD BECAUSE THE DATA SETS COMPOSITIONAL IS INFLATED, IF YOU JUST USE CORRELATION TECHNIQUES, MAYBE PUT IN SPACE ASSUMPTIONS YOU WILL GET 95% FALSE DISCOVERY RATES ARE HIGHER AND IT'S EMBARRASING TO MAKE A NETWORK (INDISCERNIBLE) NOT THAT YOU CAN'T PUBLISH IT BUT YOU SHOULDN'T. FROM A REFERENCE PERSPECTIVE MODEL BASED APPROACH IS THE WAY TO GO, IF YOU HAVE GENOMES AN MODELS, THIS IS ONE OF THOSE THINGS A FEW MILLION DOLLAR INVESTMENT GENOME SEQUENCING NOW SHOULD BE AMAZING AND IN TERMS OF HOW MUCH TO GET FROM RECRUITMENT PROCEDURES FROM THE META GENOMICS INSTEAD OF ASSEMBLY. AND IT WOULD BE SPECTACULAR. THE OTHER PROBLEM IS A LOT OF IT IS UNANNOTATED, SO EVEN IF YOU HAVE THE COMPLETE GENOME IF YOU DON'T KNOW WHAT THE GENES DO, IT'S ALSO HARD TO MODEL THAT. >> BRANDON. FIRST I LOVE MIMOSAS AND FISH TACOS, REALLY COOL. I WAS WONDERING, YOU GUYS ARE SOME ASOME MATHEMATICIANS IN SILICO MODELERS. I'M INTERESTED IN CONNECTING THOSE TOOLS TO TOOLS IN THE LABORATORY WHERE YOU CAN MAKE MICROCOSTMENTS, REPRESENTSTIVE FECAL SAMPLES TO GET THROUGH POPULATION LEVEL UNDERSTANDING OF HOW EACH PERSON'S MICROBIOME IS DIFFERENT BUT DO IN IN A LABORATORY WHERE MAYBE WE DON'T DO HUNDREDS OF MILLIONS OF DOLLARS WORTH OF CLINICALS. SO COULD YOU SPEAK TO WHAT YOU WOULD LIKE TO SEE THE TOOLS AND LAB BEING DEVELOPEDDED TO TRY TO APPLY YOUR IN SILICO MODELS TO TO BUILD THESE 10, ONE, 10, 2 SYSTEMS THAT CAPTURE SYNTHETIC HUMAN DIGESTIVE SYSTEM, I WOULD LIKE TO UNDERSTAND MORE ABOUT HOW WE CAN MARRY THOSE TWO SCIENCES TOGETHER. >> I WILL ADDRESS THE SPECIFIC QUESTION BEING -- I ADDRESS THE PREVIOUS QUESTION MORE BUT RELATED TO YOUR QUESTION, ONE PROBLEM WITH DEVELOPING THOSE TOOLS, THAT IS SPECIFICALLY TRUE FOR TOOLS TRYIN TO VISUALIZE DATA, IS THAT WE HAVE TO MAKE VERY IMPORTANT DECISION WHAT WE THINK IS INTERESTING. WHAT KIND OF VARIATION IS INTERESTING, WHAT -- ARE INTEREST AND IN MANY CASES THOSE DECISIONS ARE OBVIOUS BUT I'M A BIT CONCERNED ABOUT ALL THINGS THAT ARE MISSED BECAUSE WE BURY THEM SOMEWHERE IN THE WAY WE DECIDED TO VISUALIZE THE DATA, THE WAY WE DECIDED TO AGGREGATE THE DATA. AND I THINK THAT THIS KIND OF DISCUSSION BETWEEN EXPERIMENTAL METHOD AND COMPUTATIONAL METHOD HAVE TO BE ON GOING DISCUSSION OTHERWISE WE HAVE THIS EXPERIENCE IN THE PAST EXPERIMENTALISTS GET THE TOOLS WITHOUT REALIZING A LOT OF THOSE DECISIONS HAVE BEEN MADE AND MADE WITHOUT CONSULTING THE EXPERIMENTALIST. SO IT'S NOT ABOUT HOW WE HAVE TOOLS AVAILABLE BUT HOW TO CREATE A DIALOGUE WE ARE EARLY STAGE TRYING TO THINK WHAT'S INTERESTING AND HOW TO ANALYZE THE DATA AND WHAT SIGNAL IS INTERESTING TO LOOK FOR. >> I SEE THE NEED OF ANALYZING DATA AT OTHER TAXON LEVEL BUT MORE STUDIES, SHOW THAT STRAINS IN THE SAME SPECIES, THEY CAN SHOW VERY DIFFERENT RELATIONSHIP WITH PARTICULAR PHENOTYPE OF THE HOST, SOME MAYBE RELEVANT, SOME IRRELEVANT, SOME SHOW CORRELATION. IF YOU ANALYZE DATA AT SPECIES LEVEL YOU INTRODUCE A LOT OF NOISE ALREADY. HOW CAN YOU BE SURE THEY'RE FUNCTION IDENTIFIED ACTUALLY BIOLOGICALLY VALID? >> I THINK THAT'S A GREAT QUESTION THERE'S TWO COMPONENTS IF YOU LOOK AT THE GENETIC MAKEUP OF THE MICROORGANISM, THE PRIMARY METABOLISM, I CALL COMMON METABOLISM BECAUSE'S COMMON AMONG ALL ORGANISMS. YOU HAVE SPECIALIZED METABOLISM. THESE ARE THE MOST DIVERGENT AMONG THEM SO WE HAVE AN EXAMPLE WITH OTHER PEOPLE HERE AS WELL STARTING TO LOOK AT BACTERIA MAKE SPECIFIC ANTIBIOTIC AND IF YOU DON'T HAVE THE CAPACITY TO MAKE, TEND TO BE MORE SUSCEPTIBLE TO ACNE INFECTIONS. SO WE NEED TO KNOW THAT WE -- WE NEED TO HAVE BASICALLY GOOD REFERENCE DATA SETS. AMONG MANY ORGANISMS WITHIN THE SAME SPECIES CLASS IF YOU WILL HOWEVER YOU WANT TO DEFINE IT, SO THAT YOU CAN CAPTURE IT. THE OTHER THING TO DO IS CAPTURE THE KNOWLEDGE AND COMMUNITY DOMAINS SO SAY TAKE STAPH AUREUS FOR EXAMPLE, IF YOU HAVE TO MAKE PEPTIDE THIS, THAT STAPH AUREUS IS MORE VIRULENT THAN MANY OTHER STAPH AUREUS STRAINS SO IF WE CAN DETECT THESE MOLECULES IN THE MASS SPECTROMETRY INFORMATION YOU NEED TO START THINKING ABOUT IT BUT WE NOW -- DON'T HAVE AN EASY WAY TO CAPTURE THE KNOWLEDGE, IT MIGHT BE IN A PAPER SOMEWHERE BUT FOR ME AS SOON AS YOU PUBLISH A PAPER, THE ACTUAL KNOWLEDGE THAT ALLOW YOU TO SEARCH YOUR DATA IS ALMOST LOST. SO PARTICULARLY FOR CHEMICAL INFORMATION THIS IS READILY LOST, ALL THE INFORMATION ABOUT MOLECULES SO WE NEED TO FIND BETTER WAYS OF CAPTURING THAT INFORMATION. THAT WILL GET US TO THAT LEVEL. GOES BEYOND SPECIES LEVEL. >> SO WITH ANY TECHNIQUES THEY'RE USEFUL FOR SOME THINGS AND LIMITATIONS THAT YOU CAN'T SEE AND SO FOR EXAMPLE IF WHAT YOU CARE ABOUT IS SINGLE NUCLEOTIDE CHANGE THAT SEPARATES YOUR PATHOGENIC FROM NON-PATHOGENIC STRAIN THE ONLY WAY YOU CAN FIND THAT IS WITH DIRECT PRIMERS OR WITH REALLY DEEP COVERAGE SEQUENCING. BUT WAY TO THINK IS THOUGH THERE'S STUFF MISSING WITH CURRENT TOOLS, IT'S UNLIKELY THAT WE POSITIVE ASSOCIATIONS THAT WE DRAW ARE FALSE. YOU HAVE TO BE TREMENDOUSLY LUCKY FOR SPECIESINGS LEVEL FINDING TO NOT HOLD UP WHEN YOU WENT TO STRAIN LEVEL. YOU HAVE TO HAVE TWO STRAINS WITH THE OPPOSITE EFFECTS, PERFECTLY BALANCED AGAINST EACH OTHER. THAT'S NOT LIKELY ON THOSE GROUNDS SO THE WAY TO THINK ABOUT IT IS THE CURRENT TOOLS HIT AND MISSTUFF, YOU GET MORE DOWN TO STRAIN LEVEL AND WHAT IS USEFUL FOR THINGS LIKE SYNTHETIC COMMUNITIES WHERE WHAT WE HEARD A BUNCH OF STRAINS IN TO A PATIENT AND SEE IF THEY GET EFFECT, THAT'S THE WAY TO DO IT BECAUSE IT'S TOO COURSE A RESOLUTION. SO BEING ABLE TO GET DOWN TO THE STRAIN LEVEL IS HELPFUL FOR THAT EXPERIMENT AND DOING IT WITH ANYTHING THAT YOU FROM ATCC. >> SO I WANT TO ASK YOU ABOUT SMART TOILET, SMART MIRROR. BASED ON WHAT WE HEARD TODAY IT'S NOT OUTSIDE THE REALM OF IMAGINATION TO IMAGINE COLLECTING THE SEQUENCE DATA METABALOMICS DATA, THE BOTTLENECK IS THEN CONVINCING YOURSELF SPECIFIC RECOMMENDATIONS DIRECTLY TO CONSUMER. WHAT DO YOU THINK IS MINIMUM AMOUNT IN DATA MODEL SYSTEMS OR IN HUMANS. S IN WE NEED TO HAVE BEFORE YOU TELL A PERSON AT HOME. >> GOOD QUESTION. I DON'T THINK WE'RE LIMITED BY THE TECHNOLOGY SO MUCH AS LIMITED BY THE DATA SETS AND THAT'S WHY WE'RE TRYING TO DO THINGS LIKE GUT AND LIGHT WATCH COHORT STUFF DOS SO TRYING TO LINK UP TO FRAMINGHAM N HAYNES OTHER STUDIES COLLECTING DATA ON THAT SCALE. SO YOU CAN ASK IF YOU HAD A TINY FRACTION OF THAT DATA WOULD IT STILL BE USEFUL AND WHAT DO YOU NEED TO LOOK AT. THE OTHER THING TO CONSIDER, A WHOLE LOT OF THINGS MASS SPEC SYSTEMS NMR SYSTEMS, IF YOU TRY TO COMPARE DIRECTLY TO MILLION DOLLARS FOR WHATEVER ASK CAN YOU RECAPTURE THE SAME STANDARDS, THEY DO VERY BADLY. AT THE SAME TIME STACKS UP VERY BADLY SO CENTURY OF DEVELOPMENT WITH THE TECHNOLOGY IN TERMS OF COLOR ACCURACY AND SON. LET'S -- AND SO ON. WHAT YOU USE TO TAKE PHOTOS ON A DAILY BASIS AND ACTUALLY USE. SO I THINK THERE'S A LOT OF POTENTIAL FOR TECHNOLOGIES OUTRIGHT BLISS BUT MUCH FASTER AND TRYING TO UNDERSTAND THEM ON THEIR OWN TERMS WHAT ARE THEY USEFUL FOR. AND DOES ANY OF THIS INTERSECT WHAT YOU GET IN THE CONSUMER DEVICE. SO JUST IN THE LAST WEEK WE HAVE BEEN PLAYING WITH-MICROSCOPE IN THE LAB WRIT'S A LITTLE THING (INDISCERNIBLE) AND ACTUALLY WORKS MAGNIFICATION, DATA ON THE SURFACE USES THE LIGHTER TO ELIMINATE. AND REPLACE CONFOCAL LAB, NO, BUT YOU CAN PROBABLY DO A LOT OF STUFF THAT'S USEFUL ESPECIALLY LOOK AT WHAT'S ENABLED BY HAVING THE DEVICE ESSENTIALLY DISPOSABLE AND WHAT YOU CAN MAKE (INDISCERNIBLE) TOGETHER WITH (INAUDIBLE) AND SO ON. SO NOT SURE IF THAT ANSWERS YOUR QUESTION DIRECTLY BUT THAT'S THE WAY I'M THINKINGABLE YOUR QUESTION. -- THINKING ABOUT YOUR QUESTION. [APPLAUSE] >> WE HEARD TWO REALLY STRONG GAPS IDENTIFIED IN THIS ONE, THE NEED FOR REFERENCE DATA SETS AND NEED FOR ANNOTATION. SO THANK YOU. >> IF ANYBODY OUT THERE COULD GO GRAB EITHER PIETER DORRESTEIN OR ROB KNIGHT, THEY RAN OFF WITH THE SLIDES. I DIDN'T SEE THEM. SORRY. >> CAN EVERYBODY TAKE A SEAT PLEASE. >> NOW I'M ON. >> THIS IS SESSION 3, MY NAME IS DWAYNE LUNSFORD I MANAGE THE MICROPORTFOLIO FOR THE NATIONAL INSTITUTE OF DENTAL AND CRANIOFACIAL RESEARCH. FOR SESSION 3 STATE-OF-THE-ART TOOLS WE'RE GOING TO CONTINUE ON WITH TECHNOLOGIES AND APPROACHES PART 2. THIS WILL BE COVERING ALTERNATIVE MODELS. OUR FIRST SPEAKER WILL BE DR. ROBERT BRITTON FROM BAYLOR COLLEGE OF MEDICINE. >> THANK YOU. THANKS FOR THE OPPORTUNITY TO SPEAK. APPRECIATE THAT. I ALSO I SHOULD THANK WASHINGTON FOR MAKING ME FEEL AT HOME WITH THAT 98% HUMIDITY WALKING TO THE METRO. THAT WAS BRUTAL BUT THAT'S WHAT WE LIVE WITH ALL THE TIME. I THINK OUR DISCUSSION AT THE END OF THE LAST SESSION WAS APPROPRIATE FOR I THINK THE SESSION WE'LL GET INTO SO A LOT OF QUESTIONS ABOUT WHAT TYPES OF MODELS WE CAN BUILD TO EMULATE THE MICROBIOME OUTSIDE THE HOST OR IN DIFFERENT TYPES OF MODEL HOSTS WE HAVE MORE CONTROL OVER ORGANISMS THERE. REALLY WHAT WE'RE FOCUSED ON. WHAT I'M GOING TO DO TODAY STARTING WITH WHAT I THINK ARE MY KEY UNMET NEEDS ARE, REALLY WHAT I THIS I WE NEED TO DO IN MY LAB IS DEVELOP NOVEL MODELS FOR SETTING THE FUNCTIONS OF MICROBIAL COMMUNITIES NO JUST ASSEMBLING AND LOOKING AT STRUCTURE BUT ALSO LOOK AT FUNCTION. AS NOTED SEVERAL TIMES AND ESPECIALLY HIGHLIGHTED IN THE LAST SESSION, LACK OF SUNKSAL ANNOTATION IN META GENOMES IS A HUGE HINDRANCE FOR US. WE LOOK AT THINGS WE UNDERSTAND AND KNOW AND FINDING OUT THINGS WE DON'T KNOW IS HARD. GENETICS PLAY A HUGE ROLE. WHAT I'M GOING TO DO TODAY IS TWO EXAMPLES HOW WE TACKLE THE PROBLEMS IN MY LABORATORY AND HOPEFULLY STIMULATE IDEAS FOR THE FUTURE AND IF I HAVE TIME AT THE END I'LL TALK ABOUT CHALLENGES OF DOING THESE. MY LABORATORY IS TAKEN A MINIATURIZED APPROACH TO TRYING TO CULTIVATE MICROBIAL COMMUNITIES IN VITRO AS WAS MENTIONED DURING THE QUESTIONS EARLIER YOU HEARD TIM ONE, TIM TWO, SOME OF THESE SHINE MODEL WHICH IS ARE MORE ELABORATE IN MULTI-VESSEL CHAMBERS TRYING TO EMULATE DIFFERENT CHAMBERS OF THE INTESTINAL TRACK. WE HAVE BUILT BIOREREACTOR ARRAYS, THESE SMALL 15 ML REACTORS YOU CAN SEE HERE AND ESSENTIALLY DEVISE THESE BECAUSE WE THOUGHT THE ONLY WAY TO ANSWER QUESTIONS ABOUT IN A HURRY ABOUT FUNCTION MICROBIAL COMMUNITY IS BEING ABLE TO DO THEM IN A RELATIVELY HIGH THROUGH PUT MANNER. MOST EXISTING SYSTEMS NOW IT'S HARD TO DO MORE THAN TWO OR THREE AT THE TIME. SO WHAT WE DO IS REALLY CONTINUOUS FLOW SYSTEM FRESH MEDIA INTO THE REACTOR, THAT COMES OUT INTO THE WASTE. WE DO THIS DIRECTLY IN THE AN AEROBIC CHAMBER, THOSE ARE HEATEDDED TO 37-DEGREES AND WE HAVE A BUFFERED SYSTEM TO KEEP PH RELATIVELY NEUTRAL. AND WE CAN REALLY RUN THESE AT ANY RETENTION TIME TO MIMIC DIFFERENT PARTS OF THE TRACT WE WANT TO. THIS GIVES AN EXAMPLE WHAT ONE RUNNER REACTOR LOOKS LIKE SO HERE IS FOUR STRIPS OF SIX, 24 MICROBIAL COMMUNITIES RUNNING AT THE SAME TIME. WE RIGHT NOW CAPACITY TO DO 96 AT A TIME SO GIVING YOU A FLAVOR FOR THE AMOUNT OF THROUGH PUT THAT WE CAN DO. SO THE BIGGEST QUESTION THAT WE HAVE WE DECIDED TO BUILD A MODEL LIKE THIS IS DEMONSTRATE A FUNCTION. SO WE CHOSE CLOSTRIDIUM DID I HAVE SILL, IT'S THE -- DID I HAVE SILL, BECAUSE IT'S THE MOST COMMON CAUSE OF DIE PROPRIA, YOU CAN TREE WITH FMT. THIS IS THE IDEA OF BACTERIAL FUNCTION LOSS OR COMMUNITY FUNCTION LOSS THAT CAN THEN BE REGAINED. SO THIS IS BECOME A HUGE PROBLEM, AS YOU CAN SEE FROM THERE. WE SET OUT TO TRY TO RECREATE C DIFF SILL INVASION OF ANTIBIOTIC HUMAN FECAL COMMUNITY IN REACTORS SO WE TAKE THE SAMPLES FROM A FRESH DO MORE OR FROM FROZEN -- DONOR OR FROM FROZEN. WE BASICALLY PUT THEM INTO REACTORS TO GIVE THEM TIME OF DAY TO LET THEM GROW AND START ACOLLIMATING TO THE NEW NICHE BEFORE WE OPPOSE THE FLOW ON THEM. THEN AFTER WE DO THAT, WE START THE FLOW AND TREAT THEM WITH ANTIBIOTIC. IN THIS CASE WE USE CLINDAMYCIN WHICH IS BASICALLY THE ANTIBIOTIC THAT WAS FIRST ASSOCIATED WITH C DIFF SILL IN THE CLINIC. WE DO THAT FOR THREE DAYS AND THEN WE THEN ADD C DIFF AND SIMPLY MON TORE C DIFF ABUNDANCE OVER THAT TIME. MONITOR THE ABUNDANCE OVER TIME. SO WHAT YOU CAN SEE AND WE DID IS SHOW THAT IF WE TAKE REACTORS AND SO HERE WE HAVE N OF 10 AND YOU PUT C DIFF ON THAT REACTOR IT WASHES OUT WITHOUT EITHER RATE OF DELUSION OR SOMETIMES ACTIVELY KILLED SO THEY'RE GONE WITHIN A DAY. BUT YOU CAN SEE THERE'S NO INVASION OF THAT COMMUNITY. IF WE TREAT WITH CLINDAMYCIN, YOU CAN SEE THAT WE GET THIS NICE STABLE INVASION OF THAT COMMUNITY, THAT STAYS OUT HERE, WE CAN GO QUITE A WEIGHINGS OUT HERE WITH THIS GRAPH NOW TOO. THIS COMMUNITY IS NOW PRODUCING TOXINS, PRODUCING SPORES, ALL THINGS WE DON'T WANT C DIFF TO DO IN OUR GUT. WHEN BEFIRST STARTED I'M HOPING YOU DON'T GET 10 TO THE 6 CFU IN THE HOSPITAL AND YOU CAN SEE IF WE GO DOWN TO THE FUSE, 150 CELLS INOCULATED INTO THIS CHAMBER, YOU CAN GET A NICE STEADY INVASION. IT FINDS THE NICHE, 10 TO THE 6 CFU PER ML. THEY RECOVER AND THEY'RE UP 10 TO THE 9. WHAT YOU SEE IN A PATIENT. YOU DO NOT SEE C DIFF AS BEING DOMINANT MEMBER THOUGH CAUSING DISEASE. SO WE FEEL THIS IS A FAIRLY RELEVANT MODEL. WE HAVE DONE A NUMBER OF THINGS WITH THIS MODEL THAT I CAN'T TALK ABOUT NOW BECAUSE OF THE SAKE OF TIME, I'LL MENTION WE HAVE BEEN ABLE TO USE THIS MODEL TO LOOK AT THE ECOLOGICAL ADVANTAGES THAT EPIDEMIC TYPES C DIFF HAVE, ANY EVENT IT WAS REALLY ONE WAY WE NOW DEMONSTRATE FUNCTION OF COMMUNITY IN VITRO. SO WHAT ARE THE OTHER USES WE HAVE USED THIS FOR? WE HAVE BEEN LOOK AT A NUMBER OF AREAS HERE, I WON'T GO THROUGH THEM ALL BUT CERTAINLY THERE ARE A LOFT THINGS YOU CAN IMAGINE USING THEM FOR, COUPLE OF THINGS WE HAVEN'T DONE BUT HOPEFULLY PEOPLE THINK ABOUT USING FOR IS ESTABLISHING MICROBIAL COMMUNITIES FROM OTHER BODY SITES. ALSO USING FOR CULTIVATION OF CULTURED MICROBES. YOU CAN SEE A FAIRLY SIMPLE ROBUST TOOL AND THE BEAUTY AGAIN IS IT'S HIGH THANK YOU PUT, IF YOU HAVE ENOUGH MONEY IN THE RIGHT SETUP YOU CAN RUN 100 COMMUNITIES AT THE TIME. WHICH ALLOWS YOU TO THEN IF YOU WANT TO FORM SYNTHETIC COMMUNITIES THAT ROB WAS MENTIONING YOU CAN DO A T LOT AT A TIME BECAUSE I CAN TELL YOU WE HAVE DONE THAT AND IT'S HARD. IF YOU DEALING WITH N OF 2 OR 3 IT TAKE AS LONG TIME SO LET ME TRANSITION TO GENETICS. HOW WE TRY TO TACKLE THE GENETIC PROBLEM, SO OF COURSE AS I GREW UP IN BACILLUS AND E. COLI WITH GREAT GENETICS, WHY WE USED IT FOR FOR YEARS AS MOLECULAR BIOLOGY TOOLS, BUT UNFORTUNATELY MOST ORGANISMS THAT WE'RE STUDIENING THE MICROBIOME PROJECT DON'T HAVE THESE AND THEY'RE CRITICAL. SO WE HAVE BEEN STUDYING THE PROBIOTICS STRAIN ATCC PTA 6475, WHICH HAS BEEN ACTUALLY THE SUBJECT OF FEW PEOPLE IN THIS ROOM, IT'S AN ISOLATE THAT'S INTERESTING WITH ANTI-INFLAMMATORY PROPERTIES SHOWN TO IMPROVE DISEASE NUMBER OF SETTINGS INCLUDING AUTISTIC BEHAVIOR. WORK BY (INDISCERNIBLE). WHEN WE STARTED WORKING ON THIS STRAIN WE DIDN'T HAVE A WAY OF MAKING MUTATIONS IN A STABLE HIGH THROUGH PUT MANNER. I THINK IN THE PROBIOTIC FIELD WHEN I GOT INTO IT 12 YEARS AGO STORIES STOPPED BECAUSE IN ESSENCE THEY DID NOT HAVE GENETIC TOOLS TO GO IN AND TRY TO ASSIGN THE MECHANISMS FOR WHATEVER THAT PROBIOTIC WAS CURING OR MAKING BETTER OR PREVENTING. SO WE TURNED TO RECOMMON -- RECOME BY NEARING WE HAVE BEEN DONE AND WHAT THIS IS THE ABILITY TO MAKE UNSELECTED POINT MUTATIONS, DELETIONS AN INSERTIONS IN THE CHROMOSOME, FIRST PIONEERED IN E. COLI BUT NOW ABLE TO ADAPT TO STRAINS THAT ARE NOT -- CERTAINLY ARE NON-MODEL ORGANISMS. RECOMBINATION MEDIATED GENERATED ENGINEERING, THAT'S WHERE THE NAME COMES FROM AND WHAT I'M GOING TO TALK ABOUT TODAY IS BRIEFLY BASICALLY ACTIVITY OF PHAGOLAMB DA, E. COLI MACROPHAGE, PROTEIN BETA ERECT T. THIS IS A RECOMBINASE THAT FACILITATES HOMOLOGOUS SEQUENCES IN THE CHROMOSOME. SO OF COURSE E. COLI HAS ALL KINDS OF TOOLS, ALL KINDS OF GREAT THINGS YOU CAN DO WITH IT, IT LIKES TO TAKE UP DNA SO WHY DO WE THINK WE CAN DO THIS IN A GRAM POSITIVE ORGANISM WITH A BILLION YEARS OF EVOLUTION. THAT CAME FROM LAB HERE YOU DONE NEED TO KNOW ABOUT THE DATA HERE BUT WHAT THEY WERE LOOKING WAS ACTIVITY OF THE REBOMB BY NATION. -- RECOMBINASE. BETA IS E. COLI RECOMBINASE, THIS IS THE NUMBER OF RECOMBINANTS YOU CAN GET. WHEN THEY SCREENED A BUNCH OFISMS GRAM POSITIVE AND NEGATIVE THEY GOT THE SAME ACTIVITY IF THEY USE ENTEROCOCCUS ERECT T SO THAT'S FAR AWAY. THAT SUGGESTED THIS ACTIVITY WAS PROBABLY A CONSERVED ACTIVITY FROM PHAGOS ALL THROUGHOUT LIFE. AND THAT IS ANOTHER INTERESTING STORY. SO TO GIVE YOU THE SIMPLICITY HOW TO MAKE MUTATIONS, WE CLONE THE ERECT T GENE UNDER CONTROL OF REPRODUCIBLE PROMOTER, IT'S HIGHLY TOXIC SO IT'S ESSENTIAL FOR THE PROCESS. SO ONCE WE MAKE THE ERECT T, WE THEN TRANSFORM OLIGONUCLEOTIDE TYPE THE CELL WITH MISMATCH CORRESPONDING TO THE PLACE WE WANT TO MAKE MUTATION, BASICALLY ERECT T WILL PROTECT THESE OLIGONUCLEOTIDES FROM BEING DEGRADE BY THE CELL AND ALSO FACILITATE THE FACILITATE THE KNEELING OF THIS OLIGONUCLEOTIDE WITH STRAND OF REPLICATION. THAT'S THEN EXTENDED BY POLYMERASE. AND YOU BASICALLY END UP WITH A CELL NOW THAT HAS A WILD TYPE CHROMOSOME SO YOU SEGREGATE THOSE, AND NOW ALLOW YOU TO HAVE A MUTANT AND WILD TYPE. AND VICE VERSA, MUTANT AND WILD TYPE. THE BEAUTY IS ON STABLE PLASMID SO ONE NIGHT OF PASSAGE WE CREATED A STRAIN WITH SINGLE BASE PAIR MUTATION OR A FEW MUTATIONS THAT'S DIFFERENT. THERE'S NOTHING ELSE THAT'S DIFFERENT ABOUT THESE STRAINS. SO JUST TO FINISH, I WILL GIVE YOU AN IDEA HOW POWERFUL TECHNOLOGY LIKE THIS COULD BE. AND HOPEFULLY SUGGEST THIS IS SOMETHING TO START THINKING OF DOING IN MASS FOR MORE INTERESTING SPECIESES THAT WE HAVE IDENTIFIED IN THE MICROBIOME PROJECT. SO THIS IS ESSENTIALLY THE MECHANISM OF ACTION OF VEININGMYCIN THAT BINDS TO THE PEPTIDE WHILE SECRETED CELL WALL SYNTHESIS. THIS DIPEPTIDE IS FORMED BY THE DDL BUY LYE GAYS DLDL, THE TWO -- LIGASE. PATHOGENS GO AND CHANGE THAT LAT ALANINE TO A LACTATE OR A SERENE TO PREVENT VAIN CO-MYCIN FROM WORKING. CERTAIN INCLUDING LACTIC ACID BACTERIA ENZYMES AUTOMATICALLY DO THIS, THEY PUT IN A LACTATE SO THAT'S WHY ORGANISMS INARE -- HARVARD UNIVERSITY WHAT THEY SHOWED IS IT WAS DUE TO THIS SINGLE ACTIVE SITE TYROSINE CHANGED TO A PHENYL ALANINE SO A SINGLE HYDROXYL GROUP CHANGES WHETHER OR NOT YOU PUT ALANINE OR LACTATE. AND THAT WOULD DICTATE IF YOU WOULD BE VAIN CO-MYCIN RESISTANT BUT NEVER HAD THE ABILITY TO TEST THAT. WE USED OUR RECOME BY NEARING TECHNOLOGY, SHOT IN OLIGO, CHANGED THE AMINO ACID FROM CHANGE THE ACTIVITY AND YOU CAN SEE LACTOBACILLUS. IT'S RESISTANT TO VAIN VAIN CO-MYCIN, IF YOU DELETE THE ABILITY TO MAKE LACTATE YOU CAN GET SENSITIVITY BUT YOU CAN SEE THE SUPPRESSORS RISING HERE. IF YOU ACTUALLY THEN DO THAT MUTATION WE MADE YOU CAN SEE THAT WE GET GOOD KILLING, IT'S NOW CLINICALLY RELEVANT LEVEL VAIN CO-MYCIN, YOU MAY ASK WHY TO DO THIS, WE USE IT AS A DELIVERY VEHICLE FOR HUMAN THERAPEUTIC AND THOUGH RITTER IS NEVER SUSPECTED OF CAUSING SEPSIS WE WANT TO KILL OFF WITH CLINICALLY RELEVANT ANTIBIOTIC WHEN USED. SO REALLY WHAT I WANTED TO END WITH IS TO SHOW YOU TWO STORIES ABOUT HOW I THINK THAT WE'RE APPROACHING -- LOOKING AT MORE FUNCTIONAL STUDIES OF THESE COMMUNITIES, AND REALLY CULTIVATE USING THESE THINGS AS UNMET NEEDS OR CULTIVATING SOME OF THESE COMMUNITIES WHETHER FROM DISEASE OR HEALTHY INDIVIDUALS WE NEED TO BE GETTING MORE INDIVIDUALS OUT THAT WE CAN MIX TOGETHER. AS I SAID I THINK THAT DEVELOPING GENETIC TOOLS FOR KEY MEMBERS IS REALLY IMPORTANT BECAUSE NOW HOPEFULLY MOST OF YOU IN THE ROOM UNDERSTAND THAT STRAINS MATTER, SO KNOWING WHAT A SPECIES IS THERE, DOESN'T MAKE ANY DIFFERENCE. AS I SHOWED YOU TOTALLY CHANGE RESISTANCE TO ANTIBIOTIC. WE WEREN'T SUPPOSED TO TALK FUNDING BUT WHAT I WOULD SAY IS I GET CAN ASKED WHERE DO I SEND MY GRANTS WHERE I WANT TO STUDY MUTUALISTS OR GOOD GUYS OR GOOD IMMUNITIES IN THE ABSENSE OF HAVING TO FOCUS ON APPLYING THAT TO A DISEASE AND I DON'T KNOW THE ANSWER. I HOPE MAYBE SOMEBODY CAN TELL ME THAT BY THE END OF THE COFFINS. SO THANK YOU. [APPLAUSE] >> OUR NEXT TALK WILL BE ANGELA DAVIS AND SHE WILL DESCRIBE DROSOPHILA MODEL FOR GUT MICROBIOME RESEARCH. >> THANK YOU VERY MUCH. SO I WOULD LIKE IS TO START OFF BY GIVING AN EXPLANATION OF THE RATIONALE FOR OUR WORK ON DROSOPHILA. AFTER ALL, I THINK I'M THE ONLY PERSON SPEAKING IN THIS MEETING WITHOUT A BACKBONE. I THINK ANYWAY. SO THE RATIONALE IS FIRST WITHOUT A DOUBT THE BEST SYSTEM FOR STUDYING THE HUMAN MICROBIOME IS HUMANS AND SUSTAINED RESEARCH ON THE HUMAN MICROBIOME WILL MAKE US HEALTHIER AND ALLEVIATE CHRONIC METABOLIC IMMUNOLOGICAL AND POSSIBLY NEUROLOGICAL DISEASE. BY FAR THE BEST WAY TO GET TO THAT GOOD PLACE IS BY INCLUDING THE STRATEGIC USE OF MODEL ORGANISMS. MODEL ORGANISMS ESPECIALLY TO DETERMINE FUNDAMENTAL PRINCIPLES OF MICROBIOME SITES, SO THAT WE CAN IDENTIFY THE MOST PRODUCTIVE AVENUES FOR WORKING FOR HUMAN MICROBIOMES. IN THIS RESPECT, DROSOPHILA REALLY DOES HAVE A SPECIAL PLACE BECAUSE WE CAN CONDUCT EXPERIMENTS THAT WOULD BE ECONOMICALLY UNFEASIBLE WITH MAMMALIAN SYSTEMS AND ALSO WE BYPASS ALL OF THOSE VERY IMPORTANT ANIMAL WELFARE ISSUES THAT RELATE TO ROMANIAN AN DISPARATE SYSTEMS. IN ADDITION, DROSOPHILA IS AN AMAZING SYSTEM FOR MICROBIOME RESEARCH BECAUSE WE CAN SO EASILY TAKE THE PARTNERS APART AND PUT THEM BACK TOGETHER AGAIN. SO WE CAN GENERATE GERM FREE DROSOPHILA BY DUNKING THE EGGS TO BLEACH WHICH REMOVES THE SURFACE MICROORGANISMS AND TRANSFER THOSE EGGS INTO STERILE MEDIUM AND THE DROSOPHILA WILL GROW UP AND WE CAN MAINTAIN DROSOPHILA IF UPPED TO UNDER GERM FREE CONDITIONS FOR AS MANY GENERATIONS AS YOU WANTED THE MICROORGANISMS ARE CULTURALLABLE AND WE CAN RESYNTHESIZE THE ASSOCIATION WITH STANDARDIZED MICROBIOTA BY ADDING THE MICROORGANIZE. S OF CHOICE ON TO THE FOOD WHICH ANY DEVELOPMENTAL STAGE DROSOPHILA IS FEEDING. IT'S DOMINATED BY BACTERIA. I WILL COME BACK TO THIS POINT AT THE END BUT NOTICE HERE, NATURALLY THE DIVERSITY IS LOW BETWEEN 15 AND 100 OTUs, THAT'S AT THE 97% SEQUENCE CUT OFF FOR THE 16 RIBOSOMAL RNA GENE AND IN OUR LABORATORY SYSTEM, DOMINATED BYBACTER AND LACTOBACILLUS AND MULTIPLE OTUs OF FIVE SPECIES AND WE HAVE ISOLATED CHARACTERIZED REPRESENTATIVE MEMBERS OF THOSE FIVE SPECIES. SO THAT WE CAN GENERATE BIOTIC FLIES WITH MONOASSOCIATIONS WITH EACH OF THESE OR WITH REPRESENTATIVES OF ALL SPECIES. SO I WANT TO DESCRIBE THREE EXPERIMENTS THAT WE HAVE CONDUCTED THAT I THINK ILLUSTRATE THE UTILITY OF DROSOPHILA AND ALSO ELIMINATE SOMETHING ABOUT THE FUNDAMENTALS OF ANIMAL MICROBIOME INTERACTIONS. THE FIRST SET OF EXPERIMENTS RELATES TO NUTRITIONAL SIGNIFICANCE OF MICROORGANIZE. S. HERE IS OUR EXPERIMENTAL DESIGN. WE CAN HAVE DROSOPHILA WITH TWO COMPONENTS TO ITS DIET, GLUCOSE FOR CALORIES AND YEAST WHICH PROVIDES PROTEIN, ESSENTIAL LIPIDS AND MICRONUTRIENTS, IT'S A FACTORIAL DESIGN AS YOU CAN SEE AND GIVE YOU A SENSE FOR THE SCALE OF WHAT ONE CAN READILY DO IN DROSOPHILA WE WERE WORKING WITH A MERE 4,000 GERM FREE INDIVIDUALS. AND THOSE FOUR THOUSAND GERM FREE INDIVIDUALS COST US A TEASPOON OF BLEACH PER THOUSAND INDIVIDUALS. SO THAT'S THE COST OF WORKING WITH GERM FREE FACILITIES IN DROSOPHILA. SO HERE ARE YOU ARE ALL WELCOME TO JOIN ME AND WORK ON DROSOPHILA. HERE ARE THE DATA. ALONG THE Y AXIS IS PROPORTION OF INSECTS THAT MAKE IT TO ADULTHOOD. AND ALONG THE X AXIS IS TIME. AND NOTICE THAT THIS EXPERIMENT TOOK US ALL OF THREE WEEKS BECAUSE THIS IS FAST GENERATION TIME. TOWARDS THE RIGHT WE HAVE PLENTY OF YEAST IN THE DIET. CONVENTIONALS IN BLACK AND PERFORM WELL ROUGHLY EQUIVALENTLY, THE MEDIAN TIME INDICATED AT THE RIGHT. AS THE YEAST IN THE DIET DECLINES THE PERFORMANCE OF THE INSECTS DECLINE PARTICULARLY WHEN DIET BECOMES MORE UNBALANCED AND THERE IS A SEPARATION FROM THE CONVENTIONAL UNTIL WE GET TO THE MOST UNBALANCED DIET WHERE ALL DIE AS LARVAE. WE THEN WENT ON TO IDENTIFY WHAT WAS THE NUTRITIONAL PROBLEM BY ADDING BACK IN PROTEIN B VITAMINS TO THAT DIET AND WE FOUND RESCUE OF DROSOPHILA BY ADDING B VITAMINS AND CHARACTERIZING WHICH B VITAMINS ARE IMPORTANT BY INDIVIDUALLY OMITTING EACH B VITAMIN, EACH DATA POINT IS ONE OF THREE EXPERIMENTS, NO SIGNIFICANT VARIATION FOR THE CONVENTIONALS AT THE TOP BUT AMONG THE -- THOUGH THERE WAS A LOT OF NOISE, IT WAS PRETTY CLEAR THAT RIBOFLAVIN IS IMPORTANT WHERE VIRTUALLY NONE OF THE INSECTS ON DIETS WITHOUT RIBOFLAVIN MAKING IT THROUGH DEVELOPMENT. IN OTHER WORDS THE GUT MICROORGANISMS ARE SPARING THE DIETARY REQUIREMENT THROUGH B VITAMINS ESPECIALLY RIBOFLAVIN WITH IMPLICATION THESE BACTERIA ARE INDEED PROVIDING THESE B VITAMINS AND WE HAVE GONE ON TO ESTABLISH LACTOBACILLUS IMPORTANT. NUTRIENT SUFFICIENT DIETS WHERE DEVELOPMENT WAS UNAFFECTED IN THE XENICS WHEN EXAMINING THE ADULT FLIES WE DISCOVERED THEY WERE INORDINATELY FAT. AND THAT OBESITY WE COULD RESCUE NOT AT ALL BY ADDING BACK IN LACTOBACILLUS BUT TO A LARGE EXTENT BY ADDING BACK ACETYLBACTER AND GIVING INDICATION OF A FIRST INDICATION OF SYNERGISTIC INTERACTIONS BECAUSE WHEN WE ADDED BACK IN THE LACTOBACILLUS WHICH ON ITS OWN WAS AFFECTED WE GOT FURTHER IMPROVEMENT IN METABOLIC PHENOTYPE OF OUR FLIES. WE'RE NOW PROCEEDING FROM HERE TO USE THIS SYSTEM TO EXPLORE WHAT WE CALL COMMUNITY LEVEL METABOLISM THAT IS METABOLIC BENEFITS TO THE HOST FROM SMALL COMMUNITIES OF MICROORGANISMS THAT CANNOT BE PREDICTED AT ALL FROM THE AFFECTS AND BENEFITS FROM INDIVIDUAL TAXA IN MONOASSOCIATION. IN THE SECOND EXPERIMENT WE WORKED WITH SINGLE DIET, A NUTRITIONALLY SUFFICIENT DIET BUT MULTIPLE DIFFERENT DROSOPHILA LINES. IN THIS CASE FROM THE DROSOPHILA GENETIC REFERENCE PANEL DEVELOPED BY TRUE DIMCKID AND COWORKERS. WE WORKED WITH XENIC FLIES AND STANDARDIZED SPECIES MICROBIOTA. YOU CAN SEE OVERALL THE XENICS HAD ELEVATED LIPID, HYPERGLYCEMIC AND SOMEWHAT REDUCED PROTEIN. THIS MASKS A CONSIDERABLE AMONG GENOTYPE VARIATION. FOR EXAMPLE, IN RELATION TO LIPID, WHEN WE REMOVE THE MICROORGANISMS, SOME GENOTYPES BECOME INORDINATELY FAT, SOME BECOME LEAN. IN OTHER WORDS WE HAVE A ERALY IMPORTANT AFFECT TO POST GENOTYPE ON THESE MICROBIOTA DEPENDENT NUTRITIONAL AFFECTS. AND BECAUSE THE GENOMES ARE BEING SEQUENCED FOR THESE LINES OF DROSOPHILA WE COULD APPLY GENOME WIDE ASSOCIATION TO IDENTIFY GENETIC DETERMINANTS OF THIS VARIATION IN THESE MICROBIOTA DEPENDENT TRAITS. WE FOUND THE GREAT MAJORITY OF THESE GENES WERE EXPRESSED IN THE GUT AND NEURONS RATHER THAN OTHER TISSUES. AND ORGANS OF THE ANIMAL AND THE GREAT MAJORITY HAVE HOMOLOGUES IN MAMMALS RIGHT ACROSS THE ANIMAL KINGDOM. THIS IS IMPORTANT BECAUSE THERE IS SUGGESTIONS IN CONVERSATION SPY THAT TAXON SPECIFIC GENES OF UNKNOWN FUNCTIONING MAYBE PARTICULARLY INVOLVED IN INTERACTING WITH THE MICROBIOME. NOT SAYING THAT'S NOT TRUE BUT CERTAINLY THERE ARE DATA INDICATING THAT. WE WENT TO VALIDATE SOME OF THESE GENES, WE TOOK MUTATIONS IN THE GENES OF INTEREST AND COMPARED THE PHENOTYPIC TRAIT AND VALIDATION IS A DIFFERENT RESPONSE TO THAT MUTATION BETWEEN THE TWO MICROBIOLOGICAL CONDITIONS. AS DEMONSTRATED BY THESE TWO EXAMPLES AND FOR MOST OF THE GENES THAT WE VALIDATED BUT NOT ALL OF THEM, THE AFFECT OF THE MUTATION WAS EVIDENT IN THE XENIC FLY. IN OTHER WORDS, THE MICROBIOTA MAYBE MASKING THE PHENOTYPIC CONSEQUENCES OF HOST GENETIC VARIATION WITH IMPLICATION FOR FLIES AND POSSIBLY FOR PEOPLE THAT MAY YIELD DIFFERENT TYPES OF SYMPTOMS IN DIFFERENT PEOPLE WITH DIFFERENT GENOTYPES MY LAST EXPERIMENT IS TRANSCRIPT OMIC RNA SEQUENCE ANALYSIS THIS WITH THE FIVE SPECIES STANDARDIZED MICROBIOTA, IN 17 DROSOPHILA LINES THAT SPAN FOUR GENETIC DIVERSITY OF THE SPECIES. WE FOUND A NUMBER OF INSTANCES OF CO-EXPRESSION. THAT IS, IF THE EXPRESSION OF ONE GENE IN THIS CASE -- IS HIGH IN A PARTICULAR LINE, SO IS EXPRESSION OF A SECOND GENE BOTH INVOLVED IN INSULIN SIGNALING. IN THIS PARTICULAR INSTANCE, THIS CORRELATION OR CO-EXPRESSION WAS EVIDENT IN PHOTOBYTE BUS NOT IN EXENICS, IF WE LOOK RIGHT ACROSS THE FIRST EXTENTSIVELY EXPRESSED GENES THOSE PAIR WISE CORRELATIONS WERE MUCH STRONGER FOR NOTO BIOTIC THAN XENICC FLIES. MOVING FROM PAIR WISE COMPARISON S TO CONSIDERING MULTI-LEVEL COMPARISONS, I DETECT -- DEMONSTRATED HALF THE EXPRESSED GENES COULD BE ASSIGNED TO 11 MOLECULES OF CO-EXPRESSED GENES. SEVEN OF THOSE MODULES THE LEVEL OF CO-EXPRESSION DIFFERED BETWEEN NOTO AND XENIC FLIES. THE PATTERN OF THAT CO-EXPRESSION IS IN THE NOTOBIOTAS, THE CO-EXPRESSION WAS ELEVATED IN THE DIFFERENTIALLY EXPRESSED TRANSCRIPTIONAL MODULES NOT ONLY RELATIVE TO XENIC MODELS BUT ALSO TRANSCRIPTIONAL MODELS NOT CO-EXPRESSED INDICATING MICROORGANISMS ARE ORGANIZING THE TRANSCRIPTS IN THESE, NEARLY A FIFTH OF TOTAL OF EXPRESSED GENES ABOVE BASELINE. WE ARE HYPOTHESIZING THIS MAYBE INVOLVED IN THE PROMOTION OF ROBUST HEALTH. WE HAVE BEEN ADOPTING A TAXON GENOME TYPE APPROACH FROM WHICH WE DISCOVERED UNSURPRISINGLY NOW, THAT MICROBIOME DEPENDENT HOST TRAITS ARE COMPLEX. INFLUENCED FROM MICROBE INTERACTIONS, VARY WITH HOST GENOTYPE AND THEY HAVE MICROBIAL STRUCTURING OF SUBNETWORKS OF THE TRANSCRIPTOME, NOT JUST LEVEL OF INDIVIDUAL GENE. AND THIS BRING ME TO A SPECIFIC KNOWLEDGE GAP, WE HAVE INADEQUATE DATABASES FOR MOLECULAR TAXONMY AND FUNCTION OF EUKARYOTIC MICROORGANISMS. RECENT WORK IS EXTENDING TO FUNGAL ASSOCIATES WHICH THOUGH LOW ABUNDANCE APPEAR QUITE IMPORTANT IN TERMS OF METABOLIC AFFECTS. BECAUSE OF THIS COMPLEXITY WE'RE MOVING CLOSER TO WHERE ALL THE ACTION IS AND HOST MICROBIOME INTERFACE TO EXPLORE EXCHANGE OF METABOLITES AND INFO CHEMICALS BETWEEN THE PARTNERS AND ALSO TO INVESTIGATE COMMUNITY DYNAMICS OF THE ORGANISMS TO UNDERSTAND THEIR ABUNDANCE AND DISTRIBUTION OUR APPROACH IS TO USE TRANSCRIPTIONAL GENOMIC DATA WHICH ME AND COLLEAGUES ARE COLLECTING OVER THE YEARS AND HERE ECHOING A GREAT ADVANTAGE OF MODELING, WE'RE USING ECOLOGICAL MODELING AND METABOLIC MODELING TO IDENTIFY SOLUTIONS AND IDENTIFY SPECIFIC HYPOTHESES AND WE'RE NOW GEARING UP TO TEST THESE HYPOTHESES ADOPTING METABOLIC APPROACHES AND IMAGING APPROACHES SO WE HAVE A ERALY GOOD UNDERSTANDING OF THE SPATIAL RELATIONSHIP AMONG OUR DIFFERENT ORGANISMS. AND WHERE OUR DATA DON'T FIT TO MODELS, WHERE OUR DATA DON'T FIT TO OUR MODELS THAN WE CAN USE THAT TO REVISE OUR MODELS AND OPERATE ITERATIVE AROUND THAT. I HAVE A LARGE NUMBER OF CHALLENGES, GAPS AND NEEDS, MANY OF WHICH BEFORE I CAME TO THIS MEETING, I INTERPRETED TO BE RATHER FLY SPECIFIC BUT ACTUALLY ECHOING A LOT OF ISSUES BEING ADDRESSED TODAY BUT I WOULD LIKE TO MAKE ONE REALLY GENERAL POINT, IF YOU LACK AT MY CIRCLE HERE -- LOOK AT MY CIRCLE HERE, THESE ARE A LOT OF TECHNIQUES WHICH ARE COMING FROM COMING FROM DIFFERENT DISCIPLINES, MICROBIOSCIENCES IS INHERENTLY MULTI-DISCIPLINARY AND AS NIH TAKES ITS PRIORITIES FORWARD, LET US REMEMBER THAT WE NEED TO HAVE PROCEDURES AND WAYS TO ENHANCE AND SUSTAIN BOTH OUR INSTITUTIONAL AND FUNDING STRUCTURES TO FACILITATE THAT MULTI-DISCIPLINARITY. WHICH POINT I WOULD LIKE TO JUST THANK NIH FOR FUNDING LAB MEMBERS AND COLLABORATORS CONTRIBUTING DIRECTLY TO THIS RESEARCH. THANK YOU VERY MUCH. [APPLAUSE] >> THANK YOU, ANGELA. OUR NEXT TALK IS BY JOHN RAWLS FROM DUKE, SE BRA FISH AS A STATISTIC -- ZEBRAFISH AS A MODEL FOR HOST-MICROBIOME INTERACTIONS. Z >> MY LAB IS INTERESTED IN IDENTIFYING MECHANISMS THAT UNDERLIE HOST MICROBIOME INTERACTIONS. I THINK AS WE HAVE SEEN TODAY AND WILL CONTINUE TO SEE TOMORROW, ONE OF THE BIG PROBLEMS FACING THIS FIELD OVERALL IS THAT WE HAVE A SCALING PROBLEM. WE HAVE BEEN INCREDIBLY EFFECTIVE IDENTIFYING MICROBIAL SPECIES, STRAINS, GENES METABOLITES AN EVEN HOST GENOTYPES THAT CONTRIBUTE TO THESE INTERACTIONS. BUT I THINK THAT ANIMAL MODELS AND IN VITRO MODELS LIKE YOU HAVE BEEN HEARING IN THE SESSION HAVE AN IMPORTNT ROLE ATTACKING THE SCALE PROBLEM IN ORDER TO IDENTIFY THE MOUTHS IMPORTANT FACTOR FACTORS. SO I AM GOING TO TALK ABOUT THE ZEBRAFISH AS A MODEL SYSTEM TODAY. ONE OF THE REASONS THAT THE ZEBRAFISH AND OTHER ANIMALS ARE RELEVANT FOR HUMAN MICROBIOME RESEARCH IS BECAUSE OF OUR SHARED ANCESTRY. EVERYTHING WE KNOW ABOUT HOST MICROBIOME INTERACTIONS IN HUMANS IS PART OF OUR HERITAGE, AS ANIMALS. EVEN FROM EARLY STAGE ANIMAL DEVELOPMENT, FACETS OF OUR BODY PLAN THAT WE KNOW ARE IMPORTANT TO HOST MICROBIOME INTERACTIONS IS QUITE EARLY INCLUDING THE GUT, STEROID CELLS ADAPTED IMMUNITY ALL WHICH WERE PRESENT IN THE COMMON ANCESTRY BETWEEN FISHES AND MAMMALS. BECAUSE OF THAT WE'RE ABLE TO USE MODEL SYSTEMS LIKE THE ONES THAT YOU'RE HEARING ABOUT IN THE SESSION. BECAUSE WE CAN LEARN HOW HOST MICROBIOME INTERACTIONS EVOLVE IN DIFFERENT ANIMAL LINEAGES BUT USE EVOLUTION AS FILTER TO IDENTIFY DISTILL MECHANISMS OF HOST MICROBIOME INTERACTION THAT ARE PRESENT IN ALL ANIMALS AND THEREFORE PROBABLY PARTICULAR IMPORTANCE IN HUMAN HEALTH. SO ZEBRAFISH POSSESSES MANY TISSUES AND PHYSIOLOGY THAT WE KNOW ARE IMPORTANT IN MICROBIOME INCLUDING PROXIMAL SPECIFICATIONS AS OCCURRING IN MAMMALS, WE'LL TALK ABOUT THAT IN A MINUTE. PERISTALLSIS, MICROBIOTA, ITSELF. THERE'S ALSO PANCREAS, LIVER AND OTHER IMPORTANT TISSUES THAT PLAY A ROLE IN THE OVERALL INTERACTION WITH MICROBIOME. AS WITH ANY MODEL SYSTEM THERE ARE STRENGTHS AND WEAKNESSES WHICH ARE REALLY IMPORTANT TO CONSIDER WHEN DECIDING WHEN AND WHERE TO DEPLOY ANY MODEL SYSTEM. IN FISH THERE'S IMPORTANT BITS THAT ARE NOT PRESENT INCLUDING STOMACH, CELLS AND CRIPS. SO ONE NEEDS TO CHOOSE CAREFULLY WHEN DECIDING WHICH MODEL SYSTEM TO USE. IN ZEBRAFISH THERE ARE CLEAR BENEFITS, AS I HAVE MENTIONED THE ANATOMY PHYSIOLOGY IN THE FISH IS QUITE WHAT OCCURS IN HUMANS BUT THERE ARE SOME DIFFERENCES, FISH HAS LIMITED UTILITY AS MODEL FOR LUNG BIOLOGY OF COURSE BUT THERE'S THINGSED CONSERVEED THAT ARE USEFUL. THE FISH IS TRANSPARENT FROM THE EARLY STAGES OF DEVELOPENT TO YOUNG ADULT. THIS ALLOWS US TO LOOK AT HOST MICROBIOME INTERACTIONS AND PHYSIOLOGY IN GENERAL, USING MICROSCOPY WITH UNRIVALED TEMPORAL SPATIAL RESOLUTION WHICH FACILITATES MANY TYPES OF STUDIES THE OTHER IMPORTANT THING SIMILAR TO DROSOPHILA IS NOTO BIOTIC HUSBANDRY IN THE FISH IS QUITE SIMPLE AND SMALL SIZE ALLOWS US TO DO HIGH THROUGH PUT BIOTIC WORK AT COSTS THAT ARE ORDERS OF MAGNITUDE CHEAPER THAN WHAT IS POSSIBLE IN MICE AND OTHER ANIMALS. HOWEVER, THESE NOTO BIOTIC METHODS WERE RECENTLY DEVELOPED. THIS IS AN IMPORTANT POINT. THE ZEBRAFISH AS MODEL FOR THIS TYPE OF WORK IS A RELATIVELY YOUNG MODEL SO THE IMMUNITY OF SCIENTIST USING IT IS A RELATIVELY SMALL COMMUNITY AND IN MANY METHODS TAKEN FOR GRANTED IN SYSTEMS LIKE MICE ARE STILL ACTIVE AREAS OF RESEARCH IN THE FISH SYSTEM. HOWEVER THE NOTO BIOTIC HUSBANDRY IS A QUICK RELATIVELY INEXPENSIVE BUT ONE EDGES FOR EXAMPLE IS DEVELOPING METHODS TO GROW GERM FREE FISH TO ADULT STAGES. THIS IS SOMETHING WE CAN DO NOW BUT REQUIRES FURTHER OPTIMIZATION. DURING THE DEVELOPMENT OF FISH MICROBIOME IN THE GUT, APPEARS AN AROBES DON'T COLONIZE UNTIL EARLY ADULT STAGES. THIS MEANS THAT THE EARLY DEVELOPMENTAL STAGE WHEN FISH ARE TRANSPARENT, MOST AMENABLE TO IMAGING ARE -- THERE -- IT APPEARS TO BE A NICHE THAT'S PRIMARILY IF NOT ENTIRELY BY AROBES SO THERE'S LIMITATION OF AN AROBE BIOLOGY IN DISEASE DEVELOPMENT. THE ZEBRAFISH ARE SIMILAR TO THOSE OF HUMANS BUT WHEN YOU GET DOWN TO SHALLOW TAX NOMIC LEVEL THERE'S NOT MUCH OVERLAP. WE ANTICIPATE CHEMICAL INTERACTIONS IN METABOLISM THAT THESE BACTERIA POSSESS ARE SIMILAR TO WHAT OCCURS IN HUMANS. WORK FROM OUR GROUP IN THE LAST FEW YEARS IS A MODEL SYSTEM, THIS IS A HIGHLIGHT REEL OF THE PUBLICATIONS THAT HAVE COME OUT WHERE WE HAVE BEEN ABLE TO IDENTIFY ROLES FOR MICROBIOTA IN DIFFERENT ASPECTS OF VERTEBRATE PHYSIOLOGY WE HAVE BEEN MOTIVATED TO DEVELOP GENOMIC TOOLS AND GENETIC TOOLS OTHERWISE INTRACTABLE GUT MICROBES AND WORK FROM OTHER GROUPS INCLUDING KAREN GILLMAN'S GROUP IDENTIFY NOVEL FACTORS THAT REGULATE DEVELOPMENT OF IMPORTANT PROCESSES LIKE BETA CELL MEMBER. TWO SHORT STORIES TODAY. THAT ILLUSTRATE RECENT WORK USING THE FISH TO UNDERSTAND DEPTH OF CONSERVATION, IN VERTEBRATE BIOLOGY RELATING TO THE GUT MICROBIOTA. AND THE MECHANISMS THAT MEDIATE HOST MICROBIOME INTERACTIONS. SO FIRST WE'LL ASK ARE INTESTINAL EPITHELIAL CELLS CONSERVED AND ARE THEY REGULATED BY CONSERVED TRANSCRIPTIONAL PROGRAM? IT'S KNOWN THAT IN MOUSE AND ZEBRAFISH THERE'S MANY SAME PRINCIPLES EPITHELIAL CELL TYPES INCLUDING STEM CELLS ABSORBED IN SECRETORY GOBLET CELLS AND ENDOCRINE CELLS AND THE OVERALL PHYSIOLOGY OF THE TISSUE IS SIMILAR BUT WE DON'T KNOW IF THAT IS UNDERSCORED BY CON SERVED TRANSCRIPTIONAL PROGRAM. SECONDLY WE WANT TO ASK IF WE CAN IDENTIFY TRANSCRIPTIONAL PROGRAMS THAT MEDIATE RESPONSES TO MICROBIOTA. WE WILL THINK ABOUT THIS THROUGH THE LENS OF HOST TRANSCRIPTIONAL REGULATION. GENES TYPICALLY CONSIST OF -- YOU MIGHT THINK OF HAVING TRANSCRIPTIONAL START SITE AND APPROXIMATENAL FAMILIAL, MOST INFORMATION CONTROLLING INFORMATION IS ENCODED IN REGULATORY REGIONS THAT OCCURS VERY ADJACENT TO WITHIN OR SOME CASES GREAT DISTANCES AWAY FROM GENES. THIS IS FACILITATED IN PART BY PACKAGING OF DNA INTO NUCLEOSOME COMPLEXES. THE REASON DEVOID OF NUCLEOOWESOMES THIS OPEN ACCESSIBLE CHROMATIN IS WHERE TRANSCRIPTIONAL FOLLOWING HISTOTONE MODIFICATIONS RNA POL 2 TO PROMOTE GENE TRANSCRIPTION. I'LL TALK ABOUT TRANSCRIPTIONAL PATTERNS AND CHROMATIN PATTERNS AND HOW TO IDENTIFY THE FACTORS THAT SIT DOWN ON THE THIS DNA AND MEDIATE RESPONSES TO MICROBIOTA. IN ONE STUDY WE TOOK A COMPARATIVE GENOMIC APPROACH AND ASKED HOW SIMILAR TRANSCRIPTIONAL PROGRAMS FROM FOUR VERTEBRATE SPECIES SHOWN HERE, HUMAN MOUSE ZEBRAFISH SEPARATED BY OVER 400 MILLION YEARS OF ANIMAL EVOLUTION. WE ISOLATED FROM DIGESTIVE TRACK AND PERFORMED RNA SEQ TO MAKE LIFE MORE MANAGEABLE, WE FOCUSED ON ONE TO ONE ORTHO LOGS ENCODED IN THESE GENOMES AND ASKED HOW THEIR EXPRESSION PATTERNS RELATED WE SAW A GENERAL POSITIVE CORRELATION BETWEEN ORTHO LOG. HERE SHOWN FOR EXAMPLE BETWEEN MOUSE ILIUM AND THE ZEBRAFISH INTESTIN. THE GENES THAT ARE MOST HIGHLY EXPRESSED APPEAR IN THIS CORNER ARE GENES WE KNOW ARE IMPORTANT IN INTESTINAL BIOLOGY SUCH AS FEBP 6 AND RVP 2. IF WE TAKE THE SIGNATURES AND CLUSTER THEM, THESE IAC DATA SETS WITH MOUSE DATA SETS WE SEE THAT COMPARE TO SEVERAL MOUSE TISSUES WE SEE THE TRANSCRIPTIONAL PROFILES OF THESE VERTEBRATES CLUSTERED DINT FROM OTHER MOUSE TISSUES AND CC TECH ISSUE RESUMES 15 MINS FACTORS ASSOCIATED WITH HUMAN STRUCTURE SO DIFFERENCE BETWEEN STUDIES GI SITE, AGE, ORIGIN, WHICH HYPERVARIABLE REGION SEQUENCE, AND THE PLATFORM ALL CAN SIGNIFICANTLY AFFECT WHAT WAS REPORTED SO I THINK THIS WAS CONSISTENT WHAT WE KNOW IN HUMAN AND OTHER SPECIES. SO AS WE LOOK AT THIS THE ORIGINS OF THESE, THEY TOOK SAMPLES ALONG THE GI TRACT AS WELL AS FECES SO UPPER GI LOWER GI, THESE ARE THE THREE ABUNDANT PHYLA, YOU HAVE PROTEOBACTERIA SO YOU LOOK AT THE DISTAL BOWEL AND THE COLON, ARE THE FECES, YOU CAN SEE VERY SIMILAR TO HUMANS IN TERMS OF THE DISTRIBUTION OF THE MAJOR PHYLA. AND ALSO, BOTH FOR PHYLA AS WELL AS GENRE YOU SEE THIS GRADIANT ACROSS THE GASTROINTESTINAL TRACT SO IN THE STOMACH, MUCOSA YOU WILL SEE HELICOBACTER AND IN THE LOWER GI AND FEE SEES YOU SEE PREVATELA, A LITTLE BIT OF LACK OF CLOSTRIDUM. AT THE GENERAL LEVEL THERE'S CONSISTENCY WITH THE HUMAN. SO BASICALLY IN ALL THE SAMPLES THEY FOUND PREVETELA CLOSTRIDIUM AND 99% OF THE FECAL SAMPLES AND THEY ALSO FOUND A SET SHARED IN ALL SAMPLES REGARDLESS OF COUNTRY OF ORIGIN, DIET, AGE AND BREED. AND SO THEY WERE PROPOSING THIS AS A CORE MICROBIOME IN COMMERCIALLY REARED SWINE. AND I'LL REPORT THIS STUDY WHICH IS A -- ANOTHER RECENT STUDY LOOKING AT THE REFERENCE GENE CATALOG AND THEN META GENOMICS AND FOUND OBVIOUSLY THE META GENOME WAS INFLUENCED BY THESE FACTORS THAT INFLUENCE THE 16S. SO THE FIRST STUDY WAS BASICALLY POST WEANING. THIS IS A STUDY FROM DAVID MILL'S GROUP AT UC DAVIS SO THEY LOOKED AT PIGS IN THE FIRST SEVEN WEEKS, SO THESE FIRST BARS THROUGH DAY 21 ARE WHEN THEY WERE SUCKLING ON THE SAL. THEY'RE THEN ABRUPTLY WEANED AND THESE ARE POST WEANING SO WITHIN FIRST SEVEN WEEKS THE MICROBIOME, THIS IS A FAMILY LEVEL, FAIRLY STABLE, BUT THEN WHEN WEANED FROM THE SOU THEY CAN SEE INCREASES IN LACK FOE BACILLUS FROM COX A AND PREVATEL LA. FROM PREVIOUS SLIDE THESE WERE MORE PREDOMINANT IN THE OLDER SWINE. THEY ALSO DID META GENOMICS AND SO THE BLUE IS THE WEANING AND THE -- SORRY, NURSING AND THE RED IS THE WEANED. SO IF THEY SEE -- WHAT THEY SEE AFTER WEANING IS A LARGE REDUCTION IN THE PROTEINS ASSOCIATED WITH LAKOTAS UTILIZATION AND INDUCTIONS IN THE PROTEINS ASSOCIATED WITH PLANT DESCRIBED SUBSTRATES BECAUSE MOST TIMES THEY'RE WEANED ON TO A CORN SOY BASED DIET SO BOTH IN THE PAPER, I DON'T HAVE TIME TO PRESENT IT BUT THEY WENT BACK AND ATTRIBUTED THESE DIFFERENT GENES TO DIFFERENT TAXA. SO THIS IS SOME OF THE CURRENT OBSTACLES. SO AS WE HEARD FROM MANY OTHER MODELS THAT THE PIG AT A SPECIES LEVEL, GENERAL LEVEL, IS NOT THE SAME AS THE HUMAN. ALTHOUGH AS I WILL SHOW YOU THE PIG IS MORE SIMILAR TO THE HUMAN THAN THE MOUSE, AND AT THE META GENOMIC LEVEL, THEY'RE ALSO MORE SIMILAR THAN WHEN WE LOOK AT COMPOSITION. SO THIS WAS A VERY NICE RECENT PAPER LOOKING TO DEVELOP A REFERENCE GENE CATALOG FOR THE PIG. THEY DID DEMETA GENOMIC SEQUENCING FROM SAMPLES ABOUT 287 PIGS FROM FRANCE, DENMARK AND CHINA. NUMBER OF BREEDS AND NUMBER OF FARMS. THEY IDENTIFIED 7.7 MILLION NON-REDUNDANT GENES AND REPRESENTING 4719 META GENOMIC SPECIES. WHAT'S INTERESTING IS IF WE LOOK AT THE KEG PATHWAYS, 96% OF THOSE IN THE HUMAN CATALOG WERE PRESENT IN THE PIG. SO I THINK THIS IS SHOWING FAIRLY GOOD OVERLAP BETWEEN THE TWO SPECIES IN TERMS OF THE KEG PATHWAYS. HOWEVER, ONLY 70% IN THE PIG WERE PRESENT IN THE HUMAN. YOU WILL SEE THIS IN TERMS OF THE NEXT SLIDE TOO. SO I THINK THERE'S GOOD COVERAGE OF THE HUMAN BUT THERE'S CERTAINLY SPECIES AND AS WELL AS PATHWAYS THAT ARE IN THE PIG THAT DO NOT OVERLAP WITH THE HUMAN. I THINK THERE'S A NEED TO BETTER UNDERSTAND THAT. SO THIS IS A FIGURE FROM THE PAPER, THESE WERE THE NON-REDUNDANT GENES. AND SO BASICALLY THERE WAS ONLY .2% OF THE GENES SHARED BY MOUSE, HUMAN AND PIG SO VERY SMALL PROPORTION. WHEN THEY LOOKED AT WHAT WAS SHARED BETWEEN THE HUMAN AND THE PIG, IT WAS ABOUT 12.62% VERSUS ONLY 1.3% WHEN WE COMPARED THE MOUSE AND THE HUMAN. SO AGAIN, I THINK IT'S POINTING TO THE FACT THAT THE PIG LET IS PROBABLY A BETTER MODEL IN TERMS OF SOME OF THESE ASPECTS THAN THE MOUSE. SO THESE ARE LOOKING AGAIN AT KEG FUNCTION SO THESE WERE PRESENT IN 90% OF THE INDIVIDUALS THEY FOUND A LITTLE OVER 3,000 KEG FUNCTIONS THAT WERE SHARED BY THE MOUSE, THE HUMAN AND THE PIG. THIS REPRESENTED 69% OF THE PIG FUNCTIONS 95 AND 92% IN THE MOUSE. SO THIS GETS BACK TO OUR REFERENCE DATABASES THAT PIG IS AN EXCELLENT MODEL BUT THERE'S LESS DATA AVAILABLE ON DEFINING THESE PATHWAYS SO IT HIGHLIGHTS THE CONSISTENCY, OF MICROBIOTA AT THE FUNCTIONAL LEVEL BUT SUGGESTING A SPECIFIC SET OF SPECIFIC KEG FUNCTIONS THAT ARE CURRENTLY UNKNOWN. AND THIS IS SOME DATA FROM MY LABORATORY WHERE WE HAVE BREAST FED INFANTS SO THIS IS ALSO ANOTHER LIMITATION IN TERMS OF BREAST FED INFANTS THREE MONTHS OF AGE AND FORMULA FED AT THE PHYLA LEVEL SO YOU CAN SEE 50% OF ACTIN BACTERIA IN BOTH OF THESE PIGS, THE 21 DAY OLD PIGS LOOK LIKE ADULT HUMANS. THERE'S LITTLE BACTERIA AND PRIMARILY BACTERIA DEDEs AND FERMICUTES. THIS IS ALL BACK STEREOIN THE HUMAN INFANT AND -- BACTERIA IN THE HUMAN INFANT AND THERE'S VIRTUALLY NONE IN THE PIG LET SO THIS IS A LIMITATION. BUT WE DO STUDIES IN THE PIG LETS WHERE PROBIOTIC AND I CAN SHIFT THAT. THIS WILL CHANGE. I FEED INFANT PRE-BIOTIC IT WILL ALSO CHANGE BUT THE TRANSLATABILITY BETWEEN THESE TWO HAS BEEN A CONCERN. ONE LIMITATION I THINK I'M GOING TO SUGGEST WE NEED PORCINE MICROBIOME PROJECT. THEY'RE VERY IMPORTANT SPECIES NOT ONLY FOR PRODUCTION BUT ALSO PRE-CLINICAL BIOMEDICAL MODEL. THIS IS A REVIEW WE HAVE DONE, TO GET OVER THE ISSUE WITH INFANT MICROBIOME DIFFERENT FROM TH PIG, WE'RE DEVELOPING GERM FREE NOTO BIOTIC PIG LET. ISOLATERS ARE AVAILABLE IN WISCONSIN ABLE TO GENERATE PIGS AND I HAVE TWO MORE SLIDES WE TOOK PIG LETS AND ASSOCIATED THEM WITH HUMAN INFANT MICROBIOTA. AND THEY WERE FED, WE GAVAGE THEM AT THESE TIME POINTS ABOUT 10 TO THE 9 CFU PER ML, WE GAVE THEM FORMULA, WE GAVE THEM HUMAN MILK, FOUR TO FIVE PROTEIN, OR I HAVE HAD NIH FUNDING TO LOOK AT THE FUNCTION LIPID SACCHARIDES WHICH ARE IMPORTANT TO SHAPING. SO THIS IS TARGETED PCR, JUST TO POINT OUT IN THE PIG LETS FED HUMAN MILK WE MAINTAINED THE BIFIDA BACTERIA, THAT WAS THERE IN THE DONOR STOOL BUT NOT IN FORMULA OR 2 FL BUT THE LLMP ONE HMO MAINTAINED THAT. THERE'S NICE WORK AT DAVIS SHOWING THAT, BIFIDA BACTERIA UTILIZE TO HMO. SO IN CONCLUSION COMBINED WITH RESENTENCELY PUBLISHED PIG GENOME,S HAVING A PIG GUT GENE FAT LOG WILL ACCELERATE RESEARCH CATALOG WILL ACCELERATE COMPLEX INTERACTIONS. AS WE HAVE BEEN SAYING ALL DAY, THE INTEGRATION OF PHENOTYPIC GENOMIC AND META GENOMIC DATA WILL PROVIDE KEY BIOLOGICAL INFORMATION AND IN THE BEGINNING I THINK THE PIG LET IS A GOOD MODEL FOR US TO MODEL HUMAN CLINICAL DISEASE AS WELL AS NORMAL DEVELOPMENT. THANK YOU. [APPLAUSE] >> THANK YOU, SHARON. OUR LAST TALK IS FROM HARRIS WANING COLUMBIA UNIVERSITY WHO WILL SPEAK ABOUT THIS ISSUE OF SPATIAL TEMPORAL META GENOMICS AND MAMMALIAN GUT. >> GREAT. THANK YOU SO MUCH FOR GIVING ME THIS OPPORTUNITY TO SHARE WITH YOU WHAT I THINK IS A KEY KNOWLEDGE TECHNOLOGICAL GAP IN THE MICROBIOME FIELD. TODAY YOU HAVE HEARD A LOT ABOUT SPATIAL BIOGEOGRAPHY IN CONTEXT OF DIFFERENT LOCATIONS WITHIN THE BODY SO THEN IN THIS CONTEXT, THIS DISCUSSION I LIKE TO STRESS THAT WHAT I MEAN BY SPACE IS REALLY LINK SCALES INDIVIDUAL CELLS. THAT WILL BE REALLY IMPORTANT IN THINKING ABOUT RELEVANCE IN ECOLOGY. SO NATURALLY THE SYSTEMS ARE HIGHLY STRUCTURED WHETHER YOU'RE LOOKING AT A FOREST OR THE MICROBIOME AND WE KNOW THIS FROM VARIOUS IMAGING STUDIES THAT THE HUMAN ASSOCIATED MICROBIOTA HAVE VERY DEFINED SPATIAL STRUCTURE AND THE SPATIAL STRUCTURE IS REALLY IMPORTANT IN MEDIATING A VARIETY OF INTERACTIONS SUCH AS MICROINTERACTIONS. AS WELL AS IMPORTANT INTERACTIONS COOPERATION ANTAGONISM THAT SHAPE STABILITY AND THE MAINTENANCE OF WHAT OTHERWISE IS A VERY ROBUST COMMUNITY. THESE LOCAL INTERACTIONS ARE MEDIATED BY SPECIFIC PROCESSES WHETHER THEY BE METABOLIC, CROSS FEEDINGS SUCH AS BETWEEN VARIETY OF BACKROID DISEASE THAT E CHANGE METABOLITES THROUGH DEGRADATION OF POLYSACCHARIDES, ET CETERA, AND THEY CAN BE MEDIATING A VARIETY OF BOTH COMMENSAL ACTIVITIES AS WELL AS RESIST INVASION OF PATHOGENS THROUGH PRODUCTION OF VARIETY OF BACTERIAL SENSE AND ANTIMICROBIAL PEPTIDES. SO REALLY KIND OF THE KEY CHALLENGE WHICH I THINK IS RELEVANT IN THIS FIELD AND RELATED TO ALL THE MODEL SYSTEMS IS REALLY THAT WHEN WE STUDY MICROBIOME WE'RE ESSENTIALLY DOING A ONE DIMENSIONAL ANALYSIS IN THE MICROBIOME SPACE, WE'RE ESSENTIALLY TAKING FECAL SAMPLES, WE'RE BLENDING THEM PUTTING IN A BLENDER AND LOOKING AT ESSENTIALLY THE ABUNDANCE DISTRIBUTIONS GENERATING WHAT I THINK IS KIND OF SINGLE DIMENSIONAL ABUNDANCE INFORMATION WHICH WHEN TRYING TO USE VARIETY OF INFORMATIC TOOLS FOR ASSOCIATION INFORMATION. I THINK THIS IS ONE OF THE KEY BOTTLENECKS IN THIS AREA, AND WHAT I WANT TO PROPOSE IS A FRAMEWORK FOR STUDYING THIS AND JUST SHARING WITH YOU THE WORK THAT WE'RE TRYING TO DO IN THIS SPACE AND DEVELOPING APPROACHES AND TECHNIQUES IN THIS. I CALLED THIS SPATIAL META GENOMICS AND THE IDEA IS THAT PERHAPS WE CAN INSTEAD OF LOOKING AT ENTIRE COMPLEXITY OF THE SYSTEM, ESSENTIALLY USE HIGH THROUGH PUT RANDOM PLOT SAMPLING AND STATISTICAL RECONSTRUCTION TO INFER THE OVERALL PROPERTIES OF THESE LARGER STRUCTURES. THIS IS ACTUALLY HAS A GREAT AMOUNT OF ANALOGY TO ECOLOGY STUDIES WHERE BASICALLY PEOPLE GO INTO A FOREST AND LOOK AT INDIVIDUAL SUBPLOTS OF THAT FOREST TO COUNT NUMBER OF SPECIES AND THE INTERACTIONS TO THEN BUILD STATISTICAL INFERENCES ASSOCIATED WITH HOW THAT COMMUNITY IS STRUCTURED. YOU CAN IMAGINE DOING THIS IN THE CONTEXT OF THE MICROBIOTA BY ESSENTIALLY LOOKING AT THESE INDIVIDUAL PLOTS AND INFERRING CO-ASSOCIATION INFORMATION WHICH THEN YOU CAN INFER INTERACTIONS. SO WE HAVE BEEN WORKING ON TECHNIQUE, META GENOMIC PLOT SAMPLING BY SEQUENCING TO ESSENTIALLY IMPLEMENT THIS STRATEGY AND THE BASIC PREMISE IS ESSENTIALLY WE TAKE A TISSUE, A FIXED TISSUE OF A MICROBIOTA I IN THIS CASE A MOUSE INTESTINE, WE FIX IT IN A FIX THAT KEEPS THE SPATIAL INFORMATION INTACT. WE CAN THEN FRACTIONATE INTO INDIVIDUAL SMALL PARTICLES WHICH RETAINS LOCAL INFORMATION OF THE MICROBIOTA WHICH I THINK IS THE THING THAT WE WANT TO CAPTURE. THEN WE CAN PUT THIS THROUGH A ESSENTIALLY A DROPLET-BASED ENCAPTIONLATION SYSTEM CAPTION WITH BAR CODED BEADS THAT CAN ESSENTIALLY SIMPLY PHI THE SPECIFIC -- SIMPLY MAGNIFY THE MTA GENOMIC INFORMATION WITH THE CELLULAR CLUSTERS AND YOU CAN DO EMULSION PCR AMPLIFY CASINGS, BREAK UP THE EMULSIONS AND PERFORM HIGH THROUGH PUT META GENOMIC SEQUENCING. SO THIS IS A VISUALIZATION OF WHAT THAT PROCESS LOOKS LIKE, ESSENTIALLY IN THE TISSUE. WE CAN FILTER FOR SPECIFIC SIZES OF THESE PARTICLES, THESE ARE JUST CYBER GREEN STAINS FOR DNA ASSOCIATED WITH EACH OF THESE CLUSTERS, THESE ARE QUITE GOOD CLUSTERS. WHEN YOU PUT THEM THROUGH THIS FLUIDIC SYSTEM, YOU CAN ALSO INTRODUCE METHODS TO ESSENTIALLY BREAK UP THE CLUSTERS ONCE THEY'RE CO-LOCALIZED TO INDIVIDUAL PARTICLES. AND THESE ARE SOME DISTRIBUTIONS ASSOCIATED WITH THIS. I WON'T TWO INTO TESTIFY -- GO INTO TOO MUCH DETAIL HOW TO BAR CODE BUT THERE'S A VARIETY OF TECHNIQUES TO DO THAT INSPIRED BY THE DROPLET SEQ SINGLE CELL SEQUENCING PLATFORMS. THIS IS JUST A VISUALIZATION, KIND OF A MOVIE, SHOWING ENCAPSULATION HOVEL SIMPLE MICROFLUIDIC CHAMBER SYSTEMS, BASICALLY ENCAPSULATE TENS OF THOUSANDS OF DROPLETS IN A FEW MINUTES. SO SOME SIMPLE QUALITY CONTROL SHOWS THAT BY ESSENTIALLY TAKING A PRE-ASSOCIATED CLUSTER OF E. COLI WITH FECAL MICROBIOTA YOU CAN DISTINCTLY SEPARATE OUT THE CLUSTERS INTO CLUSTERS AND WE CAN SHOW WE CAN SEPARATE E. COLI FROM THE OTHER FECAL MICROBIOTA CLUSTERS HIGHLIGHTING THAT ESSENTIALLY EACH CLUSTER IS UNIQUELY IDENTIFIED. ONE NICE THING IS YOU CAN EXTRACT OUT BULK LEVEL INFORMATION TAKING ENSEMBLE INFORMATION OF INDIVIDUAL CLUSTERS AND THEY CORRELATE WELL WITH THE BULK KIND OF DROPLET TECHNIQUES. AS WELL AS KIND OF THE TECHNICAL REPLYCATION OF THIS STUDY. SO THIS REALLY HELPS US GAIN CONFIDENCE THIS TECHNIQUE IS -- HAS THE ABILITY TO REPLICATE ABUNDANCE LEVEL INFORMATION BUT HAS ADDITIONAL LAYER OF INFORMATION. SO THIS IS WHAT THE BROAD DATA LOOKS LIKE. SO ON THE Y AXIS ARE JUST THE OTUs I IDENTIFIED ACROSS A VARIETY OF DIFFERENT CLUSTER INDIVIDUAL CLUSTERS THAT WE CAN SEQUENCE. HEAT COLORS CORRESPOND TO ABUNDANCE LEVELS OF OTUs FOR INDIVIDUAL CLUSTER, YOU CAN SEE THAT SOME OF THESE HAVE SINGLE OTU SPECIES AND THEN SOME HAVE MULTIPLES. THIS IS THE TYPE OF INFORMATION WE WOULD LIKE TO CAPTURE. THIS IS JUST DENSITY DISTRIBUTION SHOWING NUMBER OF UNIQUE OTUs PER PARTICLE. AS WELL AS CURVE SHOWING HOW WELL WE SAMPLE THESE COMMUNITIES AND TYPES OF INTERACTIONS. HOW DO WE START TO ANALYZE THIS TYPE OF INFORMATION? SO HERE IS BASICALLY THE DIFFERENT OTUs MAP BACK TO ONE ANOTHER LOOKING AT FREQUENCY WHICH THESE OTUs ARE CO-ASSOCIATED WITH ONE ANOTHER. RELATIVE TOTAL ABSOLUTE ABUNDANCE SO MORE ABUNDANT INDIVIDUALS WOULD BE FOUND NEXT TO OTHER INDIVIDUALS BY CHANCE. SO WE NORMALIZE AGAINST THAT SO BASED OFF THAT NORMALIZATION YOU CAN BUILD FRAMEWORKS THAT ANALYZE MICROBIOTA CO-ASSOCIATED WITH ONE ANOTHER. AT DIFFERENT LENGTH SCALES HERE, THIS IS A RECONSTRUCTION OF WHAT THAT LOOKS LIKE ACROSS LINK SCALES WE THINK THIS IS IMPORTANT BECAUSE IT'S IN THE NECESSARILY WHO YOU'RE NEXT TO BUT THE TYPE OF INFLUENCE WHAT YOUR NEIGHBORS ARE ABLE TO INTRODUCE INTO YOUR PHYSIOLOGY TYPE. THAT MIGHT BE IMPORTANT RELATIVE FOR ANY INDIVIDUAL MICROBIOTA. THIS IS THE SAME MICROBIOTA SAMPLE STUDIED AT TWO LINK SCALES AND SPECIFIC OTU AND SIZE CORRESPOND TO RELATIVE ABUNDANCE AND THE EDGES CORRESPOND TO THE STATISTICALLY SIGNIFICANT ENRICHED INTERACTIONS, THAT ARE FOUND AND YOU CAN SEE THAT BASICALLY AT DIFFERENT LINK SCALES YOU'RE SEEING THESE DIFFERENT INTERACTIONS. THESE INTERACTIONS COULD POTENTIALLY BE DIFFERENT ACROSS DIFFERENT GEOGRAPHIC LOCATIONS WITHIN MICROBIOME. THIS FOR EXAMPLE IN SMALL INTESTINE WE SEE DIFFERENT MICROBIOTA IN THE LARGE INTESTINE AND INTERACTIONS ARE DIFFERENT. INTERESTINGLY FOR THE SAME OTU THAT ARE FOUND IN THE SMALL INTESTIN, WE IDENTIFY POTENTIALLY DIFFERENT TYPES OF INTERACTIONS, RELATIVE TO THE LARGE INTESTIN FOR EXAMPLE, THESE OTUs 4 AND 3 CO-ASSOCIATED IN SMALL INTESTINE ARE NOT CO-ASSOCIATED IN THE LARGE INTESTINE. WE CAN IDENTIFY NEGATIVE INTERACTION, NOT JUST POSITIVE CO-ASSOCIATIONS. WHICH MIGHT TELL YOU SOME THINGS ABOUT SPECIFIC ANTAGONISM ASSOCIATED WITH THESE MICROBIOMES. FOR EXAMPLE, HERE, THIS IS A NEGATIVE INTERACTION BETWEEN THIS LACTOBACILLI AND BACKROID DISEASE SPECIES HERE. SO YOU CAN SEE IN THE CONTEXT OF PERTURBATIONS WE MIGHT BE FAMILIAR WITH. THINGS LIKE ANTIBIOTIC TREATMENT, AS WELL AS DIETARY MODULATION. I THINK WE'RE BEGINNING TO ONLY SCRATCH AT THE SURFACE OF STARTING TO LOOK AT THE MICROBIOME INTERACTIONS IN CONTEXT OF PERTURBATIONS ONCE WE ORIENT WHERE THEY ARE RELATIVE TO THEIR NEIGHBORS. I THINK WHERE I'M HOPING WHERE THIS AREA GOES, REALLY IS JUST NOT JUST BEYOND IDENTIFICATION OF INDIVIDUAL STRAINS THEMSELVES BUT KIND OF FUNCTIONAL INFORMATION. SO FOR EXAMPLE NOT ONLY CAN WE START TO THINK ABOUT THE SPECIES LEVEL INFORMATION WE'RE WE CAN START TO PERFORM THIS SPATIAL META GENOMICS ON THE WHOLE 'NOTHER GENOME SO NOT ONLY UNDERSTANDING THE SPECIES BUT THE GENES THAT ARE ASSOCIATED WITH THEM AS WELL AS TRANSCRIPTIONAL PROFILE IN THE CONTEXT OF BIOGEOGRAPHY. SO YOU WOULD EXPECT THAT CO-LOCALIZATION WITH CROSS FEEDING PARTNER MAY INTRODUCE ADDITIONAL TRANSCRIPT OMIC CHANGES THAT ARE RELEVANT ONLY IN THAT LOCALIZED CONTEXT WHICH IS NOT NECESSARILY GOING TO BE EASY TO DECONVOLUTE IN A BULK STUDY. YOU CAN ALSO LINK THIS TO OTHER IMMUNOHISTOCHEMISTRY APPROACHES WHERE FOR EXAMPLE YOU CAN TAG THE ASSOCIATION OF A MICROBIOTA TO LOCALIZATION OF INDIVIDUAL MOLECULES OR EVEN HOST TISSUE ITSELF. ALL THIS I THINK REALLY HAS ADDITIONAL DIMENSION OF TEMPORAL PROFILING WHICH WE NEED TO DO AT THIS LINK SCALE. THIS ALSO IS COMPLIMENTARY THE MORE ADVANCED IMAGING BASED APPROACHES FOR THIS, I THINK THE KEY LIMITATION FOR THESE IMAGING STUDIES IS REALLY THAT WE DON'T HAVE THE LEVEL GENOMIC RESOLUTION THAT WE CAN GET BY DOING DEEP SEQUENCING AND AS WELL AS GENOMIC META GENOMIC TRANSCRIPT OMIC ANALYSES. WITH THAT, I WOULD LIKE TO WRAP UP AND SAY THAT I THINK MAPPING THE MICROBIOME AND SPATIAL BIOGEOGRAPHY OVER TIME IS REALLY IMPORTANT IN UNDERSTANDING MECHANISTIC INSIGHTS. SO I THINK WE GET A LOT OF CORRELATIONS BUT THE MECHANISM REALLY REQUIRES US TO THINK ABOUT AT THE LINK SCALE RELEVANT FOR THE MICROBIOTA WHICH I THINK ARE ON THE MICRON SCALE. THIS WILL HELP TO INFER ECOLOGY AS WELL AS FUNCTION. MAJOR SPATIAL STRUCTURING IN THE GUT, SEEMS TO BE ONLY OCCURRING OFTENTIMES THE LEVEL INDIVIDUAL SPECIES WHICH IS REALLY HARD TO DECONVOLUTE USING IMAGING METHODS SO THESE TYPES OF SEQUENCING APPROACHES ARE REALLY IMPORTANT. AND THE MICRON SCALE INDIVIDUAL TAXES COULD BE HETEROGENEOUSLY DISTRIBUTED WHICH MAYBE REALLY IMPORTANT IN THE CONTEXT OF BIODIVERSITY. CERTAINLY VARIETY OF DIFFERENT GI LOCATIONS, MAYBE EXHIBITING DIFFERENT TYPES OF ASSOCIATION PATTERNS RELEVANT TO THE TISSUES AND THE TYPES OF ENVIRONMENTAL QUEUES MEDIATING THESE ACTS. ADDITIONALLY THESE LINK SCALE INTERACTIONS STUDYING DIFFERENT LINK SCALES IS -- AS WELL AS VARIETY OF HOST VARIATIONS IS REALLY IMPORTANT. I THINK POTENTIALLY MAYBE THESE SPATIAL LOCALIZATION INFORMATION POTENTIALLY ALSO SERVE AS ADDITIONAL CLINICAL BIOMARKER. THIS MIGHT TRANS LATE TO ANALYSIS STUDYING THE FECAL MICROBIOTA FROM ANIMAL STUDIES IT SEEMS THE FECAL MICROBIOME SPATIAL INFORMATION SEEMS TO RECAPITULATE THAT TO DISTAL GUT MICROBIOTA INFORMATION. SO WITH THAT, JUST LIKE TO THANK MEMBER OF MY LABS WHO -- COLLABORATORS, WE HAVE HELPED DO THIS WORK AND -- YEP, THANK YOU FOR YOUR ATTENTION. [APPLAUSE] >> THANK YOU, HARRIS. WE CAN TAKE QUESTIONS NOW. PLEASE IDENTIFY YOURSELF FIRST. >> BRANDON ACRE. I LIKED THE LAST TALK THAT WAS AMAZING. THANK YOU SO MUCH. I'M AN ONCOLOGIST SO I LOOK FOR KEYSTONE SPECIES WAY TO DEFINE ECOLOGICAL HEALTH AND I WONDER IF YOU THINK THAT OR ANYONE OF YOU THINK THAT THAT MIGHT BE AN ACCEPTABLE WAY TO GO ABOUT DEFINING A HEALTHY MICROBIOME. I HEAR STORIES FROM OTHER SCIENTISTS SAYING THAT WE DON'T KNOW WHAT A HEALTHY MICROBIOME IS, YET WE CAN WALK INTO A KELP FOREST AND TELL YOU IT EHEALTH BECAUSE IT HAS SEE OTTERS AND SEA OTTERS KEEP THE URCHINS AT BAY SO WE HAVE A RESILIENT RESOUNDING ECOSYSTEM SO THOUGHTS ON THAT. >> SO I THINK KEYSTONE SPECIES IS REAL IMPORTANT IN A LOT OF ECOLOGY, OFTENTIMES VERY DIFFICULT TO IDENTIFY THEM FROM THESE BULK STUDIES BECAUSE THEY ARE FOUND IN VERY LOW ABUNDANCE SO ONE OF THE MOTIVATIONS FOR THINKING ABOUT SPATIALLY ORIENTING THEM IS THAT YOU REMOVE ABUNDANCE LEVEL INFORMATION SO YOU CAN DRILL DOWN LOW ABUNDANCE INDIVIDUALS ASSOCIATIONS MAYBE IMPORTANT IN THAT CONTEXT SO CERTAINLY I THINK THAT'S GOING TO BE REALLY RELEVANT IN A VARIETY OF STUDIES HERE. >> I DON'T WANT TO STEER TOO LONG TO SPATIAL BUT THAT'S INTRIGUING AS WELL. ARE YOU LOCKING AT DIET AND LIQUID DIET MORE CONSISTENCY THAN SAY SOLID DIET ESPECIALLY WITH HETEROGENEOUS FOODS? LOOKED AT ANYTHING LIKE THAT? >> YES. CERTAINLY WE -- THIS IS -- WE'RE AT THE BEGINNING OF LOOKING AT THIS, AND DEFINITELY WE SEE BIG DIFFERENCES BETWEEN DIETS AND HIGH FAT VERSUS HIGH FIBER DIETS IN TERMS OF ASSOCIATION PATTERNS. SO I THINK THAT REMAINS TO BE SEEN WHAT THE RELEVANCE OF UNDERSTANDING THE ECOLOGICAL STRUCTURE IS. THAT'S A GREAT SUGGESTION THERE. >> I'M CHRIS LYNCH. I HAVE A QUESTION FOR -- I ENJOYED THESE TALK. I HAVE A QUESTION FOR DR. RAWLS ABOUT ZEBRAFISH MODEL. I WANTED TO KNOW IF SOME PROBLEMS, I HAVE READ ABOUT THIS MODEL STILL EXISTS. ONE IS THAT THERE A FEW YEARS AGO IT WAS A LOT OF PAPERS COMING OUT THEY HAD NO REFERENCE DIET AND THAT COMMERCIALLY AVAILABLE DIET SOME OF THE NUTRIENTS LIKE IRON WHICH CAN AFFECT THE MICROBIOME, WERE MAYBE FIVE OR EIGHT FOLD DIFFERENCE BETWEEN DIETS AND WAY OVER THE REQUIREMENTS. AND THEN ANOTHER THING WAS THAT WHEN ZEBRAFISH WERE KEPT AT NORMAL LABORATORY UNDER NORMAL LABORATORY CONDITONS WITH A LOW FAT COMMERCIAL DIET, THAT THEIR ADIPOSITY RANGED ANYWHERE FROM 18 TO 45 IN MALES AND FEMALES. SO IN HUMANS, AFTER 35 YOU'RE ELIGIBLE FOR BARIATRIC SURGERY. GIVEN THAT OBESITY IS LINKED TO THE MICROBIOME, HOW DO YOU ADDRESS THAT PROBLEM IN ZEBRAFISH? >> >> THAT'S A GOOD QUESTION. SO THE QUEST FOR A REFERENCE DIET OF THE ZEBRAFISH THAT IS ADOPTED BY HOPEFULLY A BROAD SPECTRUM OF RESEARCH COMMUNITY IS STILL ELUSIVE. THE ZEBRAFISH MODEL REALLY GREW AS A LABORATORY MODEL WITH NUTRITION NOT BEING AT THE FOREFRONT. AND THE DIETS THAT ARE USED COMMONLY IN MOST FISH LABS ARE ADOPTED FROM OTHER TROPICAL FISH SPECIES WITHOUT SPECIFIC NUTRITIONAL REQUIREMENTS OF THE ZEBRAFISH BEING KNOWN OR UTILIZED IN THIS DECISION. THIS IS STILL A PROBLEM IN THE FIELD. I MENTION THE IMMUNITY OF RESEARCHINGERS LOOKING AT HOST MICROBIOME, ZEBRAFISH RELATIVELY SMALL WITHIN THE FIELD, SAME WITH NUTRITION. IT'S RELATIVELY SMALL NUMBER OF FOLKS IN THE FIELD THAT ARE PAYING CLOSE ATTENTION AND THINKING CREATIVELY HOW TO SOLVE THESE SORTS OF PROBLEMS. THERE ARE SOME STUDIES THAT SUGGEST STANDARD LAB DIETS FOR FISH PRODUCE RATES OF ADIPOSITY THAT WOULD BE CONSIDERED OBESE BY MAMMALIAN STANDARDS. IN OUR WORK LOOKING AT HOST MICROBIOME INTERACTIONS WE DON'T USE THOSE DIETS, WE HAVE CUSTOM DIETS WE UTILIZED WHERE THE NUTRITION CONTENTS ARE MORE DEFINED. AND FOR LONGER TERM NOTO BIOTIC WORK WE USE PROTOZOA AS THE DIET WHICH IS MORE REPRESENTATIVE WE THINK OF WHAT THEY EAT IN THE WILD. SO THAT OPENS UP A WHOLE OTHER SET OF QUESTIONS. THIS IS SOMETHING THAT THE FIELD IS STILL STRUGGLING WITH. >> THIS IS KIND OF AN IDEA MORE THAN A QUESTION. BUT IT RELATES TO A QUESTION FROM THE PREVIOUS SESSION ABOUT HOW TO LINK BIOINFORMATICS TOOLS LOOKING AT GENE AND STRAIN LEVEL ANALYSIS TO IN VITRO TOOLS LIKE THE BIOREACTORS WE HEARD ABOUT SO IT'S SOMETHING I WANTED TO ASK ROBERT THOUGHTS ON. CONNECTING BACK TO HOWARD'S KEYNOTE THIS MORNING, ABOUT THE BIOLOGICAL SPECIES CONCEPT AND HOW MUCH RECOMBINATION THERE ARE BETWEEN CELLS OF -- THAT WE'RE CALLING SAME SPECIES I WOULD ECO WHAT HE SAID, WE SEE VARIATION WITHIN WHAT WE CALL BY OPERATIONAL DEFINITION AS SPECIES. SOMETIME THERE'S A LOT OF GENE FLOW SOMETIMES NOT, WE HAVE SEEN THAT IN HE WAS LOOKING AT GENOMES, WE HAVE SEEN THAT IN META GENOMES WITH THE TOOLS THAT I TALKED ABOUT. SO HERE IS THE IDEA, QUESTION, COULD WE GET SOME OF THOSE STRAINS AND TEST HOW MUCH GENE FLOW THERE IS IN YOUR BIOREACTORS AND HOW FEASIBLE IS THAT, WHAT WOULD BE THE LIMITATIONS? >> GREAT QUESTION, IT'S ACTUALLY SOMETHING THAT WE'RE DOING FROM A LEVEL OF GENE FLOW BUT TRYING TO ASSEMBLE MORE DEFINED COMMUNITIES MORE SIMPLIFIED TO DO DEEP SEQUENCING AND LOOK AT EFFECTS ON DIFFERENT ENVIRONMENTAL BASIS WE CAN DO AND HOW GENOMES CHANGE OVER TIME SO THAT'S ONE OF THE STRENGTH OF THE BIOREACTOR IS YOU WILL BE ABLE TO SAMPLE FIVE TIMES A DAY, TEN TIMES A DAY DEPENDING ON WHAT KIND OF DATA THAT YOU WANT. AND YOU CAN TAKE THAT OUT, RUN THEM OUT AS LONG AS TWO MONTHS. SO THAT'S SOMETHING THAT CAN BE DONE, SOMETHING WE'RE LOOKING AT WITH DIFFERENT PERTURBATIONS SUCH AS DIET, OTHER THINGS TO DO THAT. WE'RE WORKING RATHER THAN WITH COMPLEX FECAL COMMUNITIES, THE NUMBER OF STRAINS THAT ARE IN THERE ARE SO GREAT WE WANT TO START WITH MORE DEFINED 10, 20 TO START ASKING THESE QUESTIONS. ONE OF THE CHALLENGES WE'RE HAVING IS FIGURE OUT WHO ARE THE GUYS ASSEMBLE TOGETHER, STAY TOGETHER AND GROW REACTORS. THAT'S DEFINITELY AN APPLICATION OF REACTORS. >> SO WE HAVE TIME FOR ONE MORE. >> (INDISCERNIBLE) JUST TO FOLLOW-UP FROM PREVIOUS SESSIONS THIS MORNING, STRAIN LEVEL DIVERSITY, STRAIN LEVEL CHANGES (INAUDIBLE) SEEMS TO ME MODEL SYSTEMS MAY HAVE MORE MINIMUM MICROBIOTA, WOULD BE A GOOD PLACE TO START ADDRESSING FUNCTIONAL STAIN CHANGES AND IN THAT REGARD MY QUESTION IS TO ANGELA. ANGELA, IN DROSOPHILA IF YOU LOOK AT WHY DROSOPHILA ARE FROM YOUR LAB VERSUS ANOTHER LAB, HOW MUCH STRAIN LEVEL DIFFERENCES DO YOU SEE CONSIDERING THE DROSOPHILA IS RELATIVELY SPEAKING LOW IN COMPLEXITY? >> SO STRAIN DIVERSITY IN TERMS OF BACTERIA, IT'S REALLY IMPORTANT. AND WE HAVE DEVELOPED A METHOD WHICH CAN DISCRIMINATE PHENOTYPIC AFFECTS AND RELATE THAT TO GENE CONTENT, SPECIFIC GENES OF THE BACTERIA, MEDIATING THE PHENOTYPIC TRAIT OF THE HOST. I DIDN'T TALK ABOUT THAT IN HERE BUT I WOULD BE VERY HAPPY TO DISCUSS IN MORE DETAIL LATER. >> GREAT. LIKE TO THANK OUR SESSION 3 SPEAKERS AGAIN. IT'S BREAK TIME UNTIL 4:30. >> OKAY. FOR THE PEOPLE ONLINE, WE HAVE MANY PARTICIPANTS ONLINE -- I THINK THEY ARE HEAR ME ONLINE THOUGH. I'M JUST TALKING TO THE PEOPLE ONLINE. YOU KNOW, WE WANT TO REMIND YOU THAT THE PEOPLE ONLINE THAT WE SET UP A MECHANISM FOR YOU TO, YOU KNOW, PARTICIPATE IN THIS, EVEN IF YOU WEREN'T HERE. AND SO IF SOME OF THE SPEAKERS RAISE QUESTIONS FOR YOU OR YOU'D LIKE SOMETHING CLARIFIED IN QUESTION SESSION OR BEFOREHAND, WE SET UP A GMAIL E-MAIL ACCOUNT YOU CAN SEND QUESTIONS TO, THAT LITA OR SOMETHING ELSE IS FOLLOWING. IT'S ETMICROBIOME@GMAIL.COM, A SAFE E-MAIL ACCOUNT, NOTHING WILL HAPPEN TO YOU IF YOU SEND YOUR QUESTION IN THERE. AND WE ALSO HAVE FOR THE SOCIAL MEDIA LOVERS A TWITTER ACCOUNT, HASHTAG #ETMICROBIOME. SO IT'S ETMICROBIOME@GMAIL.COM AND HASHTAG #ETMICROBIOME. IN A NUMBER OF SESSIONS THIS MORNING WE'VE COVERED SOME DIFFERENT OPPORTUNITIES AND SOME SPEAKERS MENTIONED OPPORTUNITIES IN MICROBIOME RESEARCH. IN THIS NEXT SESSION WE'RE GOING TO HIGHLIGHT SOME OTHER GENERAL ISSUES THAT HAVEN'T BEEN DISCUSSED YET THAT IMPACT HUMAN MICROBIOME RESEARCH AND IDEAS ON HOW TO ADDRESS THEM FOR THE FUTURE OF THE FIELD. AND THEN AFTERWARDS WE'RE GOING TO HAVE A ROUNDTABLE MODERATED BY MIKE REDDY. THE FIRST SPEAKER IN THIS SESSION IS DR.ED THATTED THAT, AND HE'S THE PROFESSOR OF IMMUNOLOGY AND CHIEF OF DIVISION OF LABORATORY AND GENOMIC MEDICINE AT WASH U SCHOOL OF MEDICINE, TALKING TO US ABOUT FUNCTIONAL ROLES OF THE MICROBIOME IN ANIMAL MODEL EXPERIMENTATION. THANKS. >> THANKS FOR THE NICE INTRODUCTION, CHRIS. WE HEARD SOME REALLY GREAT TALKS IN THE LAST SESSION BUT SOME INTERESTING MODEL SYSTEMS, SOME MAYBE ARE LESS EXPLORED THAN OTHERS. WHAT I'M GOING TO FOCUS ON I THINK IS A MODEL SYSTEM THAT'S HIGHLY EXPLORED, WHICH IS THE MOUSE SYSTEM. I THINK ALL OF US THAT WORK WITH MICE KNOW THAT IF YOU'RE WORKING WITH A STRAIN OF MICE WHERE ALL THE MICE ARE GENETICALLY IDENTICAL WE SEE DIFFERENCES IN PHENOTYPES. THIS TYPICALLY IS REPRESENTED IN CAGE EFFECTS WE SEE. WE ALL KNOW THIS. WE ALL HAVE SEEN THIS. THIS IS ONE EXAMPLE THAT WE HAD DISCOVERED A FEW YEARS AGO IN OUR FACILITY. WE'RE VERY INTERESTED IN FUNCTION OF IgA, IMMUNOLOGY OF IgA IN THE SOUTHWEST -- INTESTINE. IN THE WILDTYPE MOUSE COLONY IN THE FACILITY THERE WERE MICE THAT HAD DETECTABILITY FECAL IgA, MICE IN OTHER CAGES THAT DIDN'T. THIS IS INDEPENDENT OF IgA PRESENT IN THE SERUM. WE SAW THIS IN OUR FACILITY AND BEGAN COLLABORATING WITH SKIP VIRGIN, PASSED HORIZONTALLY AND VERTICALLY, THIS CAN BE TRANSFERRED THEN HORIZONTALLY AS WELL. YOU CAN TAKE IgA HIGH AND LOW MICE, PUT THEM IN THE SAME CAGE ALL THE MICE WILL BECOME IgA LOW. WE WENT ON TO SHOW THIS WAS BACTERIAL SPECIES DRIVING US BUT THE REAL LESSON HERE IS THIS IS SOMETHING WE ALL KNOW WE HAVE TO DEAL WITH, IN THE MOUSE COLONIES. THERE'S THIS TRANSMISSIBILITY OF THE MICROBIOME. THAT'S THE EASY PART. THE HARD PART IS WHEN WE WANT TO START LOOKING AT MODELING HOST-GENETICS AND MODEL SYSTEMS PARTICULARLY TRYING TO MODEL MUTATIONS WE SEE IN HUMAN DISEASE. THIS IS WHERE THIS GETS A LITTLE BIT HARDER, WHERE PEOPLE STOP PAYING ATTENTION I THINK TO THE CONTRIBUTIONS OF THE MICROBIOME. AND WHAT I'M GOING TO GO AHEAD AND PUT MY CHALLENGES SLIDE UP. I THINK A LITTLE BIT OF THIS IS PREACHING TO THE CHOIR BUT SOME IS THAT THIS COMMUNITY HAS TO GO OUT AND REALLY EXPAND BEYOND OUR BOUNDARIES AND LET PEOPLE KNOW THEY NEED TO BE THINKING ABOUT MICROBIOME PARTICULARLY IN ANIMAL MODEL EXPERIMENTS. SO THE BASIC ISSUE IS THAT THERE'S -- THERE ISN'T A COMPLETE APPRECIATION IF THE MICROBIOME CONTRIBUTES TO PHENOTYPE IN THE INTESTINE AND LUNGS, REALLY ON A SYSTEMWIDE LEVEL. YOU CAN FIND EXAMPLES IN ALMOST EVERY ORGAN SYSTEM WHERE THE MICROBIOME CAN AFFECT THAT PARTICULAR ORGAN. IN MANY CASES, I SEE THIS AND I'M SURE YOU'VE SEEN STUDIES THAT LACK EXPERIMENTATION THAT LACKS FOR CONTROLS FOR THE MICROBIOME. THESE CHALLENGES REALLY OCCUR AT MANY LEVELS. THIS IS AT THE LEVEL OF SENIOR SCIENTISTS, JUNIOR SCIENTIST, PEOPLE AT THE BENCH, BUT ALSO GOES UP TO PEOPLE THAT ARE ADMINISTRATORS AND EVEN EDITORS OF JOURNALS. THIS NEEDS TO BE TAKEN SERIOUSLY ACROSS MANY LEVELS. HOW DO YOU APPROACH THIS? WHAT'S THE BEST WAY TO CONTROL FOR MICROBIOME? MOST OF US WOULD AGREE THE BEST WAY TO DO THIS IS IF YOU HAVE A MOUSE THAT'S MUTANT, AND GROWING SEPARATELY FROM CONTROLS, YOU SEE A PHENOTYPE, THE THING YOU HAVE TO DO IS BREED THEM FOR LITTERMATE CONTROLS. THIS I THINK AS MANY PEOPLE ARGUED, INCLUDING MYSELF AND SKIP VIRGIN, WE THINK THIS IS THE GOLD STANDARD. THE KEY THEN IS TO DO THIS BREEDING AND THEN TEST TO SEE UNDER THESE CONDITIONS NOW ARE MUTANTS NOT EQUAL TO CONTROLS, THIS WOULD FAVOR A HOST GENE MECHANISM. THEN YOU CAN GO AHEAD AND STUDY YOUR GENES. IF YOU DO THIS ON THE CONTROLS AND MUTANTS NOW HAVE THE SAME PHENOTYPE THIS WOULD FAVOR A MICROBIOME DOMINANCE, YOU'RE TRYING TO FIGURE OUT THE MICROBE DOING THIS. THERE ARE CAVEATS. IF YOU THINK HARD ABOUT THIS, IT'S NOT ALWAYS TOTALLY BLACK AND WHITE WHERE THIS IS GOING TO HAPPEN. THERE ARE MANY EXAMPLES NOW IN THE LITERATURE WHERE YOU CAN HAVE TRAITS THAT ARE CLEARLY INFLUENCED BY A GENE BUT THAT GENE IS FURTHER INFLUENCED BY SPECIFIC MICROBES. WHEN YOU WIND UP INTO THIS LAND HERE IN THE MIDDLE, YOU NEED TO BE ABLE TO THINK ABOUT DOING EXPERIMENTS THAT CAN THEN TEST FOR THESE COMBINATORIAL TRAITS, TAKING THE FORM OF A VARIETY OF DIFFERENT EXPERIMENTATION, INCLUDING CO-HOUSING, INCLUDING FECAL TRANSPLANTS, INCLUDING ISOBIOTIC MICE, TO NAME A FEW. AND DO LITTER MATE CONTROLS MATTER? I THINK THE ANSWER IS QUESTION. THERE'S AN INTERESTING PAPER THAT JUST CAME OUT IN "IMMUNITY." IT WAS LOOKING AT NLRP6, YOU'LL HEAR MORE FROM DANA PHILPOTT TOMORROW. THE PUNCHLINE HERE, THERE WERE PAPERS PUBLISHED SEVERAL YEARS AGO ABOUT LITTERMATE CONTROLS, INTERESTING GENE AND PHENOTYPE, DIFFERENCES IN MICROBIOME. WHEN YOU BREED THE MICE AND DO LITTERMATE CONTROLS THERE WERE NO DETECTABLE DIFFERENCE IN RECOVERY FROM INJURY OR THE MICROBIOME. THIS IS SOMETHING THAT NEEDS TO BE -- I THINK IT'S BEGINNING TO BE TAKEN SERIOUSLY. I THINK THERE ARE OTHER EXAMPLES OF THIS THAT HAVE OCCURRED AND THAT ARE COMING ALONG, BUT THIS IS JUST ONE THAT I WANTED TO HIGHLIGHT. SO YES, LITTERMATE CONTROLS DO MATTER. WHAT CAN WE DO TO FACILITATE REPRODUCIBILITY, THERE ARE A NUMBER OF THINGS INCLUDING REPORTING DETAILS OF OUR EXPERIMENTS. THIS IS ANALOGOUS TO WHAT WENT ON WITH MICROARRAY EXPERIMENTS IN THE '90s WHEN THERE WERE CRAZY THINGS HAPPENING AND PEOPLE BEGAN REPORTING SPECIFIC DETAILS OF HOW THEY ACTUALLY DID THEIR HYBRIDIZATION. THIS HELPED CLEAN UP THE FIELD. WE CAN DO THE SAME THING HERE. WE CAN REALLY REPORT DETAILS OF HOST-GENETICS, EXPERIMENTAL DETAILS HOW YOU'RE CONTROLLING FOR THE MICROBIOME. HUSBANDRY DETAILS WHICH ARE CRITICAL, MANY CAN HAVE A PROMINENT EFFECT ON THE MICROBIOME, AND HOW YOU'RE DOING YOUR MICROBIOME ANALYSIS, ALL THESE THINGS REALLY MATTER. THEN ONE LAST THOUGHT HERE IN THIS SEGMENT OF THE TALK IS THAT WE OFTEN GET -- WE SEE A PHENOTYPE IN A HOUSE AND GET VERY EXCITED WHEN WE FIGURE OUT AND PUBLIC THAT PAPER. THE TIME WE SHOULD GET EXCITED IS SOMEONE COMES UP TO US IN A MEETING OR PUBLISHES ANOTHER PAPER THAT AGREES WITH WHAT WE FOUND. AND THOSE ARE THE THINGS THAT WE SHOULD BE STRIVING TO DO AND HAVE THOSE CONFIRMATORY STUDIES I THINK IN THE LITERATURE. THEY ARE UNDERAPPRECIATED AND UNDERVALUED. BUT I WOULD PROPOSE THAT THOSE CONFIRMATORY STUDIES ACTUALLY ARE JUST AS VALUABLE AS INITIAL STUDY THAT MAYBE FOUND A PHENOTYPE WITH A PARTICULAR GENE OR MICROBE. WHAT THIS IS INCUMBENT UPON US TO SHARE OUR MICE, AS A FIELD, AND REALLY TEST THIS IN DIFFERENT FACILITIES. WE FIND THE SAME THING, GREAT, IT REALLY THOSE IT'S ROBUST UNDER DIFFERENT CONDITIONS. IF WE DON'T THEN IT'S AN OPPORTUNITY TO FIGURE OUT WHY IS IT DIFFERENT, AND IS THERE A COMPONENT OF THE MICROBIOME THAT'S INFLUENCING THE PHENOTYPE. EITHER WAY, I WOULD SAY YOU CAN'T LOSE. AND WE SHOULD TRY AND EMBRACE THIS AS A FIELD. OKAY. WHAT I'M GOING DO IN THE SECOND HALF OF THE TALK IS JUST SHOW AN EXAMPLE OF HOW WE'RE BEGINNING TO LOOK FOR PHENOTYPES THAT ARE REPRODUCIBLE THAT WE'RE INTERESTED IN HOW THEN TO APPROACH THIS. EVEN HOW EVENTUALLY TO TRY AND TIE THINGS WE KNOW THAT ARE VARIABLE IN HUMANS, WHICH IS A DIFFICULT SYSTEM TO WORK IN, TO TRY AND MODEL THIS IN MICE. SO WHAT WE'RE INTERESTED IN IS THIS VARIATION IN HUMANS, IN RESPONSE TO INFLAMMATION AND INFECTION. I'M GOING TO FOCUS ON ONE PARTICULAR PATHOGEN, INFLUENZA, HERE. THIS IS A HIGHLY CONTAGIOUS VIRUS. HUGE GLOBAL BURDEN, HUGE NUMBER OF CASES OF MORBIDITY AND MORTALITY EVERY YEAR. THE INTERESTING THING IS THAT YOU CAN HAVE HUMANS, DIFFERNT HUMANS THAT ARE EXPOSED TO THE SAME STRAIN OF FLU, AND THERE'S VASTLY DIFFERENT RESPONSES TO THIS, FROM JUST A MILD UPPER RESPIRATORY INFECTION TO DEATH. AND SO WE'VE KNOWN THIS BUT WE DON'T REALLY UNDERSTAND WHY THIS IS THE CASE. THERE'S BEEN A NUMBER OF INTERESTING STUDIES THAT HAVE BEEN DONE IN MICE, BOTH IN ANTIBIOTIC-TREATED MICE AND GERM-FREE MICE, WHERE FLUIDS GIVEN AT A DOSE THAT KILLS 50% OF THE MICE, AND THEN WHEN YOU GIVE ANTIBIOTICS TO MICE IN THAT SAME FACILITY OR USE GERM-FREE MICE THEY ARE EXQUISITELY SENSITIVE TO THE SAME STRAIN AND DOSE OF FLU. INSTEAD OF KILLING 50% OF THE MICE YOU KILL NEARLY ALL OF THE MICE. SO THIS IS ACTUALLY REPLICATED NOW MULTIPLE TIMES IN MULTIPLE DIFFERENT LABS, PUBLISHED, AND IT'S BEEN SUGGESTED THERE'S A ROLE FOR THE INTESTINAL MICROBIOME OR MICROBIOME IN GENERAL, AND ACTUALLY MEDIATING THIS. THE QUESTION IS WHAT ACTUALLY -- WHAT IS IT, WHAT ACTUALLY IS THE COMPONENT IN MICROBIOME, AND HOW DO YOU GET AT THIS? SO OUR FIRST STEP WAS WE HAD A HYPOTHESIS THAT PERHAPS TYPE 1 INTERFERON SIGNALING WAS RESPONSIBLE FOR THIS. THERE MIGHT BE VARIATIONS IN TYPE 1 INTERFERON SIGNALING, IN PATIENTS, AND MAYBE WE COULD MODEL THIS. SO WHAT WE DID IS WE PICKED ON A MOLECULE CALLED INTERFERON RECEPTOR FRN 1 AND LOOKED AT KNOCKOUTS OF THIS GENE, IT BINDS TO INTERFERONS, THERE'S AMPLIFICATION DOWNSTREAM. WHEN YOU DO THE EXPERIMENT WITH CONTROL OR ANTIBIOTICS, NOW THERE'S NO DIFFERENCES IN EITHER MORBIDITY OR MORTALITY WITH THESE MICE. SO WE THINK THAT -- WE HAD THE IDEA THEN THIS WAS GOING TO BE DEPENDENT ON THIS PARTICULAR SIGNALING PATHWAY. HOW DO YOU THEN GO FROM HAVING THIS IDEA ABOUT A SIGNALING PATHWAY TO UNCOVERING WHAT THE MOLECULES ARE THAT ARE ACTUALLY DOING THIS. THIS IS OUR HYPOTHESIS. WE THOUGHT THERE WERE SPECIFIC MICROBIAL PRODUCTS THAT ACTUALLY MIGHT BE AFFECTING THE ENTERIC MIGHT ENTERIC MICROBIOME TO IMPACT INFLUENZA PATHOGENESIS. WHY METABOLITES? THIS IS ONE WAY, THERE ARE A NUMBER OF WAYS FOR MICROBIOME FOR FUNCTION. THESE ARE NICE BECAUSE THESE ARE SMALL MOLECULES INDUCED OR PRODUCED BY THE MICROBIOME, CAPABLE OF RAPID DIFFUSION, CAN PASS INTO THE BLOODSTREAM AND AFFECT DISTANT TISSUE. THESE ARE NICE BIOACTIVE MOLECULES TO THINK B THEY ALSO THEN ARE AGNOSTIC OF THE TYPE, THE STRAINS AND SPECIES OF MICROBES PRESENT IN THE INTESTINE. WE DID A SCREEN, WE TOOK A POOL OF METABOLITES SHOWN TO BE PROMINENT IN WILDTYPE MICE. AND THE NICE THING IS THEN THESE MOLECULES, MOST OF THESE WE COULD BUY FROM A CHEMICAL COMPANY LIKE SIGMA, AND WE DID A CELLULAR-BASED ASSAY. WE WERE INTERESTED IN TYPE 1 INTERFERON AND OBTAINED FROM MIKE HOLZMAN A REPORTER LINE ESSENTIALLY THAT READ OUT TYPE 1 INTERFERON SIGNALING. WE DID THESE METABOLITES ALONE AND IN COMBINATION WITH ESSENTIALLY MIMICKING AND AFFECTION WITH POLY IC OR ADDING TYPE 1 INTERFERONS, AND HAD A SIMPLE LUCIFERASE ASSAY. WE HAD A NUMBER OF HITS WITH THIS ASSAY, A NUMBER OF METABOLITES AND THIS INITIAL SCREEN SEEMED TO UPREGULATE THE ACTIVITY OF THE REPORTER, WHICH WE THOUGHT WAS EXCITING. AND THEN WE DID SECONDARY SCREENS WHERE WE WANTED TO LOOK FOR DOSE-RESPONSIVENESS, AND THINGS THAT MATCHED, METABOLITES THAT WERE PRESENT IN THE SERUM OF THESE MICE. AND FOUND ONE METABOLITE THAT REALLY PIQUED OR INTEREST, WHERE WE SAW THIS DOSE-RESPONSIVENESS, IN COMBINATION WITH TYPE 1 INTERFERON OR POLY IC, DESAMINOTYROSINE, FROM POLYPHENOLS OR FLAVANOIDS, KNOWN TO BE PRODUCED IN THE INTESTINE AND ENHANCES ACTIVITY IN VIVO WHICH I'M NOT GOING TO SHOW. THE BIG QUESTION, DOES TYROSINE PROTECT FROM INFLUENZA, WE COULD DELIVER THIS IN THE DRINKING WATER OF MICE, AND WE COULD GIVE PLUS OR MINUS DAT, AND PRIOR TO INFLUENZA, AND THEN MONITOR THE MICE OVER TWO WEEKS. AND TO OUR DELIGHT WHAT WE FOUND IN THESE EXPERIMENTS IS WHEN WE DELIVERED THIS SINGLE METABOLITE IN THE DRINKING WATER WE COULD PROTECT FROM DEATHS FROM INFLUENZA. SO THIS SINGLE METABOLITE PRODUCED WE THINK BY INTESTINAL MICROBES WAS ENOUGH TO PROTECTED. WE COULD TREAT FOR ANTIBIOTICS. THESE MICE ARE SUPER SENSITIVE TO INFLUENZA, WE COULD ADD DAT PRIOR TO INFLUENZA, AND WE SAW SIGNIFICANT PROTECTION, THE MAJORITY OF MICE WERE PROTECTED BY DESAMINOTYROSINE. WE THEN LOOKED INTO THE LITERATURE AND HAD BEEN -- THERE HAD BEEN INTEREST IN FLAVANOIDS IN THE '90s, MOSTLY BECAUSE THEY ARE IN RED WINE AND PEOPLE LOVE TO DRINK RED WINE. SO PEOPLE BEGAN STUDYING THESE AND LOOKING AT THE PHARMACOLOGY OF THESE, PHARMACOKINETICS OF THESE. AND THERE HAD BEEN A NICE SCREEN OF HUMAN MICROBES LOOKING FOR THE ABILITY TO DEGRADE FLAVANOIDS INTO DAT, ONE WAS CLOSTRIDIA, WE WERE ABLE TO COLONIZE MICE READILY WITH IT AND TESTED MICE THEN THAT WERE GIVEN ANTIBIOTICS, AGAIN SUPER SENSITIVE TO FLU, AND THEN EITHER COLONIZED WITH CLOSTRIDIUM OR CONTROLS INCLUDING ENTEROCOCCUS FECALIS. THE KEY NOW THE MICE THAT HAD RECEIVED, THESE MICE WERE PROTECTED FROM FLU. AGAIN, SO AGAIN THE CORRELATION HERE IS THAT DESAMINOTYROSINE IS A SINGLE METABOLITE THAT CAN PROTECT, AND THIS IS PRODUCED BY SINGLE. THIS ALSO IS DEPENDENT ON TYPE 1 INTERFERON. WE LOOK AT KNOCKOUT MICE, THEY WERE COLONIZED BUT NOT PROTECTED FROM DEATH FROM FLU. SUMMARY HERE, WHAT WE COULD DO IS TAKE A REALLY COMPLEX QUESTION, HAVE A CELLULAR SCREEN AND THE RIGHT POOL OF METABOLITES AND PULL OUT SOMETHING THAT WAS BIOACTIVE AND SEEN TO HAVE ACTIVITY BOTH IN VITRO AND IN VIVO. SO WE THINK THIS IS AN INTERESTING WAY TO CONVERT WHAT WE KNOW ABOUT THE MICROBIOME INTO FUNCTION. AND I THINK THIS IS SOMETHING THAT WE'RE GOING TO SEE NOW OVER AND OVER AGAIN IN THIS PARTICULAR FIELD. I WANT TO SAY THANKS TO THE PEOPLE IN MY LAB WHO DID THIS STUDY, ASHLEY STEED IS A CRITICAL CARE PEDIATRICIAN IN MY LAB WHO DROVE THIS. AND GERRI KAIKO CONCEIVED OF THIS DREAM AND DID IT. WITH THAT I'LL SAY THANKS. [APPLAUSE] >> WE'LL HAVE QUESTIONS AFTERWARDS. SO OUR NEXT SPEAKER IS MILDRED CHO, ASSOCIATE DIRECTOR OF THE CENTER FOR BIOMEDICAL ETHICS AND PROFESSOR AT THE DEPARTMENT OF PEDIATRICS AND MEDICINE AT STANFORD UNIVERSITY. THE LAST TEN YEARS SHE'S BEEN THE P.I. OF AN NIH-FUNDED CENTER OF EXCELLENCE, ETHICAL AND GENETICS AND LEGAL AND SOCIAL IMPLICATIONS OF RESEARCH, SPEAKING ON ETHICAL ISSUES IN HUMAN MICROBIOME RESEARCH AND BEYOND THE USUAL SUSPECTS. THANK YOU. >> THANKS. THANKS, CHRIS, FOR INVITING ME, AND LITA. SO I'M GOING TO TALK A LITTLE BIT ABOUT WHAT I THINK ARE CRITICAL GAPS IN THE PROGRESS OF HUMAN MICROBIOME RESEARCH FOCUSING ON TRANSLATIONAL ASPECTS, BRINGING THE KNOWLEDGE THAT WE'VE ALL HEARD ABOUT TODAY AND WILL BE HEARING ABOUT OVER THE NEXT COUPLE DAYS, TO BE ABLE TO APPLY IT TO HUMAN HEALTH. SO AS YOU'VE HEARD, WHEN HMP1 STARTED OUT AND THE FIELD WAS JUST GETTING GOING, THE INITIAL FOCUS WAS ALMOST EXCLUSIVELY AND STILL LARGELY THERE'S A LOT OF FOCUS ON CHARACTERIZATION AT THE GENOMIC LEVEL, THE WHOLE POINT OF THIS, THE STUDIES ALLOWED YOU TO CHARACTERIZE POPULATIONS AT THE GENOMIC LEVEL. THEREFORE THE ASSOCIATED ETHICAL, LEGAL AND SOCIAL IMPLICATIONS TENDED TO FOCUS ON THE COLLECTION AND USE OF DATA AND SAMPLES, NATURALLY. AND SO ETHICAL ISSUES THAT PEOPLE HAVE TALKED ABOUT OVER THE LAST SEVERAL YEARS RELATED TO HUMAN MICROBIOME RESEARCH RELATE TO THINGS LIKE RETURNING RESULTS TO HUMANS, DATA SHARING, OWNERSHIP, PROTECTING PRIVACY AND SO FORTH. THESE ARE ALL ISSUES THAT RELATE TO THE DATA AND THE SAMPLES, AND HOW DO YOU GET THEM, WHAT DO YOU TELL PEOPLE ABOUT THEM AND WHAT DO YOU DO AFTER YOU COLLECTED THEM. AS YOU'VE HEARD QUITE A BIT ABOUT, THERE'S BEEN A RAPID SHIFT FROM THE MORE OBSERVATIONAL STUDIES TO EXPERIMENTAL RESEARCH THAT INVOLVES INTERVENTIONS, THERE ARE HUNDREDS OF TRIALS CURRENTLY LISTED IN clinicaltrials.gov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n-OF-1 TYPE STUDIES. THERE'S ALSO THE GREAT POTENTIAL FOR SELF-SELECTION BIAS. THERE ARE ONLY CERTAIN KINDS OF PEOPLE WHO ARE INTERESTED IN DIY SCIENCE, OR PARTICIPATING AND WHO HAVE THE TIME TO ENGAGE IN THESE ACTIVITIES, SO THERE'S A BIG QUESTION ABOUT EQUITABLE ACCESS, TO PARTICIPATION AND RESULTS, AS WELL AS POTENTIAL FOR THERAPEUTIC MISCONCEPTION, CONFUSING CLINICAL PRACTICE AND EFFECTIVENESS WITH THE UNKNOWNS OF RESEARCH. SERIOUSLY CONFLICTS OF INTEREST, NOT THE FINANCIAL CONFLICT OF INTEREST WE TYPICALLY TALK ABOUT, BUT THE MORE THE KIND OF CONFLICT OF INTEREST WE THINK IF WE THINK ABOUT A DESPERATE PATIENT, FOR EXAMPLE, AND THEIR ROLE IN CONDUCTING RESEARCH AND ANALYZING DATA AS WELL AS LACK OF MECHANISMS OF ACCOUNTABILITY. WE ASSESS WITH RISKS AND BENEFITS, AUTONOMY AND JUSTICE. WE TYPICALLY THINK ABOUT THE INTEGRITY OF RESEARCH BY THINKING ABOUT WHETHER DATA AND MATERIALS ARE SHARED, WHETHER IT'S PUBLISHED AND DISSEMINATED, HOW RIGOROUS, IS IT REPRODUCIBLE, AND SO FORTH. BUT IT'S REALLY UNCLEAR HOW TO THINK ABOUT THESE PRINCIPLES AND WHETHER ANY OF THEM APPLY IN THE SITUATION OF PARTICIPANT ORGANIZED SCIENCE, DO THEY HAVE ANY OBLIGATIONS TO -- EVEN IF THEY WERE TO FIND SOMETHING THAT WAS VERY EFFECTIVE SUCH AS FMT FOR C. DIFFICILE, IS THERE ANY OBLIGATION TO DISSEMINATE THAT OR TO -- IN THE SPIRIT OF DUTY TO RESCUE FOR HELPING OTHER PEOPLE WITH THAT KINDS OF INFORMATION. OR ALSO ARE THERE ANY OBLIGATIONS TO MINIMIZING RISK TO PEOPLE WHO ARE GOING TO PARTICIPATE IN THAT KIND OF ACTIVITY. AND DOES INTENT MATTER. DOES IT MATTER WHETHER YOU'RE TRYING TO CURE YOUR OWN CHILD? OR JUST PLAYING AROUND IN YOUR KITCHEN? AND SO I'LL JUST FINISH UP BY SAYING THAT THIS AMBIGUITY OF OBLIGATIONS DOES HAVE REAL IMPLICATIONS FOR BEING ABLE TO DEVELOP AND ASSESS MICROBIOME-RELATED INTERVENTIONS, AND ALL WE'VE HEARD A LOT ABOUT SUCCESSFUL CLINICAL STUDIES HERE TODAY, SOMETIMES THESE CAN GO NOT SO WELL, AS DESCRIBED IN THIS PAPER OF A CLINICAL STUDY IN WHICH THEY RECRUITED 150 INDIVIDUALS TO RECEIVE FMT INTERVENTION, AND AT THE END ONLY HAD THREE PEOPLE WHO COMPLETED THE TRIAL. AND PART OF THE WAY THROUGH, AS THEY WERE ELIMINATING PEOPLE IN THIS TRIAL, THEY FOUND THAT MANY OF THEM BASICALLY MANY POTENTIAL PARTICIPANTS LIED ABOUT CRITERIA THAT MEANT THEY WERE EVENTUALLY -- HAD TO BE ELIMINATED FROM THE STUDY, OR THEY WERE DECEPTIVE IN OTHER WAYS OR BROKE PROTOCOL AFTER BEING ENROLLED. IN THE END THEY ONLY HAD DATA FROM THREE SUBJECTING, PART IS AN ESPECIALLY ACUTE PROBLEM FOR AREAS OF RESEARCH SUCH AS MICROBIOME RESEARCH WHERE THERE ARE OTHER AVENUES IN WHICH PEOPLE CAN TRY TO GET AT WHAT THEY WANT, OR WHAT THEY THINK THEY WANT, TREATMENT OR PARTICIPATION IN STUDIES. TO CLARIFY THE ETHICAL OBLIGATION OF ALL PARTICIPANTS IN ORDER TO FACILITATE REAPING BENEFITS IN A JUST WAY. THANKS. [APPLAUSE] >> WE HAVE TIME FOR SOME QUESTIONS, IF ANYBODY HAS QUESTIONS. DON'T FORGET YOU CAN SEND QUESTIONS IN ONLINE TOO. >> I'M DECIDING IF I SHOULD ASK THE QUESTION ABOUT THE BEAUTIFUL INTERFERON STORY, OR THE ETHICS ONE. I'D LIKE TO ASK ABOUT THE SECOND. THAT'S THAT I'M SO GLAD THIS TOPIC IS AT THIS MEETING. WE THINK OF THIS AS UNNECESSARY BECAUSE WE PRESUME ETHICALITY TO OUR ACTIVITIES BUT YOU POINT OUT THE COMPLEXITY OF THAT. MY QUESTION TO YOU, AS AN ETHICIST, IT SEEMS CULTURALLY WE'RE AT A TIME WHEN THE BELIEF OR EVALUATION OF ETHICS IS AT A NADER, WHAT IS THE APPROACH THOSE IN THE ETHICS COMMUNITY ARE THINKING ABOUT TO RAISE THE CONVICTION, THE IMPORTANCE OF ETHICS? >> THAT'S A GOOD QUESTION. I WAS THINKING ABOUT THAT IN TERMS OF HOW ONE MIGHT TRY TO INCREASE MOTIVATION OF PEOPLE TO THINK ABOUT ETHICS AS THEY ARE PARTICIPATING IN RESEARCH, ALSO PARTLY BECAUSE OF THIS IDEA IT'S NOT JUST SORT OF PEOPLE WHO HAVE TO TAKE REQUIRED COURSES, YOU KNOW, THAT ARE -- THAT GET NIH FUNDING IN RESPONSIBLE RESEARCH, BUT IT'S ALSO POTENTIALLY PATIENTS AND PHYSICIANS AND OTHER PEOPLE WHO ARE NOT TYPICALLY KIND OF IN THE FOLD OF THE TRADITIONAL SCIENTIFIC COMMUNITIES THAT ALSO NEED TO BE CONSENTED, AND SO I DON'T KNOW WHAT THOSE INCENTIVES ARE, BUT THINKING ABOUT ETHICS, NOT SO MUCH IN TERMS OF REGULATION, BUT IN TERMS OF SETTING UP SYSTEMS SO THEY CREATE INCENTIVES FOR PEOPLE TO THINK ABOUT ETHICS AND WHAT IT MEANS TO DO THE RIGHT THING. MAYBE SOMETHING THAT MIGHT BE MORE EFFECTIVE. >> HI. I AGREE THAT I WISH I WOULD GET TWO QUESTIONS, ONE FOR EACH OF YOU, THOSE WERE FABULOUS TALKS. I'M GOING TO ASK A QUESTION BECAUSE I THINK IT'S A PART OF WHAT YOU YOU WERE TALKING ABOUT, DR. CHO, WHICH IS SO HOW DOES IT CHANGE IT IF RESEARCH IS BEING CONDUCTED ON THE GROUP WHO ARE ANALYZING THE DATA, LIKE IF PEOPLE USED LAB MEMBERS, OR IF THEY USED THEMSELVES, OR IF THEY USED THEIR CHILDREN, BECAUSE THAT SEEMS TO ME KIND CAN OF A BLUR THAT YOU WERE SORT OF TALKING ABOUT THERE IN THE CONTEXT OF CLINICAL BUT THAT ALSO COULD BE APPLICABLE TO RESEARCH STUDIES. >> YEAH, SO THIS IS SORT OF THE CONFLICT OF INTEREST, THAT'S ONE OF THE POTENTIAL CONFLICTS OF INTEREST. I KNOW THAT WE'VE HAD -- THERE'S TYPICALLY A SENSE THAT PHYSICIANS SHOULD NOT PRACTICE ON THEIR FAMILY MEMBERS, FOR EXAMPLE. AND THAT'S PARTLY BECAUSE, YOU KNOW, OF THE POTENTIAL THAT YOU WON'T BE AS OBJECTIVE, AND SO I THINK THOSE SAME KINDS OF CONSIDERATIONS APPLY TO DOING RESEARCH ON YOUR COLLEAGUES OR EVEN ON YOURSELF. SO YOU MAY BE, YOU KNOW, EITHER OVERESTIMATING OR UNDERESTIMATING RISKS OR BENEFITS OR GET TOO WEDDED TO A HYPOTHESIS OR SO FORTH, AND SO I THINK SO SCIENCE HAS MECHANISMS TO DEAL WITH THAT SUCH AS PEER REVIEW AND, YOU KNOW, DSMVs, IT MAY MAKE THOSE THINGS MORE ACUTELY REQUIRED, BUT I THINK WHEN YEAR TALKING ABOUT DESPERATE PATIENTS, I THINK THAT'S JUST -- THAT'S JUST A BAD SETUP, FROM THE GET-GO. SO I THINK THAT AGAIN MAYBE THE MECHANISMS OF SCIENCE THAT ENCOURAGE COLLABORATION AND PEER REVIEW AND HAVING OTHER PEOPLE GET INVOLVED IS ONE OF THE MECHANISMS THAT COULD BE TRANSFERRED OUTSIDE THE LAB. >> A QUESTION FOR DR. STAPPENBECK. THE 80-ODD METABOLITES, WERE THEY FROM FLUID-INFECTED MICE OR WHERE DID IT COME FROM? >> SORRY, YEAH, I BLEW THROUGH THAT. THIS IS A STUDY WHERE THE GROUP ON TARGETED METABOLOMICS, EARLY DATA, 2012 PAPER, SO THEY TOOK GERM-FREE MICE AND GERM-FREE MICE COLONIZED WITH BASICALLY NORMAL MICROBIOME FOR MICE AND THEY BASICALLY LOOKED FOR METABOLITES THEN THAT WERE ENRICHED IN THE PRESENCE OF MICROBES. AND SO THIS WAS A STARTING POINT FOR US, FOR THIS PARTICULAR STUDY. >> IT LEADS TO POTENTIAL FOR MANY MORE. 83 IS NOT A LARGE NUMBER. >> OH, YEAH. >> THAT'S ONE WAY TO DO THE EXPERIMENT BUT FLUID INFECTED VERSUS NON-FLUID INFECTED COULD BE INTRIGUING, FIND METABOLITES AND GO THAT ROUTE. POTENTIALLY THERE'S A WHOLE NUMBER OUT THERE. >> EXACTLY. >> WHAT ARE YOUR THOUGHTS? >> I WOULDN'T SAY THIS IS THE ONLY METABOLITE. IT EXPLAINS I THINK THE MOUSE STORY VERY NICELY BUT LOOKING AT HUMAN-TO HUMAN METABOLOMES WOULD BE INTERESTING, WOULDN'T SURPRISE ME IN SOME METABOLITES INHIBIT. >> ARE YOU TAKING THIS WHEN FLU SEASON ROLLS AROUND, IN THE SPIRIT OF SCIENCE? >> YOU HAVE TO HAVE THE RIGHT BUG. WE ONLY KNOW ONE BUG. THE KEY IS TO FIND THE MACHINERY WITHIN THIS MICROBE THAT CAN MAKE DESAMINOTYROSINE AND SEE WHAT OTHER MICROBES ACTUALLY HAVE THIS. AGAIN, IT WOULDN'T SURPRISE ME IF THIS IS THE ONLY BUG. BUT THIS IS REALLY EARLY PHASE FOR THIS WORK. >> HI, DR. CHO. LITA PROCTOR. YOU DIDN'T ADDRESS DIRECTLY BUT MENTIONED GROWTH OF COMPANIES, STARTUPS AND OTHERWISE. AND IT HAS TO DO WITH WHO OWNS THE MICROBES. THERE'S THIS NOTION THAT, YOU KNOW, WE ALL HAVE OUR OWN UNIQUE MICROBIOME, RIGHT? IF YOU WANT TO MAKE A PRODUCT OR SOMETHING OUT OF IT, YOU KNOW, CAN YOU CASH OUT ON THAT? IT CAME OUT EARLY ALSO IN THE FIELD WHEN PEOPLE WERE GOING TO THESE REMOTE COMMUNITIES LIKE THE BRAZILIAN INDIANS COLLECTING MATERIALS, THERE'S THE ENTIRE ISSUE OF EVEN TRYING TO COMMUNICATE WITH THEM ABOUT WHAT YOU'RE DOING, WHY THAT AFFECTS SOCIETY, THEM, AND SO ON. AND THEN THERE ARE OTHER PEOPLE TRYING TO GO TO REMOTE COMMUNITIES TO COLLECT, YOU KNOW, ARCHETYPAL MICROBIOMES IN ORDER TO DISCOVER THESE NEW MOLECULES OR NEW MICROBES. ON THE OTHER HAND, THERE'S THE OTHER SIDE OF THIS STORY WHERE THE CONCEPT IS THERE'S MICROBES ARE EVERYWHERE AND THE ENVIRONMENTAL SELECTS, NO SUCH THING AS PERSONALIZED BIOME. WHAT'S YOUR COMMUNITY DISCUSSING, WHO OWNS, WHO SHOULD BENEFIT FROM ANY PRODUCTS, INTERVENTIONS, SO ON? >> YEAH, THAT WAS A GREAT QUESTION. I THINK ON THE ONE HAND, THE FACT THAT, FOR EXAMPLE, EVERYBODY'S INDIVIDUAL MICROBIOME IS -- IT'S NOT SOMETHING YOU CAN STANDARDIZE. IT FLUCTUATES IN TIME AND SPACE. SO IN TERMS OF THINKING ABOUT PACKAGING HUMAN MICROBIOMES AS PRODUCTS, THAT'S SORT OF A NON-STARTER. AND SO ON THE ONE HAND, THAT MAKES IT HARD TO SORT OF ENVISION SORT OF COMMERCIALIZATION PATHWAYS THAT ARE VIABLE, BECAUSE YOU TYPICALLY NEED TO HAVE SOMETHING THAT'S PRETTY STANDARDIZED, THAT YOU CAN EVALUATE, THAT'S REPLICABLE IN DIFFERENT ENVIRONMENTS. SO ON THE OTHER HAND, THAT'S MAYBE A GOOD THING, BECAUSE THEN THE -- THERE CAN'T BE SORT OF MONOPOLY OWNERSHIP OVER IT. IT'S HARD TO THINK ABOUT HOW TO PATENT, YOU KNOW, SOMEBODY'S MICROBIOME. OR EVEN ASPECTS OF A MICROBIOME OR A PROCESS THAT INVOLVES MICROBIOMES BECAUSE IT'S SO VARIABLE. IT DOESN'T FIT WELL INTO OUR PARADIGMS OF INTELLECTUAL PROPERTY, AND SO FORTH, BUT THAT CUTS BOTH WAYS. ON THE ONE HAND, THAT IS SORT OF WHAT INCENTS COMPANIES TO MOVE FORWARD CAN DEVELOPING PRODUCTS. ON THE OTHER HAND -- YOU KNOW, THE WIDE ACCESSIBILITY OF IT MAY BE THAT, YOU KNOW, IT CAN KIND OF THROW IT OPEN TO DIFFERENT COMMUNITIES TO FIGURE IT OUT. WITHOUT HAVING TO DEAL WITH OWNERSHIP ISSUE. BUT THAT DOES SORT OF RAISE THE OTHER QUESTIONS OF IF IT'S NOT STANDARDIZABLE, HOW CAN IT BE REPEATED. >> RIGHT, RIGHT. PEOPLE ARE APPARENTLY GOING TO AIRPORTS NOW, AND SAMPLING THE SEWAGE -- PUMP SEWAGE, BECAUSE AIRPORTS NOW SAMPLE ALL THESE POPULATIONS FROM ALL OVER THE WORLD AND THEY GO TO THE REALLY LARGE AIRPORTS AND THEY TAKE THE BILGE AND TRY TO ISOLATE EXOTIC BUGS. THE IDEA IS NO ONE OWNS THIS BECAUSE IT'S A WASTE PRODUCT. >> RIGHT. WELL, LEGALLY WASTE IS NOT OWNED. >> RIGHT. RIGHT. THE MINUTE IT LEAVES YOUR BODY, RIGHT. >> YOU LEGALLY DON'T OWN IT. >> RIGHT. THE REASON I JUMPED, MATT HENN IS HERE SOMEWHERE. SO I THINK HE TOLD US, I DON'T WANT TO MISREPRESENT THE PROJECT, I THOUGHT HE TOLD US THEIR SERIES PRODUCTS WERE ANAEROBES, CLOSTRIDIUM AND SO FORTH, I WANTED TO HEAR HOW THEY WERE DEALING WITH THE ISSUE OF WHO OWNS THE MICROBIOMES IN THE PRODUCT THEY ARE NOW TRYING TO MARKET. I THOUGHT MATT WAS HERE. I SAW HIM EARLIER. OKAY. ANY OTHER PERSON FROM A COMPANY THAT WANTS TO ADDRESS THAT IN GENERAL? OH, HERE WE GO. HERE IS SOMEBODY. >> I'M NOT AT A COMPANY BUT I HAVE WORKED IN A COMPANY BEFORE. NORMALLY THIS IS REGULATED BY THE CONVENTIONAL BIOLOGICAL DIVERSITY WHERE ALL THE COMPANIES ASSIGNED WITH A RIGHTS TO GENETIC MATERIAL WITHIN THE COUNTRY BELONGS TO THE COUNTRY AND INDIVIDUAL AGENCIES WHICH GIVE THE RIGHTS TO SOMEONE. HOWEVER, SEVERAL COUNTRIES, NORTH KOREA, IRAQ AND THE U.S., THEY NEVER SIGNED THIS. IN THE U.S. IT MEANS YOU OWN THE PROPERTY, YOU OWN THE GENETIC MATERIAL, THE RIGHTS FOR THIS MATERIAL. THOUGH IT'S REGULATED BY COMPANY. INTERESTINGLY YOU MENTIONED THE AIRPORT, I DON'T KNOW HOW THIS WOULD BE REGULATED, YOU GIVE YOUR RIGHTS AWAY BY VISITING ANOTHER COUNTRY? I DON'T KNOW. >> I HAD A QUICK ADDITION FROM AN EXAMPLE IN AGRICULTURE WHERE THERE'S NOT REALLY ABLE TO PATENT A MICROBE, BUT THEY ARE ABLE TO PATENT THE PROCESSES TO GET TO THAT PRODUCT. SO SOME TYPE OF EXTRAVAGANT PROCESS THAT BRINGS A MICROBE TO STABILITY, PUT ANYTIME A IT IN A PRODUCT TO BE SHELF STABLE, LOG UP THE IP FOR THE PATENT AGENCY BUT YOU'RE NOT GOING TO BE ABLE TO OWN THE MICROORGANISM. >> YOU COULD OWN COMBINATIONS OF MICROORGANISMS. THERE IS INTELLECTUAL PROPERTY HERE. YOU'RE GOING TO HAVE COMPANIES MARKETING THEIR SELECT COMBINATION TO ADDRESS YOUR PARTICULAR PROBLEM. IF YOU HAVE IBD, IT WILL BE THIS COMBINATION OF MICROBES THAT'S BEST. IF YOU HAVE SOMETHING ELSE, IT WILL BE THAT COMBINATION. AND SO THERE WILL BE PROPERTY THAT WILL BE OWNED, IT WILL BE LIKELY COMPOSITION -- COMBINATIONS OF COMPOSITION. >> ONE MORE QUESTION. >> WE HAVE TIME FOR MORE? GREAT SESSION. I'D LIKE TO RETURN TO SOME OF THE DISCUSSION ON THE MOUSE RESEARCH. I THINK THE POINT YOU MADE ABOUT TESTING EXPLICITLY FOR FACILITY EFFECTS IS IMPORTANT, AND MAYBE IT SHOULD BE THOUGHT OF AS A CRITICAL COMPONENTS OF PRE-CLINICAL RESEARCH, EXCUSE ME PRE-CLINICAL TRIALS. THAT BEING SAID I WONDER IF YOU HAVE THOUGHTS ABOUT HOW SOME INFRASTRUCTURE COULD POTENTIALLY BE ESTABLISHED THAT ALLOWS INVESTIGATORS TO EXPLICITTY TEST FACILITY EFFECTS GIVEN YOUR AVERAGE RO1 IS NOT GOING TO COVER ALL THE MOUSE RESEARCH IN YOUR OWN FACILITY. >> THAT'S A FANTASTIC QUESTION. AND I THINK THIS REQUIRES -- AGAIN, THIS REQUIRES LIKE ALL LEVELS BASICALLY TO RECOGNIZE THIS. I THINK THESE ARE EXPENSIVE EXPERIMENTS, AND THEY ARE NON-TRIVIAL TO DO. AND WHEN THEY ARE DONE, THEY NEED TO BE RECOGNIZED AS NON-TRIVIAL. THEY NEED TO BE FUNDED. AND THEN WHEN THEY -- WHEN WE GET RESULTS, THEY NEED TO BE PUBLISHABLE IN GOOD JOURNALS. I THINK THAT WE HAVE THESE METRICS THAT WE ALL GO BY LIKE HOW MANY TIMES OUR PAPERS ARE CITED. I THINK IF YOU DO A FOLLOW-UP STUDY CONFIRMATORY MAYBE YOU SHOULD GET 2X POINTS OR SOMETHING LIKE THAT. SOMETHING RADICAL. BUT IT WOULD REALLY SAY THOSE PAPERS ARE IMPORTANT AND WE REALLY VALUE THOSE PAPERS WHERE WE'RE TRYING TO ACTUALLY SHOW A REPRODUCIBILITY. OTHERWISE, I THINK WE'RE IN A POSITION WHERE IF WE GET IN A POSITION WHERE WE CAN'T REPRODUCE OUR WORK, NO ONE IS GOING TO BELIEVE US, NO ONE IS GOING TO FUND IT. PHARMA IS GOING TO STOP LISTENING TO US. AND THEY ARE NOT GOING TO CARE ABOUT WHAT WE SAY BECAUSE IT'S JUST A BIG HOUSE OF GABLES OR MORASS. >> I'LL LET LITA DECIDE IF WE HAVE TIME FOR QUESTIONS. >> TO CONTINUE THAT DISCUSSION, THERE'S ANOTHER EXAMPLE THAT -- OH, SARAH FROM HEART, LUNG AND BLOOD INSTITUTE. ANOTHER EXAMPLE IS WHERE YOU OBTAIN THE MICE. YOU KNOW, THERE WAS AN EXAMPLE WHERE A POSTDOC COULDN'T REPRODUCE THE WORK OF ANOTHER POSTDOC. BUT IT TURNED OUT TO BE THEY HAD OBTAINED THE MICE FROM ANOTHER VENDOR, UNTIL THEY (INDISCERNIBLE) MICE IN THE SAME FACILITY COULDN'T GET THE SAME RESULTS. TURNED OUT IT WAS THE MICROBIOTA. >> THERE ARE SEVERAL NICE EXAMPLES, DIFFERENT VENDORS WILL SHOW DIFFERENT RESULTS. ANN LIPPMAN'S TH-17 WORK IS A NICE EXAMPLE, THAT LED TO THE DISCOVERY OF A SPECIFIC MICROBE THAT WAS STIMULATING THIS PARTICULAR ELEMENT OF THE IMMUNE SYSTEM. AGAIN, I THINK WHEN WE FIND DIFFERENCES FROM DIFFERENT FACILITIES OR DIFFERENT VENDORS, WE NEED TO EMBRACE IT AND ACTUALLY -- I CAN'T READ THAT. AND THEN WE -- BUT AGAIN I THINK IT'S AN OPPORTUNITY TO FIGURE OUT WHY THIS IS HAPPENING. AND I THINK THERE ARE EXAMPLES IN THE LITERATURE FOR THAT. I THINK IT'S AN OPPORTUNITY BASICALLY. >> AND YOU HAVE BEEN REPORTING A LOT OF BEST PRACTICES, REPORTING THINGS, AND ONE OF THE THINGS THAT I'VE NOTICED A WHOLE LOT OF TIMES NOT REPORTED IS WHAT KIND OF DIET THE ANIMALS ARE ON, AND TO ENCOURAGE PEOPLE TO USE OPEN SOURCE DIETS, RATHER THAN RAT CHOW, OR PURIFIED DIETS. THEY SHOULD BE USED, AND WHAT IS USED SHOULD BE REPORTED, IT COULD INFLUENCE REPRODUCIBILITY. >> EXACTLY. WATER, HUSBANDRY CONDITIONS, EVEN AMOUNT OF BEDDING THAT'S IN THE CAGE IS REALLY CRITICAL. THE TEMPERATURE OF THE MICE IS REALLY CRITICAL. WE'VE BEEN FREEZING IN HERE ALL DAY SO OUR GLUCOCOURT CONTESTANTS CORTICOIDS ARE UP. THESE MATTER TO HUSBANDRY, ALL THESE THINGS NEED TO BE REPORTED. THEY COULD EXPLAIN DIFFERENCES BETWEEN FACILITIES. >> THEY ARE GOING TO STAY UP HERE AND THE OTHER SPEAKERS WILL IS THAT RIGHT, LITA? >> (INAUDIBLE). >> IT'S NICE TO SEE PEOPLE STILL IN THE ROOM. REMEMBER PEOPLE ARE STILL ONLINE WATCHING YOU IN HIGH DEFINITION. YOU ALL LOOKED REALLY GOOD, BY THE WAY. I LOOKED AT IT ONLINE. I'M A PROGRAM DIRECTOR IN NIGMS, THE NSF OF NIH. IT'S HOW I PERSONALLY THINK ABOUT IT. I'VE BEEN CHARGED WITH LEADING A ROUNDTABLE DISCUSSION, THE TWO PROBLEMS IS FIRST OF ALL THERE ISN'T A ROUNDTABLE. [LAUGHTER] THE SECOND, BEING AT THE END OF A VERY LONG DAY, ESPECIALLY FOR THOSE WHO TRAVELED TODAY ALSO THIS WOULD HAVE BEEN SO MUCH EASIER FOR ME IF EVERYBODY HAD A BEER OR WINE IN THEIR HAND AT THIS MINUTE. YOU CAN IMAGINE, YOU CAN PLAY ALONG. I'D LIKE TO DO ONE PIECE OF CITIZEN SCIENCE RIGHT NOW. THAT IS TO TAKE A POLL. PLEASE RAISE YOUR HAND IF AS A RESULT OF A TALK TODAY OR CHATTING WITH SOMEBODY AT A POSTER, YOU HAVE INITIATED A NEW COLLABORATION OR YOU THINK THAT YOU WILL INITIATE A NEW COLLABORATION? THAT'S WONDERFUL. EVERYBODY ONLINE? THERE IS ANOTHER SEVEN HANDS THAT JUST WENT UP. THAT'S VERY GOOD. I HONESTLY DIDN'T EXPECT THAT. THAT'S WONDERFUL. SO MOST OF YOU TODAY DID A VERY GOOD JOB OF ADDRESSING WHAT WE'VE ASKED YOU TO ADDRESS, WHICH IS CRITICAL NEED OR GAP. SO ON BEHALF OF ALL OF THE ORGANIZERS, I THANK YOU PERSONALLY AND PROFESSIONAL FOR DOING THAT. HOPEFULLY THIS IS GOING TO BE SUSTAINED FOR THE NEXT TWO DAYS. PLEASE CONSIDER THOUGH IF IT'S APPROPRIATE TO LEAD OR PUT IT MUCH EARLIER IN YOUR TALK, THE SLIDE WITH THE CRITICAL NEED OR GAP, BECAUSE THERE WAS A HANDFUL OF TALKS WHERE IT WAS THE LAST SLIDE, AND IT WAS UP THERE FOR SOMETIMES LITERALLY TEN SECONDS. OKAY? SO FOR THOSE WHO ARE IN THE ROOM OR WATCHING ONLINE WHO WILL TALK THE NEXT TWO DAYS, PLEASE CONSIDER THAT. ALL RIGHT. WHAT I'M GOING TO DO IS NOW STEP BACK BECAUSE THIS IS YOUR MEETING, AND I'D LIKE TO INVITE EVERYBODY WHO FEELS LIKE ASKING A QUESTION TO ANY OF THE SPEAKERS FROM TODAY TO PLEASE GRAB A MIC AND ASK. IF YOU CAN, TRY TO DO IT IN A BIG PICTURE WAY. RIGHT? IF YOU ASK A VERY HIGHLY SPECIFIC QUESTION, ONE PARTICULAR SPEAKER, IT DEFEATS THE PURPOSE OF THE NON-ROUNDTABLE ROUNDTABLE. >> THERE ARE TWO OF US RUNNING MICS, THERE ARE TWO STANDING MICS, AND SPEAKERS HAVE THE MICS I JUST LIFTED FROM THE TABLE. SO MAYBE IT'S STILL IN MY MIND, THAD JUST SPOKE IN THE LAST SESSION, THE POINT ABOUT THE RULE OF MICROBIOME IN PHENOTYPES, THIS AUDIENCE REALLY APPRECIATES IT BECAUSE THEY HAVE SEEN IT CLOSELY. WHAT I HAVE OBSERVED IN MY ROLE AS EDITOR IS SOME THIS, YOU HAVE TO GO OUT AND EVANGELIZE TO YOUR COLLEAGUES IN FIELDS WHERE THE ROLE OF THE MICROBIOME IS NOT APPRECIATED AND HAS PROFOUND ROLE AND SOMETIMES NOT RECOGNIZED. SO ESPECIALLY MOUSE STUDIES. SO, THAD, MAYBE YOU CAN TAKE THAT. >> THIS IS THE FIRST TIME I TALKED ABOUT THIS. I'VE TALKED IN MANY FORUMS, PEOPLE GET SO ANGRY WITH ME, YOU KNOW, IT WILL GO ON FOREVER AND USUALLY IF THERE'S ALCOHOL IT'S EVEN WORSE. SO-- BECAUSE -- AND AGAIN I THINK LAKSHMI IS RIGHT, EVERYONE IN THE ROOM APPRECIATES THIS. WE HAVE TO CONVINCE OUR COLLEAGUES IN OTHER FIELDS. I THINK IT'S REALLY INCUMBENT ON US, AND I THINK -- I LIKE THE WORD AMBASSADOR. I THINK THAT'S WHAT WE NEED TO BE. >> I'M TOM FROM OREGON STATE UNIVERSITY. EVERY SPEAKER MIGHT HAVE AN OPINION. I THINK THE HISTORY OF SCIENCE IS LITTERED WITH REVOLUTIONARY FINDINGS THAT RESULT FROM CHALLENGING ASSUMPTIONS, THE MICROBIOME IS A RIDICULOUSLY COMPLEX SYSTEM AS WE'VE SEEN TODAY THROUGH MANY DISCUSSIONS. AND WHEN WE STUDY THE MICROBIOME, WE CONSEQUENTLY MAKE SIMPLIFYING ASSUMPTION TO UNDERSTAND WHAT'S GOING ON. I'D LIKE TO KNOW WHAT THE SPEAKERS THINK SENTENCE MOST SIGNIFICANT SIMPLIFYING ASSUMPTION WE'RE CURRENTLY MAKING WE SHOULD TRY TO EMBRACE AND DESTROY TO IMPROVE OUR UNDERSTANDING OF THE MICROBIOME. >> I THINK THE COMMUNITY AS A WHOLE OFTEN ASSOCIATES ASSOCIATION WITH CAUSATION, AND I THINK WE HAVE TO WATCH OUT FOR THAT. THE EARLY DAYS OF MICROBIOME RESEARCH, THAT SEEMED TO SHOW PROMINENTLY. I THINK WE PROBABLY HAVE TO BE A LITTLE CAREFUL ABOUT OUR LANGUAGE, WOULD HELP I THINK MITIGATE SOME OF THAT. THAT WOULD BE PROBABLY THE NUMBER ONE THING I KEEP SEEING POP UP. WELCOME TO HEAR OTHER PEOPLE'S THOUGHTS. >> ONE OF THE OTHER THINGS WHICH HAS COME UP A BIT IS THE IMPORTANCE OF GETTING BEYOND SPECIES OR BELOW SPECIES, BECAUSE SO MANY TRAITS OF BACTERIA DO NOT MAP WELL ON SPECIES. WE KNOW BECAUSE OF HORIZONTAL GENE TRANSFER WE HAVE HAVE TRAITS THAT ARE A LOT OF FUNCTIONAL REDUNDANCY AND IN ADDITION TO THAT WE CAN HAVE A LOT OF HETEROGENEITY THAT WE CAN'T DETECT TAXANOMICALLY, AND OF COURSE WE ALSO HAVE PHENOTYPIC HETEROGENEITY. >> I'M REPRESENTING THE ET SOCIAL MEDIA TEAM, JEN FROM VTU, THE FIRST FROM JULIANNA, TWEETED OUT EARLIER. THE QUESTION WAS DURING THE KEYNOTE FOR HOWARD OCHMAN'S TALK, WHY IS GYRASE A GOOD TARGET FOR PHYLO TAGS, AND FOLLOW-UP QUESTIONS ABOUT WHAT PROPORTION OF THE HUMAN MICROBIOME CAN'T BE CLASSIFIED, WHAT PROPORTION ARE WE MISSING USING A NUMBER OF TECHNIQUES DISCUSSED TODAY? >> I WON'T SPEAK TO GYRASE SPECIFICALLY, MAYBE HOWARD WANTS TO. BUT I THINK THERE'S QUITE A FEW PROTEINS THAT ARE GOOD TAXANOMIC MARKERS. THE SECOND QUESTION I THINK IS MORE IMPORTANT, ABOUT WHAT WE'RE MISSING. I'LL JUST RECALL A SLIDE FROM MY TALK ABOUT WHAT'S -- IF WE ARE INTERPRETING OUR DATA IN THE CONTEXT OF WHAT WE ALREADY KNOW FROM THINGS WE'VE SEQUENCED BEFORE, THE ANSWER IS MOST, WE'RE MISSING MOST. THAT VARIES DEPENDING ON WHAT ENVIRONMENT WE'RE STUDYING. SINCE WE TALKED ABOUT ETHICS AT THE END TODAY JUST TO MENTION THAT THERE ARE BIASES BASED ON CERTAIN POPULATIONS OF PEOPLE, PARTICULARLY NORTH AMERICAN AND EUROPE, DOMINATE WHAT WE KNOW. AND IT'S NOT CLEAR HOW THAT'S GOING TO PLAY OUT AS WE GET GENOMES FROM MORE DIVERSE GROUPS OF PEOPLE. I THINK THAT'S REALLY IMPORTANT FROM THE PERSPECTIVE OF UNDERSTANDING KNOWLEDGE AND IMPORTANT ETHICALLY THAT WE GET GENOMIC -- WHOLE GENOMES FROM MORE DIVERSE ENVIRONMENTS INCLUDING MORE DIVERSE TYPES OF PEOPLE. >> (INAUDIBLE). >> YEAH, GOOD POINT. I AGREE WITH WHAT MIKE SAID. MOSTLY BACTERIA. THE POOR MICROBIAL EUKARYOTES ARE SUPER IMPORTANT. DID YOU WANT TO ELABORATE? >> NO. [LAUGHTER] >> (INAUDIBLE). >> YEAH, TOTALLY. ESPECIALLY THE FISH. >> OKAY. I HAVE COMMENTS ON TWO THINGS. ONE IS THIS (INDISCERNIBLE) QUESTION, MANY PEOPLE ASSUME THAT YOU CAN ONLY STUDY THOSE BACTERIA IF YOU CAN CLASSIFY THEM. YOU CAN GIVE THEM A NAME. BUT THIS IS ACTUALLY A MISCONCEPTION. WHEN YOU HAVE A UNIQUE SEQUENCE, YOU KNOW IT'S REPRESENTS BIOLOGICAL ENTITY, NO MATTER YOU CANNOT GIVE A NAME OR NOT, YOU CAN STILL WORK ON IT. YOU CAN STILL DO STATISTICS, ALL KINDS OF CHARACTERIZATION. THAT'S THE PURPOSE OF SEQUENCING, IF YOU'RE ACTUALLY WORKING ON THE SEQUENCE. I DON'T THINK WE -- MANY PEOPLE WORK ON CLASSIFIED SEQUENCES, AND THEY DISCARD THE REST UNCLASSIFIED SEQUENCES. SO THAT'S PROBABLY, YOU KNOW, THAT'S ONE COMMENT. ANOTHER COMMENT IS WE CAN NOW WORK ON TO STRING LEVELS, BECAUSE WE IS ASSEMBLE HIGH QUALITY THROUGHOUT GENOMES OF BACTERIA, PARTICULARLY FROM INTERVENTIONAL TRIALS. THE QUESTION, ANY SINGLE STRAIN, IF IT'S SHARED BY MORE THAN 20% OF SAMPLES WOULD BE ALREADY CONSIDERED PREVALENT BACTERIA BUT YOU HAVE A LOT OF ZEROES IN YOUR DATASET, IN MANY OF THE INDIVIDUALS. AND SO I THINK WE SHOULD INTRODUCE THE CONCEPT OF (INDISCERNIBLE) WHERE YOU LOOK AT THE CO-OCCURRENCE OF INDIVIDUALS, AND IN ONE OF THOSE STUDIES WE SHOWED YOU CAN ACTUALLY IDENTIFY ABOUT 10 TO 20 AMONG 200 STRINGS, AND THEN EACH GUILD, THE MEMBERS INCREASE OR DECREASE TODAY. THEY CAN BE FROM VERY DIFFERENT PHYLA BUT THEY WORK TOGETHER. SO THEN IF YOU GET ABUNDANCE AT THE GUILD LEVEL THEY CAN CORRELATE WITH HOST DISEASE PHENOTYPES VERY NICELY BUT INDIVIDUAL STRINGS CANNOT. SO PROBABLY I THINK WE PROBABLY COULD NEED TO CLASS BACTERIA BASED ON WHAT THEY DO TOGETHER AND WHO DOES WHAT, WITH WHOM, RATHER THAN BASED ON WHO THEY ARE, WHAT WE CALL THEM. IT'S JUST A COMMENT. I'D LIKE TO HEAR YOUR FEEDBACK. THANK YOU. >> THE ONLY THING I WANT TO SAY, I AGREE WITH EVERYTHING YOU SAY, BUT I THINK THE ONE COMMENT I WANT TO MAKE IS WITH WHAT MIKE SAID ABOUT THIS ASSUMPTION THAT WE USED TO MAKE ABOUT ASSOCIATION, CAUSATION, A SIMILAR ASSUMPTION IN MICROBIOME CORE OCCURRENCE, WE NEED YOUR ACTION, THIS IS ANOTHER ASSUMPTION I THINK WE SHOULD VALIDATE BEFORE WE TAKE THIS INTO ACCOUNT AND IN MANY CASES CO-OCCURRENCE HAS NOTHING TO DO WITH INTERACTION, HAS TO DO WITH EXTERNAL FACTORS. THE IDEA OF GUILD IS POWERFUL AND USED IN RESEARCH, I DO THINK BEING ABLE TO IDENTIFY INDIVIDUAL PLAYERS FUNCTIONALLY, IT'S NOT ABOUT NAMING, IT'S KNOWING WHAT THEY DO, IS CRUCIAL FOR A LOT OF FUNCTIONAL RESEARCH WE WANT TO DO. >> YES, SO BEAUTY OF GETTING THE NEARLY COMPLETE HIGH QUALITY THROUGHOUT THE GENOME IS BECAUSE YOU'RE ABLE TO LOOK AT THE FUNCTIONAL GENES, AND IN ONE CASE MANY -- ABOUT 30 STRINGS ASSOCIATED WITH THE DISCERN CONCENTRATION POSITIVELY, BUT IN HALF OF THEM TWO GENES CONVERTING CHOLINE INTO GMA, OTHERS ARE MERE ASSOCIATION BUT DON'T HAVE THE FUNCTIONAL GENE, YEAH. >> JUSTIN SONNENBERG, STANFORD. WE HEARD TALKS ABOUT LONGITUDINAL STUDIES IN HUMAN, WITH SO MUCH VARIABILITY AND SUCH COMPLEXITY APPLYING MULTI-OMICS TO PEOPLE OVER TIME SEEMS LIKE A GREAT WAY FOR DISCOVERY AND ACTUALLY LEARNING THINGS ABOUT THE COMPLEX SYSTEM. FOR THOSE OF US TRYING TO DESIGN STUDIES IN THE CONTEXT OF AN RO1 BUDGET, AS SOON AS YOU START SAMPLING AT A LOT OF TIME POINTS AND APPLYING OMICS, YOUR N GOES DOWN DRASTICALLY. AS CURTIS SAID THERE'S NO SILVER BULLET FOR WHAT MEASUREMENT YOU WANT TO MAKE. THIS IS DISCOVERY. GENERATING AS MUCH DATA AS POSSIBLE IS WONDERFUL. AND SO I'M WONDERING FOR THE PEOPLE THAT HAVE BEEN CONDUCTING LONGITUDINAL STUDIES IF THERE ARE ANY PRINCIPLES THAT YOU COULD PASS ON OR THAT YOU'RE AFTER THAT YOU COULD DESCRIBE TO US THAT MIGHT HELP INFORM THE DESIGN OF SUCH STUDIES BECAUSE IT SEEMS LIKE IT WOULD BE A MAJOR THEME GOING FORWARD. >> IN NO PARTICULAR ORDER, PROBABLY MOSTLY THINGS THAT YOU ALREADY KNOW, BUT AS GENERAL PRINCIPLES, THINK AS OWEN SAID EARLIER, THINK A LOT ABOUT BASELINE METADATA AND CONSISTENT FORMAT, RECONTACTING IS INVALUABLE, SAMPLES IN A FORMAT THAT ALLOW YOU TO COME BACK AND DO TARGETED CULTURE, MICROBIOLOGICAL IN ADDITION TO OMICS IS DIFFICULT IN LARGE SCALE HUMAN STUDIES BUT REALLY WORTH IT. AND FEWER SUBJECTS WITH DEEPER CHARACTERIZATION, AS MIKE SAID EARLIER, CAN BE VERY POWERFUL. THOSE ARE MY QUICK TOP OF THE HEAD COMMENTS IN THAT VEIN. MIKE, DO YOU -- >> YEAH, I HOPE THE RESEARCH WILL APPEAR VALUABLE TO THE EARS LISTENING, THAT THEY WILL LAUNCH LARGE SCALE THINGS. I MEAN, I PARTICIPATE IN LOTS OF LARGE SCALE PROJECTS, MANY OF YOU KNOW, AND THEY HAVE A ROLE AND IT'S VERY DIFFERENT FROM THE ROLE OF SMALL PROJECTS, INDIVIDUALS, PROJECTS THAT ARE EQUALLY IF NOT MORE IMPORTANT AS A WHOLE BUT WE NEED THESE LARGE SCALE PROJECTS. THEY ARE EXPENSIVE BUT REDUCE REDUNDANCY. I REMEMBER WHEN I WAS A NEW ASSISTANT PROFESSOR SOMEONE IN MY LAB SPENT IS A YEAR SEQUENCING GENES, TWO LABS WERE FUNDED BY RO1 RESEARCH, A LOT OF BUILT-IN REDUNDANCY OUT THERE WITH PEOPLE DOING THE EXACT SAME THING, AND I THINK THE ADVANTAGE OF THESE CONSORTIA, YOU CAN TAKE ON LARGE PROJECTS. YOU CAN PULL DIFFERENT KINDS OF DATA, DIFFERENT EXPERTISE, EVERY CONSORTIA I'VE BEEN IN PEOPLE SEEM TO SHARE IDEAS AND THINGS, IT DOES PULL EXPERTS TOGETHER TO BE MORE EFFICIENT THAN RO1s ARE NORMALLY. I HOPE THAT WILL SHOW VALUE FROM LARGE SCALE PROJECTS, AND AGAIN RELEVANT PEOPLE, SOME I KNOW ARE IN THIS ROOM, AND THERE WILL BE EXTENSIONS, WHAT ARE THE NEXT SETS OF QUESTIONS WE CAN PLAY MULTI-OMICS ASSAYS. THEY ARE EXPENSIVE, NO WAY OF GETTING AROUND THAT. THROUGH THE PRICE GOES DOWN, BUT WE ALWAYS GO DEEPER. WE ALWAYS SEQUENCE A LANE OF HiSEQ, WE GET MORE READS AND SEE MORE. THEY DON'T SEEM TO GET AS CHEAP. IT'S NOT PERFECTLY CHEAPER WHEN YOU GET MORE DEPTH BUT YOU KNOW WHAT I'M SAYING. IT WOULD BE NICE IF WE CAN CONTINUE THESE KINDS OF THINGS. SPEAKING FOR MYSELF AND OTHERS, I'VE LISTENED TO HERE, WE'RE LOOKING FOR OUR NEXT PHASE. SO THAT'S SELF INTEREST SPEAKING, I GUESS. >> CAN I JUST ADDRESS IT ALSO FROM A PROGRAM PERSPECTIVE? THE PURPOSE OF THE HMP WAS TO BUILD THOSE DATABASE, REFERENCE DATABASES. WE'VE DONE THINGS LIKE GONE IN TO SEE HOW MANY OTHER PEOPLE USE THE REFERENCE DATA TO TEST A NEW HYPOTHESIS, OR BUILD A NEW COMPUTATIONAL TOOL. OVER THE YEARS WE FOUND ROUGHLY HALF OF PEOPLE WHO ARE NOT FUNDED BY THE HMP USING THE HMP REFERENCE DATA ARE TESTING NEW HYPOTHESES. SO IT'S KINDS OF LIKE FREE DATA, WHAT IT COSTS YOU IS SERVER TIME BUT THE EXPERIMENT HAS SORT OF BEEN DONE FOR YOU AND MAYBE ALLOWS YOU TO DO DRY EXPERIMENTS BEFORE YOU COMMIT TO A SET OF ASSAYS OR WHATEVER. SO THAT IS ACTUALLY THE PURPOSE OF THE HMP RESOURCE. >> I JUST HAVE ONE THING TO ADD TO WHAT MIKE AND OTHERS HAVE SAID HERE. AND IT'S BASICALLY THAT I THINK PRIOR PLANNING IS A REALLY GOOD IDEA AND MAYBE THIS IS ONE PLACE WHERE THE COMMUNITY COULD POTENTIALLY HELP. WHEN WE STARTED OUR PROJECT SIX OR EIGHT YEARS AGO WE PRETTY MUCH STARTED FROM SCRATCH FROM THE SEAT OF OUR PANTS, WITHOUT A WHOLE LOT OF INPUT FROM OTHER PEOPLE WHO HAD DONE LARGE PROJECTS LIKE THIS. I THINK WE COULD HAVE LEARNED A LOT FROM OTHER PEOPLE WHO HAD ALREADY DONE IT AND PROBABLY THERE ARE PEOPLE THAT COULD LEARN FROM US NOW. I THINK AS YOU'RE GOING INTO A BIG PROJECT LIKE THAT, LONGITUDINAL STUDIES, TAKING HUNDREDS OF SAMPLES FROM DOZENS OF PEOPLE, THAT IT PROBABLY MAKES SENSE TO MAKE SURE YOUR IRB IS RIGHT, YOU'VE GOT YOUR DUCKS IN A ROW BEFORE YOU START BECAUSE IF YOU HAVE TO CHANGE SOMETHING IN MID-STREAM, IT'S A REAL DIFFICULT CHALLENGE. SO IT'S SOMETHING THE COMMUNITY MIGHT BE ABLE TO CONTRIBUTE, SOME KIND OF GUIDELINES OR HELP OR BOILERPLATE PROTOCOLS FOR PEOPLE TO USE. >> I THINK WE HAVE TIME FOR ONE MORE QUESTION. >> (INDISCERNIBLE) FROM OFFICE OF RESEARCH, NIHOD. MY QUESTION IS A VERY NAIVE QUESTION, I CAME LATE TO THE MEETING, SO MAYBE I MISSED THIS. SO WHEN WE'RE TALKING ABOUT MICROBIOME ARE WE SPECIFICALLY RESTRICTING ABOUT AREA, ONLY TO BACTERIA, BECAUSE THESE DAYS WE'RE LOOKING LIKE BACTERIA, VIRUS, FUNGI, EVEN PROTOSOMES, WHOLE OR JUST BACTERIA? >> I WANT TO RESPOND IN GENERAL, I DON'T DO THE WORK BUT FOLLOW THE FIELD. BACTERIA BECAUSE WE HAD HANDY DANDY BIOMARKERS AND ALL THAT. I ALL ALONG FROM THE BEGINNING WE REALIZED THERE WERE MAJOR COMPONENTS WE WERE NOT INCLUDING IN A SYSTEMATIC WAY. WE DID VIROMIC WORK, MICROBIAL EUKARYOTIC WORK, BUT EVERYTHING GOES INTO THE MICROBIOME. TOMORROW WE'LL HEAR FROM PEOPLE WORKING ON FISH AND PEOPLE WORKING ON FUNGI. THEY WILL CHAMPION THE NEED TO INCLUDE THOSE OTHER MICROBIAL COMPONENTS. >> SO BEFORE I OFFICIALLY ADJOURN -- GO AHEAD. >> WAS THERE ANOTHER QUESTION? >> TWO MORE CAME IN. DO WE HAVE TIME? >> CAN WE SQUEEZE ONE IN? I WANT TO FEEL LIKE THE ONLINE AUDIENCE IS INCLUDEED >> YOU'RE LITA PROSECUTOR, OF COURSE. >> TO GREG BUCK, IT MIGHT TOUCH ON THINGS WE HAVEN'T TALKED ABOUT. THE QUESTION WAS DO YOU HAVE PLANS TO ANALYZE PLACENTAL MICROBIOME, CROSS-CONTAMINATION, CONTROLS IN LOW BIOMASS SAMPLES. >> RIGHT. WE HAVE BIRTH PRODUCTS FROM ALL THE NEONATES BORN. WE HAVEN'T ANALYZED THOSE YET. WE HAVE PLANS TO DO THAT. WE DON'T HAVE MONEY BUT WE DO HAVE PLANS TO DO IT. THE CONCERN FOR LOOKING -- THERE HAVE BEEN A COUPLE PUBLICATIONS ON PLACENTAL MICROBIOME AND MICROBIOME ON BIRTH PRODUCTS, IT'S CONTROVERSIAL. I THINK THERE'S SOME REPORT THERE'S A PLACENTAL MICROBIOME, SOME PEOPLE SAY IT'S NOT IS A PLACENTAL MICROBIOME. THE DOGMA IS PLACENTA SHOULD BE A STERILE ENVIRONMENT, SOME DOGMAS ARE FALLING. TAKE IT CAREFULLY. WE'D LIKE TO LOOK AT BIRTH PRODUCTS. IN L AND D WE'RE WELL AWARE TAKING BIRTH PRODUCTS ARE NOT DONE UNDER COMPLETELY ASEPTIC CONDITIONS. WE'RE LOOKING PROBABLY AT A LOW BIOMASS ISSUE. WE HAVE NEGATIVE CONTROLS OR POSITIVE CONTROLS IN ALL SAMPLES. THAT DOESN'T CONTROL FOR CONTAMINATION OF THE ORGAN YOU'RE LOOKING AT, THE SAMPLE YOU'RE LOOKING AT. SO IF YOU -- ONE OF THE WAYS YOU CAN LOOK FOR CONTAMINATION, FOR EXAMPLE, IF YOU LOOK AT A PLACENTA OR BIRTH PRODUCT, YOU COULD EXPECT MAJOR CONTAMINATION TO COME FROM VAGINAL ENVIRONMENT. IT'S NOT ENTIRE TRUE BUT YOU WOULD EXPECT IT TO BE COMING FROM A BODY PART OF THE WOMAN, AND SINCE WE HAVE DATA ON THAT, IF YOU SAW A MICROBIOME PROFILE THAT LOOKED LIKE VAGINAL PROFILE YOU'LL SAY MAYBE THAT WAS A PRODUCT OF CONTAMINATION. IF IT'S VERY DIFFERENT, YOU SAY, OKAY, IS THIS REAL OR IS IT ENVIRONMENTAL OR DOES IT COME FROM THE REAGENTS THAT YOU'RE USING? I THINK YOU HAVE TO BE CAREFUL THERE BECAUSE IF YOU'RE LOOKING AT LOW BIOMASS SAMPLES, YOU HAVE TO BE VERY CAREFUL THAT YOU'RE NOT LOOKING AT CONTAMINATION. WE HAVE PLANS TO LOOK AT IT, WHEN WE GET AROUND TO IT, AND HAVE ENOUGH MONEY TO DO IT. WE'LL TAKE THESE THINGS INTO ACCOUNT. >> OKAY. SO I JUST WANT TO FINISH BY SAYING THE FOLLOWING. SO IN 2008, I LEFT ACADEMIA AND MY BELOVED HT4 AND STARTED TO BE ROTATING PROGRAM DIRECTOR AT NSF WHERE I WAS FOR A TWO-YEAR STINT. I HAVE NOTHING BUT GOOD MEMORIES THERE. BUT THE BEST THING THAT HAPPENED TO ME IS THAT I MET LITA PROCTOR AT NSF, OVERLAPPED WITH HER AND WAS THERE AT THE MOMENT, RIGHT AROUND THE MOMENT SHE GOT A A CLUE SHE WAS GOING TO LEAD THIS, AND WHEN SHE LEFT NSF. EVERYBODY KNOWS HOW HARD SHE WORKS, THE DRIVING FORCE ON EVERY LEVEL A DRIVING FORCE COULD BE DEFINED. SHE'S A WONDERFUL PERSON. I THINK HER MODESTY -- [LAUGHTER] I THINK HER MODESTY WAS MANIFESTED WHEN SHE INTRODUCED HERSELF AND ASKED DR. CHO A QUESTION A WHILE AGO. THE THING THAT'S MOST SPECIAL ABOUT HER, THAT YOU PROBABLY DON'T KNOW, THAT SHE HAS THIS INCREDIBLE ABILITY TO TREAT PEOPLE BETTER THAN THEY TREAT HER. I VERY OFTEN HAVE SEEN HER OR HEARD HER ON OUR MANY, MANY, MANY, MANY PHONE CALLS, AND PLANNING MEETINGS, ABOUT THIS VERY DAY, AND THIS VERY WEEK, WHERE SHE DID EXACTLY THAT. SO I'M GOING TO ADJOURN TODAY BY HAVING US ALL THANK LITA FOR BEING LITA.