>>WELCOME TO THE INAUGURAL
WALS LECTURE FOR THIS SEASON.
I GATHER THIS IS THE 28TH
SEASON.
IT'S NOT EXACTLY THE NORMAL
PLACE AND TIME, BUT THIS YEAR IT
WILL BE IN THIS ROOM AND ONLINE
AS IT USUALLY IS, SO WE HOPE TO
SEE YOU ALL IN FUTURE WEEKS AS
WELL.
AND IT'S A REAL PLEASURE FOR
LAMBDA LUNCH, A PROKARYOTIC
INTEREST GROUP TO WELCOME JILL
BANFIELD TO GIVE THIS FIRST
LECTURE.
THIS IS ALSO THE ROLLA DYER
LECTURE, WHICH APPARENTLY HAS
BEEN GOING ON SINCE 1950, WELL
BEFORE WALS STARTED, AND THAT
LECTURESHIP HONORS A FORMER NIH
DIRECTOR, WHO WAS AN AUTHORITY
ON INFECTIOUS DISEASE.
SO EACH YEAR, THE DYER LECTURE
IS PRESENTED BY AN
INTERNATIONALLY RENOWNED
RESEARCHER WHO HAS CONTRIBUTED
SUBSTANTIALLY TO BIOLOGICAL
KNOWLEDGE OF INFECTIOUS DISEASE
AND IN THIS CASE MICROBES IN ALL
PLACES WE FIND THEM.
EACH YEAR, LAMBDA LUNCH,
ALONG WITH OTHER INTEREST GROUPS
AND PEOPLE ALL OVER NIH NOMINATE
SPEAKERS.
LAMBDA LUNCH SOLICITS
NOMINATIONS FROM OUR MANY
MEMBERS, AND WE VOTE AND JILL
WAS AT THE TOP OF THE LIST, I
THINK NOT JUST THIS YEAR, BUT
THIS YEAR WE GOT -- OR LAST
YEAR, WHEN THE INVITATIONS WENT
OUT.
SO WE'RE REALLY DELIGHTED THAT
SHE COULD COME AND GIVE THIS
TALK.
SHE STARTED HER EDUCATION IN
AUSTRALIA, WHERE SHE COMES FROM,
CAME TO MARYLAND, TO HOPKINS FOR
HER PH.D. IN EARTH AND PLANETARY
SCIENCES, MOVED TO THE
UNIVERSITY OF WISCONSIN AND WAS
ON FACULTY THERE UNTIL 2001,
WHEN SHE MOVED TO UC BERKELEY.
THIS IS HER FIRST TRIP TO NIH.
SO WE THOUGHT IT WAS MUCH
OVERDUE.
MAYBE THAT'S NOT SO SURPRISING,
GIVEN SORT OF THE FIELD SHE
COMES FROM HISTORICALLY, AND I
THINK ALL OF US UNDERSTAND THAT
SOME OF THE BEST SCIENCE COMES
OUT OF PEOPLE FROM ONE FIELD
MOVING INTO OTHERS OR LENDING
THEIR EXPERTISE AND THEIR
DIFFERENT WAYS OF LOOKING AT
PROBLEMS TO ANOTHER FIELD.
SO SHE COMES TO US FROM EARTH
AND PLANETARY SCIENCES, WHERE
SHE GOT HER PH.D., AND THE
DEPARTMENT SHE'S IN NOW IN
BERKELEY ARE MATERIALS SCIENCES
AND ENGINEERING EARTH AND
PLANETARY SCIENCES,
ENVIRONMENTAL SCIENCE POLICY AND
MANAGEMENT.
SO NOT WHAT WE USUALLY GET TO
HEAR, BUT THAT'S BETTER YET.
HER WORK HAS REALLY -- ON
NATURAL MICROBIAL COMMUNITIES
HAS REALLY SPANNED FROM
EX-TREATMENT ENVIRONMENTS TO THE
INFANT GUT, SHE'S DONE A LOT OF
WORK ON THE TREE OF LIFE.
SHE'S RECOGNIZED WITH A LONG
LIST OF HONORS, SOME OF THEM IN
GEOCHEMISTRY, SOME IN
MICROBIOLOGY, SOME IN JUST
EVERYTHING.
INCLUDING ELECTION TO THE
NATIONAL ACADEMY OF SCIENCES.
FOR THOSE OF YOU WHO WANT TO
HEAR MORE AFTER TODAY'S LECTURE,
THERE IS A LAMBDA LUNCH TOMORROW
IN BUILDING 37.
IT WILL ALSO BE ONLINE.
IF YOU DON'T KNOW, THAT'S AT
11:00.
IF YOU DON'T KNOW WHERE AND WHEN
THAT IS OR NEED THE LINK, EMAIL
ME, SUSAN GOTTESMAN, AND I'LL
SEND TO YOU.
AND TODAY'S LECTURE IS OBLIGATE
SYMBIONTS AND OTHER INTRIGUING
MEMBERS OF HUMAN MICROBIOMES.
I'M DELIGHTED TO WELCOME JILL TO
NIH.
[APPLAUSE]
>> OKAY.
GOOD AFTERNOON.
CAN YOU HEAR ME?
THANK YOU, SUSAN, FOR INVITING
ME AND OTHERS WHO ARE INVOLVED
IN THE INVITATION, AND CHRIS FOR
MANAGING ALL OF THE
ARRANGEMENTS.
I REALLY WONDERED ABOUT THE
WISDOM OF ALL THIS TRAVEL AT
THIS TIME THAT I HADN'T BEEN TO
NIH BEFORE AND I'M LIKE, I'VE
JUST GOT TO GO.
SO IT'S BEEN GREAT TO BE HERE SO
FAR, I'VE MET ALL SORTS OF
INTERESTING PEOPLE AND I HOPE
I'LL GET TO MEET MORE OF YOU IN
THE NEXT DAY.
AS SUSAN MENTIONED, I'M AN EARTH
SCIENTIST.
I'M REALLY INTERESTED IN THE
ENVIRONMENT AND ENVIRONMENTAL
CHALLENGES OF CLIMATE CHANGE,
AND MICROBIAL ROLES IN THOSE,
BECAUSE AFTER ALL, THEY'RE RUN
BY MICROBES.
SO TODAY I'M GOING TO TALK TO
YOU AT NIH ABOUT A TOPIC THAT
CROSSES BETWEEN EARTH SCIENCE
AND THE HUMAN MICROBIOME.
BUT I WANTED TO START OUT BY
SAYING THAT THE CONNECTION
BETWEEN MICROBIOLOGY AND EARTH
PROCESSES HAS BEEN IN PLACE
SINCE THE VERY BEGINNING OF LIFE
ON EARTH.
OBVIOUSLY EARTH PROCESSES SUCH
AS METAL DEGASSING AND THE
APPEARANCE OF OCEANS, CHEMICAL
WEATHERING, CHANGE THROUGH ITS
ENVIRONMENTS AND PROVIDE
OPPORTUNITY FOR BIOLOGY BUT THEN
BIOLOGICAL INNOVATION FED BACK
WITH CHANGES IN THE ENVIRONMENT,
AND SO THOSE THINGS CYCLED OVER
AND OVER AND OVER AGAIN, OVER
AND OVER, OVER TIME.
THE BIGGEST INNOVATION WE ALL
RECOGNIZE IS THE APPEARANCE OF
OXGENIC PHOTO SINT CYST
OXGENIC PHOTOSYNTHESIS.
WE HAVE THE APPEARANCE OF
EUKARYOTES, DIVERSIFICATION OF
YOU'RE KAY YOTS WITH PUNCTUATED
CHANGES REMINDING US ACTUALLY
THAT ALL OF GEOLOGY, ALL THE
GEOSCIENCES WAS FOUNDED ON
BIOLOGY BY THE PAIL RECORD.
ACTUALLY THIS SORT OF FRAMES THE
TOPIC I'M GOING TO TALK ABOUT
TODAY WHEN WE LOOK AT THIS
CARTOON, WE CAN SEE THAT THERE'S
THIS SYSTEMATIC CHANGE IN LIFE'S
MICROSCOPIC DIVERSITY AND OF
COURSE ALONG WITH THIS CAME
CHANGES IN THE MICROBIAL
CONSORTIA THAT INHABIT THOSE
ORGANISMS.
SO AS WE LOOK TO THE MORE RECENT
TIME PERIOD, WE MIGHT ASK WHERE
DID THE ORGANISMS COME FROM THAT
COLONIZED ANIMAL BO BODIES?
THE MOST TRACTABLE PART OF THAT
QUESTION WOULD HAVE TO BE THIS
LAST PART WHERE IT'S RECENTLY
INVOLVED HUMANS.
IN PARALLEL WITH THIS, I
INCLUDED A PICTURE OF THIS TREE,
I'LL TALK ABOUT IT AGAIN IN A
MOMENT BUT AS I'M SURE YOU'LL
REALIZE, THE ORIGIN OF LIFE
WOULD BE SOMEWHERE IN HERE, ALL
THE LIVING THINGS ARE AT THE
TIPS OF THE BRANCHES.
SO ALL THESE BRANCHES OF
ORGANISMS THAT APPEARED ACROSS
DOMAIN BACTERIA AND ARCHAEA, OF
COURSE, COME FROM THE FULL
DIVERSITY OF ENVIRONMENTS,
INCLUDING ANIMAL AND HUMAN
MICROBIOMES.
SO THIS IS THE QUESTION THAT I'M
CURRENTLY RATHER INTERESTED IN:
WHERE DO THE ORGANISMS THAT
COLONIZE THE HUMAN BODY COME
FROM?
DO THEY DIFFER SUBSTANTIALLY
FROM THE ORGANISMS THAT EXIST
FROM THE ENVIRONMENT AND
ASSUMING SO, HOW DO THEY DIFFER?
HOW OFTEN WOULD THEIR
TRANSITIONS FROM THE ENVIRONMENT
INTO THE HUMAN BODY, AND I THINK
A CORRELATE THAT WILL BE THE
OPPOSITE DIRECTION BUT WE'RE NOT
WORKING ON THAT YET, AND THEN
FINALLY, WHAT WAS INVOLVED IN
HABITAT TRANSITION, WHAT
PROCESSES OCCURRED, WHEN DID
THEY OCCUR RELATIVE TO THE
COLONIZATION EVENT.
SO I'M WORKING ALMOST
EXCLUSIVELY IN WAYS THAT ARE
FOUNDED ON GENOMIC -- MANY OF
YOU ARE FAMILIAR WITH THE BASIC
IDEA, MAYBE NOT ALL BECAUSE I
KNOW A LOT OF PEOPLE DO SORT OF
THE LABORATORY CULTIVATION,
ISOLATION, GENETICS,
BIOCHEMISTRY.
THIS IS A KIND OF PARALLEL
APPROACH, IT'S SOMETHING THAT I
BEGAN WORKING ON RIGHT AT MY
VERY EARLY START IN MICROBIOLOGY
AROUND THE YEAR 2000.
WE EMBRACE THE IDEA OF
COMPLEXITY AS EARTH SCIENTISTS,
THAT'S FUNDAMENTAL TO US, WE
KNOW WE HAVE TO DEAL WITH
COMPLEXITY, WE JUST DO THE BEST
WE CAN TO SORT IT OUT, SO BY
CAPTURING THE COMPLEXITY, WE
HAVE THE OPPORTUNITY TO
UNDERSTAND A LOT OF THE
INTERACTIONS AND ASSOCIATIONS
THAT WE MISSED IN PURE CULTURE
WORK.
MOST IMPORTANT, WE CAN STUDY
ORGANISMS THAT ARE NOT AVAILABLE
IN PURE CULTURE.
INCLUDING PHAGES AND VIRUSES.
SO THE APPROACH JUST STARTS
SIMPLY WITH COLLECTION OF A
SAMPLE THAT REPRESENTS THE WHOLE
MICROBIAL COMMUNITY.
WE THEN EXTRACT THE DNA, WE
FRAGMENT IT.
MOST OF THE WORK WE'VE DONE HAS
BEEN WITH SHORT READS, ASSEMBLED
INTO CONTINUOUS GENOME FRAGMENT
THAT ARE THEN BINNED BY SOME
ALGORITHM OR SERIES OF
ALGORITHMS.
THE BINS ARE TAKEN TO REPRESENT
PARTIAL GENOMES, DRAFT GENOMES.
SOME OF THOSE DRAFT GENOMES WILL
COME FROM NON-CHROMOSOMAL
ELEMENTS, AND I'M GOING TO TALK
A LITTLE BIT ABOUT THOSE TODAY
AND MORE IN THE LAMBDA LUNCH
TOMORROW.
AND THEN THERE'S THE POSSIBILITY
THAT WE CAN IMPROVE THOSE DRAFT
GENOMES AND ULTIMATELY ACHIEVE
GENOME COMPLETION.
NOW THIS IS NOT VERY OFTEN
PERFORMED AND I'LL TALK AGAIN
ABOUT THIS TOMORROW IN A LITTLE
BIT MORE DETAIL, BUT IT IS
POSSIBLE AND IT'S ACTUALLY
REALLY IMPORTANT FOR SOME OF THE
WORK THAT I WILL TELL YOU.
I'M NOT GOING TO TELL YOU WHAT
WENT INTO IT.
IT'S QUITE TEDIOUS AT THIS TIME.
BUT IT'S SUPER IMPORTANT IF
WE'RE TO HAVE RELIABLE
SEQUENCES.
SO OFTEN I GET THE KIND OF
COMMENT THAT, WELL, WHAT CAN YOU
REALLY LEARN FROM METAGENOMES,
THEY'RE JUST NOTHING AND ALL YOU
REALLY SHOULD BE WORKING WITH IS
EXPERIMENTS.
WELL, I TOTALLY DON'T BELIEVE
THAT.
AND I THINK NOW THE DATA ARE
ACCUMULATING THAT WE CAN BEGIN
TO HAVE CONFIDENCE IN SOME OF
THE KINDS OF INFERENCES WE CAN
MAKE FROM GENOME SEQUENCES FROM
ENVIRONMENTAL SAMPLES.
AND SO I AGAIN PRESENT THIS TREE
OF LIFE THAT WE PUBLISHED IN
2016, WHICH WAS INTENDED TO
CAPTURE A SENSE OF THE DIVERSITY
OF LIFE THAT HAD COME TO LIGHT
THROUGH GENOMES THROUGH
METAGENOMES.
SO THIS IS BASED ON GENOMES, AND
THE GENOMES AT THE TIME WERE
COMING FROM ALL OF EARTH'S
ENVIRONMENTS.
ESPECIALLY TERRESTRIAL
ENVIRONMENTS THERE HAD BEEN VERY
LITTLE STUDIES TO DATE.
WHAT WE REALIZED TRUE THROUGH
CONSTRUCTION OF THIS TREE
CAPTURING ALL THE DIVERSITY IS
THAT THE MAJORITY OF LINEAGES IN
BACTERIA AND ARCHAEA ARE NOT
REPRESENTED BY GENOMES IN PURE
CULTURE.
THEY REPRESENT APPROXIMATELY
PHYLA -- AND EACH RED DOT MEANS
THAT LINK YAJ LINEAGE HAS D
REPRESENTATIVE.
SO THAT MEANS WE'RE LEAVING OUT
IN CULTIVATION-BASED STUDIES A
HUGE MAJORITY, ACTUALLY, OF
LIFE'S DIVERSITY AND PRESUMABLY
BIOCHEMISTRY AND GENETICS.
ONE OF THE FEATURES THAT REALLY
STANDS OUT ON THIS TREE AND THE
TREE WE'VE MADE PREVIOUSLY IN
2015 IS THIS COLLECTION OF
ORGANISMS FROM LINEAGES THAT
HAVE NO ICE ISOLATED
REPRESENTATIVES.
THIS IS A MONO -- PRETTY MUCH
EVERYONE WHO MAKES THESE TREES
FINDS THE SAME RESULT AND ALL OF
THE ORGANISMS HAVE NO ISOLATED
REPRESENTATIVE.
THE GENOMES ARE ALL SMALL IF NOT
VERY, VERY SMALL.
A SYMPTOM THAT WE PREDICTED
WOULD MEAN THAT THE CELLS WOULD
BE TINY.
SO HERE WE HAVE A PREDICTION
FROM THE GENOMES, BY FILTRATION
THROUGH 0.2-MICRON FILTER, WE
SHOW WE COULD ENRICH THOSE
ORGANISMS.
NOW A LOT OF SURVEYS, INCLUDING
THE SURVEY -- CAPTURED CELLS ON
TO A .2 AND EVEN .4 FILTER,
THESE GO THROUGH, SO REALLY
LIFE'S MINIMUM SIZE.
THIS IS SHOWN NOT ONLY BY
FILTRATION BASED ENRICHMENT BY
CRY YOE TM.
WE ALSO CAN PREDICT FROM THE
GENOMES THAT THE CELLS SHOULD
HAVE AN S LAYER, A SURFACE PROAT
NAISHES LAYER AND SOMETHING WE
CAN DIRECTLY VISUALIZE.
WITH CRYOTM.
THIS IS JUST A SLICE.
BASED ON THE GENETIC REPERTOIRES
OF THESE ORGANISMS, WE PREDICTED
THEY WOULD BE OBLIGATE
SYMBIONTS, AND BECAUSE OF THE
KINDS OF ENVIRONMENTS THEY CAME
FROM IN PART, WE SUGGESTED THAT
THEY WERE PROBABLY SYMBIONTS OF
OTHER MICROBES.
THIS IS REALLY IN CONTRAST TO
MOST SYMBIONTS KNOWN -- WHICH
WERE MICROBIAL SYMBIONTS OF
EUKARYOTES.
SO THIS IS ACTUALLY SOMETHING
THAT WE KNOW A LOT MORE ABOUT
NOW THROUGH CO-CULTIVATION
STUDIES AND FOR -- FROM
ADDITIONAL CRYOTM OF SELECT
ENVIRONMENTAL SAMPLES.
JUST TO GIVE YOU A SENSE OF
THESE ASSOCIATIONS, IN THE TOP
LEFT-HAND CORNER, I APOLOGIZE
IT'S A BIT HARD TO SEE, WE HAVE
KIND OF THE ROAD MAP FOR THIS
SLIDE.
NOW IGNORE THE MOST PROMINENT
FEATURE, WHICH IS THE FILM --
THAT NET IS JUST THE SUPPORT.
FOCUS ON THIS BIG GREY BLOB,
WHICH IS A SINGLE MICROBIAL CELL
OF NORMAL SIZE.
IN B, WE'VE EXPANDED THE VIEW OF
THIS AND WHAT WE CAN SEE IS
ATTACHED TO THE SURFACE OF THIS
HOST CELL, IS A CHAIN OF CELLS
UNDERGOING CELL DIVISION.
THE CELL SIZE IS AROUND .2,
.3 MICRONS IN DIAMETER.
SO REALLY, REALLY TINY CELLS.
AGAIN, WE CAN SEE THROUGH THESE
CRYO TM DATA, MANY PILLAE
SURROUNDING THE CELL, AS WELL AS
PENETRATING THROUGH THE CELL
WALL OF THE HOST INDICATING A
MECHANISM FOR COMMUNICATION.
WHICH IS SOMETHING THAT ALSO CAN
BE DEDUCED FROM THE GENOMES FROM
META GENOMES.
SO I'M GOING TO TALK TODAY ABOUT
THE ORGANISMS THAT COLONIZE THE
HUMAN BODY, BUT ALSO HAVE
REPRESENTATIVES IN THE
ENVIRONMENT, FOCUSING ON THOSE
LINEAGES FOR WHICH WE DON'T HAVE
A LOT OF DATA FROM ISOLATE-BASED
STUDIES.
AND IN THE CPR, I SHOULD SAY --
LET'S GO BACK HERE A SECOND,
THIS IS THE SPR, THESE TINY
EPISYMBIONTS.
WE HAVE THREE LINEAGES THAT ARE
ROUTINELY ENCOUNTERED IN THE
HUMAN.
SACCHARIBACTERIA, TM7, BACILLAP
BACTERIA AND ABSCONDITABACTERIA.
AS WE LOOK ACROSS EARTH'S
ENVIRONMENTS, WE FIND THAT THESE
ORGANISMS OCCUR AS RELATIVELY
LOW ABUNDANCE, SORT OF IN THE
1%, SOMETIMES TO THE 10% MAXIMUM
LEVEL, BUT THIS IS ACTUALLY NOT
TO SAY THAT THEY'RE RARE
COMPARATIVELY SPEAKING BECAUSE
IN MANY OF THESE COMPLEX
ENVIRONMENTS, THE MOST ABUNDANT
ORGANISM IS ONLY 1% OF THE
SAMPLE.
WE ALSO SEE THE BLUE DOTS FOR
SACCHARIBACTERIA ARE MORE
NUMEROUS THAN THE OTHER DOTS,
INDICATING THESE ARE THE MOST
COMMONLY ENCOUNTERED GROUP OF
THESE BACTERIA.
IF WE ZOOM IN ON THE
ANIMAL-ASSOCIATED GROUPS, WE
FIND THAT THEY ARE FOUND IN TWO
MAIN ENVIRONMENTS.
BOTH IN HUMANS AND IN OTHER
ANIMALS.
IN THE GUT AND IN THE ORAL
CAVITY.
OTHERS HAVE WORKED ON THIS AND I
WANT TO ACKNOWLEDGE THE WORK OF
THE FORSYTHE INSTITUTE WHICH HAS
BEEN ABSOLUTELY GROUND BREAKING
IN UNDERSTANDING THIS KIND OF
SYMBIOSIS IN THE HUMAN BODY.
SO THIS IS A PAPER FROM THE
FORSYTHE INSTITUTE, WHICH REALLY
IS ONE OF A SERIES OF PAPERS
THAT DEFINITIVELY SHOWED THAT
SACCHARIBACTERIA IN THE ORAL
CAVITY ARE AT THE SYMBIONTS OF
ACTINOBACTERIA, SO NOW WE HAVE A
HOST MICROBE EPI SYMBIONT PAIR.
AGAIN WE SHOW IMAGES IN THIS
CASE THESE IMAGES FROM THE PAPER
INDICATE THE SACCHARIBACTERIA AS
RED TINY DOTS, COMPARED TO THE
BIG, BIG, BIG ATINOBACTERIAL
CELLS, AND THEN ON THE THIRD
SLIDE, THIRD IMAGE, WE CAN SEE A
SCANNING ELECTRON MICROSCOPE
IMAGE.
I DON'T KNOW WHY THIS IS A
LITTLE DARK, BUT YOU CAN SEE
HERE THESE GREAT BIG THINGS,
THOSE ARE THE ACTINOBACTERIA AND
THESE ARE THE EP PI SYMBIONTS
THAT DECORATE THE CELLS.
THIS IS A CRYOMT IMAGE IN
COLLABORATION WITH THEM, AND IT
GIVES YOU A SLIGHTLY MORE
DETAILED VIEW CLOSER UP VIEW OF
THIS ASSOCIATION, YOU CAN SEE
THE TIP OF THE ACTINOBACTERIA.
AND THEN THE TINY LITTLE
EPISIMBIOTIC CELL.
I'M NOT GOING TO DWELL ON THIS,
THIS IS NOT OUR WORK BUT I WANT
TO ASSURE YOU AT NIH THESE
PROBABLY DO HAVE MEDICAL
SIGNIFICANCE.
THERE ARE OTHERS WORKING ON
THIS.
THERE ARE INDICATIONS THAT
SACCHARIBACTERIA HAVE AN IMPACT
ON THE INCIDENCE OF
PERIODONTITIS AND ARE INVOLVED
IN REDUCING, AS I BELIEVE, BONE
LOSS.
DUE TO ASSOCIATED INFLAMMATION.
SO THAT'S THE WORK OF OTHERS.
I THINK IT JUST POINTS VERY
CLEARLY TO THE NEED TO STUDY
THESE ORGANISMS IN MORE DETAIL,
AND THE NEED FOR INFORMATION
ABOUT THE MECHANISMS BY WHICH
THEY ASSOCIATE WITH THE HOSTS
AND IMPACT THE HUMAN.
BUT THE QUESTION I'M GOING TO
TALK ABOUT FOR A LITTLE WHILE IS
WHERE DO THEY COME FROM, HOW DO
THEY GET THERE, WHAT COMES ALONG
WITH THESE MIGRATIONS.
SO WE HAVE DATA WHERE WE CAN
FIND THESE ORGANISMS IN A
VARIETY OF ENVIRONMENTS, WE'VE
GOT GENOMES OF THE ORGANISMS IN
THE MOUTH, FOR EXAMPLE, OR THE
GUT.
WE CAN ASK WHAT CHANGES IN GENE
CONTENT WERE THEY, AND WHETHER
DID THOSE CHANGES IN GENE
CONTENT OCCUR AND HOW OFTEN HAVE
THESE MIGRATIONS TAKEN PLACE?
SO WE'RE JUST BEGINNING TO BUILD
THIS PICTURE, BUT I THINK IT'S A
VERY INTERESTING TOPIC AREA FOR
UNDERSTANDING EVOLUTION OF
MICROBES AND THE HUMAN
MICROBIOME.
SO THIS IS A PHYLOGENIC TREE ON
THE LEFT FROM A PAPER BY ONE OF
MY RECENTLY GRADUATED PH.D.
STUDENTS, ALEX JAFFE.
IT SHOWS THE THREE GROUPS THAT
OCCUR IN THE HUMAN BODY
ROUTINELY.
THIS TREE IS CODED IN COLORS
THAT INDICATE THE ENVIRONMENT
FROM WHICH THESE ORGANISMS WERE
DERIVED.
THE TAKE-HOME PICTURE FROM THE
THREE SEGMENTS OF THIS TREE WILL
BE SHOWN IN THE NEXT SLIDE AND
IN THE SLIDE ON THE RIGHT, WE
CAN SEE IN BROWN COLOR THE
LINEAGES OF ORGANISMS THAT ARE
IN THE HUMAN BODY.
AND WE CAN SEE THEY'RE RELATED
TO EACH OTHER IN CLAIFS BUT IN
THE CASE OF GRACILIBACTERIA,
SUGGESTING THERE WERE SEVERAL
MIGRATION EVENTS INTO THE HUMAN
FROM NATURAL ENVIRONMENTS.
IF WE LOOK AT THE FRANKING FLANG
CODING, WE CAN SEE THESE WERE
PROBABLY AQUEOUS FRESHWATER
ENVIRONMENTS.
THE DATA FOR ABSCONDITABACTERIA
ARE VERY SLENDER.
AT THE MOMENT THERE'S JUST ONE
GROUP OF ABSCONDITABACTERIA
FOUND IN THE HUMAN MOUTH.
I NOTE HERE THESE TWO GROUPS USE
AN ALTERNATE GENETIC CODE.
I'M NOT GOING TO TALK ABOUT THAT
IN THE CONTEXT OF THESE
ORGANISMS BUT I WILL TALK ABOUT
IT LATER IN THE CONTEXT OF
PHAGES.
OKAY.
SACCHARIBACTERIA, MUCH BETTER
SAMPLED.
IN THIS CASE, WE CAN SEE SEVERAL
LINEAGES OF ANIMAL-ASSOCIATED
SACCHARIBACTERIA, AND AGAIN,
GENERALLY SPEAKING, THE CLOSEST
RELATION TO ORGANISMS ARE FROM
THE AQUEOUS ENVIRONMENT.
IT KIND OF MAKES SENSORILY, YOU
CAN IMAGINE IF ORGANISMS ARE
GOING TO GET INTO THE HUMAN
BODY, THEY COULD VERY EASILY
COME FROM FRESHWATER.
WITH MULTI-PAL MULTIPLE CO.
THE NEXT THING WE COULD ASK, HOW
DO THESE ORGANISMS DIFFER?
THE FIRST THING WE WANT TO LOOK
AT IS GENOME SIZE.
WHAT COMES TO LIGHT WHEN WE LOOK
AT THE GENOME SIZES OF THESE
THREE GROUPS IN -- ACTUALLY THIS
ONE JUST SHOWS SACCHARIBACTERIA,
ONE OF THE THREE GROUPS.
IN THESE DIFFERENT HABITAT TYPES
WITH GENOME SIZE ON THE X AXIS,
THIS HERE IS PROTEOME SIZE,
BASICALLY A PROXY FOR GENOME
SIZE.
WE HAVE ACCOUNTED FOR THE FACT
THAT MANY OF THESE GENOMES ARE
ONLY PARTIAL, EVEN ACCOUNTING
FOR THAT, IT'S PRETTY CLEAR THAT
THE ANIMAL-ASSOCIATED ORGANISMS
HAVE SUBSTANTIALLY SMALLER
GENOMES THAN THOSE THAT -- THEIR
RELATIVES THAT OLE KUR IN THE
ENVIRONMENT.
SO THAT MIGHT MOTIVATE YOU TO
ASK WHAT ABOUT THEIR METABOLIC
CAPACITIES, HOW DO THEY DIFFER,
WHAT IS THE PHYSIOLOGICAL CHANGE
THAT TOOK PLACE ONCE THESE
ORGANISMS BECAME ANIMAL OR
HUMAN-ASSOCIATED?
WELL, TO DO THIS, WE'RE GOING TO
USE A PROTEIN FAMILY-BASED
APPROACH, AND I'M GOING TO
EXPLAIN TO YOU BEFORE I SHOW YOU
THE DATA.
YOU START WITH ALL THE PREDICTED
PROTEINS FROM ALL THE GENOMES.
AND THEN YOU GROUP THE PROTEINS
TOGETHER BY BUILDING HIDDEN
MARKOFF MODELS, SUCH THAT YOU
CAN GROUP THINGS INTO FAMILIES
WHERE THE FAMILY HAS A FUNCTION
MORE OR LESS REPRESENTS ONE
FUNCTION.
SO ONE WHERE WE KNOW THE
FUNCTION.
IT DOESN'T MATTER IF YOU DON'T
KNOW THE FUNCTION, YOU STILL
HAVE THE SEQUENCE.
SO YOU CAN INCLUDE EVERYTHING IN
THE ANALYSIS.
AND SO WE THEN GO GENOME BY
GENOME AND WE ASK, DOES THIS
PROTEIN FAMILY, AND WE'RE
TALKING MAYBE 20,000 PROTEIN
FAMILIES, DOES THIS PROTEIN
FAMILY OCCUR IN THIS GENOME, YES
OR NO?
THIS PART IS GOING TO BE A
YES-NO PLOT WHERE YES IS BLUE
AND NO IS WHITE.
AND SO THIS IS JUST A 2 BY 2, 2
GENOMES, TWO PROTEIN FAMILY, YOU
CAN SEE HERE WE'RE GOING TO CODE
IT, TRUE AND FALSE.
FOUR GENOMES, THREE FAMILIES,
WE'RE GOING TO GET A SENSE OF
WHERE THESE PROTEIN FAMILIES
OCCUR ACROSS GENOMES AND THEN BY
MAPPING ON THE ENVIRONMENT
ACROSS THE ENVIRONMENT.
SO WE CAN CORRELATE FUNCTION TO
ENVIRONMENT IF POSSIBLE.
SO THE NEXT SLIDE, WE'RE GOING
TO ZOOM WAY OUT AND SEE
THOUSANDS OF PROTEIN FAMILIES
AND HUNDREDS OF GENOMES.
BUT IT'S BASICALLY SET UP LIKE
THIS.
SO THIS IS WHAT IT LOOKS LIKE,
AND THIS IS JUST FOR
SACCHARIBACTERIA.
THIS PARTICULAR SLIDE.
AGAIN, COLUMNS OF PROTEIN
FAMILIES, PRESENCE, BLUE,
ABSENCE, WHITE.
THE GENOMES ARE ARRANGED BASED
ON THE PHYLOGENETIC TREE BASED
ON THE ANALYSIS OF
PHYLOGENETICALLY INFORMED GENES.
SO RIGHT AWAY, YOU CAN SEE THAT
THERE ARE SOME PROTEIN FAMILIES
THAT ARE WIDELY DISTRIBUTED IF
NOT UBIQUITOUS ACROSS THESE
DRAFT AND PARTIAL LIQUEUR ATED
AND COMPLETE GENOMES.
THOSE OBVIOUSLY THE GENES
INVOLVED IN CONSERVED FUNCTIONS,
SUCH AS RIBOSOME CONSTRUCTION,
TRANSLATION, TRANSCRIPTION.
BUT WE ALSO SEE GROUPS OF
PROTEIN FAMILIES THAT ARE
REPRESENTED BY BLOCKS OF BLUE
THAT ARE SPECIFIC TO CERTAIN
ENVIRONMENTS.
AND BY GOING IN AND LOOKING AT
WHAT THE PROTEIN FAMILIES ARE IN
THE INDIVIDUAL CASES AND THEN IN
GROUPS OF PROTEIN FAMILIES, WE
START TO GET A SENSE OF WHAT
THESE PROTEINS DO IN THE CASE
THAT THEY ARE
ENVIRONMENT-SPECIFIC.
THERE'S NOT A LOT OF INFORMATION
IN THESE ORGANISMS BECAUSE WELL
OVER HALF THE GENES HAVE NO
PREDICTED FUNCTION, SO THERE'S A
LOT OF PROTEIN FAMILIES THAT
HAVE NO FUNCTIONAL PREDICTION,
BUT WE CAN START TO IDENTIFY
THINGS LIKE AMINO ACID UPTAKE,
CRISPR CAS SYSTEMS FOR PHAGE
DEFENSE, ET CETERA THAT, ARE
SPECIFIC TO THE HUMAN GUT
ASSOCIATED AND HUMAN MOUTH
ASSOCIATED ORGANISMS.
WE CAN DO THE REVERSE, WE CAN
IDENTIFY CERTAIN KINDS OF
CHARACTERISTICS OF CAPACITIES
THAT ARE ABSENT IN HUMAN, AND
JUST AS ONE EXAMPLE WOULD BE
AEROBIC METABOLISM.
SO THERE ARE SUBSTANTIAL CHANGES
IN GENE CONTENT ASSOCIATED WITH
ORGANISMS THAT HAVE COLONIZED
THE HUMAN BODY.
SO THE NEXT QUESTION WE CAN ASK
IS, WHEN DID THESE CHANGES TAKE
PLACE?
ONE POSSIBILITY IS THAT THEY
PRECEDED MIGRATION INTO THE
HUMAN HABITAT, OROKURRED AROUNDD
CONTINUOUSLY AFTER MIGRATION.
THIS APPROACH, THE APPROACH TO
ANALYZE THIS, REQUIRES THAT WE
BUILD TREES FOR EVERY PROTEIN
FAMILY AND COMPARE EACH TREE TO
THE PHYLOGENETIC TREE.
AND THAT CAN BE DONE MANUALLY
AND WAS DONE BY ALEX TO SOME
EXTENT MANUALLY, BUT BASICALLY
THAT'S COMPUTATIONALLY TRACTABLE
USING BIOINFORMATIC TOOLS.
WE USE A TOOL DEVELOPED BY
OTHERS CALLED THE ALE METHOD
THAT BASICALLY DOES THIS IN A
PROBABLISTIC KIND OF WAY, AND
INFERENCES.
THIS IS AN EXAMPLE OF THE KIND
OF RESULTS YOU CAN GET.
THESE ARE DOTS THAT ARE CODED
FOR PROBABILITY THAT INDICATE
THE INFERRED TIME OF ACQUISITION
OF GAIN, SO VERY FEW GAINS
ACTUALLY OR LOSS OF PROTEINS.
OR PROTEIN FAMILIES, MORE
ACCURATELY.
SO FROM THIS, IT WOULD APPEAR,
ANALYSIS OF THE DETAILS OF THESE
KINDS OF PATTERNS WOULD APPEAR
THAT THE GENE LOSSES DID NOT
PRECEDE OR CO-OCCUR WITH
MIGRATION INTO THE HUMAN BODY,
BUT PROBABLY TOOK PLACE
CONTINUOUSLY AFTER THE
TRANSITION.
SO WE CAN ANSWER A COUPLE OF
QUESTIONS OR BEGIN TO ANSWER A
COUPLE OF QUESTIONS FOR THESE
GROUPS, AND THOSE ANSWERS WOULD
BE THAT THE HABITAT TRANSITIONS
ARE PROBABLY NOT ACCOMPANIED BY
A HUGE CHANGE IN GENOME THAT
OCCURRED AROUND THE TRANSITION
TIME, BUT RATHER CONTINUOUSLY
OVER TIME POST COLONIZATION, AND
THAT THE COLONIZATION EVENTS
PROBABLY HAPPENED MULTIPLE TIMES
AND MOST LIKELY FROM
GROUNDWATER-ASSOCIATED LINEAGES.
SO THE CPR ARE JUST ONE EXAMPLE
OF THIS BUT THERE ARE OTHER
EXAMPLES WE CAN TURN TO SEE IF
THE PATTERN HOLDS UP IN OTHER
LINEAGES.
I THINK THESE ARE INTERESTING
GROUPS BECAUSE THREAR NOT THE
ONES MOST PEOPLE WORK ON IN THE
HUMAN MICROBIOME SO I'M REALLY
FOCUSING ON CPR AND THESE TWO
NEXT EXAMPLES.
THE NEXT EXAMPLE IS ACTUALLY NOT
A CANDIDATE PHYLUM, IT'S CALLED
ELUSIMICROBIA AND I THINK
THERE'S A COUPLE, MAYBE THREE
ISOLATES AT THIS PRESENT TIME.
THERE ARE ANALYSES THAT INDICATE
THE GREAT DIVERSITY OF THESE
THINGS AND ONLY RECENTLY HAVE WE
BEEN ABLE TO ADD GENOMES FOR
WHAT ARE INFERRED TO BE THE MOST
LINEAGES.
THE TOP HERE INDICATES THE
PLACEMENT OF ELUSIMICROBIA WHERE
IT FALLS IN THE TREE.
THE CLOSEST GROUP YOU MIGHT BE
FAMILIAR WITH ARE A CONVENTIONAL
PHYLUM.
HERE WEE COLLAPSED ALL THESE
DOWN AND JUST OPENED UP THE
ELUSIMICROBIA RADIATION.
THE DIFFERENT LINEAGES ARE
COLORED HERE ON THE TREE AND
NUMBERED BUT THE MAIN POINT I
WANT TO GET ACROSS NOW IS THE
ENVIRONMENT OF ORIGIN OF THESE
GENOMES.
AND THEN WE HAVE A BIG SAMPLING
OF THE GENOMES, WE CAN COMPARE
THE ORGANISMS THAT HAVE COME
FROM THE NATURAL ENVIRONMENTS TO
THE ONES IN THE HUMAN/ANIMAL
ASSOCIATED ENVIRONMENTS AND WE
CODE THE ANIMAL-ASSOCIATED ONES
IN THE OUTER RING, IN ORANGE,
AND THEN JUST FOR EXAMPLE THE
GROUNDWATER IN BLUE.
SO FROM THIS, WE CAN SEE BY JUST
FOCUSING ON THE ORANGE THAT
THERE ARE AT LEAST TWO MAJOR
GROUPS OF ELUSI MICROBIA THAT
OCCUR IN THE HUMAN ENVIRONMENT
AND IND KAIPTING THAT THERE'S
BEEN AT LEAST TWO MIGRATION, TWO
LINEAGES DIVERSIFIED INTO THE
ANIMAL HABITAT AND THE CLOSEST
FLANKING GROUPS OF GROUNDWATER.
WE CAN ALSO LOOK AT THE GENE
CONTENT FROM THE ANIMAL
ASSOCIATED GROUPS AND THE ONES
THAT HAD BEEN BEST ARE REALLY
THESE HUMAN ASSOCIATED GROUPS
REPRESENTED BY ISOLATES, THESE
TWO.
WE CAN MAKE A LIST OF THE
FUNCTIONS THAT WE EXPECT TO FIND
AND WE DO FIND IN GENOMES AND WE
CAN COMPARE THAT SET OF
FUNCTIONS AND BASICALLY THE
TAKE-HOME POINT WITH THE BLUE
SHADING INDICATES ENVIRONMENTAL
SAMPLES, THE WHITE ARE THE HUMAN
ASSOCIATED ONES, THAT THERE'S A
SUBSTANTIAL LOSS IN METABOLIC
DIVERSITY ASSOCIATED WITH THE
HUMAN MICROBIOME COLONIZATION.
WHICH IS REALLY NOT SURPRISING
BECAUSE IT'S A MUCH MORE MAYBE
NUTRIENT-RICH AND CONTROLLED
ENVIRONMENT.
THE THIRD GROUP WERE ORIGINALLY
REPORTED AS BACTERIA ASSOCIATED
WITH THE HUMAN GUT.
YOU THINK, WHAT THE -- IS GOING
ON HERE?
CAN THAT BE TRUE?
SO ACTUALLY I MET RUTH LAE, AND
SHE TOLD ME ABOUT THESE
CYANOBACTERIA, THEY TRIED TO GET
SINGLE CELL GENOMES AND THEY
COULDN'T GET ANY.
THIS GOES BACK EARLY 2000s.
I SAID, 1%, NO PROBLEM.
GET US SOME SAMPLES AND WE'LL
GET THE GENOMES.
WE ACTUALLY GOT THREE -- I THINK
THREE COMPLETE GENOMES.
SHARON DID THE GENOMICS.
AND WE COULD ADDRESS THE
QUESTION OF WHAT THEY WERE DOING
IN THE HUMAN GUT.
WELL, IT TURNS OUT, AND I'M JUST
PUTTING A LITTLE BIT HERE ABOUT
WHY PEOPLE MIGHT CARE ABOUT IT,
IT'S NOT MY FOCUS TODAY, IT
TURNS OUT THEY'RE NOT PHOTO
SYNTHETIC.
ACTUALLY, IF YOU LOOK AT THE
PHYLOGENY, I THINK MOST PEOPLE
AGREE THEY'RE NOT SIGH CYANO.
THE LINEAGE STRUCTURE OF THE
TREE IS CHANGING PRETTY
RADICALLY.
THESE ARE THE CYANOBACTERIA.
THIS IS A NEW GROUP WE CALL THE
MELAINABACTERIA.
IT WOULD APPEAR THAT THESE
ORGANISMS ARE ACTUALLY
FERMENTING IN THE GUT, AND
PRETTY DISTINCTIVE, BASAL TO THE
CYANOBACTERIA.
THERE ARE TWO OTHER BASAL LINK
YAJS AND THEY'RE ALSO
FERMENTATION BASED METABOLISMS
FOR THE MOST PART WITH A LOT OF
HYDROGEN METABOLISM INVOLVED.
BUT THAT'S REALLY I THINK MOSTLY
INTERESTING FROM THE PERSPECTIVE
OF EVOLUTION OF OXOGENIC
PHOTOSYNTHESIS.
WE CAN RENDER A CELL CARTOON.
I DON'T EXPECT YOU TO READ THIS,
UNDERSTAND IT, BUT I JUST WANT
TO SHOW THAT ALL THE GENES AND
PATHWAYS, PARTICULARLY YOU'VE
GOT A GENOME THAT'S REALLY HIGH
QUALITY OR COMPLEELT CAN BE USED
TO DO A RECONSTRUCTION OF THE
METABOLISM.
AND THIS IS THE KIND OF WAY WE
PRESENT IT, YOU'LL FIND THESE
VERY COMMONLY ALSO IN ISOLATE
GENOMES, SO IT'S BASICALLY VERY
ANALOGOUS TO THE KIND OF
RENDERING OF DATA THAT WE WOULD
USE THERE.
SO WE CAN TO THE SAME KIND OF
ANALYSIS, WE CAN ASK ABOUT
PROTEIN FAMILIES, WE CAN ASK
ABOUT ENVIRONMENTAL ORIGIN.
THESE ARE LINES, ROWS OF
GENOMES, THEY'RE GROUPED BY
ENVIRONMENT AND THEN THE COLUMNS
ARE CAPACITIES.
THIS IS A SLIGHTLY DIFFERENT WAY
OF PRESENTING THE DATA, THE
GENOME COMPLETENESS, ONE IN A
BOX MEANS IT'S GOT ONE --
THEY'RE ALL REALLY GOOD QUALITY
GENOMES.
PRETTY CLEARLY, THE GENETIC
CAPACITIES OF THE GUT ASSOCIATED
MELANABACTERIA ARE PRETTY
SUBSTANTIALLY LESS THAN THOSE OF
THEIR ENVIRONMENTAL
COUNTERPARTS, AGAIN POINTING TO
THIS IDEA OF GENE REPERTOIRE
LOSS IN GENOME REDUCTION
ASSOCIATED WITH HUMAN
COLONIZATION.
I WANT TO TALK TO YOU ABOUT
PHAGES BECAUSE I'VE BEEN VERY
INTERESTED IN THE VIRUSES IN
BACTERIA FOR QUITE A WHILE.
ACTUALLY SOME OF THE MOST
INTERESTING ONES TURN OUT TO BE
THE ONES FROM THE HUMAN
MICROBIOME.
IF YOU LOOK AT THE AVERAGE SIZE
OF PHAGE GENOMES IN PUBLIC DATA,
AT LEAST WHEN WE DID IN 2019, IT
WAS 55KB, WHICH IS PRETTY TINY.
BUT WHEN WE WERE WORKING ON A
PARTICULAR COHORT OF INDIVIDUALS
FROM BANGLADESH, IT CAME TO
LIGHT THAT THERE WERE SOME
REALLY HUGE GENOMES IN THERE,
MUCH BIGGER THAN WE HAD REALLY
EXPECTED.
AND ALL OF THESE WERE MANUALLY
CURE WRAITED TO
CURATED TO COMPLETION, IT'S
ACTUALLY A HANDFUL OF INDIVIDUAL
SUBJECTS, BUT THE BIGGEST ARE
THE MOST INTERESTING, PERHAPS
THOSE ARE AROUND 540 AND SOME A
LITTLE LARGER NOW, SO ROUGHLY 10
TIMES BIGGER THAN EXPECTED,
BASED ON PUBLIC DATA.
SO LET'S TAKE A LOOK AT THESE
TWO GENOMES, OR THE GROUP OF
GENOMES THAT THESE TWO GENOMES
REPRESENT.
BECAUSE THEY ARE SO DISTINCTIVE,
WE GAVE THEM A NAME AND THE NAME
COMES FROM THE NAME OF THE
VILLAGE WHERE THESE SUBJECTS
WERE RECRUITED, HUMAN SUBJECTS.
AND SO WE CALLED THEM THE LAK
PHAGES.
SO THESE ARE THE FIRST TWO
CLAVES, A1 AND A2.
FIRST LET ME JUST ASK, WHY DOES
IT MATTER THAT PHAGES HAVE LARGE
GENOMES?
FIRST OF ALL, IT'S NOT EXPECTED
SO THERE'S GOT TO BE SOMETHING
INTERESTING THERE, A WAY OF
BEING FOR A PHAGE.
WE MIGHT ANTICIPATE BECAUSE OF
THEIR SUBSTANTIAL GENETIC
REPERTOIRES, THEY MAY BEHAVE
DIFFERENTLY DURING INFECTION.
PEOPLE HAVE SUGGESTED MAYBE THEY
DON'T ACTUALLY DO ANYTHING, THEY
JUST HANG OUT ALMOST LIKE A
PLASMID.
WE DON'T KNOW THAT TO BE THE
CASE.
THEIR LARGE CARGO CAPACITIES IS
POTENTIALLY MEDICALLY RELEVANT
AS WELL AS BIOLOGICALLY RELEVANT
FROM THE PERSPECTIVE OF THEIR --
I DON'T WANT TO SAY LIFESTYLES,
BUT EXISTENCE STYLES, AND I
WOULD JUST NOTE THAT THE MEDICAL
IMPORTANCE ASSOCIATED WITH BEING
ABLE TO TRANSFER MANY GENES MAY
COME ABOUT THROUGH THE ABILITY
TO MOVE ANTIBIOTIC RESISTANCE
GENES AND VIRULENCE FACTORS.
I THINK MOST PEOPLE DON'T THINK
ABOUT PHAGE SPREAD OF DISEASE
BETWEEN ANIMAL HUMAN WISE
BECAUSE THEY'RE ALL FOCUSED ON
VIRUSES OF EUKARYOTES.
I THINK THERE'S ACTUALLY A KIND
OF PARALLEL PHENOMENON THAT
MIGHT BE POSSIBLE HERE, IN THE
CASE WHERE THE PHAGES CARRY IN
PENNSYLVANIA
TOXINS THAT MAKE THE MICROBES
PATHOGENIC.
THIS IS JUST A LITTLE LIST OF
DISEASES THAT ARE INTRODUCED
INTO HUMANS BY THAT MECHANISM.
SO IT'S ACTUALLY A PRETTY GOOD
LIST.
AND SO THIS RAISES A QUESTION
THAT I THINK IS PRETTY
UNDERSTUDIED THAT POINT IS,
COULD MIGRATION OF PHAGES FROM
ANIMALS INTO THE HUMAN
MICROBIOME ACTUALLY BE A
MECHANISM FOR TRANSFER OF
DISEASE?
AND I PARTLY MAYBE CAN ANSWER A
LITTLE BIT OF WHY THAT MIGHT NOT
BE AS TRUE AS I'D ORIGINALLY
THOUGHT IN THE COMING SLIDES.
SO THE NEXT QUESTION WE HAVE IS,
WELL, OKAY, WE'VE GOT THESE HUGE
PHAGES IN THE HUMAN MICROBIOME,
WHAT DO THEY REPLICATE IN?
THE ANSWER AS INFORM BID CRISPR
SPACE, I WON'T GO INTO THE
DETAILS, IS VERY CLEARLY
PREVOTELLA.
RS THE THE REPRESENTATION IS N
THESE GOLD COLORS, IT'S THE MOST
ABUNDANT GENUS.
AND THESE INDIVIDUAL LITTLE
BLOCKS WITHIN THE BAR ARE ACTUAL
GENOMES.
SO MANY DIFFERENT SPECIES OF
PREVOTELLA.
ONE OF THE THINGS THAT CAUGHT
OUR EYE IMMEDIATELY PONZIING
THESE HUGE GENES, GENOMES, I BEG
YOUR PARDON, IS THE FACT THAT
WHEN WE PREDICTED THE GENES, THE
PREDICTIONS JUST LOOKED
COMPLETELY WRONG.
NORMALLY THEY HAVE ABOUT 90%
PLUS CODING DENSITY, AND THESE
HAD UP TO 50% REGIONS WHICH
PRETTY MUCH TELLS YOU SOMETHING
IS WRONG.
MOREOVER, GENES THAT YOU WOULD
HAVE EXPECTED TO BE MADE OF
THESE TWO PARTS WERE FRAGMENTED,
SUGGESTING THAT SOMETHING WAS
WRONG IN THE GENE CALLING.
THE ANSWER, AS HAS ALSO BEEN
SEEN IN THE CPR BACTERIA I
MENTIONED, THE BACTERIAL TYPES,
AND IN ONE PRIOR STUDY IN A BIG
SURVEY JGI DID IS THAT THE
PHAGES USE AN ALTERNATE GENETIC
CODE.
AND IT'S NOT COMPLETELY
MYSTERIOUS, IT'S JUST SIMILARLY
THAT A STOP CODON HAS BEEN
RE-ASSIGNED FROM AN AMINO ACID.
WHEN WE TELL THE PROGRAM THIS
PARTICULAR STOP CODON, WHICH I'M
GOING TO REFER TO AS TAG OR UAG
AS YOU PREFER, IS NOT REALLY A
STOP CODON.
IT'S AN AMINO ACID.
AND WHEN WE TELL THE PROGRAM
THAT AND WE DO THE GENE
PREDICTIONS, YOU CAN SEE WE
RECOVER GOOD CODING DENSITY AND
FULL PROTEIN PREDICTIONS.
SO PRETTY CLEARLY, THE CODE OF
THE PREVOTELLA AND OF THE PHAGE
THAT AFFECTS IT, THIS PHAGE THAT
AFFECTS IT OR THIS GROUP OF
PHAGES IS DIFFERENT, WHICH
RAISES ALL SORTS OF INTERESTING
QUESTIONS WHEN IT COME TO
TRANSLATION.
SO YOU'VE GOT ONE RIBOSOME AND
TWO GENETIC CODES FEEDING IN,
HOW DOES THAT WORK AND WHY WOULD
THAT BE THE CASE?
SO JUST TO MAKE THAT REALLY
CLEAR, A STOP CODON IS NOW READ
THROUGH AND AN AMINO ACID IS
INCORPORATED, SO THE NEXT
QUESTION MIGHT BE WHAT AMINO
ACID?
I SHOULD SAY THERE'S THREE STOP
CODONS.
TAG, TGA AND TAA.
IT TURNS OUT NOBODY'S EVER FOUND
TAA RE-ASSIGNED, BUT BOTH TAG
AND TGA CAN BE RE-ASSIGNED, SO
IT CAN JUST CODE FOR AMINO ACID.
SO WE CAN MAKE ALIGNMENTS OF THE
VARIOUS SEQUENCES OF THESE
PHAGES, AND BY LOOKING AT THE
AMINO ACID CODED FOR IN THE
POSITION THAT'S NOW READING IN A
WAY THAT WE WOULD THINK TO MEAN
STOP, WE CAN FIGURE OUT THAT THE
UAG IS TRANSLATED AS GLUTAMINE.
SO WHEN WE LOOK AT THE
DISTRIBUTION OF RE-ASSIGNED STOP
CODONS ACROSS THE GENOMES, ONE
THING THAT BECAME REALLY OBVIOUS
IN THESE LAK PHAGES IS THAT IT'S
REALLY HETEROGENEOUS.
SOME GENES HAD NO RE-ASSIGNED
CODON, OTHERS HAD MANY.
AND IF WE LOOK AT THE CATEGORIES
OF GENES THAT HAVE MANY STOP
CODON, IT'S ALL THE STRUCTURAL
PROTEINS.
AND LATE STAGE PROTEINS.
I'LL COME BACK TO THAT IN A
MOMENT.
SO WE ASKED, WELL, WHERE WE FIND
THESE LAQ PHAGES AND LAE
FIND CERTAIN KINDS OF
PREVOTELLA.
IN WESTERN DIET, THE BACK BAS
GENUS.
IN THE U.S. WE FIND ALMOST NONE
AND WE FIND THE LAK PHAGES IN
PREVOTELLA AND BABOONS, HUNTER
GATHERER COMMUNITIES, CHILDREN
FROM INDIA AND CHOLERA-IMPACTED
BANGLADESHIS AND SO FORTH.
SO WE ASKED, THEN, OKAY, LET'S
LOOK AT LAK PHAGES MORE BROADLY
AND SO WE DELIBERATELY COLLECTED
A TON OF DIFFERENT ANIMAL
MICROBIOME SAMPLES AND MADE A
PHYLOGENIC TREE IN WHICH WE
REPRESENT EACH GENOME AS A
BRANCH AND WE CODE THE BRANCHES
BY ORGANISM OF ORIGIN.
SO ANIMAL ORGANISM OF ORIGIN.
WE CAN SEE HERE, FOR EXAMPLE, IN
THIS BRANCH ON THE RIGHT, WE
HAVE MANY GREEN AND YELLOW DOTS.
THESE ARE ALL BABOON-ASSOCIATED
ORGANISMS.
HERE INTERESTINGLY ENOUGH, WE
HAVE GREEN AND PINK AND BLUE
WHICH ARE A MIXTURE OF HUMANS
AND QUITE DISTANTLY RELATED
ORGANISMS, WHICH WOULD BE PIGS
AND HORSES, SO DOMESTICATED
ANIMALS.
BY THE WAY, THE LARGEST GENOME
IS NOW 660KB, SO FOR A
HUMAN-ASSOCIATED ORGANISM.
WE CAN ASK NOW THE SAME KIND OF
QUESTION ABOUT PROTEIN FAMILIES
BY MAKING EXACTLY THE KIND OF --
SAME KIND OF ARRAY I SHOWED YOU
BEFORE BUT HERE CODING PRESENCE
IS GREY.
WE CAN SEE THERE ARE GROUPS OF
PROTEIN FAMILIES THAT ARE
SPECIFIC TO PHAGES THAT ARE
FOUND IN DIFFERENT MICROBIOME
TYPES.
SO FOR EXAMPLE, WE CAN PUT BOXES
AROUND PROTEIN FAMILIES THAT ARE
SPECIFIC TO PIGS AND THEN
PROTEIN FAMILIES THAT ARE
SPECIFIC TO ALL BABOONS AND SOME
KINDS OF BABOONS AND OTHER KINDS
OF BABOONS.
SO THIS ACTUALLY TELLS US THAT
PROBABLY IF NOT IMMEDIATELY UPON
MIGRATION, OVER TIME AFTER
MIGRATION OF THE PHAGES AND
PROBABLY THE BACTERIAL HOSTS
INTO THESE NULL OR DIFFERENT
ANIMAL MICROBIOMES, THERE'S BEEN
PRETTY SUBSTANTIAL CHANGES IN
GENE CAPACITIES.
SO I THINK I'M GOING TO SKIP
THIS SLIDE ON THE ORDER OF TIME
BUT SAY VERY BRIEFLY THAT THESE
LIVE PHAGES ARE NOT RARE AND THE
CODING STUDY IS NOT RARE.
NEXT I'LL TALK ABOUT THE LARGER
ANALYSIS OF THE CODED PHAGES NOT
JUST LIMITED TO LAK.
LOTS OF -- THIS IS JUST 10
SAMPLES, LOTS AND LOTS OF
INSTANCES OF BIG GENOMES AND
ALTERNATE CODED PHAGES THAT ARE
QUITE ABUNDANT.
SO WE CONDUCTED A STUDY
PUBLISHED RECENTLY IN WHICH WE
BASICALLY SURVEYED ANIMAL AND
HUMAN MICROBIOMES AND WE
BASICALLY CLASSIFIED EACH OF THE
PHAGE GENOMES BASED ON WHETHER
OR NOT TAG OR TGA WAS
RE-ASSIGNED.
AND WE FIND BOTH.
AND WE FIND THAT THE GENOMES
HAVE QUITE A WIDE DISTRIBUTION
OF LENGTH SO IT'S NOT JUST
ASSOCIATED WITH BIG GENOMES.
AND THAT IT VARIES QUITE A BIT,
AND IT'S VERY SUBSTANTIALLY MORE
PREVALENT IN HUMANS WITH A
NON-WESTERN DIET COMPARED TO
WESTERN DIET.
SO I WON'T GO INTO THIS IN
DETAIL, BUT THIS IS A PHYLOGENIC
TREE THAT BASICALLY ON THE
OUTSIDE IS DECORATED WITH BARS
TO INDICATE GENOME LENGTH.
SO AGAIN, YOU CAN SEE
SUBSTANTIAL DIFFERENCES IN
GENOME LENGTH.
AND SHOWN IN THE COLORS HERE,
JUST AS THESE BLOCKS OF COLORS
ARE THE DIFFERENT -- WE FIND
FOUR DISTINCT FAMILIES OF
ALTERNATIVELY RE-CODED
BACTERIOPHAGES, THAT INFECT
FIRMICUTES.
THIS IS A MUCH BROADER PHENOMENA
THAT MIGHT HAVE BEEN INDICATED
BY MY ONE INTRODUCTORY STUDY OF
THE LAK FAIDGES.
PHAGES.
WHAT'S EVEN MORE INTERESTING, I
THINK, IS THIS RESULT
ILLUSTRATED HERE WHERE WE HAVE
CLOSELY RELATED PHAGES, CLOSE
TOGETHER ON THE TREE THAT HAVE
YELLOW, GREEN AND GREY CODE.
THAT MEANS STANDARD CODE, TAG
RE-ASSIGNED -- THEY CAN BE
CLOSELY, CLOSELY RELATED AND USE
DIFFERENT GENETIC CODES.
THIS IS NOT SOMETHING WE
EXPECTED AS ANOTHER EXAMPLE
HERE.
SO OVERALL, BETWEEN 2 AND 6% OF
THE PHAGES WE FOUND IN HUMAN
MICROBIOME USE AN ALTERNATE
GENETIC CODE.
SO IT'S NOT REALLY, REALLY
COMMON, BUT IT'S CERTAINLY NOT
RARE AND PROBABLY STILL
UNDERRECOGNIZED.
SO EXPANDING ON THIS JUST A TINY
BIT MORE, THE DIFFERENT CLAVES
ARE ILLUSTRATED BY THE ROWS, THE
BLOCKS, VERY CLOSELY RELATED
PHAGES CAN USE DIFFERENT GENETIC
CODES.
THIS IS AN EXAMPLE WHERE WE'VE
DONE WHOLE GENOME ALIGNMENTS,
WHICH YOU CAN ONLY DO WITH
CLOSELY RELATED GENOMES.
AND HERE IS 90% AVERAGE
NUCLEOTIDE IDENTITY.
AS WE CAN SEE HERE, THERE'S
INTERSPERSING OF TGA RECURRING
PHAGES, AND STANDARD CODE
PHAGES.
WHEN WE ALIGN THE GENOMES, YOU
CAN ALIGN THE WHOLE GENOMES HERE
AS SHOWN BELOW, WE FIND AGAIN
IT'S STRUCTURAL AND ACTUALLY
LYSIS PROTEINS THAT HAVE
ACCUMULATED THESE IN-FRAME STOP
CODONS OR WHAT WOULD BE STOP
CODONS IF READ IN THE NORMAL
WAY, AND WHAT'S PERHAPS EVEN
MORE INTERESTING IS THAT THE
STOP CODON THAT'S BEEN
RE-ASSIGNED HERE IS ALMOST NOT
USED IN THE STANDARD CODE PHAGE.
SO IT WOULD APPEAR THAT A
PRECURSOR, AND THIS IS MORE
GENERALLY TRUE, BY THE WAY,
PRECURSOR CODE SWITCH IS
PROBABLY REDUCTION IN USE OF THE
CODON THAT'S BEEN RE-ASSIGNED.
ANOTHER DRIVER APPEARS TO BE LOW
GC.
SO LOW GC, STOP CODON AVOIDANCE,
AND THE CODE CAN SWITCH.
SO THIS TELLS US THE GENETIC
CODE IS EVOLUTION MORE DYNE
EXPECTED.
WE THINK THE RE-ASSIGNMENT OF
STOP CODONS MAY BE IMPORTANT IN
TERMS OF THE PROCESS OF
INFECTION AND SUCCESSFUL
INFECTION BY THE PHAGES FOR THE
FOLLOWING REASONS.
WE SEE THAT MANY OF THE PHAGES
ENCODE SOME MACHINERY KNOWN TO
BE REQUIRED FOR CODE SWITCH.
THESE REQUIRE -- THIS INVOLVES A
TRNA THAT CAN RECOGNIZE THE STOP
CODON.
IN SOME CASES, WE CAN IDENTIFY A
SYNTHETASE AND THAT WOULD
RECOGNIZE STOP CODONS.
WE THINK DURING THE EARLY PART
OF INFECTION, THE GENOME IS READ
WITH CODE 11, THE HOST'S
BACTERIAL CODE.
AND THEN THE PHAGE MANAGES TO
PRODUCE THIS CODE SWITCH
MACHINERY, AND NOW IT FLIPS THE
RIBOSOME.
SO THAT IT READS THE STOP CODON
AS THE AMINO ACID OF CHOICE.
AND WE THINK THAT THIS IS A
SPECULATION, WE NEED TO DO
EXPERIMENTS TO VALIDATE THIS,
THAT POSSIBLY THIS IS BECAUSE
IT'S REALLY IMPORTANT THAT THE
PHAGE NOT PREMATURELY PRODUCE
THE PROTEINS INVOLVED IN LYSIS
AND STRUCTURAL PROTEINS.
SO IT MAY JUST BE AN INSURANCE
POLICY FOR THAT REASON.
I WANT TO SAY THE ALTERNATE
CODED PHAGES -- WE'VE BEEN ABLE
TO IDENTIFY INCORPORATED INTO
THE GENOME, IN OTHER WORDS, PRO
PHAGE, THAT USE THE ALTERNATE
GENETIC CODE.
SO THIS IS JUST TWO EXAMPLES,
ONE IN THE PREVOTELLA GENOME,
QUITE SMALL PHAGES, AND LIKEWISE
IN A FIRMICUTE GENOME.
SO WE CAN PICK THIS OUT VERY
EASILY BECAUSE THE NORMAL TBEENE
PREDICTIONS GIVE YOU SUCH LOW
DENSITY.
SO THE LAST PIECE OF WORK IS NOT
PUBLISHED YET.
IT DONE WITH LONG TERM
COLLABORATORS WHO DO PROTEOMICS.
WE'VE PROVIDED THEM WITH HUMAN
MICROBIOME SAMPLES THAT CONTAIN
ABUNDANT ALTERNATIVELY CODED
PHAGES AND THEY'VE BEEN ABLE TO
CONFIRM THE BIOINFORMATIC
PREDICTION THAT THE STOP CODON
READS AS, IN THIS CASE,
GLUTAMINE.
THIS WAS ACTUALLY -- WHEN WE SAW
THE LAK FAIDGES BECAUSE E
LISTING OF ALL GENETIC CODES
THAT EXIST IN BIOLOGY, TOOK US A
WHILE TO REALIZE IT GOES 11, 12,
13, 14, 16.
SO THERE IS A CODE 15.
WHEN I CONTACTED NIH AND I SAID,
HEY, BY THE WAY, THERE IS A CODE
15, THEY TELL ME IT'S NEVER BEEN
SEEN IN BIOLOGY, BUT HOPEFULLY
NOW WE HAVE PROTEOMIC
VERIFICATION NOT JUST BIOIB FOR
MA
BIOINFORMATICS, WE CAN FIX THE
LISTING.
SO I TELL YOU, CODE 15 REALLY
DOES EXIST, I THINK VERY CLEARLY
NOW, AND THIS IS JUST A DIAGRAM
OF THE TWO PHAGES THAT WERE
STUDIED WITH THE ASTERISKS
INDICATING WHERE THERE WAS
PROTEOMIC CONFIRMATION THAT TAG
EQUALS GLUTAMINE.
SO I THINK IT'S A GOOD TIME TO
WRAP UP, GIVEN THE HOUR.
I WANTED TO MAKE A FEW
CONCLUSIONS.
I FIRST WANT TO BACK OUT AND SAY
AGAIN THERE'S A LOT IN THE HUMAN
MICROBIOME THAT WOULD BE MISSED
BY CULTURE INDEPENDENT
APPROACHES AND THE ENVIRONMENT
MORE BROADLY, OF COURSE, AS
WELL.
THEY'RE NOW KNOWN TO SOME EXTENT
THROUGH GENOME RESOLVED META
GENOMICS.
THERE'S A LOT WE CAN PREDICT, A
LOT WE STILL DON'T KNOW.
MANY OF THESE ORGANISMS MAY HAVE
MEDICAL SIGNIFICANCE.
AND THE EVIDENCE IS EMERGING
FROM THE STUDIES OF OTHERS THAT
THEY DO.
AS I SAID, WE'RE INTERESTED IN
WHERE DO THEY COME FROM, HOW
DOES THE ENVIRONMENT IMPACT
HUMAN MICROBIOME DEVELOPMENT.
WE THINK THAT THEY, GIVEN THE
LATE APPEARANCE OF HUMANS, MUST
HAVE COME FROM THE ENVIRONMENT
AND PROBABLY THEY CAME FROM
GROUNDWATER.
COLONIZATION WAS PROBS BLI PROBY
ACCIDENTAL FIRST BUT OVER TIME,
IN EVOLUTION OF THE ASSOCIATION,
THERE WERE CHANGES IN THE JEAN E
REPERTOIRES MOSTLY ASSOCIATED
WITH LOSS OF CAPACITIES AND
GENOME REDUCTION.
I THINK IT'S REALLY IMPORTANT WE
KEEP OUR EYES ON NOT JUST THE
MICROBES BUT THEIR ASSOCIATED
BACTERIOPHAGES OR VIRUSES.
WE SEE CLOSELY RELATED PHAGES IN
NOT VERY CLOSELY RELATED
ORGANISMS, AND WE SEE NOT SO
CLOSELY RELATED PHAGES IN
CLOSELY RELATE ORGANISMS.
FOR EXAMPLE, HUMANS AND BABOONS,
THEIR PHAGES ARE VERY DIFFERENT.
HUMANS, DOGS AND HORSES, THEY
SEEM TO BE MUMP CLOSER.
MUCH CLOSER.
SO ASSOCIATION MAY BE IMPORTANT
IN TERMS OF -- INTO THE HUMAN
MICROBIOME.
I PERSONALLY FIND THAT THIS
TOPIC OF ALTERNATE CODING OF
PHAGES IS REALLY FASCINATING.
I CAN'T TELL YOU WHY IT'S GOING
TO BE IMPORTANT YET, BUT I KNOW
ACTUALLY THE PERSON I SAT NEXT
TO ON THE PLANE COMING OUT HERE
RUNS A NON-PROFIT IN OAKLAND ON
PHAGE THERAPY, AND SHE WAS GOING
TO A CONFERENCE WHERE SHE'S
GOING TO CONVENE A SECTION ON
SUCCESSFUL IMPLEMENTATION OF
PHAGE THERAPY TRIALS AND SO
FORTH, AND I THINK THAT THERE
MAY BE SOME REASON TO LOOK AT
THE GENETIC CODE AND HOW IT CAN
BE USED BY PHAGES TO JUST ADD
THAT LITTLE BIT MORE PROBABILITY
OF SUCCESSFUL INFECTION.
PERHAPS MORE BROADLY
EVOLUTIONARY SPEAKING, I THINK A
REALLY FASCINATING -- THE IDEA
THAT A PHAGE CAN SWITCH THEIR
CODE VERY EASILY.
THEIR CODE SWITCH IS VERY
FACILE.
IT'S NOT FIXED, IT'S NOT STATIC.
PROBABLY IT CAN SWITCH ONE WAY
AND PROBABLY BACK AGAIN.
THERE ARE OBVIOUS COMPONENTS OF
THE MECHANISM OF CODE
ADAPTATION, BUT I'M SURE THERE
WILL BE A LOT MORE TO LEARN AS
WE START TO GET ALTERNATE PHAGES
INTO CULTURE, SO WHY HAVE WE NOT
DONE THE EXPERIMENTS ALREADY?
THERE IS, TO MY KNOWLEDGE, NO
ALTERNATIVELY CODED PHAGE IN
CULTURE, AT LEAST NOT ONE
PUBLISHED TO THIS DAY.
I WANT TO THANK OBVIOUSLY OUR
FUNDING SOURCES WHICH INCLUDE
THE NATIONAL INSTITUTES OF
HEALTH AND SOME OTHER
ORGANIZATIONS.
I LISTED PUBLICATIONS
THROUGHOUT, BUT THE PEOPLE WHOSE
NAMES HERE ARE, WITH ONE
EXCEPTION, JOANNE SANTINI AT THE
TOP ARE MEMBERS OR PAST MEMBERS
OF MY LAB AND WE'VE BEEN REALLY
LUCKY TO WORK WITH MEMBERS OF
THE FORSYTHE INSTITUTE ON THE
TH7 SACCHARIBACTERIA.
I'D BE HAPPY TO TAKE QUESTIONS.
[APPLAUSE]
>>I'M GOING TO START FROM ONE ONLINE
THE APPEARANCE OF A GROUP OF
SYMBIONTS THAT HAVE LOST AEROBIC
METABOLISM RAISE THIS QUESTION:
I HAVE ALWAYS THOUGHT THAT THE
ORIGINAL MITOCHONDRION WAS
ENGULFED WHEN IT CONTAINED ALL
OXFOS CAPABILITY.
DO YOU SEE EVIDENCE THAT THOSE
ORIGINAL ORGANISMS,
QUOTE-UNQUOTE, MAY HAVE ALREADY
LOST MOST ETC PROTEINS, IE, ARE
THERE NASCENT NEW MITOCHONDRIA
OUT THERE AS SYMBIONTS?
>>OH, I LOVE THIS QUESTION.
BUT FIRST OF ALL, IT'S A BIT
BACKWARDS.
TRANSPORT CHAIN -- THEY GO
TOGETHER, I THINK IT'S ACTUALLY
THE OPPOSITE.
I THINK THAT THE ORGANISMS IN
SOIL PROBABLY GAINED THE
POSSIBILITY -- IT'S NOT THAT
WELL REPRESENTED AT THIS TIME.
AND MOSTLY THEY'RE ASSOCIATED
ORGANISMS.
I THINK THE VAST MAJORITY OF
THESE CPR ORGANISMS ARE AN
AEROBES AND THAT SEEMS TO BE THE
NORMAL MODE OF LIFE IN EARTH'S
ENVIRONMENTS WHERE THEY OCCUR.
AND IN THE HUMAN BODY.
SO I DON'T KNOW ABOUT THE -- I
DON'T THINK THE ANALOGY WITH
MITOCHONDRIA IS QUITE
APPROPRIATE IN THIS KAY.
I THINK IT'S MORE LIKE ANOTHER
KIND OF ORGANISM, ORGANISM
ASSOCIATION, SO ON THE CONTINUUM
OF ENDOSYMBIOSIS WHICH WOULD BE
THE MITOCHONDRION AND LOOSE
ASSOCIATION -- THIS IS A CASE
WHERE THEY HAVE DIRECT PHYSICAL
CONTACT OR EPISIM SYMBIOSIS.
I THINK THAT'S AN EVOLVED
STRATEGY, I THINK IT'S A VERY
COMMON STRATEGY AND I THINK IT'S
EXTREMELY UNDERSTUDIED, BUT I
DON'T THINK IT'S ANALOGOUS IN
QUITE THAT WAY.
>> HI.
THANK YOU FOR THE LECTURE.
MY QUESTION IS ABOUT LAK PHAGES,
BECAUSE YOU SAID THAT THEY CAN
BE REALLY VARIABLE IN THE GENOME
SIZE, BUT IT ALSO MEANS THAT
THEY HAVE TO BE ABLE TO PAD THIS
GENOME IN THE CA PSI.
AS YOU SHOWED ON ONE OF THE
TREE, SOME OF THEM REALLY --
LIKE SOME GROUPS REALLY WERE IN
THE GENOME SIZE AS OTHERS ARE
NOT.
DO YOU SEE ANY DIFFERENCE IN THE
CAPSIDS OR PROTEIN THAT FORM
THOSE CAPSIDS?
>> I THINK BY WAY OF
CLARIFICATION I WANT TO SAY I
TALKED ABOUT TWO THINGS, I
TALKED ABOUT LAK PHAGES FIRST
AND THEIR GENOME SIZES RANGE
FROM 465KB TO 660.
SO IT'S NOT A HUGE RANGE IN
SIZE.
BUT IT'S LINEAGE-SPECIFIC.
SO THERE'S A FEW MAJOR LINEAGES
OF LAK PHAGES.
SO I THINK THERE'S NO BIG
MYSTERY WITH THE CAPSIDS.
WE CAN IDENTIFY THE CAPSID
PROTEINS, BUT SO THEY'VE EVOLVED
DIFFERENT SIZES BUT THE SIZES
AREN'T HUGELY DIFFERENT AND
CLOSELY RELATED LAK PHAGES HAVE
THE SAME SIZE.
WHAT I SHOWED YOU IN TERMS OF
THE HUGE RANGE IN GENOME SIZE,
THEY'RE ALL-OF-US TERNTIVELY
CODED PHAGES.
IN THAT CASE, THEY'VE GOT
DIFFERENT HOSTS, DIFFERENT TYPES
OF PHAGES.
THEY'RE JUST ALL OVER THE TREE.
AND SO I'M SURE THERE PROBABLY
WOULD BE DIFFERENCES IN THE
CAPSID PROTEINS BUT I HAVEN'T
LOOKED AT THAT IN DETAIL.
>> BUT I MEAN, YOU HAVE SOME
CLOSELY RELATED GROUPS THAT VARY
IN SIZE, YES, FOR ALTERNATIVE --
THE ONE WITH ALTERNATIVE.
SO FOR THE CLOSELY RELATED
GROUP, HOW YOU EXPLAINED THAT
THEY CAN TACK THESE GENES --
>> I SEE WHERE YOU'RE GOING WITH
THIS.
SO THAT'S A PRETTY ZOOMED OUT
VIEW OF THE TREE, AND I DON'T
KNOW HOW REALLY VERY CLOSELY
RELATED THEY ARE, BUT YES, IT
TENDS TO BE, AND I'M PRETTY SURE
ABOUT THIS, THAT CLOSELY RELATED
PHAGES HAVE THE SAME GINO SIZE.
SO IF WE FIND ONE LARGE PHAGE,
WE FIND A CLAVE OF THEM.
CLADES OF HUGE PHAGE ACROSS
THOSE ENVIRONMENTS.
SO ONE, YOU FIND MORE BIG.
AND MORE DISAT THAT PARTICULAR
TIMELY BRANCHING, WE FIND THE
SMALLER ONES.
SO I DON'T KNOW ANYTHING BEYOND
THAT IN TERMS OF THE MECHANISM,
BUT I THINK IT'S QUITE A BIT OF
EVOLUTIONARY TIME THAT SEPARATES
THEM.
>> THANK YOU.
>> ANY OTHER QUESTIONS?
SUSAN, GO AHEAD.
>> LET ME START WITH ONE BACK
WHEN YOU WERE SHOWING THE
ACQUISITION OR LOSS OF METABOLIC
THINGS AND SORT OF INDEPENDENT
EVENTS.
IT LOOKED LIKE THEY WERE IN
GROUPS AS IF THERE'S NOT A
CAPACITY THAT MUST BE GAINED
WHEN YOU GO FROM THE
ENVIRONMENT, THAT YOU CAN DO IT
MANY DIFFERENT WAYS AND IT'S
NOT -- YOU KNOW, THAT YOU MUST
GET SOMETHING IN PARTICULAR.
IS THAT ACCURATE?
>> I THINK THAT'S FAIR, YES.
AND THE FACT THAT -- I MEAN,
THESE ARE PHYLUM LEVEL VIEW, SO
IF WE SAY A BRANCH -- THOSE HAVE
REALLY DIFFERENT ORGANISMS, SO
DIFFERENT STARTING POINTS, AND I
DO THINK IT'S REALLY -- AS IT
SHOWED SO FAR, CONTINUOUS
MODIFICATION, NOT ONE
REQUISITE --
>> THING THAT YOU START WITH,
YEAH.
>> IN THE CASE OF THE LAK
PHAGES, IT'S REALLY INTERESTING
THAT WHAT STANDS OUT IS THE
GAINS.
IN THE CASE OF THE MICROBES,
IT'S MORE THE LOSS, LOSS OF
DIVERSITY.
DIVERSITY OF CAPACITIES.
>> MAYBE WHY YOU CAN DO MORE
EASILY.
>> OR WHAT YOU DON'T NEED TO DO,
YOU SHOULD.
ONCE YOU GET TO THE HUMAN BO BO,
IT'S REALLY DIFFERENT THAN BEING
IN AN AN AN AQUIFER OR SEDI.
>> I JUST HAD A COMMENT, NOT A
QUESTION.
>> OKAY.
I REALLY LOVE THE ALTERNATE
TRANSLATION CODE.
THAT'S REALLY FASCINATING.
BUT OF COURSE IN THE MODEL IN
WHICH -- SO THE PHAGES ARE
CARRYING THE MACHINERY TO DO
THAT.
>> FOR THE MOST PART.
>> AND YOU THINK THOSE ARE SORT
OF EARLY GENES THAT ARE COMING
IN, BUT NOT ONLY ARE THEY GOING
TO AFFECT WHEN THE PHAGE CAN
MAKE THOSE LYTIC ONES BUT
THEY'RE GOING TO DO STRANGE
THINGS TO THE HOST TOO.
AND DO YOU SEE ANY -- I MEAN, I
GUESS YOU NEED ONE THAT DOESN'T
DO IT AND ONE THAT DOES TO KNOW
WHETHER THE HOST HAS ADAPTED AT
ALL.
>> I HAVE TWO HUGE QUESTIONS AND
THIS IS A REALLY INTERESTING
QUESTION.
I THINK THAT -- WELL, WE JUST
DON'T KNOW, ARE ALL THE
RIBOSOMES SWITCHED, IS IT JUST A
SUBSET S IT A COMPLETE SWITCH?
THERE'S A LOT OF QUESTIONS
THERE.
WHAT WE COULD LOOK FOR ARE
PEPTIDES THAT ARE TERMINATED AND
CLASSIFY THEM AS TERMINATED
PHAGE PROTEINS, AND TERMINATED
HOST PROTEINS.
BECAUSE ONCE WE HAVE THE GENOMES
CULTIVATION-INDEPENDENT, REALLY,
WE CAN PLEA PREDICT THE PROTN
SEQUENCES AND THE PEPTIDES AND
WE CAN VALIDATE THEM.
SO WE REALLY NEED TO ASK THAT
QUESTION, DO THEY MAKE THE
TERMINATED -- THE PREMATURELY
TERMINATED BACTERIAL PROTEINS,
AND THE ONE QUESTION I WOULD ASK
ON TOP OF THAT IS, DOES THE HOST
BACK
BACTERIA HAVE A WAY OF SWITCHING
THE RIBOSOME RIBOSOME BACK?
BASED ON THE OTHER THINGS WE
KNOW ABOUT THIS INTERACTION, I
BET THERE'S A WAY THAT THE
BACTERIA GOES, NO, YOU DON'T.
AND NOBODY HAS THE RESOURCES YET
TO DO THE EXPERIMENTS.
I THINK CAN YOU DO SOME WITH
CULTIVATION INDEPENDENTLY, WE'VE
JUST NEVER HAD THE RESOURCES TO
DO IT.
OKAY.
>>ONE MORE ONLINE
THIS QUESTION IS FROM OUR
COLLEAGUE, HECTOR ROMERO.
HELLO, THIS WAS A FASCINATING
TALK.
I'VE WORKED WITH BACTERIA PHAGES
IN THE PAST AND HAVE ALSO BEEN
REALLY INTERESTED IN THE WAYS
THAT BACTERIA PHAGES FROM THE
SAME CLUSTER CAN VARY IN THE
WAYS THEY ACHIEVE LISOGENY.
THERE ARE THOSE THAT AFFECT THE
SAME HOST SPECIES BUT ONE MIGHT
AFFECT THROUGH LYSIS THE OTHER
PREFER INTEGRATE.
DO YOU THINK THAT THE
DIFFERENCES IN THE INTEGRATION
MECHANISMS USED BY
BACTERIOPHAGES IS ALSO RELATED
TO ALTERATIONS FROM THE
ENVIRONMENTAL ASSOCIATIONS?
>> I REALLY DON'T HAVE A
RESPONSE TO THAT.
>> I DON'T EITHER.
>> I THINK THAT'S A TOUGH
QUESTION.
IT'S AN INTERESTING POSSIBILITY,
BUT I DON'T THINK THERE'S ANY
DATA TO REALLY SPEAK FROM IN
RESPONSE.
>> AND ONE MORE, THEN WE CAN
WRAP UP?
>> SURE.
THANK YOU.
SO THANK YOU, THAT WAS REALLY
GREAT.
I JUST WAS WONDERING, TO FOLLOW
UP ON SUSAN'S QUESTION, GIVEN
THAT YOU'RE FINDING A LOT OF
PREF TA
PREVOTELLA WHERE THE LAK PHAGES
ARE DOES THAT MAYBE SUGGEST THE
PREVOTELLA IS FINDING A WAY TO
RESIST, MAYBE IT'S FOUND A WAY
TO SORT OF --
>> GREAT QUESTION.
I GET YOU.
YES, THE ANSWER IS ACTUALLY
FIRST OF ALL, LET ME GO BACK TO
HOW WE IDENTIFIED PREVOTELLA AS
THE HOST FOR THE LAK.
THE ANSWER IS -- TARGETING,
THAT'S CRISPR.
BUT WE NEVER FOUND THE CRISPR
SPACES THAT CONFER IMMUNITY IN
THE SAME MICROBIOMES THAT WE
FIND THE LAK PHAGE.
WE USE CRISPR SPACE TARGETING TO
DO FIRST HOST-PHAGE LINKAGES FOR
10 MORE YEARS.
THIS IS ACTUALLY THE NORMAL
PATTERN.
THE PREVOTELLA THAT HAVE THE
LACK LAK
PHAGES HAVE DIED MOST PROBABLY,
BEEN PREDATED BEFORE THE LAK
PHAGES APPEARED.
WE HAVE TIME SERIES DATA TOO, SO
WE HAVE FOUR CONSECUTIVE-DAY
SAMPLES, SO THE LAK PHAGES ARE
REALLY CHANGING VERY QUICKLY,
THESE ARE VERY DYNAMIC SYSTEMS.
SO I WOULD SAY NO IMMUNITY, LAK
PHAGES PREVALENT.
IMMUNITY, WE DON'T FIND THE LAK
PHAGES, IT'S ONLY GOING ACROSS
THOSE TWO SAMPLE SETS WE CAN
MAKE THE CONNECTION.
SO THE IMMUNITY IS AT LEAST BY
CRISPR, MAYBE OTHER MECHANISMS
AS WELL.
BUT WE DON'T KNOW THE LIFE STOOL
OTHER THAN THERE'S NO EVIDENCE
THAT THEY INTEGRATE, THEY NEVER
BECAME PRO PHAGE, AS BEST AS WE
CAN SEAL FOR ANY OF THESE -- ANY
HUGE -- THAT WE KNOW THEY DO
THAT.
SO WHETHER THEY HANG AROUND AND
ARE SOMEHOW BENEFICIAL TO THE
HOST THAT MAKES THEM MORE LIKE A
PLASMID, I THINK THAT'S ON THE
TABLE STILL.
SO HOW DEFENSIVE THE PREVOTELLA
HAS TO BE IS ALSO IN QUESTION.
THANKS FOR THE QUESTIONS.
>> THAT'S WONDERFUL.
I GUESS WE'RE SUPPOSED TO FINISH
UP BECAUSE WE'VE HIT THE HOUR.
LOTS TO TALK ABOUT, REMIND
EVERYONE HERE AND ONLINE THAT
THERE WILL BE A LAMBDA LUNCH
CHAPTER 2 TOMORROW.
AND CONTACT SUSAN GOTTESMAN IF
YOU NEED THE LINK.
AND THANK YOU SO MUCH FOR
COMING.
IT'S BEEN WONDERFUL, A LOT OF
FUN AND LOTS OF THINGS TO KEEP
TALKING ABOUT.
[APPLAUSE]
>>THANK YOU.
THANKS FOR THE QUESTIONS.