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"'cause" you just get started right
okay so one singular much for the
introduction to think you on what the
you're sort of the the meeting
organiser all you cannot hear noise
okay okay okay good. Um voice you
saying okay okay so I think in the
meeting all basically the opportunity
on the present well we've done in PGI a
I start to feel bad that I sort of
change to my talk from yesterday to
today it seems like become more and
more challenging to to give talks I
don't really have anything new to say a
after so many a fantastic talks
enquiries but I'm fine I so on a you
see these people of of course well what
I'm trying to present is actually to
use a systematic not skill mix way try
to see if we can sort of softball apply
this kind of you encouraging issues
that we've been discussing over
previously and this morning there on
polish has become really information by
people really sort of choice like blind
men try to are touched then if I guess
what the and if I'm not back are smart
people will have some cats may see mine
may not oh I'm actually a morse I don't
actually have a mine are well written.
So long as the problem. Um I remember
like almost ten years ago. I keep a
call to you know when nature sort of
interview me I said I don't really have
a pretty high wanna have muscle on but
actually few years ago in nature select
BSD the ten sinus matters that year. I
said I if you really don't have a brain
you don't know how to move the muscle
but yes it's actually trying to
demonstrate the problems of the current
particles starting is trying to get
something interesting on you a high
process is something based on
incomplete data set any we actually far
from doing. So are you know to to
really to look like sort of you can
what the and it look like you basically
need the whole picture. So you
basically stealing of very early face
collecting data. So you become that
very sort of important for PGI a which
is trying to do is can we started and
forget about hypotheses forget about
all the models conclusions knowledge
whatever on you control from those data
just collecting the data I mean just
collect whatever data I mean forget
about draw a conclusion from hundreds
of examples whatever how about the
meeting samples so how about getting a
multi a mix data well one meeting
individuals from all kinds of layers
contracting collecting. And worry about
all these hypotheses as you is made are
so this is basically a lot ideas there.
So we started to economics data back to
I mean the melody angst data back to
almost ten years ago. Um together with
just goes in every project we made a
great contribution there for these room
and whatever cover a story at that time
would be first time assembled are the
three meeting human opportunities
instant know objectively genes from
shop rates which is only thirty five
whatever fifty basically there but you
don't really believe that we can do
that job where we actually simple that
oh you have to be really prove for
success and people really use that as a
reference jean catalogue for many of
those studies they are we know it's not
enough you we probably give you the
most upon that one in the european
populations there is you far from
complete so we keep connecting are
Charlie samples American sample since
you know a sample more and doing more
analysis other publish this paper this
year together with again dominican
social. So we got a meeting jeans but I
don't think it's really enough real. So
of course no presentation is today it's
talking about thirty meeting jeans. I
don't know how many genes that there
but from this ten meeting jeans we've
constructed we've done the kind of
assessment there. Um is already cover
something like ninety five percent for
most of those sort of common jeans you
can see from individuals. And if you
look at from this remaining two ten
meeting genes are most of those genes
we discovered are kind of know what
currency in jeans which really
contributed most to expensive science.
So once again it's they're those other
re jeans and the the rear categories
you're a human got categories if you
look at all these functional difference
between those commenting reached on
individual specifically reached jeans
there. Um as you can probably guess
consult the you're commenting supply
functions essentially forcing by right
off but then this would be just
specific genes that we at all you know
recently on the reflected that station
to be a hosting immune systems admiring
factions in the body treatment you know
all these challenges that you actually
interact with the environment. And
tarzan whatever. So this is really not
really special case but then we started
to put all these data into a database
right so this is what you can download
the data you the data. And whatever so
one is constantly updating so is still
every so twenty four hours we had more
genes and functions whatever species on
their samples well but this is the the
first thing in the G level stuff right
all based on that people have been done
a lot of association study like the
chinese that that we do study with with
like you years ago european type two
diabetes study we you know the
obviously study and many more of those
isuzu studies. And that I need you know
a developed do not acknowledged just
started from the show reason to
assemble that you know the species that
stuff because I mean it's not a three
meeting meeting in columns crises this
silence species that people want to
study on I'm people also move onto this
is all americans comics Amanda proton
except. There's also lots of this kind
of sort of projects ongoing there. I'll
but we know then imitation of the
technology right you all sequencing all
assemble just from a strong reason to
it you know level or whatever MLGOMG
whatever you're talking about this
group of genes that have the S same
opponents. Um well actually have an
imitation of the they're they're not
actually speech said we cannot see any
difference cross this and all this
variations that the may have a very
important functional impact if people
in the fermentation bitterness they
know a for you call I'll for any of
those species just like one base pair
mutation work have different functional
impact. So what be very important to
develop the college that you can
sequences species travel and actually
basically get DNA from sort of along
not so long a fragment of DNA in
sequence yet at a sample point. So this
is what we've done so we've quite a
company call completing a mix of
practise two years ago. And was
starting to develop the technological
therefore to up to a level where you
can sequence well every matter sample
Eurospeech species that so the idea is
basically you get a hundred to three
hundred KBDNA match extra bar coded
icicles that bar coded in a so you
actually get a three hundred K be non
fragments of sequestered in a venue
assemble from there people in this
world with sort of sick was you would
know if you got through and make a B
assembled uni from bacteria you would
be able to assemble to to achieve that
what was species that so by that you
probably could recover basically a
matter to you know really are not
imaging level but the matter species in
the a sequences. And this whole type I
don't really have the data to show yet.
Um because we actually got a
preliminary results just a few weeks
ago. And hopefully next year we will
start to advance the real results are
in our instruments you meetings are
that week as started to sequence the
species level from them at a a samples.
So this is just a retail you that what
PGI is this I mean for collecting data.
And developing technologies to generate
more accurately cheaper outdated. Um
how about the other species I'm gonna
talk about human right but we're not
just to human mom matter samples we've
done a lot of other animals like pagan
mouse the which people we use a lot oh
I'm a dog reasons which is quite an
important of course would be important
to ask I mean do they actually you may
share the same inner sort of a couple
tubers which you probably needing to
different conclusions we used MS animal
models. So without the mouse the using
the same way of doing shotgun
sequencing sample and so a first of all
this is the comparison between mostly
human so you can see the mouse
catalogue your greater difference to
the human kind of energy level then the
functional now in not away. So that
share a similar function but not the
same genes which in some way it's good
if you study the function there on the
remote I I don't I that's as you can
see there you are but realised what
make use ratios use difference there.
But the actually come going away so
they're not really that much so the
difference. And if you add in pay there
what you want be more complicated first
of all the here jean between those
three species of quite small. So they
can you know gene that they don't cheer
but in the functional that was you know
a lot it tells you again if you want to
use that as use the mouse model opaque
motto as active function allowances you
may be fine but not look you mean to be
G levels yet. And if you do this P box
possibly analysis with all these
different colours here. Um you see lots
and yellow here. But the yellow
represent pay a some specific. So that
tells you actually the we got specific
past we whatever cables copper more
functional module so humane Miles
probably imply the pickup environment a
kind of different in human. And mouse
maybe more function to to supplement
tend to physiology anyway so this is
the comparison between human pecan
models. But that's them bodily some
state right are we even sequence more
than just the model exams for example
kinetics I mean it looks nice wee
sequence that we've got operation. BMC
yet you know things honest started
sequence side you know with norwegian
group which you actually siamese a big
farming business. So can we sort of
understand why you know the Simon B is
so different even you feed them the
same thing I still all this kind of
project a out of curiosity we are even
sequencing the the fickle sample from
wherever which basically you can
probably walks through the use and talk
somewhere else and get the sample be a
lot and you can get chance of because
samples there. Um but that's a quite
interesting expect edition so we have
some I can't Norwegians and this and
we've sort of hunting both well so it's
it's quite experienced. Um but again
this is just for fun I mean that seems
really a serious or whatever I can not
say this is not zero size is it is a
serious eyes but this is just part of
our program to collecting all these
fickle samples and and sequence that
interacting and to enrich our gene Cox
anyway so we have three more species
any of those speech I mean panned out
for example idea this the pictures you
so it's sequence to got to use a pen a
polar bear and just right I mean any
species you can think of we can send a
sample we will do a but this is just
the one thing right to construct a
reference in a sort of catalogue
somebody has to do it and we are happy
to be that kind of digital museums to
store all those data and sequence. Well
then of course the second parse would
be can we start it attracted managing
angst all mixed data from different
time points right so this is what we've
done together with Frederick at for
swedish a whole again four hundred us
one hundred samples but then for time
three point at some three time points
with the other sample. RS project
already shows you some of the data five
just try to sort of show you some of
those jeans and you whatever matter how
to use we've got right so hard they
assemble whatever and you know the
matter species whatever is kind of
normal so it's not a sure enough people
but they also sure very very low
abundance like so they actually
sometimes goes away after one but
anyway so again that tells you it's
those things up quite specifically
quite kind of personalised those are
the signatures of the got echo system
in different states from you bound to
be a mother as you can see the the
shifting here yeah is because of the
diets in the physiology I don't really
go into the details of this carrots but
I'm happy to show you you are
interested. Um so the but then noticing
will be interesting to collecting from
different the geographic location one
thing with down for example is a
comparison between chinese and things
which you we've got a lot of managing
onyx data first of all you can see that
different right so the the president
human got but what we could use really
unique at least on yeah you buy. PC
analyses you can realistically always
each other there. And that's even there
is also similar to you upon is you
preeminent or as you can see here is
really compatible. But if you really
look carefully they have lots of
different for example that then string
colossal wine which yeah figured out
from their got materials. And drink
lots of milk to I mean we I don't
really I'll have lots of new but we
have actually very very so it'll be the
big expense relative expense you know
prior you up but tier. And more
importantly we are consuming more
anybody got whatever treatment. So you
see from our couple tours which we
chinese individuals have more
antibiotic resistant genes are we
probably we used and but anyway this is
not really good a few again is all
meetings so that they would be taxed
difference there. Um as you can see the
the energy and the time reasons a
couple had remote I'm reasons you know
it's quite different there remembering
transporters you know the anabolic by
decorations is quite different the two
the show you more specifics. Um chinese
like to eat all these sorted for small
whatever stuff there which may contain
some of those solid years which is not
really good sorry here so then you
already see actually which from chinese
calls the which probably also expensive
for ten so Europeans Devine china maybe
it's not very good for them if they
don't really have a box to add your
with by the way so you know so because
of the price difference so we need
actually a lot of MS it's sort of
synthesising and be the missus facing
materials say because from the times we
don't really you have enough. And if
you look at the pin type that there is
actually have produce sort of more
casting away so they find more which I
hardly noticed but I actually are
noticed afterwards after I think it's a
but the chinese tires which yeah with
relatively sufficient protein assembly
that means a license may actually have
more but your is this sort of thing the
size been I mean B complex essentially
masses and so on as you all could see
it from this summarised the rockets my
it's just a kind of a to show that
there is a big difference because of
that your graphic locations of people
of colour saying probably genetics all
is probably that's why or environment
whatever. So I actually initiate
another project to see for the chinese
beseech chinese we should genetic is
chinese the probably boring you know
them more you're your or united states
try to see what stick sort of
difference of what tears and is you
don't have to Medicare sort of
difference over there to see the
difference there but we don't have the
yeah but again this is a way of sort of
connecting different geographical
locations ages sequence MO but more
importantly you want to collecting all
this angst data from different disease.
So you can see from all it's nice to
almost every disease are sort of
metabolic right and Dave anything
metabolic has that not wanna get "'em"
is you need to sequence the camp accuse
also we started from the type that
media switch your published a few years
ago I think that's one of the first to
study is using the kind of do you lost
type of analysis but on the puppeteer
start not like the human study which we
need tens of some samples to get a
minimal sort of P value or whatever
significant signals there by just doing
them editing a mix analysis you only
need to do hundreds of samples that
just shows you the diapers either all
be signal the statistical power there
is quite strong only need hundreds
examples already give you some results
for example we gives you very very good
real rock or whatever to tell you the
you can find out the perfect by
marketers just by sequence the the
disease and control samples we did a
wide use all this fifty up by markers
as just show you two can clearly
separate have leds and controls there
there we go either monitoring I mean
this is the some of those patients the
gastric bypass treatment you can if you
just look at least fifty apart markers
there you can see the create she from a
kind of bad materials to a community to
have that are back to committee. So
that's just show you the those kind of
markers again could be potentially
interesting to be used to be mechanical
level for the that classes to to see a
how good treatment is still useful
really for the talk from just go
talking about all these obesity in
America a consortiums there I'm not
going to talk more there but we've done
another study on the kind of us got
disorders that this is the current
understanding of a kind of possible is
whatever physiology about you know kind
of ask the disorders but there is
people knows it's important on this
later but not much information. So we
were trying to think out can we feeding
the cats there can we sort of try to do
something thereby just multi a mix
analysis. So we started general also
data not just got the copious but also
the host them at that point a mix. So
we tested this zero butterflies there
we tested the euro metabolised. And by
sequence also a lot of cup of tears and
start to make links right situation. So
this is the correlation between the got
cold using the host a metabolised so
you started to make you know
associations between different
metabolised in different box has
started to have this kind of tables
they tried to see you know this
specific metabolites probably have a
strong began situation with respect
here is some of those but yours I don't
even have a name or anything like that
but we know it's there. And then we
started to fill in the gaps. So you you
have some sort of smart guess. Um I
know I don't have a smart oh right but
still you you have enough data you
could draw all these lines you know by
christian may possibly for example that
easy stuff that all these red star what
you stuff that you could start feeling.
Um so this kind of thing is this real
you the multi all mixed power right so
more and more sort of individuals have
the multi layers information then just
by statistics you try to make for them
to go this is another example is that
we've done between the chemical peels
the conferences found this study is not
just trying to find out by markers for
it is thing the the the colour cancer
patients and the controls of course we
actually did find some markers. But
more importantly can we find out
interesting markers to a sort of to be
the markers of different stage so we
collected all the sample from you know
state one two three and four and you
can discover for example the don't be
jeans is quite interesting if you to
sort of follow up that become a stage
apart markers. So that actually us
shows you again the progression of of
the cup material changes day and to the
potential by Marcus you can discover
from different states I'm not a scene
with down I mean this is again from
different point of study so from this
from each other strategies which try to
collect lot just a fickle sample but
also the dental sample for seventeen
which is just so shy to see if they
have the same a situation the bucks we
stick you know the disease and controls
in to see if they shared a lot. Um but
first of all again the as usual so we
we've discovered markers that the
related with the argument limited are
we starting patients there and actually
you discover gram actually got you know
probably be protective against the
disease which is good. But then you you
do all this study what this is another
one based on the cup active analysis
but then have a very specific a
phenotype characters here trying to see
if you can bring again the materials
reason this specifically not that makes
you RP level whatever IDT level there.
So it just this is just another way of
looking at the data this is that that
elevated right so you got a dental data
comparison with this other heavily data
and we got paid. Um a become a very
interesting for example some of those
materials are really representative in
this in the all these samples then
actually this study shows sometimes the
dental sort of markers is even stronger
associated. So you know what be weekly
because doctors told me that sometimes
the the puppeteer is could actually a
big into the bloodstream just from the
models I don't really need to go
through the got in stocks but anyway.
So that tells you that that will this
but to is is also very very important.
Uh for the rendered of structures are
not just to to develop a by matter from
but then so but ear is to to say this
is important but markers for a patient
step and also they're really useful I
mean we did we sort of find out to
compare with that because sample
instead of a sample but the total
samples are kind of more useful for the
evaluation of the university which is
the traditional. T so the correlating
the best to see you know if you have
certain materials actually these
treatment would be more efficient or
actually lasting peace you could become
a very interesting study there again so
this is just different part of the a
tier is how how that that these
disease. So we are collecting a lot of
those kind of information and basically
every possible easy samples we could
collect it over the country in china.
And sequence all of them and put it
into our database. And well there's a
lot of things that we've trying to do
again the collecting all mixed data
from the for intervention. So well we
know all the food directly sometimes
directly influence the got Mccall be
able to sometimes they sort of just
affect the the the release date active
the greetings there and there is a a a
very magic at Madison co traditional
chinese Madison which is being sort of
a documented for thousands of years and
all well nobody knows why and we sort
of just try to see you anything we
could do regarding to those tradition
tennis madison's that we made in this
to something that people think he's
probably important for the different a
sort of a physiology of human. And we
start to test tomorrow I mean I know it
sewing chinese I don't know how to
transit that you do initially anyway
but I just show you some of those
examples there like for example this is
the for this is come to the top on the
list is just a lou. Um it evaluates of
very different pictures of the remote
computer from the PC controls. And you
can look at the the but to resume
posting is actually the shortage pretty
aspect to this which is in general so
it's quite an amazing. So I I'm taking
a low everyday and so just to just to
be you the safe side. And another why
is the kind of to which is again a very
interesting results is sure especially
for the you know by assisting creation
my wife does not really like me to to
have gotten or every day but I do that
rely on the actually a outside of a by
the way so we are keep doing all this
kind of seems to not just from the
mouse study but also pick stuff too but
also human study too. So we we could
volunteers most of them. P gentle
always because we have six on employees
so they have that would the cool there.
So we have the interesting sort of
contain which we could a cafeteria
which you could put all these things
there. And some people sign up to say
now I want to do this study. And they
started you don't work I'd probably
every day thing we saw tested before
and after and all these things so just
trying to see how that affects all this
property to an odyssey of course people
have been discussing is cool robotics
you are provided. It's important that
so we've tried isolated all these high
P values stuff from all this disease
control starting okay. So for example
this one this a but tier is RTF one
zero one is one but here is that we got
it is healthy but you receive detect
like really said analysis that so then
we use that one mouse model issues a
very very good potential or problematic
sort of you could be used it in a way
to protect you against the have it
beeps again we're recruiting people in
PGI but then P jacket poised too young
so we recording their parents oh so the
parents you know newly discovered
directly D.'s whatever so I have
several sorry there it's loose that are
up robotic try to to see if they have
any better. And then we started because
we have a national team back at PGI and
we started to use a national team bank
become a nationals to back which is
good actually so we save all these
different kind of stews with different
each sex whatever we don't people that
means three toleration so it's not like
I so forty dollars at oh by the way so
well hopefully we can do more there.
And is still not very class and of
course to do fickle right estimation so
it's what you would be much better to
develop a pool tables still cocktail
solution which I so of beach yeah it's
really trying to do. So then from this
people back oh that's too bad we
selected all these individuals and then
it started to screen out all this
transpired just non targeted waiting.
Um so the work has been carried on
voting almost a year. I we've got
twelve point restraints entice about a
whatever twenty species. And which is
quite good. This is just the copper
species party in this entire. Um a got
up too three yeah hopefully we will get
it the sort of the whole colour
coverage in the a couple years time but
we are are trying very hardest really
labour intensive. It's quite
interesting okay so but from that we
are trying to look into do to develop
kind of cocktail solution so when
people come to be jointly sequence the
cup of tea or is the MP we give them a
or pale. And and probably sometimes a
card or other blue or any of those
traditional Madison so along try to
help manage or else. Okay eventually a
soul everything just has to be done in
which people are talking about a
collecting samples canonical samples
hundreds of samples there. But it's not
enough rain we as I say at the very
beginning we did meet with the meetings
and so we need more T a mixed data for
one meeting each at least I mean that
stuff I mean is the start if you look
at the cost but you know you've already
seen. It's you can solve more small. So
long as ten solid and your starter
people talking about once on your
stomach but we this right in ten years
you would be just one dollar just
really the way it is free I mean
everybody to sequence the in a minute
you know whatever for free. I think BTI
will all three four three couple of use
because the value of the data would be
much more than just generating the
data. So when you process rush. And
when you know exactly how to use the
data apply today to sequence the data
to generate data would be free and
obituaries on the way to to towards I
think next year we was started to
provide services to do a whole genome
sequencing at the level of several
hundred dollars you have dot how would
you know sequence with like a an almost
can have cafeteria sequencing at I
don't twenty thirty dollars whatever.
So everybody can afford to it. And
there would be a very interesting are
sort of interface we call voyager to
really demonstrate all these data. And
sort of make a community of people so
people if I have a one mini users in
these systems. So people could call
friends like they're competing with
their running competition so the
recorder friends to say okay so now we
are you need to do this steering group.
So to see how the but here it changes
and Ellis study would be done in is
that if you have enough data users. And
this is what PJ I will do in the next
two three years. And from that's
hopefully we will get in the first a
database a minute you know meeting all
makes database for well for the follow
up study. And from there I hope we can
have some complete picture of whole
picture of something at that time if I
was still get invitation from this
conference I may just tell you the real
sort of whole picture not by hypothesis
is true but actually dated even see
conclusion that I can show you but
anyway there is a lot of people join
the work as you can see just go and
Frederick has already give that talk to
a lot of others thank you very much for

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Conference program

Introduction of the Session 1 : The Gut Microbiome: Facts and Figures
Josef Penninger, Institute of Molecular Biotechnology, Vienna
23 Oct. 2014 · 9:07 a.m.
The role of commensal bacteria in the gut
Willem de Vos, Wageningen University, The Neterlands
23 Oct. 2014 · 9:31 a.m.
Q&A : The role of commensal bacteria in the gut
Willem de Vos, Wageningen University, The Neterlands
23 Oct. 2014 · 10:29 a.m.
Gut microbial richness impacts human health
Dusko Ehrlich, INRA, Jouy-en-Josas, France
23 Oct. 2014 · 11:07 a.m.
Q&A : Gut microbial richness impacts human health
Dusko Ehrlich, INRA, Jouy-en-Josas, France
23 Oct. 2014 · 11:44 a.m.
Cross-talk between the mucosal immune system and environmental factors
Hiroshi Kiyono, The University of Tokyo, Japan
23 Oct. 2014 · 11:56 a.m.
Q&A : Cross-talk between the mucosal immune system and environmental factors
Hiroshi Kiyono, The University of Tokyo, Japan
23 Oct. 2014 · 12:31 p.m.
Introduction of the Session 2 : Host - Microbiome Interaction
Susan Suter, University of Geneva, Switzerland
23 Oct. 2014 · 1:41 p.m.
Mechanisms of cross talk in the gut
Annick Mercenier, Nestlé Research Center, Lausanne, Switzerland
23 Oct. 2014 · 1:55 p.m.
Q&A : Mechanisms of cross talk in the gut
Annick Mercenier, Nestlé Research Center, Lausanne, Switzerland
23 Oct. 2014 · 2:34 p.m.
Relationship of diet to gut microbiota diversity, stability and health in older people
Paul O'Toole, University College Cork, Ireland
23 Oct. 2014 · 3:52 p.m.
Q&A : Relationship of diet to gut microbiota diversity, stability and health in older people
Paul O'Toole, University College Cork, Ireland
23 Oct. 2014 · 4:27 p.m.
Gut microbes and their role in malnutrition and obesity
Rob Knight, University of Colorado, Boulder, USA
24 Oct. 2014 · 9:16 a.m.
Q&A : Gut microbes and their role in malnutrition and obesity
Rob Knight, University of Colorado, Boulder, USA
24 Oct. 2014 · 10:01 a.m.
The gut metagenome - your other genome
Jun Wang, BGI, Shenzhen, China
24 Oct. 2014 · 10:19 a.m.
Q&A : The gut metagenome - your other genome
Jun Wang, BGI, Shenzhen, China
24 Oct. 2014 · 10:53 a.m.
Fecal transplant to mine for novel probiotics
Max Nieuwdorp, Amsterdam Medical Center, The Netherlands
24 Oct. 2014 · 11:04 a.m.
Q&A : Fecal transplant to mine for novel probiotics
Max Nieuwdorp, Amsterdam Medical Center, The Netherlands
24 Oct. 2014 · 11:25 a.m.
Introduction of the Session 4 : Nutritional Interventions
Keiko Abe, The University of Tokyo, Japan
24 Oct. 2014 · 12:46 p.m.
Interactions between gut microbiota, host genetics and diet
Liping Zhao, Jiao Tang University, Shanghai, China
24 Oct. 2014 · 12:56 p.m.
Pediatric intervention - what works and what doesn't work
Hania Szajewska, The Medical University of Warsaw, Poland
24 Oct. 2014 · 1:47 p.m.
Q&A : Pediatric intervention - what works and what doesn't work
Hania Szajewska, The Medical University of Warsaw, Poland
24 Oct. 2014 · 2:15 p.m.
Perspectives for nutrition and the gut microbiome
Nicholas Schork, J. Craig Venter Institute, La Jolla, USA
24 Oct. 2014 · 3:02 p.m.
Q&A : Perspectives for nutrition and the gut microbiome
Nicholas Schork, J. Craig Venter Institute, La Jolla, USA
24 Oct. 2014 · 3:46 p.m.