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production of and fourteen patients great to be here and talk to you'll
see some of the themes the the the um so it
wonderful here is that we will it be occurring in my dog
but to start that i really like to show a a slide that
which reminds us that you know that one can sink about the
human and this the mike about those neglected or done that
well it has made me sit and many says imagine rolling fell some disease and that
i used it that that that for chronic diseases with this live which goes one failed things seniors that
oh a couple of us go this is an n. yeah there's a the the note
amanda diseases so that the slide is get would get longer and longer so it just a bit yep but
but that an important that sink to remember also
is that chronic diseases are steadily increasing in that's so as
countries and that there is no prevention and knock you
so it is a major health problem uh
oh of course but attention of b. is currently diseases could impact that because greatly
and the simple way of viewing prevention is saying about that two components is the
direction and this guy with the asians not enough to detect there is
we also have to do something about it and they just want to call it that
the microphone for an on the risk of chronic disease can it be a target
for inter dimension ensure that you recognise some of the themes that we um
it it is but if that that that the other lacking
really tools to assess the the microphone where enough
how to assess the state of these neglected organ each and every individual
environment that could consortium we always do but that that challenge it
it by saying okay we should probably start by describing what's the status of
what's it uh uh well got to belong the other
human genome enough but collectively we can okay in
our uh uh intestinal tract and and try to find out what is the other gene on it
each and every individual and for that we developed yep approach to do it uh
maim quantitative methods are not mix of what this quantitative nitrogen onyx
quantitative methods er non x. ray start from schools samples and go all the way to
predictive models and the indication of how to go about it and how
they do that we have developed methods which make it seem to
to collect it stool samples that can now be that that can now
be done patients clones we could develop quenching liquid so it
composition of my problem is not about that for a leak but it is still samples
can then they send send a mail from the patients cons to the lab
and when the lab receives it and all the n. a. is extracted
so on that and that captures of calls all the genes that individual carriers
to find out what the the genes in the sequence a lot generate
many many sequences of the fifteen you don't sequences which capture presence
on the buttons of the jeans they're short sequences and a button for
not good on their own so we basically use them to
ma on direct ranging caught the which contains all the g. is that we have ever found
mark infinitely ma non um because the shot sequence to this reference
jane caught all the county jane so they get jean profiles
for many individuals and millions of jeans and the the
the ladies provost document data in from there they
identify the unthinkable whereas the oven has to be from others and in
principle it looks quite simple and keep these but there is it
critique of point basic needs to be standardised because it if it's a collection
is out of storage or sample processing does not done quite i than
it's very difficult to correlate sings between difference that isn't that has i sink impacted the field to sun
the the if not the most clad into different gene catalogue
is it the cut above ten million genes yeah that has just been published a few months ago
the big contribution from b. g. i. integrate to happen john
it does he meant if you expand on that that like that later on
about twelve hundred individuals that that that uh
started and caught is it one of the messages from here remember the first catalogue huh
the obvious that got this major cover the push on was one hundred twenty four individuals ten
times more than compared to him you and you know one of the main messages is
well the thing is that the common to many individuals up to don't think is very much
any long it's like a common buttons that jane is that right there is something about
at least five percent individuals well that maybe between jen from millions of these we have seen them
now what's intriguing of course is that and a jeans present in the if you will be the
just a link isn't maybe the quilt she did that to that notion that we are also
different but maybe also part of it is that some of the microbes that live
in our budget i don't to reside there but other transit in there
be as it may be seeing that this common jeans with the most informative for that
common diseases chronic diseases that we would like to that
but beyond ten even jeans i also wanted to cluster the genes in
classes of gene once they confound and we we the that that
i won't go into details of the of the procedure which really goes it
looking at the core abundance of genes in different individuals
jeez which have same abundance it was different individuals they want to the same speech
what have we found we had found if we look at the frequency of
objects class there's even foreign which caught my page among units here that
so am i allowed to have many genes and
they really the present species bacterial species which
are call methods are not mixed finishes we could describe it's also paper that came
out there that these these here we discuss it the it we call this method amongst dishes
eighty five percent of them that previously i'm no so
quinn only the gnome speeches that i thought it was jean answered being used to cannot there's back about
lines cannot present on the t. v. percent of all that is in there but that not only does a large
species and is that also smaller you wanted to chat
say less than about seven hundred genes maybe it's
i mean is it around that maybe fifty genes and they correspond to pay
just by the spasms crisper elements that sell the stuff i think
and really detailed description of this whole michael brown they can
consist construct these into action networks you can set
if age it is not a bacterium on which the page see it's
so they know about these relations and that this is a zoom on one part of this network
this particular methods among species we see some pages
which you attack we see an annuity element
and for and is even even the element is present in some strange but not in dallas and
the stage will not that back to the look at the data that a presentation of
what is going on and we can categorise oh that but neglected organ
we can assess microbe around and each and every individual to and and this and then the the the
and you can you can even think about this quantitative
methods enormous approach as a part of my possible
microscopic scanned the neglected organ waste away from i'm twenty one level
folks first microscope it some time ago yet another that person
so what can we then do i use state what we can do it in
the following sites get into a few examples we can do that last
a paper published a couple of months ago on lever settles
done in collaboration rate the other part is
that that generation university in fine huh
because i've got about about almost two hundred fifty people
patience reverse arouses that most in different ways controls people who come for
a a forecast check we speak out caught in a discover
to find out species that deeper in shape and show them
in in a few moments patience and as individuals
and train the algorithm which these diagnoses
with about ninety four percent accuracy
between patients and controls and i used the remainder of a corporate
which was never ever used to train the ability to get
exactly the same type of a precision we only seven
seven species we've had these accuracy of diagnostics so
many times people ask layout quite at the compound is we have a leaning they could
that confounded it as confound their disease state was we can
it is it accurately that the most compensate it patients and the
compensated patients may have also eliminated the effect of medication
anti virus that that bothers about the problem about if we because because we can distinguish
that most people use respective whether they take does that so not so hot
gotten standard for all the the solos that causes biopsy that season in the is it better
and you can't like it's not simple getting replacing with it the non invasive method school no it's
so we can diagnose with high accuracy
but it can also say something about beyond that that no since we can say something about the status
of the patients that i take a few minutes to you mormons guide used to these colourful slide
so first we haven't organised i'll call what this is a discovery by this
is about the ocean but into as individuals and leave us those patients
and then the the present twenty a species matter now is
speech is that that initiative uh solos and the
uh so the method journalist dishes that the marriage has individuals
but these boxes each of the boxes ideally the presence
see the genes of the species and there's a couple called for the
for the uh uh uh uh this uh presentation so ha
the problem here is one individual ninety eight a. b. c. and so on and each
line each role is a gene and fifty genes that this late so can easily see
that these twenty eight stages at present mostly in
leave aside those patients both in the discovery and evaluation corporate but these dishes
i dunno us from the patients that another there that typical for yes individuals there's it yet but
now we have also or that the other sellers patients here
in terms of the abundance of these dishes for in in the database
and what we see when we compare the quartet let's say
patients whichever least of this this is your patients which it most of the stages
the the legal schools are not lost all people
who have high load of leaves those pages
then for people who have low logo that so they can not
only diagonals patients we can also say how sick very ah
so what's going going to be the there's a massive change of michael by um in a way but so was
one parameter which i touch up on a more but later they haven't lost
that is significantly regions of that michael by on both
in discovery caught user l. c. and patience
these two species it that they're shown you in some patients it
does end up to forty percent of the microphone it's not
a small change it's a field chain button has individually we don't think find them but
a lot of people here and i guess it could you please number of these innovators and
i think they should go back and be that most because maybe they are actually seek
when you look at the species data lost from the patients which are in the region has individually
that the because the because it it's the issues that you find in the got
for most of them they don't have that so long or at niche assignment
for those that we have a well i come from the got but this the issues that we find in the patients
good mentality is actually or else the shoes there is an
invasion pass location of the michael brown from the mouse
two but that so we'll leave it normally we didn't mealy grounds of
that the yeah no mask it's not good for you to have found about
two hundred grants in your that and when you cannot live there
biochemical metabolic potential big lucy there they would impact
among at the base mind that is there is that right and these are the actually
factors that impact it hypnotic and said that and i thought i think so
there you have it it's kind of toxic might come down and it's interesting that
in the literature you can find association of santa hats
and the higher mel scores which are used to
about what's the use of the reverse sellers
okay we can perhaps we can say something about that patients
follow trying to be take that is at which these patients uh
oh it was thought it'd published last year high and low income
you some people can login car stamp you have hygiene come
they happened to be seated and you call me among
the and teletext coding count gauges that mostly
back there it is and they're not that hard in com mostly not couples and the like
if i look sick this species that they haven't eugene some or
it also ordered by the gene number login prompt
individuals ah you mean like species which
are known or suspected to be brought inflammatory and hide in crime in the us
they're talking with the shoes which are typically an right and one there
and of course this is being used by all these big difference
in amman method among species which of course the majority
but of course we just absolutely stipend is the login crank individuals and
it's one person youthful one there's something for one two three four
at least they have less fancy metabolic an inflammatory traits and that
does it gives some of the details about it but it
what it's really say see that login concretely they
just at e. p. is that people that the increase in doing the resistance this leading yeah and information
and we have not done longitudinal starts to say ah ha this
is that east but we talk to clinicians inclusion nations
tell us that they know from clinical studies that people who work these two eight is to not right
ah it had basic attacked about it is kind of
us go these about problems and pencil not only
the clinical picture of this people say is that there had is
but also all the time over past nine he said he had an egg whites
little old gene clark all these people have pulled down significantly morally
and i didn't want people to not only gamblers all
that getting more and more into that that direction
so the analyst there michael but i'm and found that people
who habit high levels of certain methods amongst the issues
pain less way all the time and that's it displayed phoebe image shine change
big a much more when they have low level of these speeches in file level of the speech is
could these have a protected or or we don't know what they are they don't have that so manic
assignment but they can place them kind of when you get it but
produces maybe just wander but it's not one of the important facets
of that not that not that it was absurd the ins and event and look
it french and a fine basically the same type of change
that these by motel at the distribution of individuals
hide income volume cow make to these bios saying that that and are not the call what was
lower smaller so the power was it's that that a lot
so we found only a species but popping out of this eighteen but also highly busting danish study
the train our algorithm to distinguish low and hygiene
con people on forty now nine range
six methadone long speeches could identify thanks to ninety five percent accuracy
and the same algorithm the same algorithm works as the out for banks
the rains
french we went to touch you can't that would that look at
lincoln centre spouses because see once again these an even
distribution the it's less clearly by mogul nineteen percent one out
of five that's what big selected them to be healthy
in this has a guy see see that these these keen on methadone long speeches and
they bias in distribution the same algorithm that button potential and the and the
a dangerous for that as well and that legal parameters go in the same
direction so we do see this huge difference in all of
them and and to try to put the microphone
the potential of michael but i'm in login kong individuals
let me see say this a good friend of ours i can man's yet is low
due to produce new production is a lot that is low bit about the room seemed to be
well and what this high l. p. f. producer tore inflammatory it guys so it'll sink bit
michael button in login count individuals is less fancy so that
we get this kind of meta analysis on about sixteen hundred people some people uh
yeah see and i have had encountered it hygiene count the uh
most of them about operational separate sodium content hide income
that danes looked at spain spain yeah says that i combat in the moment this tool
but when that one both to patients say all these types about it is nash
or i'd be beating up i'd be is that is the last but one day because that it this is kind of exception
and that it's into an interesting exception but in many of these diseases
this neglected organ seems to atrophy so how about these actual costs we
don't know but there is a real no logical see that
well by that that maybe some problem with it because all these
guys that analysts they didn't like the pipeline directly develop
so there are some differences for the other two and if you look at the project that imagine onyx
then one can distinguishing the two parts of the d. n. a. sequencing and
by informatics which we sink was rather standardised across this that is
but there are some differences sample collection processing these two says and we just don't know whether
it's an real loss on that part of the last in this court wasn't important is to establish
because it may using the standardisation his critical and we really need to look into it
so yes we can detect the sky
but read and we also need to alleviate can microphone be
a target for intervention in the sink about this
mike about that to be a should not as a package and which can saying it's not a
abel alliance it's kind of population change like you topic lakes
okay the the stroller micro by um and that
it be tempted to do that in michael b. is that it
forty nine all of it or bees french which are
following colour yes they could die for six weeks and maintenance that was six weeks
that was that and and responsibility of putting them on from your
subject yeah sure but i was caught the middle east
study the dietary intervention as i said was colonial as they did
hi propane law about that and the seven and the the the the fibre
what we observed of course is that all the metabolic that on it does improve that's
that that was expected but what we also also is that you
can login pond individuals these gene count land that it
was improve although not fully we also so that fight unity just people believe spun better
in addition of intervention so that's stratification between respond there's and non responders
another intervention in the contest so ideas we probably ought to
exit the chip we've just got published or not
probably august people eat that these are meant that meet meet but that's what's going on
the the able to fine and number of methadone long
speeches small number of nitrogen angst the feature
impacted greatly by pro that probably ought to consumption this method announced
dishes most of them had that you carry that aspect
what else we look at the models separately mode use but clearly increase in the microphone
and they also try to do that and that too comfy and that sort of
or observation by adding probably ought to think that i think the show got system
re supposed is likely to beauty conversion so yes
we sink we can impact in different ways michael but so
one of the messages his role might that wasn't the mad about lonely just mike about appears to be
less i'll second that now simply identify individuals at least
and interventions good can corrected and possibly alleviate
various countries could have major impact on public yes
just as a reminder chronic diseases you know that i frequent and costly
four point four percent of the population scientists some type true that it is
cost usually causes that you don't use this is the deficit of
social security in in france in the passage male of
the long euros here regularly politicians that that was something about
then it goes back to that so if we could
maybe hands chronic disease by systematic analysis and treatment of market mike about that
is that section of the allegation we could perhaps impact these things
but the question they often arises when people ask me regularly
so that's what i'm going to replace it directly east
change of microbial population causal consequence of chronic disease and
i think it's a question for a lazy mind
and i think that it is a car it meant that it would be
an email and question actually because i think the people replace the mines
forget that the data is it yet another after not the and it is it
up in my problem could contribute to the disease and there is the
likely you know single clothes for chronic disease and that you know it's the
missions that it's totally and fear last this stupid question ah okay
so let me give you some examples which i have presented how could my kingdom come cheated
to the disease do all region is that my problem may be less
has intel lower beautiful produces and that in the past that has
that abandoned one find out there is the issue that systemic information which clinicians stanley
is a facet of almost all it's not all chronic diseases
the at my other example is leave aside was
quit the sink it is got macro microphone maybe toxic by producing
factors which impact and sell it and said poppy
angelo doctors she these guys like even then it's okay
and it and they feel that this okay even ah an experiment an
intervention they feel better now we understand why they would feel that
so how could that place has a toxic michael but i'm
one thing happen but try it and like to present two scenarios
who one is what i call the shots i personally
and that i think is it could be the case in little region speak a cheaper but she got to be
here so i almost made a pathogen interaction infections full of buttons
closing um what is the inflammation of sequence that in information in interested
i think that is all you we know that this michael biologists information to select
for species which dollar information which can be off if i
draw species which kennedy or there'd be a night
so that's your brought about the area which in here than
produce lots of l. p. s. and stimulate from all
information so here have aside to information say settler speeches which promote information then you get this
here's a usual second which we need to break his opera inflammatory my
problem which predisposed to add that it's chronic disease my second
scenario is loss of but here it's a it's a matter
of basing that these might may well happen in labour
said last but she can be virus infection in all about
that the obesity opinionated power right either sinks but that
we postulate leads to input by production and that has been established the dawn
discovery but as it is now the purples is a more the
but here is a little over and then this is all about the yeah and full blown pathogens it's also fine
can now get into these no leash and that at the end the
i think that ties all these motives which are not good for that so i think that
we should strive we still owe preserve health but modulate pink and if l. c.
toxic microphone and please don't nice understand icing that me understand the mechanism does
a beach we happen but please change the patent it's not called
or consequence its contribution and that type understand how it works and have the patience by
doing something about it and i think that the um also pleaded
for that but helping choose introduced my covenant public as well
as a few words about me page it more police
which was conceived by government by our government gay was nine million it nineteen
you don't you also the period to try to address these questions
may these technology available for academics medics industry tried and apple
my problem was things enjoyment has of course but also more than domestic animals that work for you know so you know
you know i mean cartons it use morse about animals as well and the number of
of applications so what is methadone up with platforms and the clinical interface
our clinical interface is because not prepared most people buy i
can program it thirteen claim all uh yeah it has
one of the because hospitals in europe so out is the patients in clinical studies
another of pop on this is cut within the rest of the on health says
for for a pickle and societal issues because we do lose sync because people can
have a great impact on the side and you'd rather be advise and help
in that the cheaper happens that operate it for buttons about operated by it in there
one has to do with samples by bond procedures automation standardisation
our objective is to have about bank of over one million stool samples and the just
a very small pilot study 'cause think about four hundred million also of europeans
around here we and we of course are integrated with bother bunks that
in um in france it one of the big hurdles is that the
data analysis that and they can standardise that best allies that's so
it works quite quite well quite big hate that but it because he
knows that it's not just the ones i've despite agenda about four
point five data bytes of of they can pick and have that in in base although
the best of this to go now is take a little longer
we also have a functional nitrogen angst local was the mechanism
what is responsible for the the elegance is we don't know
local culture all these microorganisms and waiting there would be
alone can output caught caught the but some of them we known their the enemy weeklong like for the
katie forty jeans inequalities have a library which contains about search team
mealy on jeans and then we can screen the activities
of the jeans clad in these libraries by putting them out but otherwise it's in contact
read to you kind of cell lines we have about sixteen screens immunity probably punishment
populism and others that i've been to but and number about acted clones
that are good candidates to go further saying that uh the out of
the path engaged in methadone onyx with the number of visible
papers but it's really planned for scientists of course and it it it's good to see
it that another friend so that you don't know giles a little so it's it's kind of an but that
it's not enough because to not the so side it you have
to engage industry and that we are doing that actively
but i found we had around reach as a as a mission
describe here and it weeks back to have all these but the
of each needs assessment kate by the end of the year
basically which should have been going for that so
i do think that sure my my problem hasn't see attention of into hot topic as
that was six broadcast expansion monitoring target for modulation to improve
has of course that's what we would like to do
and they sing that it could have shift the focus of might see which is mainly cute native to paint
to costly prevented them tomorrow invest say not only
until the resources but also and documents seven
so i just need to acknowledge its many good friends and
the us you see what some of them around
here like this guy may have seen before and this guy unseemly prude with me a little while
michael obvious cup collaborators ought to be made that you
not only steam it without phone nothing would be
a a nice input fat happen that i'd love and that by the commanding
you to pay good cablevision michael by author so it's
h. s. these wonderful japanese garden rich and beautiful
and it is a very final slide i'd like to invite all of
you to the next day you don't inhuman microphone information from
an michael been hundreds you should have that makes the the unit

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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.