I have the great pleasure to welcome joy Dory for a very different presentations at what we had with the animal science this morning and I would say 34 years ago we were agronomist from the same school in Britain in France bones we started at in Iran the French economical Research Institute but one became a world expert and you know which one in gut microbiome asked interaction and meta-genome and he's been known on the area for for many years he's done a lot of science on the microbiome on the meta-genome on the interaction between the microbiome Hansy host but also he always kept I would say some feet in the industry of close to the usage of the science and really developed a lot of new tools and even more more recently on how to use microbial to help the humans to you know the fans or resist to some issues so I will not go all over all the work he did but at least he obtained a lot of prize for worlds and so on so is well recognized so I will let the flow to agile for an opening or closing of the confirm button opening of our minds so let's welcome joy I would like to just express my gratitude for this opportunity to be here to be Andre and colleagues of ADC who made this possible and as Pierre Andre suggested I should start with the term holo by aunt and well modestly I will only talk of the human gut microbiota although I started with the room microbiology at inva and currently we are working also on swine or pork and poultry microbiome I'll stick to the first slide hollow biomes so hollow biota is an assemblage of very different species and it refers to the fact that on earth the vast majority of living organisms are associations especially associations of a larger eukaryotic cells and microorganisms this is true for insects for plants for large animals and all mammals essentially and it's also referring to the fact that they adjust and transform and co-evolved and evolution actually is this coevolution between the hosts and their microbes so I will also emphasize quite a lot symbiosis which is the term given at the top here we humans or babies human babies are born from a sterile environment and we develop our immune system and our gut microbiota at the same time during early times of life and that leads to a unique recognition of the microbiota as every cell every tissue or every organ of the human body as part of self by the immune system and this recognition is essential for the maintenance of health and well-being now there are conditions where there will be disruption disruption at the level of the ecological balance is consistently associated with risk of infection and we know it very well for humans for Clostridium difficile a infection which are very often into antibiotic therapy actually and there can be disruption at the level of immunity or immune tolerance and this is associated with the disease condition autoimmune or immune related disorders and so what we want to do is to build knowledge to the point where we can use the knowledge to manage the risk and mitigate the risk whenever whenever possible an aspect we have to deal with and this has been true for all my career basically starting with in our 33 years ago on the gut microbiota of the ruminants is that we only have accessed by culture in the laboratory to roughly 20 to 30 percent of the dominant gut microbiota and that stimulated a lot the molecular ecological developments that we are basing our knowledge construction today upon it essentially was centered on re-evaluating the microbiota by culture independent approaches now PR andreas suggested that I relate in my talk to a Sakurada Familia and Gaudi well the first item I want to make on that is that with this picture of of gaudiya thinking is that he was greatly inspired and in our field of molecular ecology the inspiration for me came from Carlos in Champaign Urbana Illinois in the u.s. who actually decided to pick 16s ribosomal RNA as a marker of evolution of all life forms and this has been really a unique insight towards the development of molecular ecology and so I will skip directly Malakar we started in the 70s so I will take us directly to the year 2000 basically where it became possible to address the characterization of complex microbial systems by metagenomics and using hence the characterization of the meta genome which is the combined genome of all dominant microbes within a complex ecosystem it was really a technical revolution for us and this figure just highlights the very steps that we we need to implement to do this it's essentially extracting total genetic information from human intestinal content in in this case and then applying whole genome shotgun sequencing very classical sequencing as it was applied for the human genome itself to basically characterize this second human genome by assembling and annotation of genes and one of the goals was to construct a reference gene catalog a repertoire of all the possible genes that one would expect to find and just in three clicks I have a highlight of what we have been able to built in terms of new knowledge the first item is the reference gene catalog so we are published the first one in 2010 and it was 3.3 million genes out of the characterization of 124 human human individuals in European countries in essentially done Marc and Spain and we went up to 1,200 67 individuals in 2014 and published a 10 million gene catalog it is not complete so if we add more people then we will have more and more information coming but we know that we have characterized the core the shared components already very early on in this process so we know the format as you know and we also characterize the mouse-king catalog the swine gene catalog was published last year 7 point 7 million jeans for the swine and we are currently working on the poultry metagenomic catalog what we did is we expected to find the average human configuration in that and we actually described preferred ecological arrangements and I will illustrate that further of the human gut microbiota we were very surprised actually to see that there is not one average person but rather three different types that we called enterotypes and then we also worked a lot on comparisons between patients and healthy individuals and describing at the level of the meta-genome what we call dysbiosis that we have called his bio this for now 25 years in context of non-infectious known transmissible but rather chronic infection chronic diseases sorry and they relate to disease major disease of modern societies like obesity type 2 diabetes hepatic liver cirrhosis hepatic disorders and in doing so we described lodging count or low richness of the equation as a key have strata fire and I will illustrate those two points and two types and lodging account in the next slides so if we characterize many individuals and we will present their distribution in a landscape that basically tells us all the possible microbial arrangements what we see is this we see three hot spots three dense densely populated regions and they correspond to ecological arrangements of the gut microbiota so this really came as a surprise we did not expect to find this kind of a distribution in the human population it has been documented since in mice in monkeys and also in pork actually so it's probably rather widespread in terms of observation we have sequence information so we have some level of identification of bacteria that are associated with that we know that Bacteroides the genus Bacteroides the dominant gram negatives of the human gut microbiota is highly represented in one of them and the two drivers of the other and Troy types or luminal caucus as well as methanogens and patella and we also linked this to what I call gene count or richness or diversity of the system such that back progress is on the loading count side and the others on the hygiene count side and just talking of gene count what we observed when we did this distribution of humans as a function of gene count is the the blue curve here we expected to find again an even distribution around an average gene count for the humans overall and we we observed this is king here with the low richness microbiota fragment of the population or fraction of the population and the high richness microbiota fraction of the population and as I was suggesting the entire types or ecological arrangements are not evenly distributed back toy death is highly dominant in the low richness microbiota individuals whereas the two others are more represented in high richness microbiota individuals and just after this publication caribou in the u.s. described the relationship between richness and diet dietary habits showing that those individuals with low fiber essentially a fast-food type of diet dominated will be on the web to areas dominated side or on the low richness microbiota side whereas high fiber high fruits and vegetables dietary habits will be most represented among the high richness microbiota and so what we have designed on that basis is this pipeline of analysis were we do no longer use sequence information to reconstruct genes and genome fragments but we essentially generate millions of short sequences and we map those short sequences onto the reference gene catalog so it's a very rapid bioinformatics way of counting genes essentially and we generate gene count or gene abundance matrices that we can also now transform into metagenomic species abundance matrices and obviously in the end what is important is when we relate gene counts or species counts to metadata that correspond to clinical information to physiological information or pathophysiological information and I will illustrate what we can expect from that but just at this point I need to emphasize the fact that standards and it was mentioned yesterday already for for the work and animals standards are very important we spent five years working on standardization and in 2015 we published standard operating procedures on this website microbiome - standards and they have been ever since downloaded quite efficiently actually we were within a year up to 2000 downloads of those Center operating procedures that would probably very well apply to any intestinal ecosystem you may think of and so just to summarize that each dominant microbiome gathers on average for humans five hundred thousand genes 100 plus bacterial species are represented there's other things than bacteria our feeders map bacteria phages for example quite a lot there's a viruses occasionally and also eukaryotes at some level this means 25 fold the number of genes of the human genome for each of you basically we have constructed the reference gene catalog of 10,000,000 non-redundant genes available for profiling we have a small proportion of genes that constitute a core that is most shared between individuals but we all have signatures that are personal individual and we know that humans vary in terms of genes gene counts metagenomic species and also ecology or antara types the microbiota can be characterized by rapid quantitative metagenomics and we also have been able to reconstruct genomes of non cultured microorganisms on the basis of trust during genes that are always Co abundant in any any sample so one step forward towards the construction of sacre de Familia or knowledge construction from from metagenomics is the highlight of specificities of the microbiota in disease alteration and we initially call that dysbiosis and I will emphasize the fact that we need to consider this as alteration of symbiosis it's all the hosts and the microbiota that are changing together not just the microbiota but before I go there I want to stress the fact that while we are host to 50 trillion bacteria each individual they are interacting with our cells our immune cells our neural cells our brain and they are interacting with food as well and in doing so they contribute to health and well-being and yet in spite of that they have been ignored or neglected for a long time and I will just with within three slides emphasize the fact that we have changed many things just over the recent past two over two or three generations that will have an impact on the microbiota so the first thing we change is nutrition you know of nutritional transition essentially you switch towards more protein and animal protein and fat and less fiber well that will have a strong impact on the microbiota considering fiber from the diet is more than 50% of the carbon and energy that the microbes will use and this is very recent essentially over more than 100,000 generations for the genus omo we receive sixty percent of our energy in the form of plant material and just over two or three generations we have brought this contribution down to roughly ten percent it's on average in france where i know 17 grams of fiber per day per per individual the recommendation for the nutritionist would be more than 25 grams another thing we change is exposure to chemical compounds that we call eggs in au biotics and this is there's not very many papers that document that but this one is essentially addressing the exposure or impact of the exposure to emulsifiers that are used a lot in processed food in a mouse model and mice when exposed to emulsifiers basically allowed to measure very high proportions of flagellin or lipopolysaccharide that was mentioned yesterday by our surgery era in intestinal content and that will lead to promote inflammatory responses when the microbiota of those exposed animals is transferred into germ-free animals then it actually transfers the risk it transfers the alteration of the microbiota and the risk of weight gain with a high-fat diet or the risk of developing inflammation in an induced inflammatory condition so that's exposure to xenobiotics and it would apply to many different compounds pollutants drugs and obviously antibiotics and the last thing we we changed is everything that surrounds birth we change perinatal management and environment and I just listed just a few items among many that will count that will probably impact the microbiome hence the symbiosis and essentially that relate to an alteration of mother-to-child vertical transfer of the microbes now I know it's a complex concept for the the chicken were today or nowadays the transfer the vertical transfer is really not typical of what happens but in humans what is most critical in what we see in terms of documenting in habits is a request to c-section for example certain section is on average 30% in Europe today but in some places it's more than 80 percent so in the city of Rome Romulus it's over 80 percent and there are cities towns in in the world today where it's more than 90 percent it's true in Brazil for example or in China were well the reason we hear of is just dealing with so many births that they have to basically program now this is a complete breach of the vertical transfer and it will have an impact on the development of the microbiota there's associated increased risk of disease but not not so high actually so it's not that dramatic but it will over time over generations probably have an impact and it has led to extended hygiene hypothesis or what Martin Blaser calls the missing microbes hypothesis it's also true for overall hygiene and also exposure to antibiotics in the u.s. I'm told it's at least two systemic antibiotics treatments at birth and very often three just for prevention so in that respect what we usually feel is that there should be a continuum between health on the one side and disease on the other and that's reassuring but what I want to document now is that there could be complete shift complete switch and not continuous item between between off and on disease so a break that I'll illustrate with this bead in the in the valley that may actually switch to the to the other body and one way to illustrate that is just to to see how the system can handle stress well when everything is fine you have what we call you biases of the microbiota you have normal physiological immune tone there is immune reactivity all the time and symbiosis here illustrated by cross stroke between the microbiota and the host there can be stress there can be genetic predisposition infection diet lifestyle environmental triggers and that will lead potentially to a reversible imbalance of the microbiota or a transient low-grade inflammation as an example of host deterioration and that consistently leads to an alteration of the crosstalk well if if the system is robust then basically when you remove the stress it will return to its original configuration but if the stress is so high that it goes beyond the robustness then what will happen is it will end up going into a completely different situation in this case there will be sustained oops sorry though he sustained alteration of the gut microbiota long-term alteration and on the host side sustained low-grade - overt inflammation and actually both are talking to one another such that the microbiota is essentially in this case dominated by gram-negative bacteria sending pro-inflammatory signals to the host and the host in return is sending oxidative stress signals to the microbiota favoring the non strict anaerobic bacteria that again under to entertain the the system so it's Auto aggravating condition complete switch into an alternative system this is actually from the creative transition theory that is promoted by Martin Schaffer in versioning and in Holland incidentally medicine today is only addressing symptoms so essentially dealing with inflammatory signals so you could think of a rather more although biomes related holistic way of addressing things tackling the microbiota as well as the host parameters so what we see when we look back is over the second half of the previous century as we were controlling better and better infectious conditions in humans what we saw is an increase or a rise in incidence of immune mediated disorders this is true for Crohn's disease and inflammatory bowel condition for here multiple sclerosis or type 1 diabetes which are autoimmune conditions asthma as an illustration of allergies it's also true for metabolic disease for obesity diabetes it's true for colon cancer for example and it's also true as we see it today with the neuro degenerative and neuropsychological disorder the increased curve for autism is just dramatic it's exponential uncontrolled today one birth out of 64 in the u.s. is concerned by autism it's one out of 152 in France and so it's a dramatic situation that we completely do not control part of it is explained by an improvement of diagnosis but only one-fourth roughly and so it's it's a very high concern it should be a high concern those are in my view diseases of man microbe symbiosis for which we do have no prevention and also so we have been able to document in many conditions dysbiosis in the form of alteration of the gut microbiota but in fact what we think today is what we see is an alteration of man microbe symbiosis and there are recurrent features on both sides on the microbiome side what we see is low species richness very consistent and loss of dominant menthols I'm just lighting one here Faycal you back to your own present it see I have a few more names coming in another slide they are dominant and for many of them we have documented their ability to protect the hosts in terms of inflammation or gut permeability for example and in those cases sometimes we see a rise in aura proliferation and overgrowth of gram-negative battle balloons and on the host side what we consistently see is an alteration of gut permeability and low-grade inflammation at least low-grade inflammation so if we move one step forward then what we dream of doing is using this information for well for diagnosis for example and for treatment and so in humans our our grain is to find predictors within the configuration of the gut microbiota and I was as was suggested by Phillip Jent before probably by combinations of hosts and microbiota features or parameters and so I just give some illustrations of that in the context of obesity this is the distribution curve I showed before with the low gene count hygiene count fragments of the population if we separate non obese and obese none of these in green or bees in orange what we see is it's actually by model so it's really two different populations there's roughly 10% of the population on the logical side among the non obese healthy individuals and there's 25 percent or so in the moderately obese population if we look at extreme obesity with BMI is over 40 what we see is it's 75 percent of the population on the lodging council so this parameter is actually following the aggravation of the pathophysiological condition what we can do because we have a sequence information is to try and identify signatures so this illustration this sort of barcode represents individuals as columns and species as lies for each species we have picked 40 genes and we code the abundance of the gene with a color so the more abundant is the dark color the less abundant is the light color and individuals as we have been ranked as a function of their gene count or gene richness in their microbiota so loading count to the left I didn't count to the right and what you can see is that species like Romania caucus novice or typical of loading count microbiomes whereas the two following ones taken aback urine pregnancy or metal a blue vector or typical of Hygiene count microbiome so we can identify signatures and just picking four of those then in a rack analysis what we see is that we have a model a diagnostic model that allows to completely predict whether the person will be on the loading count side or the hygiene count side well what does it tell us you will say well in fact we could connect this condition with health and in moderate obesity what we could show is loading count is consistently associated with left with less healthy metabolic and inflammatory condition it's loading counties associated with increased adiposity distribution of fat mass in the body with insulin resistance with this lipid emia in terms of blood cholesterol or blood triglyceride significantly higher in loading zone and also inflammation markers so all those parameters will predispose to comorbidities aggravation of the condition so predicting gene count is actually predicting the risk of aggravation of this particular condition we went a bit further in moderately obese individuals what we did is an intervention in forty nine individuals with low fat high protein and high diverse fiber diet and what we could show is that low richness microbiota is a predictor of the poor response to calorie restriction this is just a distribution of our subjects before we do the intervention so we have lodging count hygiene count individuals and what we can show is that the low gene count will predict a poor response this high sensitivity CRP a marker of inflammation well we do correct it quite well when we have individuals with hygiene count at the start but not so much and significantly less in individuals that have the lodging count at the start it's true for weight or weight loss for triglyceride for other parameters of insulin resistance for example yet in this condition where we have a high diverse fiber diet what we have seen is nutritional intervention able to increase microbiota gene witness for those that starts on the loading downside by by 25% and it remains stable during the second half of this 12-week intervention where it's only maintenance of reasonable dietary condition another area where we have been able to find predictors is a cancer treatment it's cancer immunotherapy and what we were able to show with Patricia Lopez my colleague in collaboration with the local seed version in Paris is that we can identify biomarkers in the microbiota that or adjuvant of cancer immunotherapy if they will help the efficacy of the treatment the way immunotherapy works or it will induce actually great permeability so cyclophosphamide is one of them it will induce permeability and passage of bacteria and bacterial molecules basically in this condition some bacteria in lymphoid tissue willing will prime a response that we call th one th 17 it's a pro-inflammatory response but in this case it will help in the tumor bed to reduce the tumor and if you have the right bacteria then you have the right immune orientation and you have the right effect on the tumor if you don't have the right bacteria then you lose completely to the point that in mice we were able to show that vancomycin will remove the bacteria and you will completely lose the efficacy of the treatment now that leads to thinking of applying that directly in the clinic and in fact our hoodies are applying directly that in the clinic in avoiding to use antibiotics that will remove the bacteria and also thinking of using the treatment combined with the bacteria as a sort of a therapeutic probiotic to basically gain efficacy in terms of percent of responders among the the patients and the last example I want to give is another condition of a blood cancer in this case where our colleague Eric Palmer in the US has shown that he could very easily run the patients as a function of diversity so this is high diversity intermediate and low diversity patients and those patients undergo what is called hematopoietic stem cell transplantation it's a bone marrow transplantation to reconstruct immunity in context were a white blood cell or cancerous and well what is known is that the survival of the patient is rather moderate after that but what Eric Palmer and colleagues were able to show is that there is a productivity of diversity the higher the diversity the better the productivity of survival so this is the curve of survival for the patients after hematopoietic stem cell transplantation and what it shows is that if you have high diversity then there's more than 70% survival within three years following intervention and conversely with low diversity it's less than 40% survival so it's a very strong outcome in terms of prediction by analysis of the microbiota again with a rather crude configuration which is diversity and so to push the dream a bit further and this is as you have seen yesterday what Sagrada família should look like by 2026 well I already mentioned that we can use microbiota as a target and nutrition is a very strong very powerful way of modulating microbiota we can increase by 25% just with a high five diet our concept here is that using high-fiber we promote fiber degrading bacteria that will actually use the fiber but also feed the rest of the microbiota and promote diversification of the overall microbiota population we we think that this should lead to new concepts basically in terms of application of what was called prebiotic and in this real probably diversity of fiber is really the key and well there's an intermediate level where what we want to do is to use bacteria as probiotics but what I'm showing here is a new generation of probiotics essentially there are a number of commensal bacteria gut commensals that have been documented for their efficacy to improve physio pathological condition or even to induce really very fine effects in terms of anti-inflammatory or protective effects on the gut barrier for example and so this is just a long list of bacteria some I have highlighted with a blue star well for those we are at a point where people are actually working very hard to culture them mass culture to live release them put them in powder stable powder and then to use them in humans to demonstrate that we can have a beneficial outcome in patients this is true for many of those for which small companies have been created to actually bring those to the ER to the clinics I have highlighted here the the colleagues scientists who were at the start of identification of those bacteria and as you see for some of them I have highlighted what is very likely the bioactive molecule so it's for example polysaccharide a for bacteria genus which is active in reconstructing a normal immune tone in an altered condition in mouse models and at the very extreme what has been developed recently is what is called microbial therapy or fecal microbiota transplantation so in this case what we want to do is to apply a complete reconstruction of the gut microbiota by inoculation of a a complex microbiota either from the person itself in autologous transplantation or from a healthy individual in allogenic transplantation so I'm not giving the example of Clostridium difficile a which has been very well documented and it's a condition in which fecal microbiota transplantation cures the pathogen in more than 90% of the patients in conditions were the complex microbiota is used people are trying to simplify that with a consortium of bacteria that do not seem to work as well but this is underway at the moment now the example I'm giving here is work by maksim you drop in diabetes so the main criterion here is actually insulin sensitivity so it's including patients that have diabetes and that either received an allogenic fecal transplantation so from a non diabetic person or as a control an autologous transplantation from themselves and what was shown in this work is that compared to healthy individuals that have insulin sensitivity the patients have at baseline insulin resistance and just the transfer of the microbiota from a non diabetic person can restore normal insulin sensitivity within six weeks after transplantation and after just one transplantation by in this case gastroduodenal intubation and administration in the georgina this is quite striking in this context autologous transplantation obviously will not do anything the impression from the data that was generated is that over the six weeks of intervention there is a constant evolution of the microbiota so probably it's tending to either go back to its original configuration or to find some intermediate configuration so we don't know whether the effect will be durable beyond that level so I mentioned that there there will be triggers that disrupt the symbiosis between the microbiota and the host and in some conditions clinical triggers like surgery chemotherapy radiotherapy antibiotics especially long-term antibiotics may actually induce complete shift of the microbiota host symbiosis to an altered configuration so if it's only moderate stress then functional food nutrition fibers may be the key to restoration of normal condition restoration of symbiosis if you go beyond the usual robustness of the system so a complete shift in a natural stable state then it may call for what what I just mentioned microbial therapy or fecal microbiota transplantation and I'm following very closely a small company in France that is promoting autologous transplantation in patients for which basically the triggers are programmed you know that you will be applying chemotherapy for example in a cancer patient and you know that in doing so you will be disrupting completely the gut microbiota so the hypothesis here is if we reconstruct the microbiota of that person with its own before then we can actually restore normal condition normal initial condition and so it's a bit complex illustration but basically what Matt Rama is doing is collecting samples before preparing conditioning the sample storing at minus 80 degrees until the patient's has finished its initial conditioning kamo therapy 15 days antibiotic 15 days and then we administering the the gut microbiota to reconstruct the the ecosystem that has already shown an impact it's an ongoing trial but essentially in terms of weight loss which is very well documented for those patients there's lots of 3 to 6 kilograms very often the weight loss continuous or the condition degrades further and then the patients are back in the hospital for a consolidation chemotherapy so they basically degrade their health condition in a way because of the treatment the context of autologous fecal microbiota transplantation what is shown is that the patient's we gain weight they not only reconstruct their microbiota reconstruct their gut transit but they also recover in terms of a very crude parameter which is a way so just as a summary we as holo biomes share a core microbiome so we have many things in common and yet we differ by genes by species and also a gut ecology and gene count gene count or gene richness which is a very important stratify er in terms of health probably because we have not found the intimate signatures that relate to that and this bio this should be viewed as an alteration of man microbes symbiosis and microbiota modulation is really something that we should use for reconstructing the ecosystem for prevention for modulation well a major way of leveraging prevention will will be nutrition ecology I know this term is really keen to do PR on race so I had to have it at the last one here thank you very much for your attention I just have a list of police why I decided to move this talk to to today because really we needed some time to listen to this very excellent presentation from John so if you have any burning questions before the lunch yeah maybe a question excellent thank you commenting are two questions just come to my mind that how later Ganga as a poultry and swine producers without is built knowledge that we have already with humans and they'll have a bird that some animals that have done much higher interaction with microbes and basically know nothing compared to what you have presented here so two questions on on the slides that you presented before first the immune caused diseases that you have shown in your right graph yeah that slide is that is that I'm extracted from age is that not related today today included aging that's tremendous so there's no relation with aging and it's known as immune aging actually or immune degradation with with very old age but it's only true for very old very old person very old very wealthy elderly is very elderly and it's not consistent in all elderly people so there are there's a very nice piece of work from colleagues from Cork in Ireland that studied hundreds of elderly people and they were showing that there's a connection with immune aging and nutrition especially showing that people who were institutionalized or living in institutions that receive a low diversity diet will have a tendency to actually evolve faster towards immune aging and so there's a tight connection between nutrition and the impact or association of aging with with degradation of the immune condition okay so Aleta thanks just to relate with your initial comment and I mentioned that for swine we generated the reference catalog of meta-genome for swine seven point seven million genes we are currently doing the same and additio is closely associated to this development with chicken so currently we have a sequenced the meta-genome of 300 chicken we have collected 600 but we want to know whether with 300 we already have a good picture of the ecosystem in terms of metagenomic reference catalog I suspect that in chicken more than in swine we will probably find differences that are typical of the location they come from or the line breeding line that we are addressing so we covered a very broad diversity but so far I cannot say more than that because it's working progress any more burning questions if not I would like to that you joined me to really warmly some joy and for this excellent presentation [Music]