[Music] so it's a pleasure to be here and I will also talk about the human gut microbiota but I thought I would start off with just spending really one minute to think about what are the different animals like and what makes them different from each other so that you have at least a little bit of context context and I wanted to link up to the poultry as well so really the microbiota and the whole gut metabolism is shaped really mostly by the diet and the gut anatomy and of course that also interacts with each other so we have carnivores on one side which mostly eat animal-based foods and they're less dependent on the gut microbiota where's the herbivores who really eat very plants that are very hard for mammals to digests they are really dependent on the gut microbiota and that is normally reflected in their gut anatomy as well they have big fermentation chambers essentially in their intestinal system and the microbiota help them really to digest the grasses that they mostly eat so that they can really get the energy out of their food sources and then we have the omnivores such as chickens and pigs and also humans of course so mostly you see a correlation here between the the shape of the gut and the importance of the gut bacteria but of course nature is messy and they are exceptions so in a classical exception of this rule upon das and one of my colleagues at the route actually did a little bit of work with the pandas that are currently at Edinburgh Zoo they're a gift alone from the Chinese essentially and the Panda is obviously a very extreme herbivore it only eats bamboo it's very hard to digest for it itself it doesn't have the right enzymes but it has a ridiculously small gut and a really poor microbiota so it's a real conundrum of the of the animal world because they're all the rules break apart so this is really also a reminder biology is messy and we can make general rules but there are always exceptions of these rules as well so I will mainly talk or I will exclusively talk about the human gut microbiota as well herve has done a lot of the job for me if on the introduction already so I won't spend very much time you are all aware we highly colonized by microbes I just want to make you aware I will only talk about bacteria but we are becoming more and more aware that there are many other microbes as well we have archaea in there which is a different type of prokaryotic microbe we have many viruses and phages we of course have eukaryotes and more and more people now started to start to study these as well so we know much more about the bacterial microbiota then the other microbes so just that you're aware I think there's a whole new revolution coming up that we better understand all the other types of microbes that also have functions if you're looking at the bacteria it's mainly to file are the Firmicutes and the back druid it is that are abundant so what you see in this in this up image here is really a this sort of phylogenetic tree depicts all the different broad microbial groups you have on the planet so anything that may live in the oceans in the soils and so on so if you're looking into got ecosystems it's mainly these Firmicutes and bacteria details that are very abundant and then we have some minor groups such as the artena bacteria and proteobacteria so it's not very diverse on this very broad scale but if you home in on to these groups so in the lower partner now you see maybe the microbiota that you may see in an individual so each of these branches on this tree here reflects a different type of bacterial species and you see that was in the firm acutest particularly each individual has many different firm acutest species strains general and families so within these two groups we have a high diversity and all these microbes have different functions and different traits so I won't dwell on this we already heard the microbiota has many functions on the hoos such as the barrier function against pathogens immune interactions and many metabolic reactions I will mainly talk about the charge in fatty acid production today but I want to make you aware also as heavy as said as well there are many different metabolic interactions that are happening between the microbiota the diet and the host so the charge and fatty acids are very important also in terms of quantity but the microbiota also interacts with phytochemical seer in the diet very much many different hundreds of different plants secondary compounds that the microbiota is involved in transforming further they make some of them by available they can change their bio activity but I won't have time today to talk about this in detail the microbiota is fueled by the diet mainly they can consume also molecules in the gut wall so they can use some endogenous molecules from the human host but diet really is the most important food and energy source for the microbes in the large intestine and was in the diet it's mainly the carbohydrates that are the food source for the microbiota and most of these carbohydrates that come from plants cannot be digested by the human host itself we just simply don't have the digestive enzymes to break down these dietary carbohydrates you maybe know them as fiber or we can also call them non digestible carbohydrates because we can't digest them ourselves so they essentially go straight through the upper intestine reach the colon where they can then be a food source and an energy source for the microbiota so we have different classes here if you think of the plant material that we are consuming in the diet we have the structural polysaccharides so there's a cell wall constituents of plant cells and we also have some storage molecules that are non digestible by us a classic one is inulin which I guess most of you will have heard about you find it in your guts nowadays or as a prebiotic so these are fructooligosaccharides that again we don't have the enzymes to digest them ourselves and they go through the system into the large intestine we can take up sugars of course and then starch has a bit of a special rule we do have enzymes in the small intestine to digest starch so principally it is available to us directly we don't need the microbiota but due to the physical chemical composition of the starch some of it will simply not be completely digested through the upper gut and reaches the colon so this fraction of the starch is called resistant starch and we'll I will come back to it in a minute so I already touched on the phytochemicals of course some of them are digestible and and can be absorbed in the upper got other ones will also go in : and the microbiota is heavily involved in their metabolism protein and fat on the other hand mostly is digested further up so on balance we can say a plant rich diet is more health promoting through the gut microbiota because it fuels and energizes the microbes and they can do their metabolism so if you think about the nine digestible carbohydrates and chemical turns we need to be aware that we have a multitude of different molecules here and there just a few examples here this is by by no means all the different molecules you will find in diet so I just wanted with this picture get the message across that you have different monosaccharide components of these different fibers we have different like Idzik like acetic linkages so you may have alpha linked ones like the resistant starch here you may have bitter linked ones and you need different enzymes to grate to degrade all these different types of fibers and not each microbe says has it so you need different microbes that then are able to break down these Mullis and these these polysaccharide chains into monosaccharides that they can then be further metabolized and are used as a food as an energy source we also have linear molecules we have branched molecules as you can see here some of them have branched points and then some of them consist also of non monosaccharide constituents such as the fuelling acid here that you find in wheat ground so the picture just shows you there's a very high diversity chemical diversity in the fiber and you essentially need a diversity in the microbiota that then collectively will be able to break this down because you need all these different enzymes to break them down and make them available so that's on the chemical side of things but we also need to consider the physical side of things and this is something I think we have maybe you can order bit too much and more and more people are now thinking about this more and looking into this in more detail so you can if you think on the physical side of things we can basically broadly categorize these into soluble and insoluble types of molecules or complexes of molecules and it appears that the insoluble complexes are much harder to break down for the microbiota many microbes have enzymes that can get at these individual polysaccharide chains but once you have it in a fragment of a plant cell wall or as a very particulate starch particle is much harder for the microbes to get access to these individual chains of polysaccharides and break them down so the picture is emerging that we need keystone so cons kills keystone species in the microbiota that have these special traits that they can actually get access to this insoluble material and I want to sort of go through a story on the example of resistant starch and that emerged in our lab over the last maybe ten years or so where we discovered that this bacterium here room in a caucus brownie ice seems to be one of these keystone species for resistant starch breakdown remember resistant starch is the proportion of starch that simply hasn't been digested by the time your digester has gone through the upper intestine and reaches the colon and there it is available for the microbial fermentation now at the time where we discovered the room in a caucus brownie I story already we knew of many bacteria in the large intestine that can break down starch so there's a few example here some of the Bacteroides species can do it a bacterium called Ubik team rectally which is one of the firmicutes can do it but it looks like they are mainly geared towards the soluble star just not these particular globular particles that come into the system so how we caught on to room in the caucus borromeo broomy I was really due to a human dietary intervention trial that we did at our Institute at the Rowett Institute we do fully controlled trials so we asked a research question and then we get our dieticians on board to design diets for us that humans are willing to eat but that have been changed in a way that we can really tackle a specific question and then these people eat our diets for several weeks and we can take samples and analyze this and the beauty is that as we provide all the diets we have an exact idea of what they're taking in we give them measured amounts they do way back so we can do we can provide the energy dependent on their individual metabolic rate and so on so it's very very controlled studies how to do how to find people who are willing to do this eating your food for several weeks but they're very gratifying because it's a very controlled experiment we can do in humans so what we did in this trial and I really only have time to give you a tiny snapshot of this aspect of the study is that we wanted to see what difference does it make to the human physiology and to the gut microbiota if we changed the type of carbohydrate in the diet so we kept for protein and fat the same the overall macronutrient wasn't changed but the the type of carbohydrate that was in was so over three weeks these people were eating a diet that was extremely rich and resistant starch and very pulling all the other non non-starch polysaccharides so very fiber pool and then in the second intervention phase or for some people it was the crossover in the first phase they got all the starch taken out and it was almost only plants of all fragments mainly wheat bran but remember otherwise that the total amount of carbohydrate fat and protein was the same in post-intervention periods there was also weight loss at the end but I don't have time today to talk in to talk about this who can't just concentrate on these phases here we had 14 volunteers I think you see the two different groups from the crossover design and what you see here is just a quantitative PCR assay where we looked at this specific group of course we did many more measurements I just show you this today so we followed each volunteer over time it took fecal samples roughly two to three times a week of these people over ten weeks so each line he has a different volunteer and you see this bacterial group was completely skyrocketing as soon as these people crossed over onto the resistant starch diet so once we bombarded their system is resistant starch the room in a caucus absolutely loved it and went massively up in quantity and as soon as we went over to the next diet they went back to their baseline levels so that showed us the room in the caucus seemed to be very important in starch breakdown in humans but you can also see that two of the people down here didn't really have this bacterial group and was what was really exciting is when we then looked at how much starch the people were actually digesting so remember fully controlled trial we knew exactly how much starch they consumed we then took fecal samples and measured starch directly in the fecal samples so we could see from what they've taken in what proportion of starch was excreted in feces and you can see for all the volunteers the starch had pretty much completely gone we measured hardly any starch in the fecal samples of most of our volunteers but for the two volunteers here that had very low lumina caucus broomy i we had massive amounts of starch excreted and faeces so we could see that the people who didn't have this bacterium could not really digest the starch so that told us that room in the caucus broomy I probably had a very important function in these in humans in starch breakdown and then one of our volunteers was happy to give us another fecal sample after we had made this observation so we got a fecal sample of this person a few years after the study and we just in the lab incubated it with starch so we took the fecal sample put it into a test tube added resistant starch and looked at how much of the starch was degraded over time and that was pretty poor most people you see the starch is nicely degraded but in this person there was very little starch degradation in vitro in the fecal sample we then added known individual bacteria that are known as starch degraders so we had before the pitcher mother the scientist you became rectally and Bacteroides theta and also our room in a caucus broomy I here which had been blooming in all the people and you can see that most of the starch degraded didn't really do very much but when we added the room in a caucus brownie I to the fecal sample we did restore the starch degradation to what you would see normal healthy person so there was further evidence that room in a caucus Rumia is special amongst the starch degraders in the large intestine so the question is what makes room in a caucus premiere special over the other starch degraders well of course nowadays we have a lot of genome information we have a lot of sequencing data so if you look at the genomes of these bacteria the question is do you see something special and the short answer is no but I'll talk you through it so basically we know which types of genes are involved in starch degradation there are many genes called glycoside hydrolases these are enzymes that are responsible for the degradation of carbohydrates and there's one group in specific the family thirteen-year GH 13r amylases they're shown in blue here so what you see here is that you see the numbers of starch of enzymes that are involved in starch breakdown in different bacteria so these are all genome based data we scan the genomes encountered all the genes that are glycoside hydrolase thirteens in blue and also other families so our room across caucus bro mia is at the end here and what you can see is that really if you just look across it doesn't look that different from the other bacteria that unknown starch degraders proof so from the courage of numbers of genes involved in starch breakdown you wouldn't really have picked that bacterium out based on its genome sequences alone so what seems to be happening is that it's the way it arranges these enzymes which really matters for some reason here we go so basically what this bacterium does is it organizes its starch breakdown enzymes on the cell surface in a sort of multi-enzyme complex it has extra domains on these enzymes which are the so-called doctrines and cohesions that can bind different proteins together it has structural proteins called scaffoldings that then can make a three-dimensional complex also link this whole apparatus to the cell surface so they basically have little machines out there which can dock onto the starch because they also have carbohydrate binding domains in these little machines and then basically through these three dimensional arrangements of all these different enzymes that can then work together to break down these particulate starch matter they are able to access the starch which the other bacteria can't do because the other bacteria have a totally different a way of organizing these enzymes so just as a comparison here we have the the starch system of Bacteroides theta out a micron it's a gram-negative bacterium so the cell surface looks different but it looks like this bacterium can get access to soluble starch chains and then it fragments them and can take the oligosaccharides monosaccharides in and consume them it itself but this apparatus doesn't seem to allow the access to very hard to digest globular impact up in insoluble starches as the room knocks brew me I can do so when we discovered this is what it was really interesting because relatives of this bacterium rumen Cox brew me I have a very similar system on their self surface this bacterium here Romina Champlain and this is a human bacterium as well but these systems were mainly discovered beforehand in ruminants in cows and sheep and this system was known as a cellulose breakdown system so here we have very closely related bacteria that use the same structural way of organizing their enzymes but the enzyme specificities are very different so structurally they use the same concept but by putting a different function in their function in the ecosystem is very different so this is very nicely visible in the genomes again you have a genome based analysis here we have out for different room in a caucus species one is a room and bacterium here so the blue ones are cellulose degraders the red one is our starch tgreider from the human gut and then we have another relative up here so what you see here is that we counted again these different enzyme families you have the starch breakdown enzymes here you have cellulose breakdown enzymes in the middle and then you have a few that started around and if you just look at the colors representing the different bacteria you can see our cellulose breakdown bacteria have many of the cellulose acting enzymes whereas our starch bacterium very quickly clearly stands out here the by circulant is the one in the middle it likes different ami cellulose --is so here the genome carriage of enzymes tells you very nicely what the bacteria do but they use a very similar biochemical approach in attacking these recalcitrant fibers okay of course this is all about the start of it all what it's all about in the end is making charge and fatty acids so they do this fiber degradation to get access at the oligo and monosaccharides that they then can ferment to charge and fatty acids the fermentation gives them energy in the charge in fatty acids essentially our by-product for the bacteria so this is a very simple depiction of the overall ecosystem in the gut the the microbial community that turns the fiber into charge and fatty acids but of course there's a lot of interaction between the individual species so just very briefly I want to highlight that this is a community action it's not individual bacteria doing this so for example if you're going back to starch now and look at a different starch degradable for the bacterial model it centers this bacterium can break down the starch and it makes form it locked it in acetate as fermentation products and then there are other bacteria that can either live off the fermentation product so for example this bacterium you hear cubic tea room Holly I can turn lactate and acetate into butyrate he have other bacteria that can turn locked 8 into propionate so it depends a bit on who's the dominant bacterium in your community whether you get more putrid or lactate from sorry putrid appropriate from lactate for example and then you have other bacteria who are not very good and degrading the hard fiber stuff but they're actually really good at siphoning off some of the oligo and monosaccharides of the primary degraders so this bacterium here Rosebery AHA - can't really digest starch itself degrade start itself but it can then really benefit from some of the sugars that are fair by the better bacterium and current can turn them into butane so just that you get the idea there's a lot of interruption in the system there's a lot of cooperation in leading to the overall production of mainly acetate butyrate and propionate in the system so we have already heard that the torch and fatty acids have a lot of functions on the horse I won't go into detail here because Harvey has very nicely going into this and much more and better detail than I can all these points were already covered so I will move on then and talk a little bit more about the bacterial metabolism that leads to the production of these charts and fatty acids so I'm not really expecting you to look at this in detail this is just to give you an idea of the the biochemical pathways that are behind us this is all bacterial fermentation of carbohydrates into the short chain fatty-acids you see we have different means of making propionate there's the butyrate pathway here the last step can be different in different bacteria and then of course we have other bacterial group that fit into this bigger picture so what we and others have done over many years is that we looked at individual bacteria so that we could map onto this scheme to know who is doing what so that we can if you look at which bacteria present get an idea for this is a butte reproducer this is a propionate producer so this is just some examples you see bacteria marched onto these pathways so these abusing bacteria the bacteria deities are very very important in propionate production and so on but i want to mainly show you this to also give you a caution here for many bacteria we can categorize them into butyrate or propionate producers but be aware that a bluejay producer may also make locti at the same time and for mate so they normally make a range of different fermentation assets and it can depend on the conditions whether they make more Beauty 8 on my luck Tate let's say and another thing is that there are few bacteria who are not that needs they can do different things and probably this is horizontal gene transfer that some bacteria have also got another way of fermentation through horizontal gene so I'm just highlighting two here we have copper caucus caucus that can make propionate and butyrate and also Americo Rose Berea and Yelena voor ons so just show you a few data of copper caucus cutters to make this point and we've done this in the lab if you're growing copper caucus Carter's on fructose it makes almost exclusively butyrate if you grow it on lactate it switches almost exclusively to propionate so just that you aware if you're having sequencing data from a study and you see this bacterium is present it's very hard to tell what it actually does because it depends on which carbohydrates are there or which food sources are there for it whether there's somebody else and maybe produces a lot of luck T that it can benefit from and then it's a protein a producer from carbohydrates it's a beauty producer and very briefly also to just make you aware it's not just carbohydrates also amino acid fermentation can lead to butyrate and propionate formation again very complex pathways this is not about you going in detail about these pathways just show you for butyrate formation mainly glutamate is used by different bacterias through different biochemical routes and then also lysine as a product for butyrate formation in the human gut and then it gets even more complicated when we look at protein propionate formation and many different amino acids can feed into the central metabolism of some bacteria and lead to propionate formation as well so we don't think that's a major role in the human system at least because most of the proteins are digested in the upper gut but I think it's important that people are aware of it's not just carbohydrates I want to show you one slide of a an older study from the route Institute that was done by Harry Flint and Sylvia Duncan which looked into exactly this point they gave people very high protein diets and try to take out all the carbohydrate to see what the effect of that was so these people were for four weeks on a either a moderate carbohydrate high protein or a very low carbohydrate high protein diet and what you can see here is the level of reduction in carbohydrate intakes so especially the low carbohydrate diet really was almost there was no carbohydrate in these diets this was all protein and fats the people ate and this obviously mimics the so called Atkins diet that some people really like to go onto to lose weight all the time but if you look at the change in carbohydrate in relation to the change in butyrate here in the middle the butyrate levels in faeces in these people dropped dramatically so this was a four-fold decrease in decrease in putrid but really is massive because what we see in feces is only a fraction of what happens in the system because a lot of the charge and fatty acids are absorbed by the host so if we see a massive change in faeces there's an even bigger change in the host and this drop in putrid was mainly associated with this one group of Rosemarie a species which are beaut reproduces so these bacteria really need the carbohydrate to make pre-trade protein rich diet will not make up for it even though there are some bacteria that can make betrayed from protein also incidentally the the level of a nitros the compounds which are toxic compounds from protein metabolism went up dramatically so these high protein low carb are low carbohydrate diets are really bad for human health and particularly gut health we believe because now we don't have all the protective effects anymore of putrid and the other Trojan fatty acids okay so we did a lot of pure culture work but of course it's a community as I already said we really need to think of the whole system and how it all works together we've talked about cross feeding already of luck to eat for example breakdown products we of course have direct competition between primary degraders so in this example here if we have let's say inulin coming into the system we have different bacteria you can directly access the inulin how do they interact how who's winning out how do they compete with each other and then we have environmental effects so if we have a lot of charge in fatty acid production then we lower the pH and different bacteria have different pH tolerance so the broad tendency is for the firm acutest which includes some view tray producers to be more ph tolerance if you're lowering the pH we're probably increasing vitro production in that way as well and maybe important to remind you that the each changes in the gut so if you're just looking at the colon at the proximal end of the Kulin where all the fiber enters the system we have a lower ph because there's very active fermentation happening here a lot of charge and fatty acid production so the pH tends to be mildly acidic and then the system slowly runs out of energy because the bacteria consumed the fiber now in less less and less fermentation material therefore the bacteria so the charge and fatty acid production slows down the shortened fatty acids also absorbed by the hosts to be going towards neutral in the distant cool distant : and this the cool on and b c shifts in the microbiota also incidentally there is a higher incidence of disease in the distal call and we could which could well be due to the porous apply of torch and fatty acids so we wanted to see more in more detail which different types of non digestible carbohydrates or fibers influence the microbiota which are the main beneficiaries in the microbiota if they consume these different types of carbohydrates so we did an in vitro study which you run at two different pages for their very reason to mimic the proximal and the distal colon and we tested I think it's 15 different types of fibers that fall into these different classes so we took fecal samples from several volunteers incubated them over 24 hours and then we looked at the change in microbiota we looked at the charge in fatty acid production and we used mostly qpcr but also a bit of sequencing for this so I first want to show you oh and we repeated the experiment a year later with another three volunteers just to see our reproducible the data were so if I show you the chart in fatty acid data first we really looked in this fairly simple barter system holder whole microbiota which short short term fatty acids were mainly produced and these are the background levels here of the medium without added carbohydrates then you can see very clearly that some carbohydrates were very propionate genic and particularly rum knows here was lead led to massive protein a production whereas other car bhai dates were more beauty regenexx oh the frog frog turns were generating mostly betrayed at both pages and then the alpha and beta glucans also at the lower ph again the lower ph led overall to more betray production because the betray producers tend to have more acid tolerance than the protein a produces so we can say that there are that there are carbohydrates that tend overall to more favourable for beauty producing bacteria of a propionate bacteria if you're then looking at our qPCR data so here we have all the different bacterial groups that we measured our species by quantitative PCR we have all our diets here at the two different P ages and these are average data so we looked across all our six incubations at changes that were significant across all volunteers so you can see that there are some responses that are shared between people and I'm just highlighting here again our room in a caucus broomy I which responded strongly to the starches which was fitting very nicely to our in vivo study and we have another bacterium here under this type is Hajus which was very strongly reacting to the indolence the fructose and again that tied a nicely to a human study that we've done a supplementation study before so we definitely have shared responses between different people on the other hand if we're looking now on an individual basis based on our sequencing data then you see a very different picture emerging so what we did here is we did next-generation sequencing of the 16s RNA gene which is a phylogenetic marker we can use it to really see who is there for those of you who are not aware of how this works you basically look at the sequence and you can put them into different groupings this organ also called operational taxonomic units that roughly represents species so we can see by this by the sequence which bacteria are there which species are there and then we basically went through all these and collected all the ones that are propionate for known protein a producers or known beauty a producer so i only show you a fraction of all the data here and then it goes in in decreasing abundance of the most abundant bacteria at the bottom we have it for individual volunteers at the different P ages and down here all the carbohydrates so just take in the picture don't try to read the detail but I think what you can immediately see is that the different people look very very different there's some bacteria if we found present in everybody and also responses were shared on different carbohydrates but overall it's really different propionate producers that are present or betray producers that are present in different people so if we then basically total all these up so if you take the sum of all the propionate producers in terms of abundance or betray producers and just do a simple correlation so now this is the sum of all those broken a producers and the propionate produced in our incubations you see a very nice strong correlation and we see the same for B traits so all the betray producers together lead to a nice correlation with the Beauty eight we found so basically we have functional redundancy in the system it may be beauty producer a in one person that leads to the betrayed and B in another person interestingly for the butyrate we found two correlations as you can see so for propionate there was no ph effect at all but Beauty the pH made a significant difference in the beaut reproduction so we have my higher pH reproduction at the lower pH which that's not within the beaut reproduces so we think it reflects that bacteria and relative turns make more butyrate then lactate or formate or acetate at a lower pH that's probably a within bacterium change in their physiology at the lower pH so we have functional redundancy does that mean then it doesn't really matter which microbiota somebody has well I don't think that's strictly true and you see there's still a lot of difference in different people if you look at the overall cloud in the data and I very briefly just want to show you some data from one of our old studies on inulin which was just a supplementation study where we looked specifically at Butte reproducing bacteria so what we did here is we gave people either the prebiotic inulin or we had a control phase it's again was a crossover study and we just took a little individual fecal sample at this start and at the end of each intervention period and then really used a marker against one of the beauty genes so this is just again a PCR based assay against this final gene impute reproduction and we make clone libraries and looked at the different bacteria that were present and they were all Beauty producers because now we're using a Beauty eight specific gene so here you see the different future producing group we found in our study and here are all our samples which are just really organized in Euclidean distance which means the Moores are more similar samples are clustered together and you can see that most of the samples fell into this broad I call it the normal range in this study okay the majority of people looked like this they had mostly dominated by europe bacterium rectally or respira fakest and then the other ones were present as well but you can see that three of our people here were very different now what was interesting is the people who were here didn't show a strong response to inulin so if you look at the volunteer F&B all the samples are sitting up there so it didn't matter whether it was based on controller annealing period in the Beauty producing community there wasn't a big change in community but these three people who had very different profiles very unusual profiles they showed a massive shift into that normal range after they inulin intervention so I think that was very interesting also of course it was a crossover study for some people we don't know what happened next but this person here went from this point up here after inulin and they fell right back down there in the control period they had inulin first and then controls so they really reverted back to what they were before it's a very small study it's just an observation it doesn't hold up statistically but I think it's still a very striking to see and also for this person here they had the inulin for a phase ii so we don't know what would have happened if he had another washout sample but when we looked at the fatal butyrate levels this person had a dramatic increase in butyrate after the inulin which probably likely was due to this shift in the boot rate producing community so i just want to make you aware that while many people react in the same way we do still need to be aware of inter individual variation and for some people interventions may be very important wares for other people taking a prebiotic yogurt may make little difference on a daily basis ok I'm almost at the end I just want to finish off this thinking a little bit about other factors that influence this whole thing so we're mapping on from single strains from in vitro work and also from a human studies what the different bacteria do how the community works together in degrading different fibers and producing these different charged and fatty acids but and we also then turn this into we work also on a mathematical model so to help us in silico to play around with the system to understand the system better and to design studies so here we're basically transferring all our knowledge into coding and mathematical coding that we can then run experiments in the computer just show you a little bit of data here we had a fermentation study where we looked at short chain fatty acid production at different pages just if you concentrate on the red line that's the beauty 8 so we had a low pH faced high Butte reproduce production and then a high pH faced with low Butte reproduction the the data are shown with the individual symbols and the lines are the models Sophia simulating this in the model then we can see that we're replicating the charge and fatty acid production very well it's still a work in progress we are improving the model all the time but it's a great learning tool and it's a great way to run experiments in silico and then take the best ones into the lab and confirm them in the lab so I want to use the last couple of minutes or so just to think a little bit about other factors so we can look at which bacteria do what but we can already see from our own experience bacteria may do something very well in pure culture but in the mixed system it just doesn't do it so what other factors are playing into how well bacteria compete in the microbiota and I just want to highlight this point at this group of rosamaria species here which alarm Spira CA all pretty closely related and of course carbohydrate degradation is which enzymes - these bacteria have which food sources are directly available to them this is more data of this inulin study at just shortly the Butte reproduce us on so carbohydrate utilization what can they principally eat is of course an important point now the bacteria that are really good at inulin degradation in pure culture are you bacteria Marik Tila and RESPA inulin evil runs you can see it in the name it's the best in your limb producer in on its own when there's no competition in humans we don't see it coming up so in this study despite the fact that it was really high in some people it was the u bacterium lacteal in this person for example that totally took over so it just doesn't compete why is that the case well it must be due to other traits and one thing it could be due to in this case for example is the pH tolerance again so here you see the pH tolerance of your bacterium rectally andres Barea and Alina Warren so this is decreasing pH and it's the growth rate how well can these people grow these people these bacteria grow at different PHS you see the Ubik tiem rectally holds up really well at the lower ph Kangra still grow very well where's the res Borya Angelina vorlons is crushing massively so if you're taking in a lot of inulin the pH drops massively in the proximal colon while respira an allele in linear warrants is principally able to use inulin it just may not be able to compete against this much more fast fast growing new bacteria clearly at the low pH and another thing to be aware of our other gross requirements vitamins amino acids minerals do they have any auxotrophic so we've recently done some work with the known where we looked at the vitamin requirements of these bacteria so principally how we did the experiments as we basically passage them several times through a media that didn't have any vitamins and then we looked at how many how well they could grow so with these two rows boria's here that while grospierre instant interest in ælis was auxotrophic for three vitamins in the absence of these three vitamins it could not grow the rosebery afaik is a very close relatively relative bacterium in the same genus was much less oxygen so it was perfectly happy in the absence of thiamine and also grew better in the absence of biotin so I just want to conclude then and hope I have convinced you that it releases the complexity in the non digestible carbohydrates that are very important we need keystone species to degrade particularly the insoluble dietary carbohydrates and there is a picture emerging where we believe probably a more diverse range of microbial substrates a nice diverse fiber component eat all your different fruits and vegetable vegetables try to sample from any different plant food sources leads to more diverse microbiota which probably leads to a more healthy metabolite production but I put a question mark there because of course as more research needed to really confirm this and then also I want to say again about the complexity of the microbiota we have such a tendency nowadays to do sequencing and that doesn't resolve often to species level sometimes not even to genus level if I see a paper where somebody says the LA conspiracy I did this or that I don't know what to make of it because there are so many different bacteria in that group that's do such different things so we need to be aware of this very closely related bacteria can do very different things in the system and then also the cooperation competitiveness really depends on many factors not just what can they do and we really I think need a combination of the culture and the molecular techniques the molecular techniques are great but I think we need to also have these these actual living units in the lab that we can work with to really fully understand the system so in humans at least I think into individual variation matters for many people probably responses are quite similar even though there may be different bacteria because there is functional redundancy in the system but also there will be people who have a very different microbiota who will respond very differently to treatment so probably there is a quest there is a call for personalized nutrition at least for a sub population and then it is a complex system I didn't have enough time to probably talk about the models but I think modelling Boston silica but also is working more and more with synthetic communities to work more mechanistically on what happens is a very important thing to do so I just want to thank all the people involved especially Harry Flint who has has led many of these studies that are talked about today but also all the people who did the hard work our collaborators on the mathematical modelling site and also our collaborators as where and of course all our funders thank you very much [Music]