IHSIG 2017

okay thanks for the introduction Phillip I'd first like to start by thanking the conference organizers for the invitation to come here today and tell you a little bit about our thinking in this area and fill you in on a bit of the work that we've been doing over the years it's a pleasure to have this opportunity so today I'll take you through the things that I've got up here it's going to be something of a historic overview to start with to sort of explain to you the simplicity the naivety about thinking when we first got into this area and how its hat we evolved as well we've come to understand more and more about the microbiota so I'll talk to you initially about our interest in trying to identify performance associated microbial signatures sort of bacteria that are involved in giving us good performance in birds the use of probiotics how they used at the moment and then all the step back a bit again and talk a bit more fundamentally about functions within the gut and the mic microbial interactions because I think we have to think a bit more deeply about the microbiota and how it varies along the gut and it's not just a single sort of uniform - you know you have to think of it didn't light Lemoore a sophisticated way than that I'm also interested to just briefly mention something about the origins of the gut microbiota where does it come from how does it get established and what does that mean in terms of things like the that you know sort of variability of the microbiota and that helps us to start to understand the sort of intervention points well we can go in and try and change that microbiota or repair it or you know how we can intervened to try and get the most out of our birds so you know why is the gut microbiota a good target to look at to try and improve health and productivity Phillips obviously gone into a little bit of this in his introduction to the meeting but we have to think of the microbiota is really an important that's it's almost an extra organ that we have in our bodies so it provides us very specific functions that are essential to the health of well-being of all animals essentially in the gut microbiota obviously because of its location and what it does has really big impacts on gut health and we we recognize that more and more both in the animal health industries but also in the human health area and we do work in both areas both in in poultry and in animal health and each area of work informs the other area of work a lot of the sort of fundamental stuff really has been done in in animal health and it's now being applied in to human health so it's one way in which you know we've really helped that the human health practitioners and of course gut health is so important to the overall health and productivity of birds you know the things that we really need to focus on as an industry to get the most out of the resources that we put into producing the birds and the sort of underlying sort of concept here is that as animals as humans you know we're not just our own human cells walking around but essentially we're a matter organism it's essential that we have our gut microbiota and it's it's the the unity of our gut microbiota and our own sort of biological potential that produces the organisms that we have out there functioning in the world so there is this concept around of the matter organism the capture captures that idea so just to remind people you know wasn't sure exactly how familiar everyone would be with sort of microbiota research so just put this up to remind people of what the microbiota is it's all of the microbes in a particular environment and we'll be focusing almost exclusively I think on bacteria here the microbiota does include other things such as the archaea bacteria and the protists fungi viruses so they can all have something of a role but we'll be concentrating mainly on bacteria because they have the largest functional role and it's lucky for us that they're also the ones that are perhaps easier to characterize using the the sort of sequencing technology that Philip talked about now I go back a long way further than Philip so when he said when he started getting a hundred thousand bases in in a run or something might be good when I was doing at a hundred a day if you could average that would have been fantastic I spent a whole postdoc whole year of a post doctor to sequence just a few thousand bases so the technology has come a long long way and I'll mention that again in a minute or two so to jump right in and to just list some of the many important functions that the that host microbiota interaction drives you know principally one of the very important things that the microbiota does is to release nutrients that the host can use but of course the microbiota also competes to use nutrients so there's this balance between freeing up nutrients that the host can use but also retaining nutrients within the bacteria themselves really importantly the the host microbiota room are essential if we're to digest resistant carbohydrates that we don't actually have the enzymes to digest ourselves so it's essential to get that the bio chemical potential of the the microbiota to to be our to get the full energy from those resistant carbs and really importantly to to produce short chain fatty acids from those resistant carbohydrates and the short range fatty acids is a recurring theme that I'll come back to a few during the talk both in animals but really really importantly in humans the microbiota is is essential to get proper immune development both in terms of actually developing the immune system so it can see foreign invaders but perhaps even more importantly to train the immune system to not see common food components common gut bacteria as as foreign and so to avoid unnecessary inflammatory responses because the inflammatory responses are really big drain on the energy reserves of birds so the way the microbiota orchestrates the immune response of the host is really a critical issue the microbiota are also are really important in establishing the the gut structure and integrity the amount of mucin that's produced the the the size of the villa's the providing energy for soul proliferation in the garter it affects the vascular ization of the gut the musculature of the gut the motility of the gut so the interaction of the microbiota with the host gut has all these effects that are really very central to us getting the most out of our birds the microbiota in the gut can also produce toxins and it can detoxify toxins that come in in the food too so there's sort of two aspects to that another really important aspect of the microbiota there are that they produce micronutrients that we can't produce ourselves so they produce some of these things like vitamin K and folate that I've got listed there that we can't do without we can't make them ourselves they're all important also important in recycling of bile acids they feed into endocrine hormone production touched on that a little bit later as well and of course we all know they've got a central role also in the sort of environment that's set up in the gutter and whether that can be invaded by pathogens so an important application of sort of microbiota technology at the moment is trying to exclude those pathogens from the food chain so the next couple of slides are sort of quite general in terms of the sort of functions that the microbiota have just reiterating some of the things I've I've said and expanding on them so this is from mainly a human point of view but it all applies to chickens as well so I've sort of broken it down into four main areas the sort of digestion nutrition the actual function of the gut the immune system and an area that's come up a lot in the last few years particularly in human health is this gut brain access there's a very strong connection between what's going on in the gut and what's happening in the brain that's through endocrine activity but also through direct neural activity as well linking the the gut and the brain so when these things are all going well when there's a good balance in microbiota it's functioning nicely with the host the functions that I've sort of listed up here working well and things are going ok but when things are out of balance you get dysfunction and you know in humans that can lead to obesity and of course in animals were more worried about poor growth in humans food allergies I mean gut function in humans that might be irritable bowel syndrome and related syndromes you know Clostridium difficile is really important in in humans in in poultry you know we could replace this with stratum 4 engines there's a problem when things are going wrong and in the immune system you can see inappropriately battery responses and things like asthma and diabetes and really interesting in humans there's a fair bit of work now going on to produce probiotics for some psychiatric diseases and also things like autism so there's there's great potential in this area but getting back to birds more specifically I'll now tell you a little bit about the sort of work we've been doing and really start with the incredibly naive sort of simplistic viewer we had of what we were going to do and we got into this area writing about eight years ago something like that so we're going to go in identify the bacteria that are more abundant in the high-performance Birds pull them out of birds and use them as probiotics I mean it's really easy no problem at all with that so we started our research and our goals were really to catalog and define the composition of the gut microbiota to try and understand it understand how its established and the development of it over time and then to drill down into that and understand the role of specific members of the microbiota and and the effects that they can have have on the health and productivity of birds and then finally of course is to use that knowledge to try and develop ways to to modify the microbiota to improve health and productivity outcomes and we were specifically interested in broiler chickens at this stage so to start with we took a somewhat different response a different approach to the way most other people were tackling this work so the way you know productivity trials have generally been done is to put in a few variables into the system so you might put a couple of different feeds or a feed with an additive in there and you might have a couple of different environments or different lighting conditions or something like that so you have a series of variables that you you look at and we thought this was sort of getting a bit too complicated four hours of a simplistic way of thinking about this so we decided not to go down that usual path of trying to design these checkerboard experiments and instead we went with just a single group of animals so we tried to get rid of all variables that we could so they all had the same fee the same environment they're from the same stock and then we were interested in looking at the natural variation within that group to see if that could tell us anything about the relationship between what's in their gut and the productivity of the birds so you know doesn't matter what performance variable that you measure you're going to come up with this sort of bell-shaped curve here here I've got body weight but it could be FCR it could be apparent metabolizable energy it could be time to market you know anything you put that's going to have this sort of bell curve and that means that on that curve you've got sort of low performance birds and high performance birds so what we were wanting to do is get rid of all the other variables so that was just down to the variability of the performance and see if we could link that with the structure of the microbiota so when we did that you you analyzed the microbiota within a group of birds individual birds this is and you get a particular structure of the microbiota just sort of fill people in this is just a graph showing that the composition from bird to bird so each column is one bird and the different colours are different aspects of the microbiota and different proportions there so when you get that data you can then do some statistical juggling to see how closely related one particular microbiota structure is to the next and when you do that you can then map those figures onto a tree of relationships so the closer they are on in one of these trees then the closer that samples are in the structure of the microbiota and there's really only one so a take-home message from this and that is that the high-performance birds and the low performance birds tended to group together so there are consistent differences between the microbiota and the high-performance birds and the low performance birds you know there are exceptions there are outliers but tabatin by and large they do separate into different groups so this tells us that there are things driving the differences in microbiota between the high and low performance birds so microbiota clearly is having an effect here however this is when our sort of simplistic ideas started to need some modification so you know not working in industry were working in science we're trying to get stuff published we're trying to understand the sort of rational scientific basis of these things and and one of the sort of fundamental things we have to do as scientists is to show how reproducible the work is so that was one experiment but what happens if you do it over and over again do you get the same result each time so with support from our industry body in Australia we went ahead and replicated this trial and the good news was that niche experiment we did find bacterial types whose abundance was correlated with performance so there was always bacteria that seemed to be driving that difference in performance the bad news was that the performance in each trial was associated with different bacteria so each time you do the experiment you certainly get bacteria that a driving performance but generally it's a different sort of bacteria from the previous trial you did the some overlap in the groups of bacteria and certainly the types of bacteria that are related to performance but they do vary from trial to trial so that has a number of consequences in in the way you think may think about going forward with this but this is just to sort of visualize some of the data that we are pulling it out of this so when we repeated the trial this is a different way of looking at the data so the the larger colored dots there represent the animals so that's a particular animal and the tiny dots are what we call Oh to use operational taxonomic units for which are essentially like species of bacteria so they're a particular sort of bacteria and about the species level so you can see there's lots of little black dots that's because there's lots of different species of bacteria in all these birds and within these two trials most of the black dots fall between the the bigger dots that represent the bird so that shows that they're shared between those groups of birds but the some o2u some sorts of bacteria that are only in one trial or the other these ones up here and down here but by and large they are fairly similar but when we put the third trial in that's when things got really hairy really different and in this third trial and these birds are performing just as well I mean in all cases these birds are really high performance birds so even when I say high and low performance within a group they're still all you know really pretty good performing birds but but in this third trial you can see that there are a huge number of bacteria up here that are only connected to a third trial and and have no representation at all in trials 1 & 2 so what do you do with with that sort of data how do you sort of deal with it and what does it mean in terms of development so this is just you know there's I talked about sort of statistical drug going to try and get the relatedness of bacteria within one the compare it to the next but I put this up to show just how different these trials are so there's three trials represented here with about I think it's 30 Birds or so from each trial but you know you don't have to do any statistics you don't have to do any analysis to clearly see that there's three different sorts of microbiota here I think you can clearly see that without any statistical juggling so that's the sort of variability that we have to deal with if we're going to do something with the microbiota of these birds so just to reiterate now each trial there are o to use correlated with performance the OT use these sorts of bacteria they tend to be different in each trial and we think that this complicates how you might go about manipulating the microbiota so if you pull out a bacteria that's important to the performance in one of those trials will it actually work in the other group of birds which have a different underlying microbiota this is really fundamental I think to some of the variability that we see perhaps with some of the probiotic products and even you know prebiotics that we use out there sometimes when we use them we get really good responses because they're going into a microbiota that's appropriate and they can work within that but sometimes we don't see such good responses and that may be because we're trying to use them in a background microbiota that really isn't particularly suitable for them and you know for us as as scientists we think this presents us with opportunities to really try and develop new products principally probiotics in a fundamentally new and different way that really takes into account this microbiota variation which is a fundamental finding in poultry now so with the the work we've done on looking at performance and the structure of microbiota I mean as Phillip said you know there's an awful lot we we've learned over the years but there's a there's a lot more that we don't know still and I just put up here a few things that a few themes that come out in both our work and work of many other groups around the world in terms of what actually is linked to a high performance microbiota one of the things is that the the overall structure of the microbiota tends to be more complex when you've got dysbiosis something's going wrong you tend to have less complex microbiota it's simpler that's dominated by fewer species so high complexity seems to be good you know a lot of people will monitor Oh to use lactic acid bacteria as an indicator of whether the microbiota is healthy or not you know we'd agree with that to some extent although we'd caution that you know we've certainly found lactobacillus strains that seem to be associated with poor performance as well so it does work both ways but generally o2 use you know relate of the different groups of lactic acid bacteria or a thought of as good that be cautious low proteobacteria is usually a good thing you know the proteobacteria includes a number of important pathogens unique although Salmonella and others and so generally we find that a high performance microbiota is lower in those groups of bacteria and then we get on to the presence of other more recently identified bacteria that seem to be quite beneficial I've got some names up there you can read them karley bacteria and present at CI is seem to be has a fundamental role in development of the immune system acumen SIA you seen Ophelia is involved in production of mucin and use of mucin in the gut seems to be involved in the repair of the gap quite important and then they're a group of bacteria that seemed to be really important in short chain fatty acid action and in particular butyrate production which is an important energy source for the gut and so there's a group of bacteria that are now being characterized including by Phillips group including several different sorts of Australia the important thing to note though is that there isn't one at the moment we can't define one ideal microbiota there seem to be many different routes that you can take to get to the end result of a good functional microbiota and so you know it may vary to between the sorts of diets that you're using so you know production system that's using mainly a wheat based diet may have different underlying microbiota structure to one where corn is is the main energy source so just to put up a little bit of real data here I have that were were this is illustrating the complexity issue that I've talked about that it seems that complexity is good in the microbiota and this is an experiment we published last year I think in which we're looking at the development of the microbiota over time so from day one out to day 23 and it's about a 20 23 something like that that we seem to get stabilization of that both the complexity and the structure of the microbiota so here you can see that the microbiota is so each of these is a richness level so the higher their richness value on the axis the the more diverse the microbiota is and each of those spots is is a bird and the richness of its microbiota so you can see that within any one group at any one time there's there's very significant variation from bird to bird but the trend is to great complexity and then you can drill down into that data and you can look at very specific members of the microbiota so here I mentioned Shekhar li bacterium is important in immune development and and here in this experiment we see a general trend towards an increase in in the levels of V Kali bacterium over time whereas other things here the intra bacteria are reducing which we think is probably a good thing so just to harp on the the complexity of the microbiota these are old figures really and these were generated probably before the sort of modern genome akira that we're working in now but the thought was that there's something like six hundred to a thousand different bacterial types within the gut of chickens and as Phillip mentioned also you know the majority of those can't be cultured we can't pull them out and do anything with but we can analyze them we can understand what's there it's just that it's very difficult to do anything with them at the moment but there is a lot of new technology being thrown at that as well to try and allow us to access the potential of all the bacteria that are in the gut now as I say there's 600 to maybe a thousand distinct bacterial types but even within each of those types is going to be lots of strain variation from strain to strains so you know you could have a particular vassilis say bacillus subtlest which all look very similar but they can have just one gene different you know they could be expressing an antimicrobial protein that can kill Clostridium perfringens and it can make a fundamental difference in how those two organisms work so even though there's this only a single gene difference amongst the whole genome of those organisms they could be quite different in in their actual effect on the gut and as I've shown the microbiota certainly varies flock to flock but what I didn't sort of really point out clearly was that there's a lot of variation within a flock - so just bird within the flock there's a lot of variation in the structure of the microbiota and importantly even though those microbiota is varied a lot they're all high-performing birds the other thing to keep in mind too when we're thinking about how to use these and using probiotics you know whether it's single strain multi strain or trying to pull apart the microbiota to understand their role in in performance you have to understand that these things aren't working in isolation they're working as a community so there's a whole network of function so some bacteria will produce a metabolite which other bacteria can then use and produce other metabolites so you know one bacteria may be good at producing a particular metabolite butyrate or something but it's no good if it doesn't have the feeder system going into it so as Philip said you know that we've got an awful lot to learn simply because of the complexity of this and so these are the sort of questions that are keeping us awake at night you know the first question here well I think I've clearly shown that you know there are different microbiota Xand they can have different health and productivity outcomes but we're interested to try and understand why the the microbiota is so variable and can we do anything to actually control that variability is is just the control and standardization of the microbiota a worthwhile goal in itself so you know that the trials that I've talked about we did everything we could to try and control the variation so we had the same batch of feed the same war to the same environment the same people handling there than they are going into the same rooms they come from the same genetics so with all that controlled we still got variation and that's on top of the fact that of course chickens are coprophagic so they're eating their own poo all the time so you've got this recycling of the microbiota in the gut and that's being taken up by the other birds within the flock so even with all that going on there's still a lot of variation within a flock and why is that so we and others it's certainly not you know our original idea hypothesized that the the hygiene levels in modern commercial chicken hatcheries is really the fundamental cause for a lot of the underlying variation the microbiota and that's because these days you know newly hatched chicks not exposed to the natural micro flora of birds so they're not the eggs aren't laid in a nest you know the the hens don't sit on the chicks as the the eggs and the chicks is there brooding them but instead you know the birds are coming out of these clean environments that you know we keep clean for very good reasons to try and control salmonella and campylobacter but that means that the birds aren't exposed to natural bird microbiota they have no exposure at all to that so the only exposure they have to microbiota the only place that they can establish their own microbiota is from all those random meetings with other bugs that they have so from the hatchling environment that people going in there and handling them the first feed they see the bedding they're put in the receiving environment this is the source of the microbiota that's establishing in the guts of our Birds it's not natural bird microbiota and because of that there's a great variation you know in what they're picking up where the one bird gets it mainly from a handler who's picked them up and put them in the transport box or or one Birds getting most of its might first dose of microbiota from the first feed at seeding see and it's really a sort of random stochastic process but the other important aspect of this we believe and it's difficult to get evidence for it at the moment but we believe that the founding bacteria so the first bacteria that go in can have fundamental of it's over the life of the bird so what could gets in there early actually influences how it develops after that so what we're seeing out there and what we're having to deal with is you know microbiota variability that we believe is principally caused by by this underlying process so the microbiota in birds is really fundamentally the acquisition of it is fundamentally different to two mammals because of course in mammals with the journal birth that's the first source of microbiota generally so mammals generally are acquiring the host that the animals microbiota right from the get-go whereas in birds as I say modern production it's completely random process unrelated to the adult birds at the sort of overall phylum level the sort of bacteria that are in there though between mammals and birds it's really not that different it's driven by the groups of bacteria we call Firma cuties the Bacteroides and there's Protea bacteria which we think you know it's nice if they're fairly low and a number of other sort of lower abundance types of bacteria that are in there and in birds as far as we can tell certainly in modern production the microbiota is pretty much established and fixed after sort of two to three weeks and then it doesn't change an awful lot over that the rest of the time unless something happens unless something's going wrong with the birds and it's really when things are going wrong that you know we should be thinking about using interventions and that's quite different to certainly humans where the microbiota tends to develop over a few years so it's a much longer process I've talked about the diversity increasing over time and the highest diversity in the gut of the birds is really found in the seek and the second is this sort of fermentation powerhouse that helping the bird acquire nutrients from resistant starches as a microbiologist I find the upper gastrointestinal tract so sore the duodenum jejunum even the upper ileum to be pretty bloody boring actually because it's usually completely dominated by lactobacillus so it doesn't give us a lot of sort of really interesting things to pursue there but they're really important obviously in the whole digestive process for for birds so with this sort of background information that we're sort of building up as we go along we think there are sort of reals and really interesting new opportunities to develop products in this area in particular you know microbiota or establishment products so this is going back to some of the early work from the 70s with Nurmi and and the use of very crude sequel extracts to try and colonize birds and and make them resistant to infection with Salmonella we think that actually looking at that early establishment is really an important opportunity for products so rather than dosing probiotics throughout the life of the birds can we go in at hatch and and really help the birds establish a good microbiota to put them on the path for a successful metal organism development over the course of their life the other opportunity is you know given the variability that we see in performance can we use probiotics not necessarily to increase the productivity of the whole flock but to really narrow the variation that we see within in a flock can we make the performance more consistent predictable and of course you know where a lot of probiotics are used today you know trying to fight off pathogens such as Clostridium perfringens I think still a lot of work that we can do there to to help that process in the the time remaining I just wanted to step back a bit now and go back to the gastrointestinal tract and think about the microbiota and what we want to do with the microbiota really in the context of the whole gut rather than just talking in general terms as I have up to now so so this is the real gut but I find it a bit difficult to annotate that and do things with it so I've simplified it with this cartoon which I'll use to talk about firstly the functions of the gut so each part of the gut obviously has very specific functions and you know it'll only happen in that part of the gut and not in other parts of the gut so we have to have that in mind when we're trying to manipulate the microbiota but of as well as those functional differences there are also physiological gradients that are happening across the chicken gut you know whether it's pH which I've shown here in cartoon form the level of oxygen in the gut which decreases as you go further down to the down the gut you know in the cecum it's essentially free of oxygen the the nutrient content of the gut content is going down there whether it's you know protein or carbohydrate obviously nutrients are being extracted as we go further down but things like resistant carbs increasing in the percentage that's there so all these things are happening in the gut and on top of that there are gradients in the bacteria there there's there's gradients in the actual absolute numbers of bacteria that are there which Peaks in in the seeker as maybe 10 to the 11 10 to the 12 bacteria per gram in the seeker it's basically just a bacterial paste where it's like the bacillus you know they're more abundant as percentage of the microbiota in the small intestine and reduces you go further down the gut but then there are other really important bacteria like some of the butyrate producers which were often strict anaerobes which increase as you go further along the gut so all these things have consequences in what sort of bacteria you might use we don't have time to go through that again so along with those functional regionalization throughout the gut the the physiological gradients the microbial gradients there are particular interactions between the the microbiota and the gut that are important and there they are regional things and I've just listed them some some of them up here I won't go through them or I don't really have time but you know you have to have the right bacteria in the right part of the gut so you know the one at the end there bile D conjugation I mean that's an important process to be able to recycle bile and reuse it more but you can't have that happening in the wrong part of the gut then you won't get proper fat digests and you won't get proper growth of the birds and also you know the bacteria that are involved in development of the immune system they have to be in contact obviously with the immune cells that they they act on can't be in some other part of the gut you know though it's no use having some of the butyrate producers in the upper part of the Gulf if you haven't had any pre digestion of the complex carbohydrates to feed them so now just touch on how we might go about manipulating the microbiota and there are obviously two ways to do that one is to do it directly by introduction of probiotic bacteria the other way is to do it indirectly by the use of prebiotics so things that actually feed bacteria and try and encourage the growth of the bacteria that you're interested in helping and there are obviously a lot of commercial products already out there so here's a list of some of them that you know can find out there on on the web I'm not claiming that this is an exhaustive list in any way but you know it just is there to make the point that there are a lot of products out there that are already using our knowledge of the microbiota to try and give some commercial advantage to to farmers but I'm interested in sort of actually looking at some of the claims of these products and I've just pulled out a few of these just to make a couple of little points so these are product claims straight from the websites of some of these products so inhibition of pathogen CG constraining perfringens is obviously a big one a number of products are directed at Forster idiom for engines and they clearly have activity against Clostridium perfringens and work well so that's fantastic if you've got a necrotic enteritis problem in your flock but what's the consequence of using those products if you don't have a necrotic enteritis problem I mean if they're killing Clostridium perfringens are they going to be up killing other clostridia that might be involved in in producing butyrate an energy source or for the gut so I think you have to be judicious you can't throw these things around in all situations the second one the claim was much broader so this product is is inhibiting salmonella and campylobacter and e-coli and you could think how they could all potentially be affected by a similar thing but it's also affecting spirochetes and most other pathogenic bacteria well sorry is a scientist I'm not sure what sort of magic bullet can the only target pathogenic bacteria and doesn't hit some of the good bacteria that are in there I don't know the mechanism for that and it would be great to support these product claims if there was some scientific basis for these sorts of statements and you know I guess the last and most general one up there is improving the balance of beneficial microflora that's great and you know it's a sort of thing you see on advertisements for human probiotics and all makes you feel wonderful and all the rest but you know what does it really mean I mean how is it changing the microbiota under what circumstances will it work so these are the sort of questions that I'm interested in as a scientist and as we're trying to address that and understand that I'm certainly not trying to dismiss these at all I think they they you know they genuinely do have some really useful and beneficial functions but we need to understand what they are and how they work if we're to try and develop a second generation of products that are perhaps more effective given the time sort of running out I'll just jump to the bottom point here and it's it's my personal view and I'm sure there may be many out there that'll disagree with me but the evidence that I see is that at the moment probiotics really have good application when something is going a little bit wrong with the flock when you've got dysbiosis or you've got a particular disease issued necrotic enteritis whatever that might be so I think these products seem to be quite good at rescuing performance but in our hands we're really struggling to see much effect of these products when you put them into a high-performance flock so if we put these products into a high-performance flock on a non antibiotic non coccidia stat feed that a got high biosecurity or performing really well we really struggle to see much improvement when we reuse the current range of products and I don't think that's surprising I mean the whole point of these products is to try and improve that the gut microbiota and if the gut microbiota is already fine-tuned and working well why would you think it could do more so I think we shouldn't look to them as magic bullets to to improve when they're going well so I've got a few examples here of some attempts we have made to modify the gut microbiota in the first one here we use just crude sequel content and the sequel content so this is just showing the structure of birds that we isolated the sequel content from here we took two groups of birds that had very different microbiota so this one over here has a very high level of Bacteroides and we did that just so he could distinguish them apart so he took those pooled sequel samples from these birds and put it into naive birds at hatch and what we actually found was that the the naive birds that hatch sort of picked up their own microbiota from all those random things that we talked about and we couldn't actually drive the the microbiota of the birds by adding this in the way we did in this particular experiment so this is the FCR results for what we put into the the birds so this was a poor FCR group this was a good FCR group but the birds we put into all had good FC ours again it's this problem that we've got all the time the people that we do these animal experiments with they pride themselves on on performing better than the industry standards and they do all the time and it makes it very difficult for us to get meaningful results there but then we went from using a sort of very crude total seagull extract to using a mixture of six specific cultured LA bees that we pulled out for various reasons well very specific reasons and when we put those into birds we were able to find that we were able to get increase in weight gain statistically significant over the 28 days of the trial and this is another way of showing the structure of the microbiota of these birds so this the closer they are the more similar each of these birds is in microbiota structure and the only point I really want to make here is that whether it was the control birds that didn't have any of these la bees deliberately put into them or our group of La bees that we put in they do end up with very different bacterial microbiota over and above what we're put in there I mean it's driving changes in the rest of the microbiota we've also done work on feed supplements so here we're looking at biochar bentonite and zeolite sort of biochar you'll know about and bentonite n'zeer lighter sort of clays and when we do that we we get different microbiota structures from each of those birds and perhaps more interestingly we're finding that compared to the controls each of these is reducing the level of Proteobacteria and specifically Campylobacter in these birds so that's something else that we're pursuing is a way to manipulate the microbiota so not just going down the probiotic group specifically with zeolite here we're showing a reduction in different sorts of proteobacteria as well which is an interesting property so one of the things that always frustrates me with the current probiotics is the need to continually dose them I understand that that's a fantastic product for the producers the people who are selling them but to me if you've got a really good bacteria that's doing something in the gut and if you select it and choose it in the right way you should be able to give that bacteria to the birds and that's it they're set for life so that's my recent vision of what we're trying to do so we're trying to move away from these continually dosed probiotics to probiotics that you can give either at hatch or even later later on in life and they can actually get in there and establish themselves and produce their positive effects so most of the probiotics as I understand it and I'm not privy to all the commercial development that goes on within companies but my understanding from the literature is that most of the the current range of probiotics have additionally been identified by applying in vitro tests to try and identify those that would have good properties in terms of survival in the gut so it might be a resistance to bile or the acid conditions of the gut it might be adhesion reasons to the gut cells so things that might be I'll stick around in the gut and stay there however if you this is likely to be fairly controversial but if you actually look at the literature there's virtually no controlled trials there where people have pulled out things are performed well in these in vitro assays and things that perform poorly and actually compared them all they ever do is get positive strains from these in vitro assays and put them into birds there's never the negative control there's never any formal scientific proof that these methods are actually telling us anything and we've got a fair bit of data at the moment that shows certainly in our hands that we've got strains that perform really well in these in vitro tests that don't perform well when you put them into birds and the vice versa as well so when I've got strains that don't seem to be particularly bile or acid resistant yet they perform quite well when you put them into birds they can persist in there and they seem to have some positive effect on productivity so we think there's a new way to to go about developing probiotic strains and that's really to put them through animals to start with so we're coming up with high-throughput screening methods that allow us to actually screen men many many strains of bacteria directly in birds to see those ones that can persist and stick around and do something in birds rather than just disappear and the surprising finding is that even when you go to birds a lot of the probiotics that we're using in the industry at the moment aren't even derived from chickens they might be derived from food sources or other animals or environmental sources but even when you go to chickens see a pool and Colker bacteria are out of their guts and then put them back into birds there's only a very small minority of those chicken bacteria that can reliably get back in and re-establish under variable conditions so you know depending the feed and they'll still be able to get back in there so that's that's a sort of an interesting finding that I think is is quite important and it emphasizes why does this need to be able to come up with methods to identify those rare bacteria that have these surprisingly unusual properties and so we're using where we're starting to use these methods to pull out bacteria and where the targets that we've got to use these bacteria are all the same as the ones that have talked about up to now but our hope is that they're going to be more effective and perhaps most importantly more reliable so they're going to be able to go into any sort of microbiota rather than just ones that are suited to that product so that's where I'll sort of finish the talk really but just leave you with a few more fundamental questions that have arisen as as we've gone along and done our research we're particularly interested in the origins of all the microbiota particularly as strict anaerobes I mean where do they come from in in the environment I mean some of them form spores and that's a good indication of how they survive out there in the environment but there are a lot of strict anaerobes that don't form spores so how do they how do they transfer from you know whether it's the human handlers the feed or whatever to the gut where you know there's this very special invite that they can survive in so we really don't understand that I mean it's a very fundamental question but there's still an awful lot of work to do and what are the the relative importance is of those different sources of microbiota that I've talked about is it the first fee that they go on or is it you know contamination that might be on the eggs or is it the people handling it is that just stuff circulating in the air what are the most important sources for for birds at the moment and also I mean I've mentioned that no we we analyze the microbiota from different groups of birds that were all performing well and they have quite different microbiota so how can that be how can they deliver similar functional outcomes even though the structure of them is is different and and what is it about that interaction between all the bacteria there and the host that really without our intervention can come up with this incredibly complex but different structure that works so reliably most of the time it's it's an amazing sort of evolutionary field that this can come together and work so well and really how does how do these changing networks so you know when they there's a few things that go in at the start and then they gradually get more complexity as they go on how do they stabilize and stay the same after a while so these are the sort of fundamental questions that we'd like to be are to address although how you tackle them is is not always clear at the moment lastly I just like to acknowledge four of the really key people there have been a lot more involved in the work but these ones have been really important in and the work that I've talked about and the support of our industry body the poultry CRC which is support of the work for many years thank you [Music] you