10:01:58 So, we are totally delighted to have under Splenda today as the speaker, and we Microban metabolism firm and, and I know this for a long time and admire his work and what I particularly admire is sort of that he recognized early on that for pathogenesis
10:02:19 Nikola pathogenesis metabolism is the key.
10:02:24 You know, a lot of mechanisms of patented pathogenesis and regulation has been explored. It is really a metabolic disease and similar like cancer is a metabolic disease and MDs really recognize this and explore this with someone Ella and also other and
10:02:42 Derek's to really decipher what sort of the metabolic basis is for infection and the strategies and the unique metabolism of the organisms and as I said I think he did some phenomenal contributions to that and so we are very glad to have MDS here and
10:03:05 in the first half of these three hours. He's giving a kind of a tutorial on the principles that is important for his research talk and then in the second half, we're focusing more on research.
10:03:20 So Andreas thanks again for agreeing.
10:03:23 And, the floor is yours.
10:03:25 Thanks.
10:03:27 So, as Africa pointed out, I'm going to talk about metabolic strategies that pathogens used to invade the gut ecosystems are entirely pathogens and
10:03:39 the background you need to know that you need to have to understand what the strategies are it's basically understanding this environment and that is populated by the microbiota so this is really the area that that I'm trying to introduce in the first
10:03:55 part.
10:03:57 So the, the microbiota research microbiota research is very hot topic.
10:04:13 And it became possible in the first two decades of this century to analyze these communities with non cultural techniques.
10:04:13 It was realized that
10:04:17 many diseases that had previously not been linked to the gut actually accepted some changes in the gut microbiota composition and so that was possible by doing.
10:04:27 Initially the 16 S ribosomal RNA gene sequencing or microbiome profiling for short.
10:04:35 And that's revealed that communities often change in these kind of diseases that are, you know, not hadn't had not previously been linked and it was found that, you know, these changes in the microbial communities, often accessibility disease and so there
10:04:48 has been a tremendous interest in understanding how these microbes in our large intestine contribute to disease and you know the initial focus on large intestine was felt justified because the large intestine is the place where you have the largest microbial
10:05:05 community in our body.
10:05:09 And therefore, that community also makes the largest amount of metabolites. And these metabolites that our software hosts into often affect health, and so that's why.
10:05:19 Often you see this colon here and then all the arrows to all kinds of diseases.
10:05:25 So, when you go to, to these my computer conferences that I said are very popular because many fields come together and you meet people that have worked their entire career on non alcoholic fatty liver disease or at try this or diabetes and you would
10:05:43 never meet those people.
10:05:45 But interestingly, what you don't need this microbiologists.
10:05:53 They are. Notably absent from these meetings and that is because the field was started by this technology. This microbiota profiling and that that generated large data sets and they were analyzed by people interested in bioinformatics.
10:06:11 And so, they were interested in the readout that you get from these kinds of data which is a list of all to us are now we call them ASAP so have to use this opera operational taxonomic units and as visa is out of sequence variants.
10:06:27 And those are basically species or strains that that are detected by the sequencing technology and what this micro profile profiling generators that is a catalog of species names right and that's what that field was focusing on which is very different
10:06:46 from when you when you look at the lectures in this class from afraid and better change.
10:06:52 They looking at communities, based on metabolic groupings so there's primary for mental secondary for mentors, you know Metallica Jansen so forth.
10:07:04 And species names are not that important to them I know the prominent part in this in these lectures because it was about these metabolic groupings and how electron electron flow is, you know, orchestrated between these groups.
10:07:19 But when you know the Michael by other fields started the focus was on on species names.
10:07:26 And the people were very much impressed by the diversity that we're finding so that had a large influence on the concepts driving the field and this influx from microbiology was is notably missing in that area and needs to come in at some point in my
10:07:46 opinion. So, When I. So let me start talking about microbiota and there's some terminology i will i want to clear up in the beginning, and so there's two terms that you often hear microbiota and then microbiome so microbiota is pretty an agreeable term
10:08:06 everybody agrees the microbiota are different collection of all the microbial communities that inhabit our body and Jonathan eyes and that UC Davis likes to use this analogy of Linus that you're basically covered in a cloud of microbes, you If you had
10:08:23 a microbiology class, you know, as an undergraduate, maybe you did this little experiments where you put your hand on a petri dish and you see that there's lots of bacteria growing you know that means you're covered in microbes all the time.
10:08:36 So this is kind of the idea of to my computer but then when we come to microbiome.
10:08:41 There's, there's two definitions that are floating around and that was going to make a little poll.
10:08:48 Which one you prefer, but the polling option is not active for me so I couldn't do that. But let me just tell you what the two options as one definition that kind of started the word that was used in the beginning of the of the field.
10:09:04 Men 16 as sequencing became available.
10:09:07 Is that the microbiome is basically a collection of the collection of Genes Gene products and metabolites of the gut microbiota so very microbe centric definition.
10:09:18 And that was credited by by Jeff Gordon, which is one of the godfathers of this kind of research to treasure later Burke and Nobel laureate that suggested that this is the this this is how to micro biome should be defined
10:09:39 it, you know, advice to influencing the field in the beginning because of the idea that you know that microbes have many genes that humans don't have and these genes help us to digest and then tested and for instance digest food, you know, certain nutrients
10:09:57 that we don't have and the enzymes to break down the microbes microbes provide this gene so that means it's it's it's perhaps could be viewed as an Oregon, that helps us in digestion, for instance, and that kind of Oregon metallic metaphor, kind of focused.
10:10:13 The initial research very strongly on analyzing the genes to production metabolites of the microbiota and misfit this new technology is next generation sequencing.
10:10:31 However, there's another definition that
10:10:30 is also often used and that is that the microbiota should be viewed as the microbiome should be used food as the as the microbiota and its environment so that these two components are part of the microbiome and so that environment is another component
10:10:46 that of course includes other components so this is the definition that comes from ecology and in ecology.
10:11:03 Typically the papers are about plants and and so he had it would be you know the plant and then it's a biotic environment so that's where this comes from this is the, the microbiome definition.
10:11:10 And so,
10:11:15 when the field started and and people started using sequencing to analyze communities that have not previously been really looked at in detail.
10:11:26 They were very much impressed by the diversity that we're finding and as I said you know the six, the micro biome profiling field has very much focused on this list of genes and species names.
10:11:41 And therefore, this this diversity very much jumped out at them and, and to give you an idea of what I'm talking about what I'm talking about when I say diversity.
10:11:51 I'm going to walk you in the next few slides to all the diversity that you, that is associated with the microbiota.
10:12:00 Okay, so the first observation was that when you, when you sequence the different communities and different body sides.
10:12:08 It was noticed that there is a that the species conflict composition difference and even at the file level, you would see large differences.
10:12:19 And so he can show this in this kind of pie charts, which basically a linear scale that shows you the most abundant species that are present and you see that, you know, just from the color scheme, you know, this is on the filing level here, that, that
10:12:34 all these communities are different so everybody site has different communities and, and, and they were wondering why you can look at this differently can do a so called principal component analysis.
10:12:47 So this principal component here would count for a certain percentage of the variability and this principal component for certain percentage of your ability.
10:12:55 between the microbiota and then there's some fancy math that I don't understand that is used to make these PCA plots, and you can see that the, the reason they're useful is because you can see that certain communities are very different.
10:13:15 So the rural communities for instance very different from the GI tract and so forth.
10:13:19 And often you know for some of the community actually there's no, not a single species that is in common between the community in, you know, on the skin and the community on, you know, other areas for instance.
10:13:40 I've read it and Ben had and the other speakers didn't really focus much on species names. I'm going to introduce some of the organisms that are important for microbiome research because in microbiome research there's lots of focus on on these kind of
10:13:58 taxa designations and so I'm just going to mention a few because it helps to get familiar with them to since they will be appearing again again and again and again in the lecture so there's there's one file I'm here this center bacteria.
10:14:14 That's group of positives.
10:14:17 And that includes one important species we will see which is the feedback Chairman Francis on obligate hon.
10:14:24 Then the Firmicutes often mentioned so Firmicutes is a file that contains two important classes in a first approximation.
10:14:34 They don't that phonology is getting more and more complicated and, but I'm just going to use an old division into cluster media and Priscilla and the difference here is that cluster do our applicant and ropes and Priscilla faculty diviners, so they're
10:14:51 both from positive.
10:14:52 And so, he has some of the names you might be familiar with as you probably know lactobacillus and those kind of things.
10:14:59 Then another find them that often appears to produce bacteria.
10:15:05 That is a gram negative phylum of faculties and ropes.
10:15:11 And, you know, he has things like e coli and and produce and capitalized as commensals but then there's also pathogens and sort of patterns I will be talking about someone that is part of these protein bacteria.
10:15:23 And then finally, another important tax on that we often see a departure IDs.
10:15:28 So the, the battery DTS that's the file them back to the idea would be the class. And in the Victoria, there's two important groups, there's the genius pectoral IDs and then there's the patella that and the difference in what carbohydrates to like, if
10:15:50 you look at that on in terms of the fashion industry so you would have here you're, you're producing bacteria. And then here's the battery IDs so these are from negatives.
10:16:02 And then, here's your activity bacteria and your Firmicutes so that covers a good fraction of the diversity of the known cultural bacteria. of course there's lots of uncomfortable bacteria that had been discovered recently but they're not present in the
10:16:16 human gut typically, and then down here would be occupied IKEA and as you know you carrots in the fellowship a tree.
10:16:27 Okay so that.
10:16:29 And so much about, you know, different communities and different body sites but then of course the community is also very diverse. And I just want to mention this because I'm not going to get into it much later but but in addition to bacteria, you know,
10:16:43 we heard about archaea so these are the metallic regions, but but we haven't heard much about viruses, fungi protozoa that also present and often in in very high numbers.
10:16:57 And so there's many different species on the human body.
10:17:02 And one thing that one statistic you often get thrown at you and Mike, by, by other research or microbiome talks, is that there's more cells more bacterial cells in the human body then than human cells so if you have more bacterial than human really among
10:17:19 my microbial.
10:17:21 And as I mentioned in the beginning, there's only one reason for that and that reason is the colon because it contains the largest microbial community, and you know you can read some fun papers about that fact, that is, you know, if you get into it you
10:17:38 can you can basically conclude that every time you go to a restaurant for number two, the ratio actually might change in favor of humans right because you releasing a large amounts of pictures.
10:17:52 Right. Okay, so this is the kind of micro biome research that you find on the internet.
10:17:58 Everything is being sequenced and every time there's another condition, you can wait.
10:18:03 And then a few months later, you see a paper on the microbiome changes in that condition, you know, like, Corbett 19 It took about three months and then the first Corbett 19 microbiome paper came up.
10:18:15 It's somewhat amusing but every possible condition under the sun is being sequence at the moment and, and published.
10:18:27 When you look at the genes that the microbiota converts that the ratio is even more impressive so there's hundred times more microbial diversity in the genes in our body then human genes.
10:18:41 So if that would be a democracy wouldn't work for us.
10:18:44 But anyway it contributes to this loves large complexity.
10:18:48 Okay, so then in addition to these two factors here that the different communities and different body sites and diverse communities, you have another observation that really threw everybody off and that is when people started sequencing.
10:19:03 The microbiota from different individuals.
10:19:06 They found that me and any of you
10:19:12 have only have definitely no overlap on the species level, everybody has different communities so here's this is just an early study from 2009, where this sequence 17 individuals, not the individuals but the fecal samples, and they noticed that the vast
10:19:30 majority of us operation. Operational taxonomic units, was president only in one person.
10:19:38 And there was very, very few you know maybe one that was present in everybody in 17.
10:19:44 Right.
10:19:45 So everybody has a different species composition, which made it extremely hard to understand what a normal micro micro microbial community in the gut should look like right because everybody has different species at least looking at the species list right
10:20:05 and that's what everybody was focused on this list of species if you would actually look at metabolic groupings you wouldn't see that diversity but, again, as I said, there is no microbiologists in this discipline and therefore, they're very much fixated
10:20:17 on species name and when you look at species name you don't see any similarity between different individuals.
10:20:25 Then finally, the third thing that or the fourth thing that has to be added to this is that there's also changes over time.
10:20:36 So when, when you are born microbiota assembly starts and you see rapid changes in the composition of the microbiota with the first few days.
10:20:47 And then it stabilizes somewhat that value of breastfeeding and then after you read.
10:20:53 Um, you see another major change in the community so you see all these different colors appearing so there's changes over time that that is another factor so it is there's these four factors that contribute to diversity, and you can let me grab this in
10:21:09 a different way when you you know after birth when they're my computer. My computer is assembled you have this variability and then somehow the microbiota reaches a relatively stable state.
10:21:21 And then if there's an perturbation.
10:21:24 For instance antibiotic treatment to my computer gets disrupted and there's another round of community assembly and then it reaches another stable self state but this this stable state is very similar to the stable state.
10:21:37 And that phenomenon phenomenon that after a perturbation.
10:21:44 The microbiota returns to a
10:21:48 normal or functional state.
10:21:51 Even though the species competition might be slightly different than that is terms microbiota resilience, and again, when you talk to my computer researchers that nobody really knows why we have microbiota resilience.
10:22:09 This phenomenon is not fully understood address. Yeah, you give a number, I'm sure we're giving them but before on, on the lack of overlap between individuals, and only individuals.
10:22:19 In this case, like how much overlap there will be before and after treatment, quiet for forgiving individual.
10:22:29 That depends on the participation. So if the if the litigation bikes out
10:22:37 depends on how many microbes, go extinct during the presentation so if you would be able to have an antibiotic that kills everybody.
10:22:47 Then, state and state be would have no overlap on the species level, but it would be, you know, state able to be similar.
10:22:55 So it's fighting competition to any other individual and itself, instead be right.
10:23:03 Because the microbiota will assemble again to this adult type microbiota.
10:23:09 If you have.
10:23:10 Typically when you have any good equipment you Only you only get rid of, you know, a fraction of your microbes and then that fraction.
10:23:19 After the mic, the mic, the antibiotic is so strong that fraction then gets required, but you acquiring other strains different strains from the environment, and now you have two strains that weren't wiped out.
10:23:34 They stay constant but the ones that were removed, they're replaced by similar strains from the environment and so then you have brought some new bacteria and you just depends on
10:23:54 either number some of the studies that that report for typical antibiotics treatment you will get from from some kind of infection.
10:23:58 What what it would be. Yes once, and I don't know the numbers actually, there's one study from, from MIT, he, he sequenced himself, every day for one year and in the middle of summer he had an episode of customer right Isn't he had to take antibiotics
10:24:14 and so that's what he found he was, you know there were some strange, strange going extinct and then replaced by new ones. And so you probably have, if you analyze the data set, you probably can get a number, but I don't know what the numbers, produce
10:24:35 do some of the highly abundant ones go extinct or is it mainly the low abundance. I don't know that answer to that question.
10:24:42 Depends on their susceptibility of to the antibiotics so the antibiotics usually target certain groups of organisms right there. So many buildings act against interrupts and some antibiotics act against other groupings and so it depends on what you know
10:24:55 which I assume if you have equal susceptibility and one is more abundant than the other, it's more likely that the minority species gets extinct first.
10:25:22 You might have abundant species that are fairly resistant, or abundant species that are fairly susceptible and you might see a difference. That makes sense.
10:25:23 The answer is I don't know, but I can speculate.
10:25:30 Alright, so I'll come back to this and try to explain these things but first I wanted to raise the questions that that have puzzled. This microbiome field and I think they have poisoned the microbiome field, basically because they're not microbiologists
10:25:45 and if you actually inject some microbiome microbiology and ecology, then you will see this answer to these questions but but this this diversity in the microbiota basically has raised had raised the question but what is a healthy microbiome and nobody
10:26:01 really has a good answer to this.
10:26:04 And if you don't, if you don't know what the healthy microbiome is it's also hard to define this term, just by your system and you know the microbiome is somewhat disrupted.
10:26:15 And, you know, often the mic the display. This is defined as a reduction in diversity, and a increase in potentially harmful bacteria and a tick or decrease in potentially beneficial bacteria so that's kind of the major definition of of this by users.
10:26:35 But the criticism is that if you cannot define a healthy microbiome based on species names, since we all have different species.
10:26:47 Then, that also makes the definition of disposes based on species name untenable right and so this these terms have fallen out of favor because basically it's been realized that species names and not a good way of defining homeostasis and just by yourself
10:27:05 that direction from the field that has basically only generated species names, has been to reject the terms altogether unscientific again I'm, I would disagree but we kind of get to this.
10:27:21 So, now, as I pointed out, this diversity, makes it hard to define what the healthy bite microbiome is and so the the reaction of the field has been to look at the microbiome definition that was used in the beginning that the microbiome is a collection
10:27:39 of Genes Gene products and metabolites. And so, if you want to understand the microbiome so if this is the microbiome, then you have to measure all these things so you have to measure the genes that gene products the metabolites.
10:27:52 And if you do enough of that you know he just sequence enough individuals, eventually there will be a core microbiome emerging that is common to humans, of course set of genes or causative organisms.
10:28:05 And so that was the idea and and the field has pushed a head in this direction, and analyzed every component of this microbiome. So there's the microbiota must initially analyzed the 66 s Bible some RNA, Gene mt con profiling.
10:28:28 And so that was the initial data set that gives you the species names, but then as Chuck can sequencing became more affordable.
10:28:35 More and more people are doing this metronomic which now shows you all the genes, not just the 16 s gene of these microbes so now you can have an idea of what metabolic pathways might be potentially present in.
10:28:48 in microbes. You also see viruses now in this in these data sets, and then
10:28:55 perhaps more recently, maybe move to, to RNA seek and I'm a meta transcript comics, which tells you what the microbes are transcribing so what metabolic activities they might be supporting by the transcript on.
10:29:11 And then of course you can take this further to, we're looking at the protein level at 40 on or. Finally the readout of which metabolites are produced to the metabolism so there's a lot of all mixed that can be done and have been done.
10:29:25 And so
10:29:31 that the
10:29:36 people have looked at every aspect of the microbiome right and measured and measured in detail.
10:29:47 But we still, you know, from all this data we still don't know what the healthy microbiome looks like,
10:29:54 why not.
10:29:57 I'm here sorry for a question or comment again I just want to see how you think about this, of course a lot have been measured, but from from fecal samples and you can't get only so far with know what what one is really interested in this work, if you
10:30:18 take this definition of a microbiome right in at the place where things are happening, how, how much of those kind of data there.
10:30:26 Yes, you're right. And, and that that's good criticism and of course people have not just used it, you know used to take the microbiome but also got data from biopsies and, you know, especially in animal models, you know people looking looking for detailed
10:30:45 to take the animals apart and look at everybody side and.
10:30:49 And as I said, it all it all this does in the end is increasing the diversity because different body sites have different communities and so people have done that and I've done it in excess and still, even though they measured every aspect of the microbiome
10:31:05 the Genes Gene products and metabolites enter microbiota.
10:31:09 It didn't provide the answer to the question what's, what's the healthy microbiome, why not.
10:31:19 Why, why did you know if we measure every aspect of the microbiome How come we don't understand it.
10:31:30 And so, the, you know, one as one as one answer to this question might be.
10:31:37 We haven't looked at the whole microbiome.
10:31:40 Because if you look at the second definition of the microbiome.
10:31:44 It's the microbiota and its environment, and we have not looked at the environment.
10:31:49 That was excluded from the analysis. Right.
10:31:53 And so maybe that's the reason we don't understand it and so let me make a simple example to drive that point home.
10:32:00 So let's assume we have a homeostatic community and then some disease state we find this despite your community. Right.
10:32:08 And now we want to know what's going on.
10:32:11 This is basically what the microbiome field is doing. Right.
10:32:16 So you could sequence the.
10:32:25 These plans and the genome and the transcripts and established proteome and metabolism.
10:32:28 But looked at really give you an easy answer of what is happening here.
10:32:32 Right.
10:32:35 It might but it would be difficult perhaps to see, I would argue, and the reason this is different, difficult to seniors because you're not looking at this aspect here.
10:32:49 And I'm taking this example because when you look in the environment.
10:32:53 The answer becomes trivial, a five year old can tell you what happened here.
10:32:59 We had a drought.
10:33:02 The five year olds will not be able to see anything in the in this analysis of the genome and transcriptome. And I would argue that even experienced scientists would have a hard time capitulating this change by looking at, at omics.
10:33:16 Right.
10:33:17 So leaving out the environment, leaves out such a big part of the equation,
10:33:25 that it makes it very hard to make sense of the microbiota. It also shows a few other things and that is the microbiome field. When you have a display users in the community often people try to to restore that the normal community structure by giving
10:33:48 transplants. Right. And I have to say this, this works well in one particular condition, and that is after antibiotic treatment, so that if you make that example here for the, for the for the water lilies, so he would have a lake.
10:34:02 And you dump in a lot of pesticides or herbicides to kill these water lilies.
10:34:07 After these herbicides, you know they are decomposed, you could risk reconstitute this this population, affordable is by by bringing in water lilies from another Lake right and that would work just fine and this is what a fecal microbiota transplant does
10:34:31 to you after antibiotic treatment.
10:34:27 However, if the reason for this process was not a herbicide, but an environmental change, then fecal microbiota transplants make no sense whatsoever.
10:34:38 You know, taking this water lilies and put them in the desert will not do any good.
10:34:43 Right.
10:34:45 And this example kind of drive this point home, but I'm telling you this is not at all, appreciate it and the microbiome field everybody you talk to they want to do a Michael Brito transplant for whatever disease they're working on.
10:34:57 And it doesn't make any sense because in many cases there's an environmental defect that is responsible for the disperses.
10:35:04 Alright so this is the manta ray sample. Yeah, go ahead. Excuse me have a comment right so if you sample the, the patient microbiota, I would think that the species competition would reflect the environment, like the environment eventually feeds into
10:35:19 species composition. So I guess maybe one could do this, maybe tracking over time, because the snapshot, obviously is not enough. That's my question like, it could could people then tell the, whether it's healthy versus despotic by looking at time series
10:35:34 of Absolutely.
10:35:37 You're absolutely right. So, you know, that the species composition here reflects the environment and the species competition here reflects the environment and if you know enough about the species.
10:35:48 You could use them as bio indicators and you say if you find if you see this species, you probably have behind an arid area and if you see this species, it's probably aquatic environment right and so you could use these, you could, you know, Close your
10:36:02 eyes and sample some plans. And then afterwards look at them and say hey we found a water lilies will probably be sampled plants from a lake. Right. And you can do the same thing, you know in patients, which is what we're already doing this blood test
10:36:14 right you see liver enzymes are up and you say, Oh, you know, stop drinking or maybe you have hepatitis, and you could do the same thing with the microbiota you know this tax on his app, or maybe you have this disease right so this is the goal right.
10:36:27 So yeah, you're absolutely right but this is not.
10:36:30 This is this requires you know as to incorporate this environment that we kind of find that I indicators for this particular environment by indicators right and that isn't being done because people focused very much on the microbiota alone with the comics
10:36:44 omics and not so much on the environment.
10:36:46 Does that make sense. Okay.
10:36:51 So, staying the environment so the environment.
10:37:13 In the plant fields the environment is on a biotic environment, and the microbiome field.
10:37:13 The environment is the host the host is a foundation species that provides the environment for the microbiota and therefore, it's very important in my computer composition.
10:37:16 And when you go to the GI tract there's another important contributor and that's the diet.
10:37:21 But outside the GI tract all the food comes from the host. Right.
10:37:25 So the host is really instrumental to what the environment looks like and if there's a change in the microbiota compositions, probably something changed in the host.
10:37:34 So the host factors shaped environment.
10:37:38 And the metabolites of the microbiota can contribute to health as well so this is kind of the healthy microbiome idea.
10:37:47 Now just to drive this host host point little bit home more. The host is such an important environment for micros because it's so much bigger than the microbiota it's there's a factor of a million fold bigger, that means there's lots of different niches
10:38:01 here for microbes to colonize.
10:38:04 And just to make that easier to understand.
10:38:09 If you look at a million fold increase in size you know you would looking be looking at.
10:38:16 For us, we would be looking at the state of California. And you know, you know so microbes entering the human body is basically us visiting California and you know there's lots of places to visit and lots of habitats.
10:38:28 to.
10:38:29 to encounter in and so the human being, foundation species is an important concept.
10:38:36 Alright, so let's come back to, to this question, you know, how can we make sense of this, this daunting diversity of the microbiota and be starting, I'm just going to start about this this talking about this fluctuation in the microbiota compositions,
10:38:57 over time which is basically the process of microbiota assembly.
10:39:02 To start off with, so what are the principles of community assembly.
10:39:11 And so, again, this is something that was developed long ago in the plant field and, and in the plant field. People say there's two factors that are important for community assembly and this is competition and habitat filtering.
10:39:26 So competition is typically an interaction between closely related species
10:39:36 and habits inhabited filtering.
10:39:40 In the plant feel this interaction of species with the a building environment and the human microbiome that would be interaction of species with the environment which is the host, and perhaps the diet is another important factor.
10:39:54 And when I, when I say host and diet you know these are two separate things, by the way.
10:40:03 So diet is just host behavior.
10:40:07 So, the mouse.
10:40:13 the mouse, it's whatever you know, corn starch or whatever the mouse aids and the tiger it's meet you know the and they don't really have much of a choice right there.
10:40:21 The diet is a part of host behavior, and not really a separate thing that is a bionic right.
10:40:30 So diet is really.
10:40:32 Another host control over the environment in the gut.
10:40:36 Now, importantly, so there's different outcomes of the different consequences of of computation and habitat filtering competition, the consequence of competition is that it limits the amount of similar coexisting species.
10:40:51 And so this, I chose this example here because it might hit close to close to home to graduate students and undergraduates you're familiar with this situation, but basically what you see when you look at competition as well you will see in us all to you,
10:41:06 profile of hundred species, you will see a limited number of a similar species in there. And, you know, to see that you have to look pretty closely so typically people don't consider competition as important because in the big picture of results.
10:41:22 That's not jumping out at you, but that's jumped out at you usually is in these kind of blocks is the changes in the colors right, and that is not the result of competition, but that's the result of habitat filtering.
10:41:36 So having that filtering determines which taxes are dominant.
10:41:42 So that's the outcome of habitat filtering. So basically determines which metabolic strategy strategies will be most successful in that environment and therefore, which microbes will be most abundant and since 69 sequencing.
10:41:57 You know you sequence hundred thousand reads maybe and maybe 100 species. So your sensitivities like oh point 1%.
10:42:07 So you only see microbes that are maybe abundance and its abundance like 10 to the seven times a day per gram feces if something is like 10 two to three program pieces you don't see it so you only see the most abundant.
10:42:21 You only see the let the last three four logs of, you know, the top, top most common microbes.
10:42:28 And because you're looking only at the most common microbes with this technology of 600 sequencing.
10:42:34 Everybody kind of considers habitat filtering the most important because that's really what determines the most successful species and competition is less important, but you know, I'm not sure this is really true this is just when you look at the 16 s
10:42:55 readout if you look at functional readouts competition can be more important in some cases.
10:42:53 So anyway, these are the consequences. And, and now you when you when you look at this diversity over time. Why do we see these changes in colors right so.
10:43:05 And how does habitat filtering. Select for these changes and colors, and so the number one thing to consider is.
10:43:14 Okay, how about filtering This is either host factors or dietary factors right so let's talk to the host factor.
10:43:20 So the host factor that is important in determining who is there in the large intestine is something called a PCL hypoxia.
10:43:29 And so this is a phenomenon that the surface of the colon is very poorly oxygenated it's less than 1% oxygen in the cells, normal tissue oxygenation being between three and 10%, and atmospheric oxygen being 21% right.
10:43:49 So there's an oxygen freely diffusers over membranes. So, since there's only 1% oxygen here there's very little oxygen diffusing into the lumen.
10:43:58 So this register hypoxia thing that binds conveniently to tissue that has less than 1% oxygen and so you see the surface lights up at the stain. And so, there's very little oxygen diffusing into the lumen and that helps maintain an arrow biases.
10:44:15 And if there's an anaerobic environment.
10:44:19 What you see is obligate hon dominates typically right and that's what you see in the microbiota there's a dominance of obligate ourselves all of these different colors here obligate unrolls.
10:44:32 So this is a conversion in a key ecological trade that is mediated by habitat filtering, of the host, and it's really the host who drives this because if you look in the small intestine.
10:44:44 You don't see this hypoxia the small intestine is fully oxygenated as oxygen leaking into the lumen and what you see in the small intestine is a dominance of faculty of unnerves mostly facility.
10:44:56 So the faculty of anaerobic Firmicutes but also some protein bacteria.
10:45:01 Alright, so the small intestinal community is different. It looks like, like, like a, you know, faculty interruption in the top sediment of a lake various than the you know the Unreal biases here and the large intestine changes to community to a community
10:45:18 of obligate under of studies dominant dominant obligate under upstairs minority species that are not obligate on or off we can see this in a minute. But as I said habitat filtering just determines who are the most dominant taxa.
10:45:31 Right.
10:45:32 Okay, so that is one factor and then the second factor is the diet.
10:45:39 Again, as I said, the diet is not something that is different from the host diet. In this case, is the host, because it's a maternal diet in the beginning of, of life at least in mammals, because we are getting milk.
10:45:53 right and so the diet is coming from the mother, and this basically, host of Right, right. So, and that diet triggers this dominance here of organisms that that consume.
10:46:10 One particular component and look this is milk Oracle sides. So when you, when you look at composition of milk, soy milk is composed of mostly water, but then there's some nutrients in there.
10:46:25 And when you look at what the nutrients are. So there's. So there's lactose which and, which is taken up by the baby in the small intestine for nutrition, leopards they're taking up a baby for nutrition proteins, same thing.
10:46:37 But then there's this little area here, which is, which is called HMO so these are human milk or legal rights, and this MMOs a fully absorbed in the small intestine and they go through into the colon, they do not eight and nutrition of the infant, but
10:46:58 And it's a complex mixture of short articles to her rights, which is shown here there's over 200 different species.
10:47:07 And they are consumed by microbes and it turns out that one particular species defeated bacterium longer term subspecies and fantasies long name.
10:47:18 I mentioned this organism in the beginning, with an abbreviated its name to be incentives which because I'm not from the federal budget and girls have you can forgive me, perhaps, but
10:47:32 but but but but found when the state this organism was sequence but that there was a gene cluster that that is designed to degrade several of these milk only goes to her rights and when you grow up be filtering bacterium longer term subspecies incentives
10:47:45 on this McGonagall accelerates you see that organism cross nicely and the closely related species.
10:47:52 McGonagall accelerates you see that organism cross nicely and the closely related species, by feeding back to him longer term subspecies longer term cannot crow on this, Nicholas Alright, so this is what you typically find an influence is this particular
10:48:02 subspecies here incentives.
10:48:05 And that's what what is this orange or whatever kind of color here right this is perfect bacterium. And so this dominance of definitive action was driven by the availability of this milk only costs our rights as one of the only components that reaches
10:48:24 the large intestine at that period of time and your exclusive exclusively breastfed. Right.
10:48:32 And so that's why we have this dominance of the feedback to, again, it's of course an obligate Unruh, right. So, if you feel hypoxia together with colleagues rights, gives you the field of victory and incentives.
10:48:46 And then they have meaning. And here, so just follow up on the, so this perfect of a theorem.
10:48:54 How long does a persist after, after milk. After this breastfeeding
10:49:01 taken. How long, how long does this benefit of bacteria in factors persist, after the baby stop milk feeding. Yes, so this is a good point. And so, when, when you mean the baby and you stop breastfeeding, there's no more human rights.
10:49:25 I mean, you can feed cow milk but cow milk has different legal rights and but that was the results and as a result in an extinction of the feedback to mend fences, so you don't actually find the filter by Chairman, and fantasies in adults.
10:49:37 And it's also not super clear where the feedback human factors is coming from. So actually in the Western world it's kind of declining and less and less babies have perfect perfect human factors in low income countries you see that you know 80 90% of
10:49:50 babies have the feedback German scientists.
10:49:54 But it's not clear where it's coming from it, since the mother doesn't have it.
10:49:59 And it's my computer.
10:50:01 People suspect that it comes from other babies. That might be the reason why take some time for it to appear, because you have to pick it up.
10:50:10 Somebody.
10:50:15 So menu.
10:50:17 So when you've been the baby you destroying this medical exam survive, and then at least an extinction of the benefit of perfect back to him.
10:50:26 But at the same time you introducing a new carbon source.
10:50:31 And, and that is fiber. So, one of the important carbon sources in the large intestine is fiber that is complex carbohydrates that are not degraded or absorbed by our enzymes in the small intestine and therefore they pass through into the large intestine.
10:50:46 And then, important nutrients for the microbiota and what and when you look at the microbiota and tech like kinetic enzymes what you can see when you look at legacy will hydro laces and and policy how I'd lie is is you see that the Firmicutes antibacterial
10:51:06 bucks roadies have a huge variety in these different enzymes that can break down complex carbohydrates whereas other members of the microbiota don't show this diversity.
10:51:20 And so the idea is that, because the batteries and the Firmicutes have the highest capacity to the great these kind of nutrients that leaks tend to this dominance of Australia which are the obligate anaerobic bacteria these obligate animal Firmicutes
10:51:37 and antibodies.
10:51:38 So they just so, so the as the head Firmicutes generally have this diversity of sugar degrading enzymes.
10:51:48 Also Priscilla, but the fact that if I interrupt and as I said a personal hypoxia favors the obligate on the ropes and so that's why the cluster media dominate over the back of the device Li, and then the majority is is the is the gram negative group
10:52:01 And then the majority's is the is the gram negative group that comes in. And so now this composition of Firmicutes and and red batteries. That's explained by fiber and enterprises.
10:52:15 Right, so there's these habitat filters and revises and fiber, or animal biases and mechanical satellites that are responsible for these changes we see so they're not that complicated.
10:52:27 They actually easily explained by carbon sources. Right.
10:52:32 And, you know, to go back to banner change lecture, he, he drew the metabolic flexes in the, in the room and have a cow difference in the room and to the human and testing Being that this is not a large arrow arrow arrow here in submit a very
10:52:52 small numbers in the large intestine of humans, so we do make some methane but cows are the main method producers on the planet so they have a large amount of these archaea in them and we have only a very small numbers.
10:53:06 So that's the main difference though.
10:53:09 And, and so what you basically one of my main point here is what you basically selecting for but habitat filtering. Are these primary for mentors right so these dominant species here.
10:53:19 I selected for by the substrates for the 45 primary for mentors, right so this is what you see in dominant sweater just connected to what what Ben said and to make the point about Alfred spokesman's lecture.
10:53:36 So if it has used this this graph a lot to, to say that he's focusing mostly on on the cannibalism aspect of metabolism not so much on the cannibalism because the analysis very conserved and the cannibalism is the one that distinguishes microbes.
10:53:54 If you and I think that's a very good point because if you look at this diversity here.
10:54:00 This is not explained at all.
10:54:04 By the blue arrow, because all of them have the same blue arrow.
10:54:09 What makes these changes in the community happen.
10:54:12 Are these red arrows right and so some somebody was complaining to me that my, my, you're not looking at the blue one, you know, why do you think the red one is really more important.
10:54:21 Well, the red one is the one that gives you the changes the blue one is not right. So if you're interested in these chemical communities and body composition changes, you have to look at the red arrows, right.
10:54:34 That makes sense.
10:54:38 gonna, I'm gonna ask a question. Yeah.
10:54:44 Hi, This is
10:54:53 a. My question is. So you mentioned just be just now in the previous slide that this election, or the, the impact of the diet is many absurd, or the level of the primary degree there's right.
10:54:56 I was wondering if there was any evidence of hope so these some type of coupling with the, with for mentors or secondary for mentors, meaning that for example if you change the primary degree, there is a different bacteria that maybe that sort of cascades
10:55:15 downstream, because there is something like that, that I'm familiar with in room and microbiome where there is more I think there's more of a thermodynamic coupling.
10:55:25 But in this case, we mathematicians, I mean, but in this case I'm not sure.
10:55:33 Yeah.
10:55:33 Yes, I think absolutely that is downstream effects on uncoupling.
10:55:39 And just,
10:55:42 just points to the limitation of this technology 16 s sequencing. This technology really just looks at can just visualize the most abundant species at least the way it is usually craft in these kind of bar graphs, you're only looking at the most abundant
10:55:58 species and you don't see what is happening underneath so if there's a victim going from 10 to two three to 10 to seven per gram feces you don't even see any of it.
10:56:12 Right, so that minority species are basically ignored by this technology.
10:56:18 And if there's, you know, there's interactions and other species that happened here You know that, don't reach this this height these high numbers, you will not see it, but I think.
10:56:29 So since we you know this habit that filtering here by diet kind of affects mainly the primary for mentors, I think that become the dominant species.
10:56:38 I think you don't see much of this happening but you were mentioning but I think it is happening under the surface. Yeah. Andre Andre is hide this time Schmidt if I, I'm going to be presenting next week.
10:56:51 And we're going to talk specifically about that so the connections between the primary for mentors.
10:56:58 The primary two graders a secondary firm enters in with antigens. So, good question and as Andre said they're not they're not very abundant in his expectation is right.
10:57:11 It's absolutely it's happening and so I'll show you some of the evidence for that next week.
10:57:16 Thank you.
10:57:18 Right, so you know when you have those kind of questions. You have to be interested in them and then specifically look for them and, as I said, the problem with the microbiome field has been that the interest has had been on generating this name list
10:57:31 and then when you look at the list of names, these kind of questions don't jump out at you and that that's why this has been very little follow up in those kinds of directions.
10:57:39 That's why you do need microbiologists in this field to actually raise this question and then look a little deeper into data and see whether you can find this connection, address, I have a rather basic question from the very start to ask.
10:57:53 It has to do with the name, the correspondence between nameless and the function of the, the AMA even you just now we're talking about well nameless at the firearm level, right, and okay so okay we have better read about your duties, we have Firmicutes
10:58:12 there the Polish decorated Raiders and so forth right and and the so where, where does that come from so there's a bit better bacteria has okay this HMO and so forth, it's found the infamous what what what is it about the 16 s that are associated with
10:58:32 these things why can't.
10:58:29 Why can Tibet God to pick up at this age MMOs cluster and why can some of these hydro lasers be be moved over to some of these
10:58:50 other species, either firearms.
10:58:46 So what why is this association well what is that there's some come from something earlier in evolution of the weather what was the, the.
10:58:57 Some come from something. Early on in evolution of the weather what was the, the. Yeah. Just what some basic thoughts in the in the field about about this kind of correlation.
10:59:02 And that's a good question. I don't know the answer.
10:59:05 I mean basically I'm just telling you what has been observed that this particular ability to eat milk roller coaster ride seems to be
10:59:16 the feed of bacteria and scientists seem to be one of the few organisms that that has that ability.
10:59:21 Why, why there's no. You know I just know horizontal gene transfer to another tax I don't know.
10:59:31 Andres if I could offer one observation that is related to the question.
10:59:38 So the room no caucus of befuddle bacterium that you're talking about in most of the bacteria that degrades fiber the primary to graders there gram positive bacteria.
10:59:50 And so the cell walls are different, and I've often wondered if if there's something physical limitation about anchoring in that gram positive type cell wall that prevents lateral gene transfer to suck tobacco royalties or the other Gram negative bacteria
11:00:10 there so it's not an answer. It's just a thought about the question you ask
11:00:18 another perspective.
11:00:21 I love it that we're getting this different perspective here. My take on this is that going with sort of third the final name essentially comes a core metabolic business model and the word business model comes from john Ross and I think he hit a very
11:00:39 well, which means that is sort of a core metabolism and digital bacterium have a very distinct metabolism for carbohydrate metabolism, other than Nikolai or lactic acid bacteria and.
11:00:57 And this call, metabolism so the so the red parts in this graph intuitively tie in with the flux of ATP in the cell to work and problem occupation. So in a sense, it was sort of the business core, which is.
11:01:15 So, integral for the organism and that comes sort of with with a film for largely where it comes into the horizontal gene transfer is typically metabolic upstream extension so if you have sort of a new carbohydrate, or new complex carbohydrates, but you
11:01:32 have a couple of, you know, hydro lasers that ultimately funnel these compounds into this core metabolic module or in this core metabolism. So therefore, the when when you said to me that.
11:01:49 Why can't you know other organisms have this, I think the fitness is interesting Craddick fitness that cans for specific pathways so we should have victim metabolism of glucose is different from women a caucus, that has an effect on wages trade offs and
11:02:08 so on and so forth in its context so to the environment as address head.
11:02:12 So, because of these so called metabolic property properties and cognitive running I mean just for the metabolism, but certainly metabolism has certain consequences for fitness and in terms of radio trade offs.
11:02:29 They don't change that easily and therefore, I can want Claire closely tied to a phylogenetic core was upstream extensions. I easily picked up by the horizontal gene transfer, so that's that's my two cents.
11:02:48 Okay, but I immediately have to follow up for these are these hydro lasers.
11:02:57 Such a mile. Why aren't they not just add these additional module that you can pick up
11:03:02 the selection pressure to have this to keep this hibernation. So, if, if the hydro lasers produce carbohydrates in an organism that is ultimately less competitive compared to Bishop with the bacterium they will not be maintained.
11:03:18 You don't you don't express it but then maybe especially in the okay so you're
11:03:30 fine. Okay, so yeah, so that's that's what the show about this a business models. But is that something you're going to get into more in your lecture, lecture and maybe that would be very interesting up being for for everybody to, to hear about how many
11:03:39 businesses are those are there and what what are the different types and so forth.
11:03:43 And any association was a species names, or file names. Yeah, I think I'm doing this is probably giving a good example of that and I can add some later.
11:03:52 Yeah.
11:03:54 And then Tom too.
11:03:56 There's one question in the chat.
11:04:12 But the clinical sites are broken down into salary and accessibility so there's both types of organisms. There's organisms that release these hydrolysis Hydra laces and then take up all the cosa rights. And guess other organisms that degrade the substrates
11:04:18 on the surface and transport them in right away so that nothing really is outside,
11:04:25 so dependent that depends on the pathway.
11:04:30 Alright so that.
11:04:43 Can you can you address the second question as well about. So you said that the, we have to pay attention specifically to the red arrows and not the not the blue ones, but the blue is it the. Oh, okay.
11:04:47 So am I skipped that. Yeah, well that the anabolic pathways are they don't, they don't change much because when you know but when you do what you take up here are building blocks amino acids.
11:05:02 For instance, right, or they come by synthesized inside the cell, so they don't, they don't really change the carbon sources that different. But those molecules can vary from between environments right if its dominant Lee like where you're in terms of
11:05:19 what form you're getting the nitrogen and whether you have the capacity to do appropriate reacts chemistry with it
11:05:32 mean if you take up, not an amino acid but our campuses, you know, night. So that might well be some little branches here.
11:05:45 You know that that are different between species but I think the central pathways are very conserved.
11:05:52 I feel like this is maybe an assumption that is sort of specific to the human host context.
11:05:58 I feel resistance to the idea that red is more interesting than blue, but it's not really my thing I just wanted to link it to Alfred's lecture because I thought you know this is a good example where you can make the point but you're not super convincing,
11:06:12 maybe, maybe to look at the Alfred it's just that you have to pay attention to both, you know in a broader context.
11:06:19 Alright.
11:06:21 Fair enough.
11:06:24 Okay, so
11:06:27 if you look, you know you can look at this in a, in a different way.
11:06:33 And that is, There's something called the nutrient rich hypothesis that proposes that in order for to microbes to court system.
11:06:41 Each one has to use a different resource better than anybody else in the community. Right.
11:06:47 And, and basically the abundance of this research and abundance determines the abundance of the species. And so, so easy, it's each research available in an environment.
11:06:59 But basically allow one micro to colonize. So, you know, having here an example of three different niches that determined by three different resources, but typically you know we have 100 different organisms let's say in the in the large intestine, that
11:07:14 means you have 100 different niches that that each one can be colonized by different organism. And so when doing microbiota assembly, the way this happens is that each niche is occupied by some microbe that we randomly sarcastically acquire from the environment
11:07:35 environment so the blue net she is occupied now by this by this light blue bacterium and then over time we are encountering this light pale here picture on that occupies the red niche and finally the microbiota assembly is complete by picking up the third
11:07:52 microbes that is appropriate for this Queen niche.
11:07:58 But of course you know the census is a stochastic process. This process might be different in a different individual so by chance this individual encounters that dark blue bacterium that occupies this blue niche and darker orange.
11:08:12 Trump colored bacterium that occupies this red niche and then we have a light green color that occupies this niche. So do you see the communities at different writers as.
11:08:23 The question is, you know, can be influenced this process and the important answer to this question is that once the community has assembled.
11:08:36 You cannot change it you can so we can get the community here from this mouse you can give the green bacterium to to this mouse but the light green Beckham that is already there, will have an unfair advantage.
11:08:49 And this dark green bacteria will not be able to replace it. And this phenomenon is not. You know very well understood.
11:08:58 but it's very well described, and it's called priority effects. So, the first arrival in the, in a niche.
11:09:08 The first microbe that arrives in which gets an unfair advantage so this is not a fair competition here and once the microbiota is assembled, and that's the reason why the microbiota is resistant to change.
11:09:32 Once it's assembled. So the, and so that's process that we have different microbes different individuals is known in ecology as historical contingency. That means that the text of composition here that you see in different individuals depends on the order
11:09:39 and timing of species arrival doing assembly.
11:09:41 And since this is different for each individual.
11:09:45 Everybody has different communities. That's what you saw in the beginning, it's just a consequence of of this ecological principle.
11:09:54 And then the second consequence of these priority factors that after you acquired a certain community, it no longer changes because the priority effects makes make the occupancy is superior to any competitor.
11:10:07 And as a result, you have this fluctuation in the beginning, you know if there's a species may be coming in at the beginning that is really not well suited for this niche that might be, you might be able to still replace it by a much better suited occupant,
11:10:22 but once there's a student occupied in a niche that occupied is going to kick out anybody else and now we have the state of stability. So once the assembly process is complete, and there is some variability in the beginning about it, then it becomes very
11:10:35 stable.
11:10:36 And you can sequence and individual over here and you will see no change.
11:10:41 And so this is what is called microbiota resistance.
11:10:45 And so if you now combine historical contingency.
11:10:50 This microbiota resistance, meaning that everybody assembles different communities, and then they became super stable. There's only one possible outcome of this.
11:11:01 And that is that everybody looks different.
11:11:04 So now this is just the expected outcome of microbiota assembly if you followed him some noodles. Everybody in the microbiome Phil is thrown off by this diversity.
11:11:15 But this is just a result of how ecology works. And this was described. Decades ago in the plants fields. Right, so this was not a surprise it was just a lack of reading in the right direction.
11:11:27 Right. And, you know, the music thing is that you know this initial encounter of this diversity, then was met by the community who sequences microbes by the interaction that we have to sequence more to understand this you know just sequence enough you
11:11:44 will find this core microbiome.
11:11:46 And that was the impetus to start the Human Microbiome Project in 2009.
11:11:52 And that ran for 10 years and he invested several billion dollars.
11:11:58 And this Human Microbiome Project generated 42 terabytes of multi comics data.
11:12:06 And so when that last phase ended in 2019.
11:12:11 I read some of the commentaries and the sobering conclusion was, We still don't know what the healthy microbiome looks like.
11:12:21 Mitch just you know you get to make this point, just making lists of species names and list of genes does not answer the question, what's the band's community.
11:12:31 Right.
11:12:31 And, of course, that also.
11:12:36 Then, you know, makes it hard to define homeostasis and you don't know how to define homeostasis you have this issue was defining disposes because, you know, because of historic contingency and microbial resistance these definitions here are very hard
11:12:53 to make because everybody has different microbes. I didn't that's why people have kind of rejected this and I'm going to come back to homeostasis or disposes in a second, but I want to tell you one more little thing about priority facts and that is, you
11:13:04 know, an example where you can actually visualize this. And so this was something we may not be noticed. And we worked on infant chickens.
11:13:14 And they looked at how you call that colonizes the infant gut.
11:13:19 And so he called as a faculty interrupted isn't isn't a niche that very requires oxygen.
11:13:25 And of course I told you in a large intestine oxygen is very limited so he called as a result is a minority species so you don't really see much cooler in the large intestine, but it is there, and consumes this little bit of oxygen that is available there.
11:13:38 And you can visualize this but give the call I by giving you a call it lacks operation so this is from foot ruptures luminescent, and it's an opera on the neck encodes enzymes that produce lights, and so this is called bioluminescence, importantly, this
11:13:55 reaction consumes oxygen, so it only happens when it cola has oxygen available then the color starts lighting up, and you can visualize this with a camera so you can take a bird and see that there's lights coming out of it Scott and when you take out
11:14:11 to God, you see, you know, here's the small intestine and then he has the two seekers two birds have to seeker, and then they have something called the kk which is like the colon plus of exact.
11:14:25 And so you see called I colonizes mostly the secret here, which is you know where the light is coming from.
11:14:35 So, how do you, how can you use this to look at paranoid effects so first of all what happens when you give a competitor at the same time. So you can give someone none of that also wants to have oxygen and you get the corner and someone else at the same
11:14:47 time, and then look for live production and Nicola no longer produces life meaning someone else kind of won the competition and and took the oxygen away from a corner.
11:15:01 Okay so this was, you know when to Microsoft drafted. At the same time, which almost never happens.
11:15:07 What if one of them arrives first to be CDs priority effects now so if, let's say if you give a Kudo first, and someone a second does then we go live in the competition that's you know from what I told you you would predict the call I coming in first
11:15:30 it would because of priority effects now it would be winning this competition against someone else. And that's what you see. So if you give me a call at first and then salmonella day later. Now the bird lights up, meaning and cola has oxygen and salmonella
11:15:40 was beaten by Cola, because of priority effects, right so whoever comes first, has priority access to key resources so this is the reason for my computer resistance and the reason, in essence of it microbrewery doesn't change over time.
11:16:00 If there
11:16:00 is any data on, you mentioned the antibiotic treatment, which would lower, lower the load and abundance still this recover any data, I'll say, what is the minimum required to be to be considered as a priority
11:16:18 to minimum minimal colonization. So right so you have 10 to the six or whatever the 10 to the eight and you give it a dose of antibiotics, maybe reduce it to 10 to the 610 to the fifth, and then do compete with some of our would at some point I presume
11:16:35 someone else will take over.
11:16:42 Just, just to get an idea of the number requirement.
11:16:49 If you would, you know, I mean, if you give an equal, an antibiotic that kills Nikolai but famous salmonella you would you would see someone that I know that's a industry Patricia on a call I wizard ominous understand that you, you give it the dose that
11:17:04 lower it's, it's a novel.
11:17:10 I mean, in the end, I think it's just, you know, if you if you reduce the general, if you extend the generation time of the cola enough that it loses its edge I think you will, it will at some point drop out against a clue to maybe to to ask where does
11:17:36 priority for come from.
11:17:39 Yeah, I don't know, you know, I don't know where that comes from that but you know not not not sure it's related to numbers. I think it's a spatial component
11:17:51 that you know there's an spatial niche that close to the surface where there's oxygen available that is occupied by alone and catches away, the oxygen is next arrival so much.
11:18:02 This area, you know that usually when you colonize there's some sort of bottleneck you have to pass and if you, you know you can barely pass it. But if somebody catches away the resources you you you just can't get out, but the but the bottleneck mechanism
11:18:17 that that hasn't.
11:18:20 So, there's not a good idea of what they might be,
11:18:25 or, you know, the cases.
11:18:31 There's many factors that contribute, because when you come in, you know you give it those early and in the stomach you get good reduction in the numbers of picture and then
11:18:44 from the stochastic Leon the fraction of the bacteria actually get to the location where you want to be if it's a special niche. So there's there's probably many reasons for bottlenecks that.
11:19:00 But you know that the short answer is we don't really understand these priority defects, quite as good as we would like to, I think, you know, if I would know the answer I could give you a much better and compelling answer but I haven't really found a
11:19:15 good experiment that tells me exactly what is really going on here.
11:19:20 But I think it's an interesting question.
11:19:23 So, you know, from what I've told you so far about on my computer assembly we can we can now look at assembly of the microbiota over time and try to understand what is happening.
11:19:48 microbiota which is the assembly process and then we reach the stable state. And I've told you in the beginning that this stable state here is basically the result of of normal habit of filtering in the baby which is a combination of our biases and providing
11:19:58 milk Oracle satellites and these two factors will then select for something like the fit of bacterium.
11:20:04 And so that is the first stable state, then you will have the process of cleaning.
11:20:10 MIT only across the Hawaii, are removed from the diet, which leads to an extinction of some microbes, and then fiber is given, which opens new niches and these niches, need to be filled.
11:20:38 So we have another round of community assembly that gives you some disturbance and often after weaning in agriculture animals get sick so this is like a state of instability so the microbiota is not fully functional, but then we reach a stable state again.
11:20:43 Because this habitat featuring this fiber and unroll biases gives you a dominance of Australia and factual idea which is to adults type microbiota that is stable.
11:20:56 Now if you haven't met a disruption, during life.
11:21:01 You can you can have another round of microbiota assembly so antibiotics for instance, can you know remove many species from the gut. And once you stop antibiotic treatment now you develop the microbiota will assemble again until it is complete.
11:21:16 and when you know when I say complete.
11:21:19 This is funny thing about ecosystems that usually are not fully saturated. So, the same is true for the gut, the gut is never fully saturated but for all intensive purposes.
11:21:37 It's going to be hard for anybody else to colonize.
11:21:33 But if you look close enough and you give a fecal microbiota transplant from one house to another you see that a few strains are able to interest that the kind of rare metabolic pathways that you that a box you don't often encounter.
11:21:48 But for you know for in the first approximation we can just look at the stable state, and that explains why, for instance probiotics, have to be given all the time and don't colonize is because their niches occupied and if you give a probiotic, the probiotic
11:22:02 probiotic cannot replace its competitor, because it has profound effects on its side. And so the probiotic doesn't colonize right.
11:22:10 So if you do have to stay on this after enduring treatment Oh, then you have another round of microbiota assembly. But if you don't change your diet.
11:22:21 The normal habit at filtering will resume.
11:22:27 And that will have a similar outcome and community assembly you again will have the microbes that can eat, eat those nutrients that you consume, and they will be anaerobic because you're at the theorem is hypoxic.
11:22:43 If you look closely, the strains that became extinct here in this treatment event. They will be gone and stay gone, and they will be replaced by new species however the species will have similar metabolic properties.
11:22:56 So functionally the microbiota is similar and that's what we call microbiota resilience, right that the microbiota returns to a healthy state.
11:23:06 After disruption.
11:23:10 However, if you now have a condition where you permanently change to habitat filtering.
11:23:19 Now you will, you know, let's say you have intestinal inflammation and intestinal inflammation causes many changes in the environment we're going to talk about a little bit later.
11:23:28 These changes in the environment will open new niches and destroy old bonds and so a similar thing happens as as we happens after weaning. When you have inflammation.
11:23:40 It basically opens another round of my computer assembly.
11:23:58 stable state this will be just by users, but it will be stable, because it's fed by up novel habitats filtering.
11:24:03 So if you look at this scheme.
11:24:07 Now you can say that homeostasis is just the outcome of normal habitat filtering. So whenever you have normal habitat for drink it will result in homeostasis.
11:24:18 Whereas, just for us this is the outcome of abnormal habitat filtering.
11:24:26 And so if you don't use the species definition to try to define discloses and homeostasis. And you try to define it functionally, it is actually quite simple.
11:24:37 Right.
11:24:38 Also, the answers to these questions are quite simple once you understand how the microbiota assemble so just different communities are different bodies as well this because there's different habitats filters in the small intestine, for instance, we don't
11:24:51 have a personal hypoxia so we don't have to Australia know we have Priscilla instead dominate.
11:24:58 It's a consequence of the habit of filter.
11:25:00 And the same is true for any other body surface right there's certain habits of surface that TV dominance in the, in the female reproductive tract, for instance, you have a PCR cells slough off that release glycogen glycogen is degraded tomatoes and multiple
11:25:14 trials, and that feeds lactobacillus didn't make a lot of lactate to suppress growth of other bacteria. And that's why we have the dominance of lactobacillus, the habitat filter is black region, essentially, right, and enzyme host enzymes that degrade
11:25:27 glycogen and tomatoes. Right, so every habitat has certain habits and focus that then leads to dominance of certain organisms in the female reproductive tract lactobacillus for instance.
11:25:39 And so that's the reason why all the communities at different body sites, a different outcome of habitat filtering the communities every day diverse okay this is just the reflective of how many different niches we have and different body size, and yes
11:25:55 And yes, there needs to be more research but these niches actually are.
11:26:00 But it's not super complicated to understand, but maybe it's difficult to identify its specific niche.
11:26:08 Then the taxi carriers difference between individuals which really screw people often is simply explained by historical contingency in my computer resistance so explain to you.
11:26:17 So the, the Assembly, Rules of the microbiota cannot have another outcome.
11:26:22 then taxa carriage diversity between individuals. That's a must. And finally, composition fluctuates over time well it doesn't fluctuate that much when you have a major dietary change like going from Luca Luca Sarah to fiber you see a change, but if you
11:26:37 don't have a major type dietary change this resistant to change and the fluctuation is mostly the period of assembly.
11:26:45 So now all these things that, that, that are complicated about microbiota are no longer complicated once you look at it from the point of view of a microbiologist I would say,
11:26:57 alright. So, if you define this just for yourself and homeostasis functionally as you know homeostasis being a state that is typical off or appropriate to a healthy host right that focuses on what's the function of the microbiota because normal means
11:27:18 that there should be a normal function of the microbiota. So what is the my computer do.
11:27:22 And there's a few things to my computer is important for to first in the large intestine, of course, it, it has a digestive function so the fiber degradation generates fermentation products because with this community and the large intestine is mostly
11:27:39 fermented and these fermentation products are taken up by the host for nutrition and in humans that contributes to about six to 10% of our energy budget.
11:27:49 This is much higher in organism instead of good info. So the focus for mentors and height tanker for mentors, get a lot more energy out of fiber than we do.
11:28:02 So, and as a result we don't get fed on broccoli.
11:28:05 But cows, get fed on broccoli, right. So, so the.
11:28:10 So the amount of energy that we retrieved from temptation is increased if you have better fermentation temperatures right that the colon is just very short and not super efficient.
11:28:21 The other function that is important for human health is that many of these metabolites that produce but in my computer influence the immune system and so there's this music education, and you can see this injury mice.
11:28:36 You know there's many immune functions that are not properly developed and so there's, there's an important aspect on the immune system that is heavily studied in immunology, okay so when you look at these two functions.
11:28:48 Some people argue that this is you know the microbiome is overhyped because these two functions are not really essential for life. Since Trump three miles are viable right so.
11:29:00 But I would argue that this is a flawed argument, you know, not only to Trump you might have to get a special diet and supplements. But if you take the germ free mice, out of the germ free isolator.
11:29:12 They will die from opportunistic infections.
11:29:16 And so that means there's a third function of the microbiota.
11:29:20 That is essential for life. and that is to prevent harmful microbes from entering the body is a function that I would call colonization resistance and this colonization resistance is based on the same factors that we have seen are important for microbiota
11:29:35 assembly competition and habitat filtering. So those are the two components of colonization resistance, and it is mitigated, not just by the microbiota but it's a joint venture by microbiota and host.
11:29:47 So this is the host Michael Kennedy era.
11:29:52 Okay, so let's do you guys want to have a break or should I continue think this might be a good evening, good place to have a break this this this was a great introduction and really nicely setting the framework for for the research talk.
11:30:11 So I would say suggest.
11:30:13 Let's take a 10 minute break. Like, to 1045 1140, West Coast time.
11:30:37 Is that right. Okay, so let's take a break for 10 minutes. Thanks, guys, thanks so much.
11:40:06 So
11:40:10 continue.
11:40:16 Fever talking about colonization resistance being dependent on two factors competition and habitat filtering so I'm going to first talk about competition, and I'm going to use an example that we had looked at, which is laboratory mice.
11:40:32 So does your Odyssey 57 black six miles from Jackson laboratory, or C 57 black six miles from Charles River, another vendor.
11:40:46 And you challenge these mice with someone Ella you see that the challenge goes that which, half the animals become colonized is much lower in Jackson, my mice from Jackson laboratory than in mice from Charles River.
11:41:01 So in, you need about 10,000 bacteria to colonize half demise. In from Jackson, but you need about a million bacteria to colonize half two miles from Charles River.
11:41:13 And so this could be you know due to genetic variability you know these are very similar mice genetically very similar but there are some snips, in which they differ.
11:41:21 Alternatively, it could be due to micro bio that changes between different vendors, and you can find that out by giving these.
11:41:30 The microbiota from these mice difficult microbiota to germ free animals and then challenge them with salmonella and you see in the dashed lines here this is the result of challenge of jump through my eyes you see that again the susceptibility of Of Mice
11:41:44 from Charles River is again about a million bacteria needed to colonize half demise which is very similar to the donor mice, just experiment. And the same is true for mice from Jackson so that the microbiota transferred to a totally different mouse.
11:41:59 The mouse.
11:42:01 Totally recapitulate, but those is needed to colonize the mice.
11:42:06 So what's the difference between these two different computers. So when you sequence the microbiota of these two different lines you see many differences, indicated by this color scheme here.
11:42:19 But it turns out, none of these things that you see here, actually were responsible for this difference.
11:42:26 What was responsible for this difference is this group here the intro back to Iran is. And if you look at the color scheme.
11:42:32 It's not visible in any of these mines.
11:42:36 And that's because these are minority species that are present. You know I tend to the five roughly 10 to the five colony forming units per gram feces.
11:42:48 And so as I mentioned before the sensitivity of microbiota profiling is such that you when you sequence I had thousand treats and you have 100 microbes.
11:42:58 You can only see things that are present that oh point 1% of the community and the community size, like tend to tend tend to do 11 program feces. So, the only back here you can see is, those that are higher than 27 or 28 program feces so if it's something
11:43:16 isn't this abundance, it will be in this plot.
11:43:20 If it's below that you cannot see it.
11:43:22 And basically Enterobacter your picture, these these interactive Alice here are minority species that are invisible to non cultural methods, of course, cultural good old fashioned cultural methods plating faces on McConkey have a much higher sensitivity,
11:43:37 the limit of detection is here by tentative one and interestingly in mice from Jackson, that don't have endogenous Enterobacter Alice and the ones from Charles River do.
11:43:50 The reason I may be called objects and the reason that I'm have these attributes around this is because there's something called specific pathogen free mice.
11:44:00 And the way they are made is that you derive a mouse germ free, then you give it an altar Chandler Flora to normalize my computer assembly.
11:44:11 And then he put it in a barrier facility where you monitor what is coming in. And so in checks and laboratories they try to exclude pathogens and in order to do so the screen on a clunky and kill all my that have colonists and McConkey so that keeps colony
11:44:30 colony antibacterial is free for us, other vendors like Charles River.
11:44:35 that just exclude specific pathogens which is more work.
11:44:39 Right, so they exclude someone Ella Yesenia, and and helicobacter a particles and a bunch of other pathogens, and you have to specifically screen for them but they allow my eyes to have to be colonized by commensals like a call I slept for two years.
11:44:55 So they actually do more work, but as a result, their colonies is 30, because the to actually have to natural assembly of introductory introductory Alice.
11:45:07 So this is just a way of the vent how the vendors make specific publishing free minds. So typically all mines have have entered back to Alice but artificially, they are kept out in Jackson mice.
11:45:17 And you can show that this makes a difference so you can sequence what these mice from charts we have a hat and this particular batch had a tweak or lies in the produce Mirabilis in there.
11:45:26 So this is their phylogenetic tree, compared to the stranger used for challenge with the system another stranger used to challenge demise.
11:45:36 And so now you can ask what happens if you take these three strains these three cola and produce train from Charles River mice and give them to the checks and mice.
11:45:46 And so this is shown here when when you look at the Jackson mice that just received stare on medium you have again your 10,000 Victoria.
11:45:52 I needed to colonize half demise but if you give them these three strains of introspective Alice now the dose goes up to a million that needed for to colonize 50% of the animals so that means that yes this.
11:46:08 The presence of enter picture Alice was responsible for this change and susceptibility, and these are close competitors to someone else because they're close relatives, might so here's our seminar.
11:46:20 So what we did is, you know, to show this genetically we use an another call I call it missile 1917 which is a probiotic.
11:46:29 And the news this that the fact that checks and Mize in text in my eyes The microbiota assembly is incomplete because basically the special part is in three conditions prevent a SIM, you know, completion of assembly by adding Enterobacter all this.
11:46:46 And now, What that means is we can use these mines and complete microbiota assembly by giving them a Niccolo for instance right and that you can, you could view it as a precision editing of the microbiota because it's not an infection, it's just an completion
11:47:01 of the normal process of microbiota assembly that is been, you know, artificially blocked at Jacksons by the way the house demise. And so, the nice thing about this is that you can give them any color.
11:47:13 And this is wild type, but you can also colonize another group of mice with the mutant that kind of inspired oxygen and the micro fairly condition because today be and cost itself can be the oxidase, and you can take a mutant that the compliment is mutation
11:47:26 and, and the most you know a colonized just fine but these strengths.
11:47:31 And now we can be have mice with four different mic for my computer does that differ only by, you know the presence or absence of Nikola, or if you compare these two groups.
11:47:43 The only one gene.
11:47:44 Right, so this is a kind of a neat trick for precision editing of a complex microbiota.
11:47:50 And, and now you can challenge these mice with someone else and if you do that, you see that the mice that don't have Enterobacter Alice, you challenge them at the dose tend to the five so this is here.
11:48:15 but most minds from Jackson laboratory get colonized right. So at that those most minds that from Jackson that don't have anything in them. Get colonized by salmonella.
11:48:18 When you give them a call and this 1917 you see that most mice are not colonized.
11:48:31 But if you knock out the ability to consume oxygen. Now, mice become colonized with salmonella but shows that really competing for oxygen. Right. And if you if so when when you have entered Vectra Alice to keep some of that out because they competing
11:48:38 for this critical resource.
11:48:40 And so that's the effect of competition you're close competitors that have a similar metabolism. They're competing and, you know, the effects are large, it's 100 fold difference in susceptibility.
11:48:54 And yet you see nothing in the 16 s profiling so that's why I was saying you know the competition is not easy to see. He's often minority species.
11:49:03 So in your 16 s plots that you know you might conclude the competition isn't important but competition is important you just don't see it with the technology of microbiota sequencing.
11:49:15 Okay. And so then, the next aspect is habitat filtering and so there's there's two habitat filters that need to be mentioned the first is actually coming from the microbiota so this is again very touching slide showing nicely that you know, one of the
11:49:30 main products of the primary for mentors and secondary for mentors is the acetate, and that has a pretty decent concentration in the colon even though it's absorbed by the host.
11:49:41 So supposedly like 95% of shots and fatty acids are absorbed by the host, but still what is left is still 50 million molar which is pretty high concentration and acetate is in it for liberal with acidic acid.
11:49:55 And you know just just showing the curve that that the PK value you have like a 50 50% but at the pH so this is pH dependent at the page you haven't been testing.
11:50:06 You have, let's say you know 90 to 99%
11:50:12 acetate and only one to 10% acidic acid. Right.
11:50:17 So, now, the issue is that acidic acid is not charged and can freely diffuse over membranes, but in its diffusers into a bacterium the cider soul of a bacterium has a higher pH, and in this range of Sonic pH
11:50:38 acetate is acidic acid is totally dissociated into into acetate and the proton, and the effect of this is that basically protons accumulate in the sight of soul, which disrupts pH homeostasis and that's the challenge for growth and so bacteria that that
11:50:57 different this environment has to have some way of dealing with this challenge to the pH homeostasis. And everybody who's there has has some trick doing it and often they're not understood because nobody cares, somehow, it's hard to find papers on it.
11:51:12 So people usually care about this pH homeostasis when it comes to you know pathogens overcoming stomach acid or they're interested in mentoring fermentation there's a condemnation and they're trying to figure out how you can prevent, you know, he called
11:51:24 are getting into your sauerkraut or something.
11:51:27 getting into your sauerkraut or something. But there's very little literature on the intestines, to see how they overcome it, but obviously these primary fundamentals that are present at numbers like 10 to 11 program feces to grow very well in this environment
11:51:54 It turns out, intro back to AC don't know overcome this problem probably using some trick involving respiration. And because electronics episode limited destruction festive fatty acids keep the abundance down, in part, and so this is basically habitat
11:52:03 filtering by the microbiota by producing fermentation products that can limit growth of organisms and you can see that when you, when you, when you remove this this fermentation products, for instance by antibiotic treatment.
11:52:19 So when you remove these organisms that ferment, then the products become reduced. And so you when you treat a step two mice and you see there's a massive thousand foot drop into concentration of acetate in the in the large intestine and that results
11:52:36 in a massive increase in the abundance of things like e coli for instance in the intestine. Right. And so you can see that this contributes to
11:52:47 to habitat filtering and colonization was instance.
11:52:52 However, it's not that it really kills all enter back to it but rather that you know under conditions where we do have shortened fatty acids present the cola has some resources that it uses to to deal with this problem but the resources are limited, so
11:53:09 that the numbers of the color cannot go beyond a certain point, it's just not enough of whatever they consuming.
11:53:18 Usually they use some sort of proton consuming reaction to the side of soda deal with a pH problem but whatever resource they're using is not available in large quantities.
11:53:27 During homeostasis.
11:53:29 So this is so these two effects are basically microbial effects right so competition with close competitors and then habitat filtering. So these are minority species.
11:53:39 And these are you know having to filtering is typically the dominant species that produce most of the fermentation products.
11:53:48 But then there's a third mechanism that involves the host and so that requires beauty right and.
11:53:58 But then I didn't put beauty right here and this, and this group of fatty acids. So, but it should be in there.
11:54:06 And so, edited.
11:54:10 And I think the one limitation I would say about this graph from banner change is that it's more to the host than just this absorption.
11:54:18 So, in order to understand why I single out beaut beautiful is an important factor is because it affects host physiology and so beauty rate, turns out to be an important carbon source for epithelial cells in the colon.
11:54:37 So they take a better rate and then they degrading it by better oxidation in the mitochondria.
11:54:55 And that is coupled to oxidative phosphorylation a process that consumes oxygen.
11:54:53 And, you know the oxygen and then the ATP generated you know it's used for various processes one of the processes important in the large intestine is that you've taken the contents and the large intestine bogus drawing water and in order to transport
11:55:06 water you transport sodium ions and there's an ATP is required in the buzzer lateral member introduced to sell and then chlorine and fluoride follows passively.
11:55:17 And as a result, you have water. Following boss Nordic forces and that's how we absorb water.
11:55:25 Now, this, what is important here is that the consumption of oxygen in the mitochondria is what really makes the epithelium hypoxic and I told you this is one of the main control mechanisms of the microbiota.
11:55:39 Now what happens if you, if you.
11:55:45 So what so so beautiful. It's really important to maintain this enterprises and enterprises is one of the mechanisms that keeps the abundance of entrepreneurialism really low and so this contributes to colonization resistance and inhibits and Terry pathogens
11:56:02 from entering because they also require oxygen just like a call know it's filtering it for that showed you that they compete to oxygen but of course if there's the oxygen level it's very limited that competition becomes quite fears.
11:56:13 And so these are the three components of colonization resistance if you have
11:56:21 competition habitat filtering by my microbes and targeted filtering by the host which is this unreal biases this episode hypoxia.
11:56:33 And just to compare this, what to what banner chinks was saying, in essence, this enteroviruses you know it's a very important habitat for them because it limits the range of successful strategies into colon, to those that are executed by these primary
11:56:50 Marion secondary for mentors.
11:56:53 It's very difficult for organisms that risk that require oxygen or nitrate.
11:57:00 To be successful in the large intestine because enterprises are the homeostasis of the large intestine, doesn't give them enough resources, and it's not entirely true as I said there's a little bit of oxygen, but you see what happens to a cola is so low
11:57:12 that you cannot seek it the sixth seed anymore with 16 sequencing so there is some Nikolai eating that little bit of oxygen that that leaks out.
11:57:21 But really the habitat filtering is basically determining who's dominant right and so on our biases determines that these guys here are dominant.
11:57:30 And so, yeah.
11:57:34 I find it surprising that the such a big role you attribute it to butare for enteroviruses. Imagine you don't have a bitter regenerating organism let's say you have jumpy mice, an action and I still, It's got was equally.
11:57:53 And the other.
11:57:58 No.
11:57:58 Yes, you put your finger right on the spot, I was oversimplifying because I don't think I have enough time to explain it but i i always simplify it so you write is not the carbon source.
11:58:12 That's what you see in the textbooks, but it's not true. Peter is actually a signal to activate mitochondrial activity, and that signal is generated by nuclear receptacle people gamma and Peter is the people come an agonist.
11:58:26 So I can also use liquid, but as long as the people gamma is active, you have a have a very strong activity of mitochondria so it's not that you can you can do it the same thing with limits.
11:58:35 No, no, but I mean okay i don't i don't mean literally itself the consumption.
11:58:40 the consumption.
11:58:46 I mean, I mean the host role, versus the bacteria rule. I mean the know if you if it's a host of doing whatever it's doing.
11:58:50 Right, and without this signal from literature from victory, but you have a faculty the bacteria in the gut, they're going to be taken up or their oxygen, even, even if the host is not doing anything special.
11:59:03 Well there is not enough oxygen for them to really yeah so the competitors, you know for oxygen bill in it's a it's a joint effort here of microbiota and toast so if you.
11:59:16 The key thing to understand about colonization resistance so you can remove the competitor. And then you see the petition does better I showed you that in the beginning.
11:59:24 Right, right. But you can ever they didn't show you and I'm going to show you in a minute. The other thing you can do is you can you can remove hypoxia you know you can change this episode oxygenation here.
11:59:35 And the microbiota can stay the same, and you have an expansion of the pathogen, so all you can you can compromise, each of these arrows, and it will lead to a loss of colonization resistance.
11:59:48 Giant cancer joint venture. Why can't, let's say you leave the house alone. But, but could there be enough commercial faculty that bacteria to take up the oxygens to keep the environment still and a robot.
12:00:01 Yes. So that's my.
12:00:05 Essentially, the intro back to AC contribute decolonization resistance over the short here mind.
12:00:13 So the reason.
12:00:17 Paul I protects against someone else because of that. Right, right. But so, so I want to make sure if you say, given the color that tend to spy oxygen, then it no longer works.
12:00:28 Right, right. So, that's why I was surprised by how much you attribute into the host.
12:00:38 and the mitochondria.
12:00:36 It's the difference between necessary and sufficient. Right.
12:00:40 So all three. All three points.
12:00:45 All three unnecessary but none of them is sufficient on its own.
12:00:50 Okay. Right.
12:00:53 Alright so,
12:00:56 the one thing I liked you know about furnishings talk was looking at you know what processes happened in different parts of the settlement because you can actually from this comparison see that large intestine is basically equivalent to lower layers in
12:01:16 the leg sediment in terms of its metabolism. Whereas, when you look in the upper parts of the set of mental processes that happened there are not characteristic of the large intestine, but much more what you would see in the small intestine, right so
12:01:29 so you can see similarities between microbial communities and that's why I think all this information on multiple metabolism from from studying natural environments is quite relevant to my computer research because you will see the same like metabolic
12:01:44 groupings here and actually the hop to that goal of habitat filtering by the host is to actually convert, you know, ensure that certain environments are looking, you know like, the bottom of a lake.
12:02:01 So this is kind of the summary of of colonization resistance and as you pointed out Terry that you know there's there's different components, but my point is that each of them contributes and you can eliminate, you know, the host control and you will
12:02:16 see that the host becomes more susceptible to pathogens, and you can disrupt the microbiota in in different ways and you will see this increased stability patterns.
12:02:28 So this was my initial breaking point, but I think we did this early now, so unless you want to have another one.
12:02:38 And so, can I ask a question. Yeah.
12:02:43 So I'm just wondering just since you showed this seven core. So if we are able to do a germ free certain core, are we able to inoculate this germ free coral with the human gut microbiome.
12:02:59 Oh yeah of course that's very commonly done since you take Jeffrey my as you can canonize them this human microbiota and. And that's an nice way of using germ free minds to study microbiota so by computer research you can, you know, do clinical studies
12:03:15 basically by using germ free minds and asked by the community structure itself contributes to that.
12:03:24 So, you know, if you have a disability community you can ask me that that actually affects the host over the dead as a consequence of the host being sick.
12:03:31 Right, those kind of questions.
12:03:35 Just, just to end, I think Jeff Gordon, the reverse experiment where they took seven anaerobic sediment communities actually from from the sidelines and injected this engine for mice and they typically died because of the abundance of Salford reduces,
12:03:52 which obviously captured quickly on the available nice and then produced toxic levels of hydrogen sulfide.
12:04:00 Oh, that's interesting.
12:04:01 Can we add it more like hydrogen sulfide organizers into that niche.
12:04:10 Tom would be a great person to comment on that.
12:04:16 Maybe next week.
12:04:18 So thanks
12:04:23 here so the question was about adding Sophie reduces.
12:04:28 I'm sorry. Could you repeat it.
12:04:31 Oh and just so that my previous question was, was in fact, the inverse way. I was asking if we can infect a germ free a certain color with the, the microbes from the gut microbiota.
12:04:45 And then I think Alfred reframe rephrase the question into the someone did the experiments of using the settlements microbes to trance like trance locates or inoculate into the germ free mice.
12:05:06 And here I mentioned, because of the accumulating sulfites that's why it was unsuccessful. So I was wondering if it's possible we can just, just like change the composition of this community a bit by increasing the sulfide oxidizer more than we can maybe
12:05:25 generate a healthy settlements gut microbiome community.
12:05:26 Yeah. Wow that's that's complicated.
12:05:31 Yeah, I mean, I mean interest interesting idea so I don't know, Alfred gave the best example that I know of, of, you know, colonizing a germ free mouse with some collection of microbes from the environment.
12:05:46 I don't know if anybody that's done it the reverse way but, I mean, presumably, you could play that game in the gut, you know, balance sulfite production was sulfide consumption and then it wouldn't be problematic.
12:05:58 I'm not sure what you'd learn from that.
12:06:17 But you could probably do something along those lines, xe Ting Ting, I think you brought up a really good, good point now thinking about it. In order for Sanford oxidizes to go and to keep the hydrogen sulfide level low, you need oxygen, and there's no
12:06:19 oxygen in the gut, so they would really couldn't add them, they could not metabolize to, because there is no oxygen, so my prediction would be that this edition would not solve the problem.
12:06:33 You know, although I'll bet. Andres is going to talk to you about night trade that can be available in the gut. And so you could imagine a soul fight oxidizer that instead of using oxygen uses nitrate.
12:06:45 Right.
12:06:47 Depends on the Fluxus electrons through the central cycle compared to electron flux through the nitrogen cycle. Great. Andres nitrate in the gut.
12:06:58 Yeah, a little bit. Okay, good.
12:07:03 Oh, and also. Okay, a little bit more. So if we. Yes, oxygen levels are really low, but if that the turnover rate is higher than maybe it's still feasible.
12:07:20 I mean see turnover rates of the sulfide oxidation versus self selfish reduction.
12:07:28 I think you're right in the sense that it's about one of our flexes and not so much steady state concentration. So, what we really need to know, are the flexes so sofa, nitrogen, oxygen in order to balance that.
12:07:50 Oh no problem, it's you know, it's very hard to listen to zoom talks for very long time so it's good to have interruptions, I think, so feel free to ask questions whenever you, you, you have wonder about something.
12:08:05 So this is, you know, now we understand the microbiota assembly and more importantly, how the microbiota confers this colonization resistance. So now we can finally get to the point of how someone electric and can actually invade this ecosystem.
12:08:18 And I want to make one important distinction here and that is when you talk about petitions there's these two different kinds.
12:08:24 You talk about opportunistic pathogens vs Real petitions of Frank pathogens.
12:08:32 And the defenses that opportunistic pathogens can only cause problems, if the host has some defects in its immune system, or whatever.
12:08:43 For as Frank petitions can overcome all fences defenses that we throw at them. Right, so this is the difference.
12:08:52 So opportunistic petitions supposedly an accident various bank pathogens. They use that strategy for living right so they invade the host and then transmit to the next host using the violence factors and then the process we get sick.
12:09:07 Right. Whereas opportunistic petitions they don't transmit to that strategy so if you have cystic fibrosis and you get infected the Pseudomonas Aeruginosa that doesn't transmit to you.
12:09:17 It can transmit to another cystic fibrosis patients but that's genetically very rare and the only reason that happens is because we crowd them together in a hospital.
12:09:25 So this you know opportunistic persons make you sick but that's not part of the life cycle so nothing is under selection, right.
12:09:32 All right so opportunistic pathogens.
12:09:36 The reason I bring them up is because they cannot overcome intact defenses and that, what that means is that they cannot overcome colonization resistance, and neither can commensals.
12:09:48 So, and that's just a simple reflection of the fact that the microbiota is resistant to change so this is my computer resistance, obviously also leads to colonization resistance, and since the mega pillar doesn't change over time.
12:10:01 That just means that nothing can nothing in graphs. And so we see this experimentally when we take probiotics.
12:10:09 You have to take them every day in order to detect them if you don't deck on.
12:10:14 But if you give a pathogen at a high enough dose that pathogen colonizes after one inoculation and sometimes you know, when I get reviewed by somebody from the probiotic field they asked me how often did you give someone that and I'm like why someone
12:10:29 no you give once and then invites the ecosystem. Right.
12:10:34 So this is the difference between petitions and commendable because petitions can overcome this. So how do they do that.
12:10:44 That is not to say that you know polarization resistance doesn't protect against pathogens.
12:10:50 It still has confessed a good amount of protection against pathogens, particularly at a low dose challenge but but eventually if you if the challenge doses high enough partitions can colonize, and opportunities and commensals cannot.
12:11:04 And so how does that work so we have our three mechanisms of colonization resistance that you know the habitat filtering by the microbiota which is some people call it niche modification, then competition is close relatives and people call that niche
12:11:19 preemption and then the hypoxia of the host in the large intestine.
12:11:23 And so that results that when you know the bacteria petition comes in.
12:11:28 The best seats in the House have taken there's nothing to eat.
12:11:34 So this kind of scenario. And, and then that means the punishment numbers decline.
12:11:41 And eventually the patterns in the drop out. And, and be no longer shared with the feces right so this is what happens after load those challenges but if you increase the challenge does.
12:11:54 Eventually, what you see is that the pattern, initially declines, but then it takes off.
12:12:02 And so what happens here.
12:12:05 You know initially there's the same situation that the best seats in the House are taken. There's nothing to eat and to petition them numbers decline.
12:12:13 But then there's some there's something happening here. That changes the situation and now the petition can in crafting the microbiota and colonize. So what happens here is that the pathogen deploys its virulence factors, and they change this environment
12:12:27 to make it more favorable to grow with the pathogen.
12:12:31 So somehow developments factors that targets to host.
12:12:51 colonize the new niche that has been generated by this host response.
12:12:55 So you know, here all the niches are occupied. But in this case, the host generates a new niche.
12:13:04 And that niche is then colonized by the partition right so that's the process of ecosystem invasion and I would call this particular process ecosystem engineering.
12:13:18 Because the niche that is generated here is generated by the virulence factors in essence.
12:13:25 And it's a new nutrient niche that is created.
12:13:29 And it's something that commensals cannot do.
12:13:32 Why, because what it requires is to make a sick.
12:13:39 So the various factors here trigger host response but you feel that because you have diarrhea and you have stomach pain and nausea.
12:13:48 And that creates the new niche so you know when you, when somebody does ecosystem engineering in your gut, because you get sick.
12:13:56 So that by definition commensals don't do.
12:14:01 So it's a specific strategy of pattern so let's let's get into this a little closer. So I mentioned in the beginning, you know, cola is closely related to salmonella, they, you know, everything is relative in.
12:14:15 In fact in bacterial nomenclature.
12:14:19 These two species diverged some quite some time ago, my graduate students like to point out around the time I did my PhD.
12:14:29 And after that, the pathogen acquired virulence factors so these are two types of secretion systems, I'm not going to get into much detail about them but they are targeted machineries complex.
12:14:45 14 nations syringes, the target to host these machineries are designed to transport proteins across the inner and outer membrane of the gram negative cell and across the South Pacific membrane of the host cell into the soul of the wholesale and, and this
12:15:01 virulence for the incident injected announced seldom change wholesale physiology, which results in invasion of salmonella. That's the function of the first secretion system that allows similar to enter, if you see yourselves that are non fact acidic so
12:15:15 you have to induce invasion somehow. And then the second secretion system allows similar to survive and tissue.
12:15:22 So I'm not going to bore you with details about virulence factors just for the purpose of the talk, you know it's enough to consider Nicola is, as a group of commensals and salmonella group of pathogens with these villains factors and the difference between
12:15:38 between the two is that that you know also they are very similar in the genome and have a similar genetic blueprint, the pathogen has the secretion system mount mounted on top residences the difference and can therefore entered the host tissue.
12:15:53 And then in tissue of course that the immune system debate this is why it is, you know, the immune system is very important for keeping the tissue sterile so whenever there's any microbes that enter the tissue, the immune system has the ability to distinguish
12:16:08 micro from self.
12:16:10 And then the self discrimination triggers a very vigorous innate response initially and followed by an adaptive response and these responses are designed to restore stability kill all the bacteria and tissue and keep the tissue sterile.
12:16:24 And so what that means, here is that when some of the light enters the tissue is now detected by the immune system that triggers the cytokines storm.
12:16:33 And that attracts cell types that eventually kill someone added enters the tissue and everybody who invades is basically a suicide bomber because they don't really benefit from this but there's massive changes in the lumen that that you will see the picture,
12:16:49 can benefit from.
12:16:50 So you can follow this this inflammation of a time but just looking at some of the products of inflammation so one protein that is released by to see ourselves doing inflammation is called Little kale into this is a protein that prevents iron acquisition
12:17:04 the Center for us, interacting.
12:17:08 And so you can detect little Kalan over time in the feces. And you see that when you in fact mice with someone else there's an increase in the scale and it takes about 10 days for them to get full fledged inflammation.
12:17:23 And if you in fact mice with a strain that doesn't have these villains factors, because we're genetically inactivated them. That's strange doesn't cause inflammation.
12:17:33 Importantly that strain also doesn't colonize very well so it shows you even though these villains factors,
12:17:40 they target the host, what they're really doing in the end is allowing someone to overcome colonization resistance. And you see that the light account is is way better than the mutant and that difference is artificially low.
12:17:56 Why because we used minds from Jackson, and you are now an expert on this Jackson lies don't have easy not because mice don't have enterprise GAC, but because Jackson actively kills every mouse, that is colonized was entered back to UC and so they are
12:18:12 more susceptible than conventional minds but hundred fold. So if you would have mice that have hundred bucks GAC this strain here would drop out like a stone.
12:18:23 It's colonizing here a little bit because the niche for Andrew picture Alice is empty. Right, so this is an artifact of the Jackson mice.
12:18:32 So, in real life this difference is huge.
12:18:36 Right.
12:18:40 And Vita salmonella can colonize, even though there's no bacteria is India because the virulence factors change the environment.
12:18:48 And so how does it take advantage of this environment so the first thing we found long time ago was related to suffer metabolism that happens in the gut, not as bad as and settlements but you know there so hydrogen sulfide produced, and there's enough
12:19:01 hydrogen sulfide produced by sulfite reduces the sort of every species.
12:19:08 That is certified levels will become toxic.
12:19:11 And so in order to protect the colonic at the theme from this toxic levels of hydrogen sulfide.
12:19:19 They are certified oxidizes in the ethical membrane of the colonic epithelial cells that detoxify hydrogen sulfide to tire sulfate.
12:19:28 So Tara sulfide is no longer toxic it's a harmless.
12:19:32 Oxidation productive so fight and that's typically present in the in the large intestine.
12:19:40 So what but what happens during inflammation is that, you know, some of these neutrophils migrate into the intestinal lumen in an attempt to protect that receiving from infection.
12:19:49 And these cells, they migrate out and then they undergo a so called respiratory burst which generates oxygen radicals super oxide hydrogen peroxide hydrochloric acid.
12:20:01 And these oxygen radicals can now oxidize time so fed into something called Ted to find it.
12:20:08 And if you know if you if you are someone else aficionado you know about tetra find it because we have used to define it for 100 years to enrich for salmonella in samples that contain competing microbes.
12:20:23 So if you have an infected, you have someone outbreak and you take your, you know, whatever you got infected with Excel, you know some, some raw product ice cream or something and you dump dump this into a enrichment process tetracycline it and then you
12:20:38 One day and then the second, they do selective media and SEO typing.
12:20:47 So that's how we isolate salmonella.
12:20:49 And that has been done empirically for 100 years but nobody knew why it turns out that this is the trick salmonella users and the guts to actually get some access to Alex and accepted so because type of thing it is an Alex and accepted it can use can
12:21:06 It is an Alex and accepted it can use can be used for someone else, and there's not many other bacteria that can use it that's why you can enrich for someone to learn.
12:21:19 There's one notable exception which is your senior political can also use them, which is also a pathogen. And so did someone that I can use to define it for anaerobic respiration, and that it's important for it's crossing the, the large intestine and helps it to transmit.
12:21:33 So this was the initial observation. Subsequently, we looked, you know that there's many other changes triggered by these fibrocytes at enter the lumen.
12:21:41 So far, besides produce these radicals super oxide peroxide.
12:21:47 And how is it that that can oxidize other substrates in the intestine.
12:21:56 To generate electron except us for instance, test your means and certified compounds are oxidized to s oxides and oxides and there's respiratory system for these these electron acceptor us that, that, that bacteria, typically has it as several of those
12:22:15 in the genomes of E. coli and salmonella.
12:22:19 And another important you know, perhaps, perhaps the best electron acceptor, other than oxygen is of course nitrate which is which is a product of an enzyme called, I noticed that is you know make that epithelium but it's much higher levels by inflammatory
12:22:35 mana sites that we don't see here that go into the lumen. And so this enzyme takes Argentine and oxygen and makes nitric oxide and nitric oxide can react with super oxide to form a very anti bacterial component which is called proxy nitride.
12:22:54 But that is very unstable and rapidly degrades to nitrate and so night in the gut and so you can measure nitric doubles in the gut. Go up during inflammation and that nitrate, of course can be used by anaerobic respiration, it's a great electron acceptor
12:23:09 that has a second only to oxygen it's in its rhetorics potential and can be used essentially for every process.
12:23:17 You can use oxygen.
12:23:22 And that, Then it's used by, you know for anaerobic respiration by faculty different groups and contributes to this dominance of faculty of under ops in this case seminar.
12:23:34 However, inflammation is triggered by any other condition I told you in the beginning you know if you have chronic intestinal inflammation. The microbiota changes because there's an altered habitat filtering.
12:23:43 Well, this is the oldest habit of filtering you basically generating a lot of electronic factors that weren't there. So the general biases is trying to keep the environment was similar to the sentiments of a lake even though sulfite production might be
12:23:55 a little bit less pronounced. but inflammation changes that because now suddenly it becomes available which is really what you find in the upper layers of the sediment.
12:24:05 And so that is a change in environment and as a result you will see an all the change in the community structure, there's new stress metabolic strategies that become successful due to an abnormal habitat filtering right so this is driven by the host so
12:24:20 so that's why I'm kind of emphasizing the host because many of these environmental conditions in the gut. Of course involve to host because the host is the environment.
12:24:29 Right.
12:24:31 It's not like a test tube.
12:24:34 The environment can change dynamically. Right.
12:24:37 And so that changes the microbiota compositions so when you, when you look what happens during salmonella infection.
12:24:44 You see this massive change in the in the community structure so this is again 16 as profiling, you have you have here the actual idea on the class level, and Australia and read.
12:24:57 So you see that during homeostasis and uninfected animals, 90 something percent of the microbiota is obligated under ropes of these two classes bacteria and Australia, and doesn't, and if you don't have virulence factors, nothing changes but but if someone
12:25:13 that it deploys its violence factors.
12:25:16 You have to shift from obligated to faculty different groups, there's these two new sectors that come in.
12:25:22 One is the government protein bacteria, which in this case is someone Ella, and the second one is faculty live anaerobic Firmicutes which other facility right so that you have these two sectors of faculty and Rob's coming in.
12:25:37 And another thing you notice is that the abundance of Australia goes down.
12:25:41 And that is important as I said because Australia, the main pieces of beauty rate, and then it's related to apathy oxygenation. And so that was figured out my favorite initially and I really took away his punch line he was figuring out the puter right
12:25:55 is very important for me, maintaining this this empathy al hypoxia. And so, doing some another infection, when you measure graduate levels in the intestine you see that there's a massive decrease computer right levels, and that results in a change in
12:26:10 metabolism so if you if you drop these Peter read levels, the wholesale changes in metabolism from oxidative phosphorylation and the mitochondria, to for this called aerobic like harnesses, So aerobic like homelessness is the conversion of glucose into
12:26:25 lactate, even in the presence of oxygen is a fermentation and the presence of oxygen.
12:26:32 This is the metabolism of cancer cells right and Barbara metabolism, but important thing is that this metabolism doesn't consume any oxygen. So oxygen levels in their premium increase and oxygen can diffuse into the intestinal lumen.
12:26:50 And you can you can visualize this with this hypoxia staying I was mentioning earlier so when you stay.
12:26:58 When you inject human can monitor soul into my eyes which is a chemical that conveniently attaches to hypoxic tissue. You can stain this with an antibody and you do that in the corner and you see that the surface of the colon is hypoxic.
12:27:12 So yes, the lumen is the more closer.
12:27:20 And she looked at an animal that is infected with someone else he has two sections of the more closer kind of folded on top of each other, the lumen between the middle and you see the hypoxia is totally gone, and you can ask is this really because we
12:27:27 the cluster area so you can you can add a community of 17 humans Australia so let's back to these mines that are infected the seminar. And when you do that you see that yes the hypoxia returns in these animals.
12:27:42 So it's really the depletion of Australia by the neutrophils that the changes the apathy on metabolism.
12:27:51 And that, of course, is something that faculty can exploit because they can respond oxygen. So, someone else uses this PD to circle beauty to oxidase, which is encoded by six eight.
12:28:06 And when you compare the thickness of a lot of time Simon Allah with the mutant that cannot reply oxygen under his Macrophylla conditions by infecting mice with a one to one ratio of these two strains and then asking what comes out the other end to see
12:28:19 that you get 10 volts, versus one mutant so that suggests that oxygen is available and provides some benefits to salmonella. And if you if you now at the community or 17th was tricky isolates and restore hypoxia and epithelium.
12:28:36 You see the advantage of oxygen is totally abrogated.
12:28:42 You see it's only about a tenfold effect but you know the nitrate also gives you about a tenfold in fact instead of trying to see about a tenfold effects overall it's like 1000 fold increase in numbers that comes from these three pathways.
12:28:54 And so it's a pretty sizable increase in vector numbers that you get from from respiration.
12:29:00 And again to compare this to the Emperor perfect comparison because so far producers are killing my animals, such as find out from Alfred but but still in a first approximation, you know what you have in the large intestine under homeostasis is a call
12:29:25 on that, you know, looks more like the lower layers of a sediment, very heavy in the graduate primary and secondary for mentors and doing inflammation.
12:29:36 Some of the leaves its virulence factors, so that the host changes that environment to something that looks much more like the upper layers of a settlement, and we have now oxygen and nitrate suddenly drives growth.
12:29:45 Right. And this is a tremendous trick to be done by Michael that's why I call this you know ecosystem engineering.
12:29:55 Because someone else converts this environment to this environment.
12:29:59 And I'm not sure whether there's any plans, any microbe on the planet that that can do that in legs.
12:30:07 It's a hard thing to do. Right. Someone had figured out how to do this by using the host essentially someone other uses its virulence factors to use the host lung to breathe in the gut, which is a really cool trick to make a living.
12:30:27 And you know that the whole lecture series was started by Alfred saying that you know nothing in biology makes sense except in the light of evolution.
12:30:41 And he used that as a lead into, you know, arguing that it's all about electron flow.
12:30:49 But, you know, the quantum I like in this context is from Nobel laureate from France and that basically all bacteria want from life is become to bacteria right.
12:31:04 And you know what that means for pathogen is that the pathogen that that circulates in an animal reservoir which is what the case for someone else, it doesn't it's not an environmental organisms he killed all the animals that carries someone else have
12:31:17 another will be extinct.
12:31:18 You know you can find it in the environment and lives there for a little bit, and that helps its transmission so for instance typhoid fever, which is called caused by someone a Teifi right it's transmitted through drinking water.
12:31:32 Primarily, but if you eradicate all the carriers that carry salmonella and the gallbladder you know these these type of Mary's then typhoid fever is a radical.
12:31:41 So that's what we have done in the US.
12:31:44 If you have typhoid fever in the US, that means you were you were.
12:31:48 You have a history of foreign travel, because we don't have time for us. So that means, these, these environmental reservoirs and drinking water and whatnot.
12:31:58 They're not good enough for someone to stay on this planet. You have to stay in the intestine and, and in order to be successful you have to go from an infected and testing to uninfected in testing so you have to transmit this is what the driving force
12:32:11 of natural selection is transmission in pathogens. And so for salmonella, you can ask you know is this metabolism important for transmission. And you can just mimic this by taking some mice that are in fact that the salmonella, and you put them in a cage
12:32:26 together with mice that are not infected with someone that and you can ask to the infected nice transmit salmonella to the uninfected mice it's a simple question, and the answer is yes when you call house mice.
12:32:39 The ones that are infected with someone at a cost shed salmonella, but also the ones that are uninfected after 18 days of cohousing they start to shed someone in so the transmission happens.
12:32:51 But does it need this respiratory metabolism Do you need to look like the top layer of a lake in order for this to happen.
12:33:00 And so you can activate aerobic respiration, you know, the started competing oxidase, and you see that some eyes don't transmit anymore but you still have some transmission in some cages.
12:33:12 But if you, if you can activate the ability to respond nitrate, enter ability to respond oxygen.
12:33:21 This mutant can no longer transmit.
12:33:24 So if you combine anaerobic and aerobic respiration transmission is blocked. So this metabolism is required for transmission and, and through this need to transmit this metabolism and to virulence factors, and the selection Nizza incredibly complex election,
12:33:41 selection, because the violence factors you know in some another everybody's excited about these types of secretion systems and they succeeded dozens of proteins into wholesale and each one has a target and does something very specific and you know you
12:33:53 can you can read for four weeks and weeks papers about all these factors.
12:33:59 But it's mind blowing that these effects on the host cell that you can study very mechanistic lean tissue culture actually under selection to this complicated chain of events.
12:34:11 It's just an incredibly complex election, right, that, you know, by just looking at tissue crashes, you know, have no comprehension of this.
12:34:22 You have to look at, whole animals to see how this is happening but it's still mind blowing, that these things are connected somehow.
12:34:32 Alright so, my last slide where I summarize these things for my last slide before I summarize the main takeaway points. This is a slide where I showed you know the chain of events and in one in one image but what happens during this ecosystem invasion
12:34:51 by someone other which is really ecosystem engineering in my opinion.
12:35:08 blocks.
12:35:08 Its access to oxygen and, and the bacteria produce lots of short chain fatty acids and salmonella without oxygen is inhibited but he's searching for the acid so it drops down.
12:35:21 And, you know, enteroviruses limits the amount of oxygen in the first place and the little bit that comes out is, is eaten up by cola. And so, someone who is dead in the water and it has to hang in there long enough for the virulence factors to trigger
12:35:35 this inflammation, inflammation then change the environment. So that's a critical period and and and that period if the challenge those isn't high enough salmonella will drop out and go extinct.
12:35:47 So that's why you need a politically high inoculation dose of the pathogen, so it can wait long enough.
12:35:54 You know that it's not disappeared entirely by the time you have this inflammatory response so that's kind of the challenging. The challenge for someone else and that's the reason why they need a relative high challenge chosen by low dose challenges inhibited
12:36:08 by colonization resistance, then these factors that's come out and change the environment and basically causes state of abnormal habitat filtering very now suddenly see things that we see in the upper layer of a settlement.
12:36:25 lower layers of sediment which we should see on the left, there's many other resources than other than respiration it's just nice to follow focus on respiration because it's such an important process for the flow of electrons.
12:36:39 When you look on the carbon and the very light that diversity becomes much larger and that becomes more challenging.
12:36:45 However, there's also resources coming from the host that feed into the carbon metabolism. So it's the best inventors group has shown nicely that the switch in metabolism of the hot on the host side to Arabic like policies, makes the host a major source
12:37:01 source of lactate in the intestine and actually surprisingly, most of the lactate you see doing some another infection comes from the host.
12:37:10 And the second thing he found you know you did a medical omics analysis and he found that actually lactate is the is the most abundant metabolites doing some underlie infection whereas it's a very minor metabolite she doing homeostasis very short chain
12:37:23 fatty acids so much higher.
12:37:25 But doing some of that infection lactate becomes the becomes the most abundant metabolite and it's host arrived.
12:37:32 So it's not fermentation by lactobacillus or something. But it's actually the host juicing lactate, and then salmonella using a respiratory lactate the hydrogen is that allows it to respond elected in, using suit a be, you know, the Southern Company oxidase
12:37:51 to perspire lactate to pirate rate and now you have pirate in the house itself without any Redbox balance.
12:38:00 And I think what they're using mostly is pervade format liars than to bring it to acetylcholine so you actually don't make an NIH. And now you can make everything into acetate so you get to actually some ATP.
12:38:12 There's not enough oxygen typically that bacteria actually makes you tools are there still produce fermentation products, it's just oxygen makes everything a little bit easier and more efficient you get you squeeze a few more ATP out of this acetate production
12:38:25 of lactate.
12:38:27 For instance, I mean one, but you know you get you get if you have a high throughput because lactate is the most abundant metabolite that might actually be quite effective.
12:38:38 So there's one drawback in this trilogy I told you in the beginning that's priority effects so he called I cannot kick out some of the Latino kick off the call I.
12:38:48 But, but it also means you know that the fact that the microphone is resistant to change this means that microbial warfare doesn't really work for ecosystem invasion, you often hear that you know there's type six decreasing systems and cousins and I don't
12:39:01 know what that microbes make to compete in the gut and that's not true.
12:39:07 And we know this is not true because the My computer is resistant to change so empirically we know it's not true. If it would be true that type 60 creation system allow you to craft the microbiota should be changing.
12:39:19 And it's not changing. That means just have 60 creation systems and the Collison's are not good enough for ecosystem invasion. That's the reason why commensals cannot innovate because they have lots of these, you know factors they have.
12:39:33 They're not virulence factors these types execution system and colleagues and stare at them factors you find in commensals.
12:39:40 And they cannot graph right so probiotics don't stick.
12:39:46 What takes is pathogens and my because the reference factors to to ecosystem engineering.
12:39:52 But here's the drawback of ecosystem engineering, they create a new ecosystem nutrient rich from scratch or using the host response, but this is a new niche.
12:40:05 Everybody, which is present will arrive in this niche at the same time means there's no longer any priority defects now is, is a level playing field.
12:40:16 And, and competition, a fair competition now this time.
12:40:21 So as when you ever you enter the ecosystem that has microbiota it's not a fair competition they call an idea that's already there has an advantage. But if you make.
12:40:30 If you do ecosystem engineering.
12:40:33 Now there's a level playing field and the competition is a fair game. And now, what that means is that now Ico like competes with conventional introductory see for occupying this new new nutrient niche that it's virulence factors generated.
12:40:49 and in this situation, they are using these micro.
12:40:52 These antimicrobial weaponry now. So this is in this particular situation where these become important and that's where you see the phenotypes so you know there's papers from Manama Rafa Telos lab and double standards lab and also
12:41:10 I'm blanking on the name this work done by several groups showing that this Collison's and types execution systems.
12:41:20 Denise monarchs the name. I think there's one next lab so all these these factors here, produce phenotypes, you know, an advantage of either the petition or incremental, but they all
12:41:30 tweak the system such that you looking at this ecosystem engineering and now when once there's inflammation now you see an effect of Collison's for instance, that prevents from colonized and you don't see any effect of closings if you look in an environment
12:41:45 that looks like this, like a homeostatic gut. Right. So this is kind of the drawback, or maybe the Achilles heel for pathogens that you know if you have commensals that happen to have better microbial anti microbial warfare and then the pathogen, he might
12:42:12 have a, an outbreak of salmonella, you know everybody eats the potato salad, but only half the people get sick right so there's an attack rate that might be related to variation here or maybe variation and how could competitors you have in your microbiota
12:42:27 right so there's lots of variability that that comes from the microbiota.
12:42:34 All right, so, you know, I started with in my career as being interested in the pattern and how it interacts with the host, but you know what the be learned by studying how to position index with the host is really that
12:42:51 from our perspective, we should look at pathogens, very differently.
12:42:57 Because if you're interested in microbiota, you realize that the governance factors make them excellent tools for my computer research. These virulence factors basically target the host control mechanisms that that balance the microbiota and these control
12:43:10 mechanisms are not immediately apparent when you do 16 as profiling. So these are the host control mechanisms that are disrupted typically when you have disposes.
12:43:22 And therefore, restoring host control is a very promising treatment that, you know, requires for us to know what these control mechanisms are. And for most party sites we don't really know, but habitat filters the host applies to to shape the microbiota.
12:43:39 And I think it's important to identify them because they're these habitats filters of the host, in particular, very nice treatment targets and current status of practice of pathogens on MacOS and surfaces are an excellent tool to identify these Rowlands
12:43:56 factors because they function and allowing the pathogen to enter the ecosystem by manipulating these host habitat filters.
12:44:05 Now of course,
12:44:08 others and son had virulence factors so for us to identify habitats filters positions different factors because they want to get resources so from the punishment point of view, we don't look like this we look like a bunch of resources.
12:44:22 And the virulence factors of the pathogen able to change the environment such that these resources become available.
12:44:28 And so that's the take home message, and that I am grateful for the opportunity to talk to you.
12:44:42 Thanks so much for this really wonderful
12:44:47 view of sort of how to look at metabolism within a context of a complex environment, specifically the human environment and in the end it's really to fill in how complex what appears to be complex metabolism, can be sort of a convoluted into very simple
12:45:06 ecological and microbial principles I think this this was an awesome way to really pull different aspects of physiology and metabolism and ecology together.
12:45:21 So, that is a nice, thank you so much.
12:45:24 And we have time for Christian So I really encourage the audience to pose the questions either you know to speak up or to put it in the chat room and then we'll go from there.
12:45:35 Hello, can you hear me.
12:45:38 Yes, hi undress I thank you very much for that nice election, if that's my condition here. So, I would like to ask you about your take on crowdfunding as a mechanism for community assembly.
12:45:54 And how could, let's say different environments with different dynamics, for example, this actually is not demand the environment, could change the effect of with a mechanism is most important for the community assembly.
12:46:08 Lucky mean by cross feeding.
12:46:11 So for example, we, we thought we saw before in the lectures that the organism filament organism sensor environments and they have leaky for example, reactions that provide nutrients for the others.
12:46:24 Other although I see I see, I see.
12:46:27 Yes. so I think that's, I didn't get into this.
12:46:32 But that's an important aspect of course that the order of acquisition of microbes, of course is determined in part by by these kind of crossbreeding events so if you, if you want to have a hydrogen a traffic bacteria like suicide reduces or methanogens,
12:46:50 first you have to have a microbe in there that said, primary fermented and generates hydrogen right. So there's some clear dependence that interdependence of microbes that is probably determining at which sequence certain groupings appear
12:47:09 looks at that into that but i think that's. If you look if you look for it you will probably find it it's just as I said you know the 16 s sequencing has the limitation that you're only looking at the most abundant species and for some reason.
12:47:22 That's usually the primary fermented so you might not readily see it from the 16 s data set. But if you know what you're looking for. I think you can you can probably see that picture.
12:47:38 Please go ahead. Yes, I have a question about antibiotic use, and some studies have shown that taking probiotics afterwards doesn't seem to do any good.
12:47:47 And I was hustling about that, in light of what you've taught us and so it sounds like what's going on is when you take the antibiotics you kill off a subset of cells.
12:47:58 And I would think then that afterwards if you took the probiotics you could fill that niche again with the probiotics and yet that doesn't seem to be happening and I guess I'm what I wonder is, how are you ending up with less diversity afterwards because
12:48:12 those that were not killed by the antibiotics are filling the niches and then you cannot come back and restore anything with the probiotics.
12:48:21 So, I mean there's different probiotics and the situation is probably different between those so the one set of probiotics, basically microbes that you find in sausage and sauerkraut.
12:48:34 And I would argue that just not well suited to occupy that niche and so they're there, even if you give them to a Trump three miles afterwards if you would give that nice some other microbes they will probably kick them out because you know that there's
12:48:49 a little bit of fluctuation in the beginning of microbiota assembly and I think some of it is that all of the box that you can colonize germ free minds with, but they're not really well suited for this environment, because they really good and fermenting
12:49:02 sauerkraut and not so good and, you know, inhabiting the intestine.
12:49:07 Does microbes will disappear and be replaced by something that is well suited for this environment.
12:49:14 And once you have an occupant like this, that one was will no longer be replaced so that's why you have a period of several weeks where you have fluctuation.
12:49:22 And sort of, if the probiotics are not suited I think you can give them after enduring treatment but they still want steak because they will be kicked out again.
12:49:30 You see a little bit of a better colonization of probiotics of that type after antibiotic treatment so there was a nice paper from Aaron Elena showing that but it's not.
12:49:40 It wasn't really in grafting.
12:49:42 So, there are some probiotics that good in craft craft so if you have, for instance, you call an Islam 1917 that's the human gut isolated isolated in 1917.
12:49:54 And if you, if you take an antibiotic that wipes out.
12:49:59 Joy endogenous e coli.
12:50:01 I bet you they're misaligned in 17 billion graft if you give that to a patient. I'm not sure that experiment has been done. And then there's the third situation of the fear factor mend fences, which is a human, which argument isolates.
12:50:14 And so, those in principle couldn't graph, except you have to feed human milk only goes out right. So if you don't give a prebiotic together with that probiotic it will not impressed because food is missing.
12:50:26 Right. So and. And I don't there's not many studies that actually try to give human milk all the Gaza rights with before the Benjamin Franklin's Right.
12:50:36 I mean, a little bit. David Mills is trying to do this but you know, human breast milk is super precious because there's lots of preterm birth in the US and preach from infants.
12:50:49 Too much better when they're fed breast milk. But, mothers that give preterm babies usually don't produce breast milk on at least not enough. And so there's a huge demand of getting breast milk from donors to feed those preterm infants that otherwise
12:51:10 often get sick.
12:51:12 And so it's it's a very ethically very tricky to actually divert some of that precious resource to do some animal experiments or whatever, probiotic experiments right so that's why there's not much done so in essence you have to then synthesize these
12:51:27 articles on rides, and then perhaps you can do those kind of experiments.
12:51:32 So to summarize, are you saying that after antibiotic treatment, there is the potential to recolonised but you just have to pick the right bacteria.
12:51:40 Yes, I see. Thank you.
12:51:48 You see that of course when you give a fecal microbiota transplant after antibiotic treatment and microbiota normalizes immediately.
12:51:55 Right. And all of those stick.
12:51:59 I mean, the ones that that can stick because the niches open, except these are not probiotics, not term probiotics because they're human feces. But these are all bacteria that are suited for this environment and then it works.
12:52:20 Do you think that if you use those. If you could culture, the perfect brew that it would still work if you took it orally or do you think it has to be a, like a fecal transplant.
12:52:34 Any human
12:52:36 No fecal transplants can be delivered early or delivered by the southern route and both of the seems to work, I see.
12:52:47 It's less appetizing to do it early but the people do these feeding tubes.
12:52:57 said bypass your sense of taste.
12:53:02 Thank you.
12:53:07 Yes, go ahead.
12:53:10 Hi. Yeah, thanks for your talk, I was wondering when you think about the violence factors.
12:53:19 Why is it that the human host cannot just prevent these violence factors to work. So, is there some bigger theory out there why you know why why we haven't evolved to prevent these violent factors to work, or is it just not not at this stage.
12:53:40 I mean, this you.
12:53:45 If you look at the generation time of a human versus bacteria, I think you have no chance
12:53:54 to beat bacteria.
12:53:57 It's just you know be on the planet because it's not beneficial for them to wipe us out.
12:54:02 That's about it.
12:54:06 You know, if it's if it's a pathogen, it needs to host you know as i said if you kill.
12:54:12 If you eliminate all the carriers for typhoid fever typhoid fever is eradicated. So it's not salmonella it's not in some of them as interested killed the host in fact that suicide.
12:54:21 So that's why you don't see it, but if it would be a benefit to kill us all.
12:54:28 God help us.
12:54:31 Maybe put the Jonas question, but definitely what will happen if we do something to suppress the inflammatory response.
12:54:53 You that's terrible idea because the inflammatory you know it's it's a it's a double edged sword, you know, it, it helps the bacteria to replicate.
12:54:53 In the intestine, but it also of course keeps you healthy because it removes the bacteria from tissue issue blocked inflammatory response then you die from bacterial dissemination bacteria sepsis.
12:55:07 And those.
12:55:07 That's amazing.
12:55:07 Yeah, nice and that yeah very invasive and so the, you know, one of the complications on salmonella infection that this discussion because your intestinal seminar is septicaemia.
12:55:18 So you get bloodstream infections invasive bloodstream infections that are legal and.
12:55:24 So you want your response to work.
12:55:33 Okay and tapering down doesn't help because there's such a massive response that's changing the, the ecosystem the complete ecosystem and
12:55:46 maybe I have another question so this summer supplemental look is a wonderful, I'm, I'm just wondering, the sub ok so now suppose the salmonella. Okay, so it's interested in this habitat change and then of course into doing this, now that it's colonizers.
12:56:06 What happens after that.
12:56:10 The idea will be interesting to tune down this infection and then now, it's not a niche and just stay there.
12:56:18 Is that what happens or the overall still overdoing the interaction.
12:56:22 That's a good question. I got didn't cover this because you haven't studied it but it has been studied by heart.
12:56:29 So what but similar causes is a transient gastroenteritis so it's usually your, your have diarrhea for, you know, seven days. And then you get healthy again.
12:56:42 And so what happens is when someone that they invaded triggers this massive innate response
12:56:49 and inflammation, but eventually once adaptive responses kick in and different gamma levels go up macrophages become very good killers of salmonella, and the bacteria good kid from tissue and inflammation subsides.
12:57:03 So once the inflammation is ended.
12:57:08 There is a face of maybe a month, they still shed salmonella. And we know that because someone else has a reportable disease, if you have it.
12:57:17 You're not supposed to work as a restaurant Virgo I'm food industry, because you can transmit the disease.
12:57:23 So, two people actually look with a patient's still shedding.
12:57:30 And if you're a waitress or something you know you you wanted to end quick because you want to go back to work right. so.
12:57:37 So you said for about a month.
12:57:38 And then it ends and so this is the time where you have my computer assembly again. And eventually, it was hard for showing nicely it's the microbiota that kicks salmonella out again so once the microbiota has completely assembled, since there was a disruption
12:57:54 here during inflammation. Then, then the microbiota is able to end that episode and salmonella is disappears again.
12:58:06 You know, the question is why does it not stick around like other commands that that's a good question. I don't know when that happens rarely so there's the occasional carrier that carries it for more than a year or something but typically that process
12:58:21 and
12:58:25 men inflammation subsides and then the microbiota recovers I should say that microbiota recovery is typically kind of a slow process and humans in mice, you know when the truth is antibiotics within five days.
12:58:37 They look like normal, but they're copper frantic right so they, they give themselves an FMT every day.
12:58:46 And so the.
12:58:47 That's not what you see in humans right so humans, it takes a few months until you back to normal. Typically,
12:58:56 but in principle, if it's able to behave like a call right after he establishes Nish it.
12:59:06 It could stay like the color, but maybe it doesn't behave itself.
12:59:10 Yes, in principle, yes but it doesn't so there might be a difference and the reason why it doesn't I just don't know what it is.
12:59:18 Yeah, it's a good point.
12:59:21 You know, often you think of someone I noticed like a cola was, you know, factors right and so.
12:59:30 But I think it's over, simplifying the most efficient wishes to state.
12:59:43 Some another really
12:59:44 counts on these parasites coming into the lumen.
12:59:48 He looked at that a little bit you know I just don't know whether we really understand this, but But what we found is that salmonella use is not a for nitric respiration.
12:59:59 And it can end that enzyme only works with fibrocytes when fibrocytes going to lumen, whereas he called I use this analogy for natural respiration in the gut and the connection to use that little bit nitrate it comes out of the theme, and the court and
13:00:16 salmonella cannot use them. So we have an animal model you know people come and knock on my as well which you plead regulatory T cells and in these mice, they have you know they release nitrate from the episode, and someone does not take that nitrogen
13:00:38 Nikolai takes that metric, and I'd have no idea why they have the same genes.
13:00:32 They have the same nitrogen factors but for some reason some another us is not a and Nicola users na ge.
13:00:40 And I don't know what we know from from the sentence. And that goes back to the regular trade off dead in organisms that have a less good or less efficient energetic coupling.
13:00:54 So let's say to nitrogen reduces using acetate as what I call pile of Elektra let's say let's use lactate electron donor, depending on how the energy conservation is that is that a less efficient can use lower concentrations of substrate in this case
13:01:16 it would be nitrate. So maybe there's a difference in the efficiency of the, the overall pathway that allows equal I to actually not to be less efficient but use nitrate, in order to make a living living was and salmonella might be better covered within
13:01:36 higher end ATP, for example.
13:01:43 Yes possible. I just don't understand why.
13:01:47 When you have a gut that releases night from the apathy on record I can take it was no G, but salmonella has no G and doesn't take it and that's what I don't understand.
13:01:58 The to look the same genetically, and it might be gene regulation we haven't looked it's hard to get enough transcripts, out of our guts to real time to see the struggle to that so I don't really know what the differences.
13:02:15 NET struggle to that so I don't really know what the differences. Any other questions. We are just running about out of time.
13:02:22 Then, I think it's fair to say that this was an awesome talk under Thank you so much.