10:02:26 So, um, welcome back everyone. I'm glad we again have a really high number of attendance.
10:02:38 And it is my great pleasure to introduce Tom Smith today.
10:02:43 And Tom is on the faculty of the University of Michigan and we met the first time 20 years ago, actually, something like that.
10:02:54 When we co taught the woods whole course and microbrew physiology and I really started to appreciate and understand perspective of microbial life and physiology, that comes more from an ecological perspective, whereas I was coming from my biochemical
10:03:10 perspective and we had been in contact and admiring each other's work over the years.
10:03:18 So, when thinking about someone who comes from sort of was my anchored in ecology to talk about microbial metabolism, Tom, immediately came to my mind and so I'm glad Thomas here, I should say, Tom is also a great musician, drummer, but we never got to
10:03:36 to play together. Yeah, so it's great to be back sometime maybe, maybe for the class finale.
10:03:43 Yeah, yeah, yeah. So thanks so much time for taking the time and we're looking forward to hear about microbial engineering as a gut microbiome them.
10:03:55 Yep. Thanks. Alfred I'm delighted to be here.
10:03:59 And as Alfred mentioned, I'm a, I'm a microbiologist studied the physiology and ecology of microbes in many environments. In most recently in the human gut microbiome.
10:04:16 So it was about seven years ago or so that I decided to change course of it, and focus on that, unlike gut microbes.
10:04:30 And to do that, I moved to the University of Michigan, where I'm embedded in a medical school, and I'm embedded with colleagues who understand the host side of the equation.
10:04:41 So, as Andreas mentioned last week, and I, I concur completely with him. There aren't many microbiologists in this arena, lots of clinicians lots of technologists DNA sequences, I mean, great support staff but not as many people who think about the organisms
10:05:03 and their interactions and so I thought that there was a chance where I might be able to contribute. And so what I'd like to do is tell you a little bit about the perspective that I've gained and some of the results that we've found in in studying this
10:05:24 community of organisms so I'm going to share my screen now.
10:05:33 Okay.
10:05:37 So, I modified the title just a little bit to talk about engineering the metabolism of the gut microbiome. That's really what we're after. I mean, in, in one sense, maybe we don't care so much about which organisms are there, which configurations of organisms
10:05:53 produce a specific metabolite, it's more metabolites from the gut microbiome that are interacting with the human hosts that that is the focus and by engineering, I really mean purposely manipulating the production of metabolites by the gut microbiota,
10:06:11 and I've got to start this is my absolute
10:06:18 favorite Scanning Electron micro graph of microbes from the human gut.
10:06:24 It is color eyes to highlight.
10:06:28 You know the morphological diversity of microbes that are there, but it emphasizes a couple of things that are important to think about this community of microbes.
10:06:39 One is the density. Look how tightly packed, those organisms are and so if you're thinking about the exchange of metabolites one organism influencing and other organism.
10:06:54 Have a density of microbes here that really favors those kinds of interactions, maybe a little bit different than the soil environment which I had worked on previously.
10:07:06 It also highlights to me that we've got to think about the metabolism of
10:07:14 many organisms and the interactions to do things like digest this piece of fiber that's in the gut. So there's a piece of fiber from the diet.
10:07:24 No one of these organisms can degrade that to all of its
10:07:32 elements, but a consortium of of microbes can do that. And so, again I to me there's a lot in this picture.
10:07:43 And so, I like to start I like to start out with it.
10:07:49 I'd also like to just, especially that you follow up with Andreas I mean, some of us have microbiome and microbiota a lot. And here's the easiest way that I've come across to understand the way that I think about the these terms.
10:08:20 So here's some pictures of the desert biome.
10:08:24 And what are the shared characteristics of the desert biome.
10:08:28 You know things you would imagine there's not much rain.
10:08:32 There's considerable variation between temperatures day and night, high evaporation rates course textured soil so the plants and animals that you find in a desert have have formed in response to this shared physical environment.
10:08:51 So that's the definition that ecologists would use of biome. And for biota it's the collection of organisms in a biome.
10:08:59 The collection that are there in a particular geographic region or a particular time. And the point to be made from that is that the buyout of varies between different deserts.
10:09:14 So, there are the terms as a colleges would use them and if all we're doing as microbiologist is talking about that on a small smaller scale. So the human gut is a microbiome, or maybe would call it the mammalian guts microbiome, but it has shared physical
10:09:34 characteristics. And there's little or no oxygen, except right at the periphery, pretty constant temperature, a Ph.
10:09:45 That varies a little bit along the course of the GI tract and also in between people.
10:09:52 And there's this daily flux of resources. So, as we start to think about this collection of microbes their physiology, how we might modify that physiology.
10:10:07 Here the characteristics of the gut, that are defining the gut microbiome.
10:10:14 But of course, a the microbiome difference between different people and so you may take a sample, and I'll try to be careful when I'm talking about the microbes president a sample I'd say what's the microbiota.
10:10:27 And so the microbiota from multiple people you know together defines the whole collection of organisms that might be there.
10:10:36 The mic, the microbiome. And of course that varies temporarily within a person and in between people. So, again, I start starting with ecological roots, I'd like to just define the territory that way.
10:10:52 And so that I don't just get on a roll here and keep talking I'd like to.
10:11:01 I'd like you to take this pole, if you would.
10:11:06 I'm not really sure how you respond to it.
10:11:12 But, yeah, there we go.
10:11:15 So I see people are able to participate and so it's like the majority of gut microbes in your gut right now that are metabolically active where they come in from.
10:11:40 Nobody's on to the pets thing yet.
10:11:45 was on the cover of science right, it's important
10:11:51 that we share some of our microbiome with dogs with our pet.
10:12:01 We don't have a dog.
10:12:05 I'll wait. I'll wait five, five more couple more seconds.
10:12:10 Okay, great. So, Pretty pretty interesting.
10:12:16 Anybody want to share any thoughts about that.
10:12:24 Yeah, that's not a very good. That's not very provocative question.
10:12:29 So, the majority is right.
10:12:33 We get the mostly from our family members initially and then from housemates, the microbiome that's on food or in drinking water and soil, those microbes have been selected to thrive under different environments.
10:12:52 In general, and so that microbes that are on food that on on a stock of broccoli or salary or whatever. The unless that's been irrigated with water with human microbes in it, it's unlikely that those microbes would be able to compete in the environment
10:13:17 or environmental the gut.
10:13:21 Okay, good. I just wanted to get a sense by the way I'm as a gastroenterologist this as well, and they tend to favor the food answer I mean that's the more common.
10:13:45 That's a common, common answer that I get, but as Alfred pointed out, we do share some microbes with our pets.
10:13:40 So, I'm going to move on unless anybody wants to comment on this.
10:13:50 Oh, are you seeing the results.
10:13:55 I saw them there.
10:13:58 Okay, you saw these okay. Yeah.
10:14:01 All right.
10:14:04 All right, I'd like to stop the poll now,
10:14:10 doesn't. Here we go.
10:14:18 Okay,
10:14:22 so here's what I'd like to do for the first session here to do a little bit of an overview of the evolution of the gut microbiome consider why we might want to engineer it, whether that's a reasonable thing to talk about are not focused on what rates
10:14:41 determine the composition so if we're going to engineer this, we need to know what rates, we have, we can influence and, therefore, therefore of them.
10:14:53 And so, I think, as we move forward is good good to consider those and then talk a little bit about how the metabolism is influenced by the which microbes are there and also the local environment.
10:15:06 And as I mentioned earlier, in particular, we've got some recent data on hydrogen that's kind of interesting so I'll share that. I would also welcome you to
10:15:19 ask questions,
10:15:23 provide comments I mean, make it as interactive as possible. And I'll stop from time to time because I have a tendency to get kind of excited and I just keep rolling on this so I'll leave it to you.
10:15:36 Terry Alfred whomever else to slow me down as needed.
10:15:42 So, yeah here's a evolutionary context and maybe it's maybe I've gone overboard a little bit but here's the Earth's history.
10:16:08 And, or the beginning of Earth is a sorry about one o'clock. And there's evidence for life. This is slides a little old now back to 4 billion years ago.
10:16:16 And the real point that I'd like to make here is that from 4 billion years ago, up until the Cambrian explosion. Here's the Cambrian explosion that's when most what the fossil record explodes with most of the animal body plans that we that we see today
10:16:34 for for that 3 billion years. Life was mostly microbial. And so, microbes had the chance to evolve, lots of metabolism. Before plants and animals came onto the scene and plants, animals evolved in a, in an environment where there were a sea of microbes
10:16:54 and lots of metabolism had already been invented.
10:16:58 And so, Certainly, that has this fact this diversity of microbes that were around when plants and animals evolved influence their evolution and continues to today.
10:17:15 By the way, I guess we'll we'll find out later this afternoon, if we're going to be exploring Mars is the.
10:17:25 What's the name of the lander that we're putting down, perseverance is about is scheduled to land on Mars at four o'clock this afternoon. So, We'll find out and they're going to an area about this age.
10:17:42 Looking for bio markers of life. So be kind of interesting to see what happens in the next next few years with that.
10:17:56 Sorry. So
10:17:59 just just earlier this year.
10:18:03 Shortly after they came, the, the,
10:18:09 the front end from Burgess Shale are fossils that suggests that it was that God was present in animals.
10:18:21 Just after the Cambrian explosion or yet about the same time as the Cambrian explosion. I mean here the actual images on the right, suggesting a gut. And here as artists interpretation of that and what the animals might have looked like.
10:18:42 This was a huge development in the evolution of animals. And I like to think about it as welcoming in that microbial diversity that had been evolving for 3 billion years.
10:18:57 So those organisms now have access to the insides of animals, and have had profound like I like as I suggested a profound influence on evolution of our animals ever since.
10:19:12 So, not that you need convincing but perhaps one of the
10:19:20 most obvious places where microbiome is essential, is a termite.
10:19:26 So, Alfred this is these are these are pictures that I took when I was out at the Woods Hole microbial diversity course.
10:19:36 I'm hoping that I can
10:19:40 come off.
10:19:43 I'd like to start a video here. If you have any suggestions about how I might do that.
10:19:56 It's so much better when maybe go out of the presenter mode and then try to activate it, I don't know.
10:20:10 Yeah.
10:20:12 Okay, hold on hold on just one second because I've got a couple of videos that I'd like to show.
10:20:18 Okay.
10:20:20 Are you seeing the screen now or no, no, No, you need to share it. Yeah.
10:20:28 Okay, I'm coming back I think I think I've got this Yeah. How about now do you see this.
10:20:35 No, no.
10:20:37 All right.
10:20:43 Okay, how can we give it give it one more try here.
10:20:49 Yeah, we see a screen. Okay, I'm going to try to go back to presentation mode.
10:20:55 Yeah, there we go. They Alfred good solution.
10:21:01 Anyhow, here, here at termites, and, you know,
10:21:07 these subterranean Eastern termites live on cellulose.
10:21:14 You know plant compound that has lots of different bonds holding glucose subunits together, but kind of interesting. Termites can't break down cellulose, or it can only do so marginally.
10:21:29 It's really the microbes in their gut that break down cellulose, and to acetate hydrogen, carbon dioxide and acetate is what is the primary carbon source for for the termite.
10:21:49 By the way, there's also not much nitrogen in their diet, and so it's the microbes that are also providing nitrogen actually fixing nitrogen and to from the atmosphere and providing that to the termite in it the woods whole course I mean one of the first
10:22:07 things we do to engage people as a give them a chance. Sorry to look at the microbes that are inside of a term like guts. So here they are.
10:22:25 In addition to the real conspicuous eukaryotes as we focus in and out, you'll see a spiral shaped organisms.
10:22:35 Moving out those turn out to be the major engine major nitrogen fixers that are in the gut.
10:22:48 Alright, so again as that titles say in that term right hind guts cellulose is fermented acetate is the product and. Hey, termites don't do well without a gut microbiome.
10:23:06 So, it's easy to see how termites given their diet depend on the gut microbes for their existence but you know it's not too far of a reach to look at our gut microbiome as well.
10:23:25 So here are a number of complex carbohydrates in the human diet, just presented as a picture here the same complex carbohydrates, but now using a nomenclature that identifies the different.
10:23:46 The different sub units.
10:23:48 And what kind of sugar and what kind of linkages between them. And this is kind of a fanciful picture of the large intestine, of people when the circles I just, you know, just meant to designate the microbes that are there.
10:24:05 The point that I want to make with this picture is that of all these complex carbohydrates.
10:24:13 We don't have the enzymes to break many of them down. In fact, it's pretty limited. That's it. starch and sucrose that those are the complex carbohydrates that are amylase is can degrade everything else that's shown here.
10:24:31 By the way, including the all ego sack rides that are in mother's milk are inaccessible by any of our enzymes and we depend exclusively on the microbes in our gut to break those down.
10:24:48 So, maybe not too different from the termites situation but when when you think about this diversity of complex carbohydrates and our, our limited ability to break down these carbohydrates.
10:25:10 Okay.
10:25:12 But what why is that so so that that provides some information on gut microbes a little bit of an evolutionary perspective here was the article that really convinced me that I was going to spend some time on the, on the gut microbiome.
10:25:34 This was a article from 2009. Few years ago now.
10:25:40 And they did a metabolism IQ analysis in mice. So they had germ free mice. No microbes associated with the animals at all. And then they had mice with a conventional gut microbiome.
10:25:56 And what they did was look at metabolites in a blood.
10:26:00 So, a mass spec analysis of metabolites in the blood.
10:26:06 In those two groups of mice germ free no microbes and conventional microbiome for mice. And so, yeah, just some definitions. The point of this is, there were about 300 metabolites that are in the blood that are attributed to the gut microbiome.
10:26:32 So.
10:26:34 Wow, so that I mean if we extrapolate to, people would say that you know you have a similar number of metabolites in your blood that are attributed to microbes in the gut.
10:26:48 So they've digested some complex carbohydrates in the gut. Those metabolites diffuse into the bloodstream. Once you're in the bloodstream we're now talking about just a local effect.
10:27:15 This can have a peripheral effect can affect the brain and sort of any other Oregon. So, the potential impact of the gut microbiome on any mammalian host is is large.
10:27:25 And so, we might pay a little bit of attention to the metabolism that is happening in the gut, because so many metabolites in the blood are attributed to the gut microbiome because I have a question.
10:27:38 Yeah.
10:27:40 Um, because the previous speaker was talking about how diverse the gut Michael bones are among different people. Yeah, that's the metabolites in the blood vessel, the vast majority seems to be coming from the bacteria, and then I'm curious if you sample,
10:27:57 you know say host blood relative just different people's blood. Yeah, and it don't matter below mix, how similar are that among different people.
10:28:06 Yeah sure, a good question. I mean there are core of metabolites that are common.
10:28:13 Sarah tone in which influences our moods and is largely produced by gut microbes.
10:28:23 So there are certain, there are certain our commonalities and. In an interview. And then there are variable ones and, you know, I don't have a good, I don't really have a good number for what what what percent of the metabolites are common.
10:28:40 I just don't don't don't have that at my fingertips.
10:28:43 But the other point that you raise, is that, hey, the microbiome changes a lot so wouldn't you expect blood metabolites to change a lot, and not necessarily.
10:28:56 Maybe there are different configurations of the gut microbiome that produce the same metabolites.
10:29:04 So, just something else to keep in mind as we go along.
10:29:21 As we're talking about this there was another question in the chat way so Hannah, how does the concentration of metabolites found in blood, different compared to concentration of metabolites in the gut.
10:29:24 Yeah.
10:29:26 So, some of these, some of the movement of these compounds, is through diffusion.
10:29:36 So the short chain fatty acids acetate probiotic probiotic acid acidic gas if you tear gas and they diffuse through the mucus and enter the bloodstream.
10:29:47 There are other metabolites that are actively transported.
10:29:53 So, for those that diffuse you'd expect a higher concentration in the gut diffusing into the bloodstream.
10:30:01 For those that have transporters, you might actually expect in there are cases where you find a higher concentration in the blood. Then in, in the than in aluminum the gut because they're actively being transported.
10:30:17 Yeah, good question.
10:30:21 Yeah, Alfred if you can help me with the chat so I don't see that when I'm in presenter mode, two things.
10:30:29 Okay, so that's a little bit of the overview of the apple ever the evolution of the God.
10:30:40 So, what why might we want to engine and why why screw with this, if, if evolution has provided that gut microbiome Why might we want to engineer that I mean, should we even be talking about this.
10:31:00 And let me suggest a couple of scenarios where I think we might want to talk about it and consider it.
10:31:08 One consideration would be the loss of species that are associated with the Western diet and Andreas referred to this last time. Here's some data from Justin Sonnenberg, I thought this was the nicest first example of this.
10:31:24 So, Justin and his team looked at 27 individuals from Tanzania, couple hundred from a agricultural society in a few hundred from on a more typical Western diet.
10:31:45 Let me help you interpret this graphic a little bit. So, each column represents one species of bacteria.
10:31:56 And if the column is black, the species is present, if the column is white, the species is absent. So, absent, here you know and you can just go go through black and white is just president absent.
10:32:13 The colors. Talk about the abundance. So, those species that are most abundant are in red
10:32:23 and yellow and green in decreasing amounts of abundance so you know the Malawians have some abundant microbes that are present but at very low concentrations in people on a, on a, on a Western diet.
10:32:42 And one of the points that they made from this article from this article is that there were a number of microbes that are common in individuals in Tanzania that are missing from people on our Western diet.
10:33:01 So, that doesn't necessarily say that those organisms are good are associated with health as just it's just an observation. But I would, I would let me suggest to you that that would be one circumstance where we might want to engineer the gut microbiome
10:33:21 that is if we found that any of these organisms had beneficial effects, we might want to try to restore them in the gut ecosystem.
10:33:39 So that that's one scenario, here's here's the second scenario.
10:33:45 It's related to the hygiene hypothesis and the hygiene hypothesis is this that early exposure to diverse range of microbes is necessary to train the immune system.
10:33:59 And that if we don't get that early exposure in life that we're to clean too high genetic that might lead to immune problems later in life.
10:34:11 And you know that the I'm going to show you a lot of correlations, and that's what that's what this is, we're looking at the incidence of infectious diseases from 1950 for the next five decades.
10:34:24 And it's pretty much continued on.
10:34:28 And looking at the incidence of infectious diseases. The major diseases have dropped dramatically vaccinations are responsible for some of that rheumatic fever measles, mumps, was an engineering of our water providing clean drinking water has is responsible
10:34:49 for lots of that so anyhow, the incidence of infectious diseases dropped dramatically in that 50 year period.
10:34:59 But during that 15 year period, and continuing onwards, are a number of diseases that are considered immune disorders.
10:35:15 Asthma Crohn's disease, Ms. And so, you know, there is this inverse relationship between incidence of infectious disease and maybe that's because we're exposed to fewer of these microbes and increased incidence of immune disorders.
10:35:36 So, if, if this was really related to our early exposure to microbes, we might want to consider engineering the gut microbiome, we might want to expose our
10:35:51 selves youngsters to some of the microbes that they would typically be exposed to to train the immune system.
10:35:59 So, some possibility.
10:36:01 So, another instance that might warrant engineering.
10:36:07 The third and the last example I'll get is a recurrent infections with Clostridium difficile. So CDF is a hospital acquired infection. And it's typical and people that are exposed to antibiotics, especially broad spectrum antibiotics that remove at least
10:36:28 decrease the number of microbes in the, in the gut in the large intestine CDF spores the spores of this organism are common you find them in any hospital setting.
10:36:42 And those spores reach the environment of the large intestine and they don't have as much competition there as when an individual has a healthy gut microbiome.
10:36:53 And so that leads to infection with Clostridium difficile.
10:36:58 It's a, it's a miserable condition to have.
10:37:04 And especially when it recurs, the absolute best treatment anywhere in the world for recurrent C. diff infection is a fecal is providing feces from a healthy individual.
10:37:24 In this case, provided an appeal format poop in a pill.
10:37:33 And in general, regardless of how that gut microbiome is provided, whether it's in a pill form. By the way, and most people are not to go that way because I think you have to swallow 40 to 50
10:37:48 pills in order to get a reasonable inoculate them, the more common method is through endoscopy.
10:37:56 The success rate is dramatic. And I would say that this is really why any of us are studying the gut microbiome it's because the medical community in the West realized that there was a treatment of the gut microbiome.
10:38:16 That was better than any medicine that that they had. So all of a sudden it was like, Oh, this microbiome might be important, and I really attribute this fecal transplants to the explosion of funding and interest in like in the gut microbiome.
10:38:39 I'll put this Terry I'll send me this article along with a couple others that I have LinkedIn.
10:38:45 Hey there you can find correlations with just about anything with, with lots of diseases.
10:38:53 And so, again, I would offer all of these as opportunities for circumstances where we might want to engineer that gut microbiome
10:39:07 calm before we move on, that there's some exchanges in the chat room, maybe you can address the questions, I'll be asking.
10:39:20 Sorry, I was asking, how do you compare engineering the microbiome versus engineering the diet.
10:39:32 I maybe they're the same thing.
10:39:36 Engineering the diet is
10:39:40 is one way to perhaps the best way to affect the gut microbiome.
10:39:46 But I guess I think about engineering the diet. So, to be so that the nutrients that we need that are absorbed in the small intestine are provided in the diet.
10:39:57 So lots of the vitamins that you get vitamins and minerals that you get in, are consumed from a diet absorbed in the small intestine, and they are essential for health.
10:40:11 They don't have anything to do with the microbiome. So you could imagine engineering the diet to just affect what nutrients, the host is getting.
10:40:22 But in, on the other hand you can also imagine engineering the diet to affect the gut microbiome. And that's, that's probably one of the most effective ways that we have to do that engineering.
10:40:38 May I ask you something. Please.
10:40:40 Because, so yes I think that engineering the diet will create a better environment for certain strains right but you cannot bring back a strain that you don't have anymore.
10:40:55 Right, so you cannot leave.
10:40:58 Right. Yeah. Even if you change your diet you cannot have, if, if that's trade is not anymore in your family or in your environment, you cannot bring it back out of nothing so you'd have to somehow important.
10:41:13 Yeah, that's a thank you that's that's a that's a good point I should have included that that's part of the answer to the last one too.
10:41:21 By the way, that's what a probiotic is. Yeah. Right. And so you can go to local pharmacy and buy all kinds of probiotics. So people are familiar with that idea of introducing organisms.
10:41:37 I mean, the problem is is that most private probiotics are come from food.
10:41:44 They come from yogurt or.
10:41:50 kimchi or kombucha. I mean, They're fermented there ferment they perform fermentation is in foods. We've been eating him for hundreds of years and so they're generally regarded as safe and, and now they're packaged and sold as probiotics.
10:42:09 There are not many, but there are some, I'll show you some probiotics it really came from the gut microbiome right that's what we, that's where we need to get the probiotics from.
10:42:23 And in fact there's an effort to try to preserve microbes in from indigenous peoples that have some of those things from a few slides back that were identified as missing microbes it's like, hey, maybe we ought to start preserving those in case we find
10:42:41 out that they're valuable necessary. Yeah, Thank you, a good point. Thank you.
10:42:52 Alright,
10:42:55 so you're, you're already there what what determines the composition what what can we engineer.
10:43:03 And so, again, I like to think of it from an ecological standpoint and any of you that have had any ecology have probably been exposed to the island biogeography the seminal work from MacArthur and Wilson.
10:43:22 And they talked about, what, What is it that determines what organisms are on an island.
10:43:31 And so these volcanic islands are essentially sterile at least in terms of plants and animals, when they're born from volcanoes. And, you know, maybe in, so is the infant gut.
10:43:46 So maybe we should look to Island biogeography for what rates are determining what plants and animals are there.
10:43:55 And it doesn't do it justice but uh you know it's really, it's immigration MacArthur and Wilson, come to show the immigration and extinction or what drop it drive the composition of the islands biota.
10:44:16 So what organisms how close to shore is the is the island. So, that influences what organisms can integrate, what are the conditions on the island that determines what organisms go extinct or can thrive there.
10:44:32 So Island biogeography has been extended a little bit.
10:44:37 And people now talk about for rates.
10:44:40 So, immigration, what organisms are coming in.
10:44:44 What's the birth rate. what's the death rate, and what's the immigration rate.
10:44:49 And so, as we're now moving on to engineering the metabolism of the gut microbiome. Here's what we've got to work with that dictates what organisms are there.
10:45:04 And, you know, in one sense it's a little bit easier for the human gut microbiome so okay so here is a human gut splayed out in two dimensions, starting in the upper left with the mouth, through the stomach, through the small intestine.
10:45:22 Hey this is real. Isn't that incredible 510 1524 feet or so of small intestine is packed in their abdomen.
10:45:31 And that's where, again, that's where a lot of nutrients from your diet are absorbed.
10:45:36 But when people talk about the gut microbiome, they're really talking about the colon, or the or the large intestine. And it's a it's a smaller environment it's about four feet long.
10:45:52 From here to the anus. But this is the ecosystem that we're talking about, and kind of nice in the sense that it's defined it's like, it's got walls.
10:46:05 It's got an input and it's got an output. And so if we're thinking about engineering it's a, it's a, I don't know it at least.
10:46:15 It's a little more tractable to think about this system.
10:46:19 And so we got immigration most of the immigration comes in this way.
10:46:24 So, it's important to gotta survive the pH too acidic conditions of the stomach.
10:46:32 It's gotta run the gauntlet through the small intestine arrive in the large intestine, and then be able to compete with organisms that are there.
10:46:44 So, for microbes we talk more about growth rate than birth rate but I just wanted to preserve. So think about birth rate and growth rate of microbial population as equivalent.
10:46:56 I just wanted to preserve the ecologist definitions.
10:46:59 There's death rate organisms are dying. And, you know, emigration rates kind of a.
10:47:13 Yeah, I'll use the term anyhow, but we lose a lot of our microbiome on a daily basis. So, and that's important. So, I mean, we have a question Tom just, yeah.
10:47:22 Krista, where are most of the microbes are they even the district muted. And is there a in test small intestine microbiome as well.
10:47:32 Yep. So there are microbes in the small intestine.
10:47:37 Not as much.
10:47:39 The density is much less, and that's controlled partly by flow rate. So the flow rate through the small intestine is much greater than the flow right through the large intestine.
10:47:56 There are bile acids is there that are a little bit more, that are inhibitory to microbes. So, yes, there are microbes there, but they're not not nearly as dense, and I mean there's a condition called small bowel overgrowth where it seems like there is
10:48:20 overgrowth, there is growth of bacteria in the small intestine. That's generally pathological state. So, in general, the density, the metabolic activity of microbes is in the large intestine.
10:48:50 Where did that did that get that. Was there another part of that question or did that get that. I think that was good there was another one there good estimates on how important death rates are compared to growth and sort of dilution.
10:49:00 Yeah.
10:49:04 Know what a good question though because of these are the rates, we have to deal with,
10:49:10 with the better estimates you have of them, the better. We do have a pretty good estimate of the immigration rate. It's about 50 times 10 to the 14th microbes a day.
10:49:24 So that means, by the way, that that number of microbes needs to be replaced every day.
10:49:33 And talk about. Wow. So, so you have the potential to change the composition of the microbiome considerably. If you're replacing that number, half, half of the microbes every every day.
10:49:47 So, I mean this is a healthy individual and.
10:49:52 Yeah, so, so, so we have evidence we have some ideas about immigration rate immigration rate.
10:50:02 I mean, so probiotics housemates, I mean it. In general I suspect it's pretty low. I mean when Clostridium difficile is a member of that.
10:50:15 That's a little more problematic but I think that you're focusing your attention in the right place. What determines the growth rate of microbes in the gut and what determines their death rate, and so certainly there are cross feeding interactions that
10:50:30 influence growth rate hydrogen concentrations, the dietary complex carbohydrates that make it through the small intestine, those resources can also call them prebiotics are huge in determining birth rate pH so all of the basic things that a microbiologist
10:50:52 would think about influence birth rate and I think my bias is is that this is where we have the biggest potential to intercede and engineer the gut microbiome.
10:51:07 So I just have a question about the number yes there.
10:51:11 Do you really mean 50 times 10 to the 14. Yeah, because that's many, many, many leaders, So do you mean 50% of the of the 14.
10:51:19 Well, that's the number of microbes. But if they bought a cubic micron each.
10:51:24 So tend to the fifth end of the 15 of them is a leader.
10:51:30 I'm tend to the 15th is a leader you say, yeah.
10:51:35 Would you be 50% of 10 to the 14, maybe. Yeah.
10:51:41 I honestly I don't remember where I got that number for him but, you know, we, we, it's a.
10:51:47 I mean, we have a couple of pounds of matter. Two to three pounds of matter in our large intestine at any one time, and you lose about, you know, about half of that passes through every 24 hours.
10:52:02 So I don't think I suspect I suspected me it's 50%. Anyways, yeah, yeah, yeah, yeah. Hey, say, I'll go back in and check that it's, it's a big number, we lose about half of the microbes that are there, and we have the potential to replace those.
10:52:21 So that so that so that's the point and, yeah, you're back of the envelope calculations that yes that's a little bit high.
10:52:32 So, so just along these lines then would you then expect that the average doubling time is about 1212 hours of the, of
10:52:44 the average might have been to get that or, depending on what assumptions you make a.
10:52:52 I've calculated down to be an average of four hours.
10:52:56 So, something in that range.
10:52:59 But yeah, if you consider that 24 hours. I see I see how you got there. Yes, the average it has to be something on the order of 12 of 12 hours. So, by the way from an experimental point of view.
10:53:14 After working in soil for so long, where we had to do a treatment one year, and wait for the next season to see some effect. this was a really attractive environment to work in.
10:53:25 If you poke this system, you're going to see changes, a much faster, and for somebody who's not very patient like me, it's a it's a one, a wonderful experimental system.
10:53:44 What, what, what else to say there.
10:53:58 Well, we'll come back to this but, again, we're going to focus on in the research I can give you will focus on these factors that are affecting the birth rate.
10:54:06 Let me give you just a couple of examples from the literature, immigration. This is a paper by Jen's Walter beautiful paper. He gave a probiotic one that came from the human gut microbiome digital Bactrian long gum in gave it over the course of several
10:54:23 days to individuals in this study, and then looked six months later, to ask whether or not that strain of digital back came along and persistent or not.
10:54:36 So some people it persisted in some people, and it didn't persist and others that is it colonize these people didn't colonize these people kind of not an unexpected result but Jen's and his group went further, and what they find it they could predict
10:54:55 who was going to be colonized because that niche that's occurred by befuddle vector in long them seeing that to have. They were underrepresented
10:55:08 in Bactrian long that is these white spaces are trying to indicate hey there's room there's a niche that's available.
10:55:18 There wasn't shotgun minute genomes underrepresented under representation of genes from carbohydrate utilization.
10:55:28 In, is a relatively small study.
10:55:32 A few dozen people, and higher resource availability. So, these are all measured characteristics of people that were more likely to have this organism.
10:55:53 In graft is the is the term that they use long term persistence in this case long term was six months. So, people ask me well can you actually. Are there examples of where you've introduced an organism, and it's completed successfully.
10:56:04 And This to me is the absolute is the first and best example of that happening.
10:56:09 So, we can do it.
10:56:15 And we're thinking about.
10:56:18 It was a nice study in mice, where they combined a probiotic, the probiotic was
10:56:28 lack of caucus lack this strep throat marvelous.
10:56:34 In some other organisms, with a with a prebiotic prebiotic a substance that induces growth or activity of micro organisms. In both cases, the definition is something that has health benefits, although that's sometimes a little loosely defined.
10:56:50 But this was a study in mice in New Zealand is one of these Carbo hot complex carbohydrates that we can't degrade it in mice can degrade it passes through the small intestine untouched, makes it to the large intestine and so when they did this experiment.
10:57:09 Again, this was one of the first ones that showed some potential. What they found was that the short chain fatty acids that are common fermentation products in acidic acid probiotic acid and BK acid.
10:57:26 All of them were stimulated by the, the feeding of activity.
10:57:36 And the score, looking at inflammation oh this is a collider score
10:57:42 improved.
10:57:44 So, a lower number is better. So these are the Fed mice. This is just feeding the non fermented milk product, sort of, like, one of the questions earlier well you can feed you know the substrate but if the organisms not there it's not going to have the
10:58:03 same effect. That's really demonstrated there perfectly and then just Sham feeding and handling had the worst the highest score for for colitis. So, there, there are lots of studies, since then I tended to pick one of the first ones that showed the potential
10:58:23 to engineer.
10:58:32 Okay. Hey, I'm going to go through this, this one last one, just a few slides here.
10:58:43 And now, Now we start okay we've looked over the evolution of the gut microbiome why we might want to engineer, what rates we have. Okay, now we're going to dig into the metabolism a little bit, and ask about how metabolism is influenced by which microbes
10:58:59 are there in in the local environment.
10:59:04 And so, this, this might, you know be familiar to some of the
10:59:12 slides from Bernards presentation, a couple weeks ago.
10:59:19 Anyhow, just a flow of glucose to set through some major metabolites in an ad hoc system that has no other terminal electronic sectors.
10:59:33 And, I mean, the way that I like to think about this is it, bacteria that find themselves microbes that find themselves in this position, and they can get ATP out of this reaction but they're left with these electrons, but they've got to do something
10:59:49 with those electrons they have to.
10:59:53 There has to be something for them they can't just accumulate.
10:59:58 So, in the gut environment. One of the common mechanisms is the reduced protons with them.
11:00:08 That is dumped electrons and protons and make hydrogen gas, and these this enzyme this hydrogenated that is responsible for making hydrogen is common in a lot of gut microbes.
11:00:23 So, this is a strategy that lots of microbes make, of course hydrogen accumulates in the gut, and as hydrogen accumulates this becomes less favorable reaction.
11:00:36 And so, bacteria, the Firmicutes, one of the major phyla of bacteria in the gut tend to dump their electrons on to acetate and reduce it to beauty right.
11:00:50 So here's one of the major fermentation products, and they get some ATP out of that.
11:00:56 So, I mean I'm generalizing here a lot to say that this is Firmicutes to do it but it is a common feature of the, of the Firmicutes course Pyro aid can be reduced to lactate.
11:01:10 It can also be reduced. And this is done, often by Bacteroidetes to pro p amp a so appropriate acetate and Beaterator the three short chain fatty acids that are most common in the mammalian got the mouse gut human gut.
11:01:31 And so i mean i i don't know i'm not going to go into this very much because I'm hoping that Bernard and Alfred may have touched upon elements of this.
11:01:42 Let me, let me just add a couple more the animations and then I'll open it up for discussion.
11:01:49 The hydrogen is a source for other microbes in the gut we know that we, all of us carry a number of a seed engines organisms that can consume hydrogen and reduce carbon dioxide to acetate, and about, depending on your age of about a third of us have active
11:02:13 pathogenesis, you take a sample of your breath and detect whether or not gut microbes are reducing that hydrogen the methane in your large intestine.
11:02:22 And he had the point that I want to make here is that hydrogen concentration is an important local parameter for controlling the flow of electrons.
11:02:37 And one of the hypotheses that we have in terms of the human cohorts and I'll show you this data is that when there's more hydrogen.
11:02:46 That was a little backwards pressure on this and we tend to get more beauty rate, or more appropriate. And when hydrogen is less a greater percentage of the carbon flows to acetate and there's less less of you right.
11:03:03 So we're going to focus on beauty right later. That's why I have this hypothesis there.
11:03:07 So, I'm going to pause there for just a minute, and I don't know, ask anybody to chime in if they're interested.
11:03:22 I'm a bit.
11:03:24 Thinking back to the start of the presentation where you said that you, the one thing that, like, we actually can digest is glucose right that's not necessarily thing that the microbes need to eat was just wondering how much of the glucose actually ends
11:03:38 ends up in the microbes and how much is your hockey a great. Oh yeah, great, thank you I should modify this slide, answer is no. If you drink any glucose.
11:03:52 If you're having a coke right now, or whatever. None of that's going to make it down to the large intestine, that it's going to travel through 20 feet of small intestine it's all going to be absorbed.
11:04:05 So I took a shortcut here that I shouldn't have.
11:04:09 But the resistant starches
11:04:13 that are in lots of the dietary fiber, they're broken down first the glucose, and then glucose enters central metabolism.
11:04:24 Thanks for pointing that out glucose shouldn't be the starting point on this slide. It should be resistant starch or England, and we should go through fructose as, as well.
11:04:36 Yeah, thank thanks for bringing that up
11:04:46 some privacy so Sandy has a questions.
11:04:49 What the flow going to h2 but I guess you answering the depends on the hydrogen partial pressure, and all that, this maybe I'll follow up on the question.
11:05:00 The, so I guess it's not so easy to get rid of the hydrogen just by diffusion of the week.
11:05:11 Yeah, the gas and what what what's, What's the problem.
11:05:19 Production versus
11:05:25 how much is produced in and how much escapes. So, so let's talk.
11:05:31 It's a good thing let's talk about it for a minute. So first of all, some of the hydrogen the fuses into your bloodstream exchanges in your lungs and you can detect it in your breath.
11:05:43 So that's the basis for looking at tests for lactose intolerance or, you know, they they're measured Hi, we don't make hydrogen, but we're exhaling, it, it, we're exhaling it because back to your microbes in our gut or making it.
11:06:00 So that's one route of escape.
11:06:02 The other route is something that is through flatulence so you know a lot of any high, you know, Junior High student knows that hydrogen is flammable.
11:06:16 And so we do pass some hydrogen in flatulence, but their local concentrations still get high and a real challenge in my mind is determining how high they get.
11:06:36 I'm not sure how we do that.
11:06:41 So, there's no way but the fact that you look, but there's gotta be some evidence that that shows the accumulation of the hydrogen in is responsible for some of the other effects on be iterative things, things like that, maybe not absolute level but there's
11:06:57 a, there's fluctuation in hydrogen accumulation in that that that is that just just getting rid of by natural causes diffusion Federation's is not not enough to your issue.
11:07:12 Terry you bring up, bring up a lot of good points, including that that variation over time. I mean, you can track hydrogen in your breath and, you know, about two hours after you eat hydrogen starts going up in your breath and so concentrations locally
11:07:28 in the gutter going to change based on when you last eight, but roughly what is the magnitude of this change I was talking factor of two factor of 10.
11:07:47 So you're really asking about low local concentrations of hydrogen what what the microbes are seeing. Yeah,
11:08:03 I don't know.
11:08:00 And I
11:08:03 did this diagram also suggests that pH might have an effect on.
11:08:11 Right. Yes, absolutely.
11:08:14 QUESTION So, does it is it relevant variable or is it sort of buffered too tightly to.
11:08:23 Yeah, thank you for bringing that up I think it is a relevant variable in people.
11:08:30 The the pH in the colon varies from 5.5 to seven.
11:08:37 And there are a lot of factors that influence that I mean the host is buffering, the stock the acid is comes out of the stomach with by carbonate. So it's I mean it's neutralizing that fermentation in the colon and certainly lowering the pH.
11:08:53 So there are a number of factors that influence pH, and I think that pH is one of the important variables that we haven't given enough consideration to, because 5.5 to seven that's a mean that bacteria certainly you're going to respond to that to that
11:09:14 range, so I i think it's crucial journal pH right.
11:09:18 It's the intimate for this kind of reaction to internal pH that that matters.
11:09:24 Inside of the bacterium so while I'm not talking about inside the bacteria.
11:09:29 But, I mean, Boris was pointing to that reaction diagram and it's the proton inside the material.
11:09:37 Oh.
11:09:38 Gotcha.
11:09:40 So, but that's that's an equilibrium also with the outside.
11:09:46 Hydrogen partial prices because hydrogen can diffuse. So the big implication of the hydrogen partial pressure as Tom said, and the proton concentration is that it determines the Redbox potential of the pier hydrogen protons.
11:10:03 And with that, whether or not the electrons as Tom has drawn in from pirated oxidation can be used for proton reduction or need to be consumed with your direct production, that's that's an intrinsic set of thermodynamics trade off.
11:10:19 Yeah, where the, the rhetorics potential of the hydrogen is absolutely crucial for shifting the segmentation balances.
11:10:30 So a question. The if it's difficult American see how difficult it would be to measure the partial pressure locally in the gut but what about.
11:10:42 What about pumping in some hydrogen, maybe not a human but on some other organism, and then seeing the effect that you may have idea of. That's a good idea.
11:10:54 As far as I know, no one's done that.
11:10:56 There are also this tech technology called nano bubbles, where hydrogen is it very small bubbles is infused water.
11:11:10 So I think there's some ways that we could do that, let me show you just, I've got two slides in about hydrogen.
11:11:28 Okay, so, so here's a pure culture of Rosebery and test analysis. One of the common beauty rate producing bacteria from the gut. and it was grown under atmosphere.
11:11:45 I mean always have nitrogen, the solid bars or one atmosphere of hydrogen. And just like you would expect from that previous slide.
11:12:04 When hydrogen is present acetate is consumed from the medium.
11:12:15 That's the night that's the negative sign, and it's reduced to eat.
11:12:19 Beauty rate so there's more beauty a production, there's also more for me produced. So, these results are in.
11:12:28 So that under one atmosphere.
11:12:31 Local pressure I can tell you that it does make it doesn't make a difference for this organism.
11:12:38 I'm going to throw a little bit of a curve at you. Here's another prominent gut micro organism that does not have a hydrogen Ace doesn't make hydrogen doesn't consume hydrogen.
11:12:51 As expected, whether this has grown under a nitrogen or a hydrogen atmosphere, there's, there's no difference in the fermentation. These fermentation products.
11:13:04 We do.
11:13:07 This might be too much. So, for those of you who are more interested in hydrogenated carbon monoxide is an inhibitor of carbon of hydrogen as, so we can get this mirror those results that with hydrogen by including carbon monoxide.
11:13:24 So this was just to get a mech and is it the hydrogenated or not.
11:13:29 So, okay, so those are the slot slides I wanted to show you about microbiota so if you have more Firmicutes or more Bacteroidetes you might get more beauty rate or more appropriate respectively.
11:13:44 The local environment was somebody brought up pH I think it's a hugely important parameter, hydrogen, of course hydrogen is going to be important in that, in that flow of carbon and so I just wanted to provide some.
11:14:00 So, you know, some basic experiments some, some ideas for thinking about what we are going to tackle when we try to engineer that gut microbiome.
11:14:13 And then, right, I'll leave you with this and then we can we can discuss it, you know from Michael Pollan so right he's talking about the extent that we're bearers of genetic information the majority of that's microbial.
11:14:27 And that microbial second genome exerts an influence on our health. And what he mean the punch line is in the red, while your inherited a genes are more or less fix it may be possible to reshape even cultivate your second genome.
11:14:43 So, I'll
11:14:49 alpha that's, that's what I was going to stop in terms of the tutorial. But, I mean, maybe we have a few minutes for conversation.
11:14:59 I think this would be great.
11:15:00 I'm just, I'm working on some questions in the chat box but we could probably
11:15:12 Jonas Do you have you had a question maybe if you can articulate this about hydrogen release.
11:15:25 Not yet. A question and just also comment right so I really tried to dig into the numbers to really find out what's the most important release path for hydrogen.
11:15:37 And, you know, fat loss and breath and consumption by cross feeders. And I was surprised how little is known quantitatively about the different paths.
11:15:51 But what seems to be clear is that the hydrogen levels in the gods are really high and so at least we have. So there are some partial pressure measurements out there.
11:16:01 I don't know how reliable they are but so I completely agree it's a really important factor. And the question why that is why hydrogen is not just released through the got a PC view.
11:16:16 I think that might have to do i mean speculation but it might have to do with the fact that the garden moment needs to stay anaerobic at the same time right so it might just be hard to design an MPC VMware the hydrogen can give us out without the oxygen
11:16:33 diffusing,
11:16:37 the other hand the rate of hydrogen formation is really high.
11:16:42 Yeah, no, I mean, no question so I think that regardless of that release rate that there's going to be local concentrations of hydrogen that are important.
11:16:58 There was a discussion on, you know, to what extent appropriate formation could also be as an electron. So, basically this this triangle of acetate formation acetate and hydrogen formation reiterate formation and appropriate formation, how this plays
11:17:20 into sort of strategies to balance for meditative electrons. I think that's how I would summarize the, the chats. Yeah. Hey, what's interesting is that sort of the rule of thumb in terms of the proportion of those different short chain fatty acids and
11:17:41 humans. It's about 60 2020 60% acetate 20% beauty rate 20% protein eight. Yeah, you know, approximately. So that's in a healthy person that's the proportion of the, the molar proportion of those different short chain fatty acids.
11:18:08 But I can just add to that. So, from a microbiome point of view.
11:18:13 If you assume glucose fermentation, and metabolically you can either produce procreate or acetate plus hydrogen and hydrogen is covered because of the the the maintenance of electrons so the electrons that you oxidize from glucose you need to recover
11:18:31 somewhere.
11:18:34 There's a significant ATP implication of producing acetate versus beauty rate. Because when you, when organisms produce acetate and hydrogen.
11:18:47 There is more ATP form, so that's beneficial to the organism and and it's fitness, the trade off of that is that it needs a hydrogen partial pressure that is low, which basically means it depends on the other organisms, which means that the overall pathway
11:19:05 is essentially specie aided to two organisms and then that's the beginning of the metabolic interaction between organisms.
11:19:14 It's it's essentially driven by by the energetics and pathway length of the individual cells.
11:19:23 That's that's my view. And again, the, the other sink for hydrogen, that we have to keep in mind or the mythology ends in the regions. So, I, if you go to indigenous peoples and almost everybody has nothing antigenic their gut microbiome is are on the
11:19:46 fan of genomic.
11:19:47 And so, I mean it's just an observation, but most mammals in fact are authentic authentic also. So, I mean, it's just the other factor to consider that the rate of consumption by microbes is going going to be important for local concentrations as well.
11:20:06 So there's not just escaped into the blood escaped through flatulence there's consumption of hydrogen by other groups of microbes.
11:20:17 I would really agree with that of course but but it's really an open question how important the consumption is their processes right and and that's really, then at the end the open question How important is this cross feeding in shaping really the growth
11:20:35 of the primary fundamentals, or can be. I mean, obviously they play some role right, but maybe in first order we can forget about them, or maybe they're the most important thing right.
11:20:58 Jonas I I agree completely with that, I don't know.
11:20:53 But it's something that has not gotten much attention, at least in the environment of the mammalian got it has a cow Romans and and termites.
11:21:04 But it's not a factor that we've given much consideration to maybe to ask this question a different way.
11:21:15 You know, although viewing this, the large intestine, as a kind of a chemo stat was a 24 hour dilution, but this is really growth is not really a problem, in principle, many of these organism can grow very rapidly right the evil and aerobically they can
11:21:35 grow very rapidly.
11:21:37 So, I'm not even sure whether ATP is a cancellation or whatever right but it's the grain at the one 10th of the potential of with it could be greener, and that the struggling with something.
11:21:50 And can we put our finger on that something that it is my I really am not convinced that growth is the issue.
11:22:03 Yeah, they're competing that I mean it's a competition.
11:22:08 It's preferential interactions I mean we. I can't remember if I have the data in there or not but we find that the some of the bacteria that degrade resistant starches.
11:22:22 That's external to the salad that takes place so there's some release.
11:22:26 The motto trios, there's some bacteria in the gut that specialize on multiple trials and so that they do well.
11:22:39 So there are those kinds of cross defeating reactions as well. No, I mean, competition is a big deal if growth is a primary thing right and then, if, if you have too much food and and that's if we are the let's say the common enemy is too much hydrogen,
11:23:04 just stops everything from going, then it's not so much about competing for what it is rather about somehow getting rid of these things. Yeah. Gotcha.
11:23:03 Now I know I understand what you're saying. I don't think there's always an abundance of resources that for the gut microbes. I think there's that I think there's competition for those.
11:23:13 And it's on a daily cycle. I mean in the morning when you get up if you measure your breath hydrogen, there's very little that is it my interpretation is is that the resources that were available to the gut microbes are largely extinguished by morning.
11:23:29 Now after you eat.
11:23:32 You know that, depending what you eat that may change that situation so that there certainly is this fluctuation of resources coming into the gut. So I think they're going to be times where there is competition is important, and other times when there's
11:23:46 resources of plenty,
11:23:50 or the, The other part to that is that
11:23:55 the good soluble compounds in the diet have been resolved. So what ends up in the lives God is pretty much insoluble polymers. So the rate of polymer hydrolysis and uptake is the rate limiting step in the growth of gut microbiota.
11:24:20 I have people look at me, if, if, what if the input the research is a is a at least a possible bottle that. As far as just getting enough of things to make the biomass, then there should be a big difference between people that either log or just kind
11:24:37 of a people that are close to salvation army deep, but the more or less of the, I mean we have a couple of. kilograms of biomass at hand. Right, yeah.
11:24:49 Sorry. No, go ahead. Please bar Scott, I mean I think this is a great discussion but I think it's really that that's so if we eat more fibers and if he eat more resistant starch, then the biomass being produced is really going up a lot, it's it's a one
11:25:07 to one correlation basically I'm much more training.
11:25:22 once every week. Okay. And it's not like he's got like 10 times more biomass. No, no, but the data is pretty key at least you know i don't know any friends whiteness hard to argue but if you look at the studies where people looked at bio master and over
11:25:32 over the pending on Fiverr consumption all that you really see a linear increase with the fiber and resistant starch content of how much back mass is released.
11:25:43 Yeah, so it's it's really it is that the major bottleneck is really the complex carbohydrates.
11:25:50 Hey, and let me just also toss in that there's been there been some nice studies that have identified the mammalian gut as a nitrogen limited environment.
11:26:01 So you keep pouring in all those car complex carbohydrates you want, but if there's not sufficient nitrogen available through amino acids or other sources that that's going to limit the breakdown and that the fiber passes through.
11:26:19 So, I mean, we've got a, we've got to think about the whole or the whole microbiome and, you know, nitrogen in this environment nitrogen is a crucial factor.
11:26:32 There is a question for Korea and maybe you can create an AVI have questions maybe you can post them directly.
11:26:42 Yeah, sure, that I think this talk has been really cool. I especially like the emphasis on like the ecological aspects of it. So one thing that separates, and host associated bacterial community from perhaps other ecological communities is the host of
11:26:59 alive and is probably assisting or altering these communities in some sort of way. So I'm curious about what role you think that host regulation aside from diet.
11:27:10 So I'm thinking more like typical signaling from the host is going to influence community composition.
11:27:15 And then the second question was, do you think that historical contingencies are playing a role in these community compositions now, because if you're introducing a new taxa to this environment where you're also doing is performing an invincibility experiment.
11:27:33 And so are there situations where you think these early life experiences, or the status of the community at the time is going to determine whether or not you can actually manipulate it with specific microbes at a later date.
11:27:50 Corn Wow, that was a wonderful perspective and questions there. So, in regards to the the First Avenue, how much is the host influencing.
11:28:03 Certainly there are mechanisms by which the host can influence the composition of the, of the microbiome it secretes antibodies into the lumen that that that can play a role mucus that is produced continuously in the gut microbiome that that is a resource
11:28:25 that's used by the microbes as well.
11:28:29 And so, some mucus production is mucus that's produced in the colon is is a another source of resources.
11:28:43 And I think we don't have a good idea of other than how important other hosts derived products are in determining the gut microbiome but I think the basic notion that you're proposing there is an important one is not to forget about that, that the host
11:29:02 may regulated.
11:29:04 Others may have more to add there contingencies also an important one Marty blazer.
11:29:13 Really, really favors contingency as an important factor in the development of disease in our 30s and 40s depends on what microbes were there. Originally, and so I yes contingencies is going to be important.
11:29:35 How much is that going to influence our ability to modify a microbiome, I mean, I don't know, let's say, for instance I maybe took an adult and get gave a regular treatment of antibiotics of broad spectrum antibiotics, you could remove lots of the microbes
11:29:51 that are there.
11:29:53 So does that. I mean I guess that I turn that back to you I mean, does that does that remove the contingency, or
11:30:03 does the host is it hosts still going to respond differently based on what it's seen earlier in life. Yeah, it's a it's a good question to raise. Yeah, I mean, that helps, um, I'm wondering you know if there is host regulation is associated with this,
11:30:18 then that contingency doesn't just exist in the community. It will now exist within the community and the host right so you're dealing with and visibility from this micro trying to enter into this factual community.
11:30:31 You might be dealing with.
11:30:34 Yeah, for lack of a better term like host training on which microbes it's supposed to be accepted yeah absolutely yeah like a lot. Yeah.
11:30:44 And can you just business. Another question, what is actually a composition of mucus and what does it add
11:30:53 mucus is the backbone of mucus is Musa NMUCINX a protein.
11:31:01 It's enriched in just a few amino acids.
11:31:07 I'll think of those in a minute but anyhow so musician is the backbone, and that back and use and backbone is like isolated.
11:31:15 So there's lots of glide constellation that take that takes place so lots of carbohydrates that could be cut off.
11:31:24 Its CL elated psychedelic acid is added to it so that Newson backbone a protein backbone is decorated with carbohydrates. And so you have both a good carbon source and a good nitrogen source coming from use and for the, for gut microbes.
11:31:43 By the way, if you eat a low fiber diet bacteria that are there, tend to turn the abuse in and start degrading more of the museum, that's seen as that's typically detrimental to the host.
11:31:59 And there was another question.
11:32:04 Are there any data on biomass per species in the gut, in some environments that can be huge difference hundred for differences so rare microbes can contribute significantly to biomass turnover, anything like this in the gut.
11:32:22 You know we're stuck mostly on these relative measures of the microbial community relative abundance of 16 as genes are relative abundance of jeans and a meta genome.
11:32:37 There are really good biomass at I'm not aware of good biomass s estimates for different groups of microbes but, yeah, the mythos antigens, I can tell you this, I'm a fan of genes are one group that has been measured, and they're never very abundant there
11:33:06 great.
11:33:08 So I suggest maybe we'll take a 10 minute break and then get back at 43 1143, West Coast time.
11:33:23 Right, thank you all for the great questions.
11:33:27 Thank you.
11:43:07 So Tom I am rejuvenated.
11:43:12 I am.
11:43:15 Alright, hey, there was another question maybe before we get into your research, Doc.
11:43:22 Is there any guts organized already built being built.
11:43:27 Yes, the gut Oregon boys are, are being used widely, both as three dimensional structures, where they inject bacteria into the lumen of that, Oregon.
11:43:53 And we, what we're doing is we take the Oregon oil and splay it out and grow it as a monolayer in a trans well system. And we've got those trans wells in our anaerobic chamber, so that the upper side the atypical chamber the top, the lumen facing side
11:44:04 of the cells are seeing and toxic conditions and we uncover we cultivate strict and robes in that. And then the base of lateral side of the chamber, we have 5% oxygen 5% co2 pumped, you know, flowing in through that to feed the epithelium So, yes, those
11:44:25 are all they're both the three dimensional and two dimensional models are derived from colonic stem cells. And so you can he could do that on an individual basis, said the same thing from mice, but we're doing it with humans because that's one of the
11:44:43 few chances where you haven't, you know can actually look at the gut microbe interaction. Right.
11:44:49 Thanks.
11:44:51 I'm fine. That's, that's fresh enough that I don't, I don't have any, so I'm not going to talk about that at all. I don't have the results from that
11:45:01 will take it away.
11:45:03 Hey, I'm Alfred I was going to but I decided to get a cup of coffee and instead.
11:45:10 If we covered things that have come up in the chat.
11:45:15 Most of the part I would actually encourage folks from the chat box to ask questions directly because I think they are much more interesting and create much more lively discussions, if, if you, you know, ask them directly rather than having them send
11:45:35 anonymously into the chat room so I encourage everyone who has not who still has an open question to, to ask Tom and in while we're going ahead. Justin and Tom can be interrupted anytime, So.
11:45:55 Yeah.
11:45:55 And by the way, I think, I think I have less in this second half. So, so we have plenty of time for discussion, and I I'll modify accordingly. If there's a little bit more discussion, then I'll modify as we go along.
11:46:11 So don't be hesitant and I agree with it Alfred I'd like to hear from you.
11:46:19 So,
11:46:19 I mean, before we. Before I start, were there any quite Did somebody have something in the chat room that they felt hadn't been addressed yet by me or someone else.
11:46:32 I was curious like if you just measure the growth rates of some of the more abundant header tropes in the gut on model fibers in an anaerobic condition if if Terry is right that like growth is not a problem.
11:46:47 In other words like dude what are their doubling times on the typical substrates that are that are in the that are in the gut.
11:46:55 So, so these got animals that we're working with have doubling times, you know, hour and a half.
11:47:04 On a soluble substrate.
11:47:08 It's a little more difficult with some of the insoluble substrates because the bacteria attached to the surface of measuring growth is a little harder but again it's it's having a matter it's on the order of couple of three hours.
11:47:22 So, I think that that capacity for growth isn't a problem.
11:47:29 Got it. Thank you. Yeah.
11:47:31 I have a question. So, I understand it's very difficult actually to define an species.
11:47:38 But how many percent of the gut microbiome helping cultured in monocultures in define the minimal medium.
11:47:50 So if you would have thrown in that last piece about a defined minimum medium.
11:47:55 That boy that complicated. Not many, not many loopholes, like English medium or undefined medium and in minimum medium, like how many percent.
11:48:06 I would guess that it's, it's about 60% or more.
11:48:11 So much medium
11:48:14 rich, rich media, and all kinds of different rich media. Yes, you know, after Mansa Musa Phyllis, the Virgo microbiome, you know that's growing on a meat mucus based medium.
11:48:30 So, but it's not as dire as in some environments where you know you do a shotgun meta genome or something we can't find, you know the organisms are identified.
11:48:43 We've got cultivars for lots of, lots of the organisms, then I would guess I'm guessing it's about 60%.
11:48:54 And I see So how have people reconstituted Lexi the minimal gut
11:49:01 microbiota that that has a function or like cannot have the computer function but at least major functions, right of this of the gut microbiome.
11:49:12 So, yeah, I gotcha. Good, good question. So, so people have put together lots of synthetic communities.
11:49:20 10 member communities and colonized mice with them.
11:49:26 And
11:49:30 so certainly experimentally it's a tractable thing to put together, you can model colonize mice or put in communities of microbes and, you know.
11:49:45 Yeah.
11:49:44 Most of those microbes what will colonize especially in the model colonization situation I gets that there's no competition.
11:49:55 So people have done that but in terms of the, the other concept that you bring up is sort of a core microbiome and I don't know if there is such a thing for humans there seem to be multiple configurations of the microbiome that are common so there's a
11:50:13 people have called these arrow types. So, There's one private Tella is a dominant organism or room no caucus or the batteries are more common and so there are, I would say, it looks like there are three or four different types of microbiome and healthy
11:50:33 people.
11:50:35 Thank you.
11:50:40 Okay. Hey, well I'll go ahead and start sharing my screen but, uh, his questions come up, please, please feel free.
11:50:49 I think, Terry was just launching another question.
11:50:54 It's okay. I can't wait. I can't wait until the end. It's kind of thing so discuss some of the this this this feel we can sit, sit around and discuss for five hours.
11:51:03 All right, well here here's it here's a slide for you that I that I just added
11:51:10 about hydrogen. So, This was the first effort in a pretty good effort.
11:51:18 They convinced 44 people to basically not eat him and lay down on the table for 10 hours, and they collected the gas in this man a metric rake and analyze the composition.
11:51:37 So, this is, this sort of a typical environment. Typical atmosphere in the gut microbiome. So I don't know if that helps at all in terms of the conversation we were having about hydrogen partial pressures but for yeah there's what you're dealing with
11:51:57 sort of in a, in a general sense.
11:52:01 Jonas in one of his chat room posted was saying that he found some number as high as 50% hydrogen.
11:52:11 Yeah, there's a lot variation from person to person. So 53 extreme person to person and over time as well. Yeah.
11:52:21 And I understand there's also this mystery about methane production.
11:52:25 That just some people do it some people don't.
11:52:30 Yeah, especially in the West, so I'm not sure I think I have some data on that in the slide and so yep unclear why it's important, NASA was studying it for a while because they thought that it might be related to flatulence, and if you're up in space,
11:52:51 you know, with no gravity.
11:53:04 Gas isn't a good thing to have, but once they found out that it wasn't related to flatulence they kind of lost interest in it and so nobody's really studying.
11:53:04 It's just an observation that people make. Yeah, maybe. Can I ask another question which might. I'm not sure if it's a good point here but. So, if you say 60% can be cultured again guess most of the more abundant ones can be cultured right and so I always
11:53:26 have this question, we know that there are so many species around, but how many species to be really need to, to, to, to, to understand something, right.
11:53:36 And it sounds like you are pretty critical with considering a call microbiota.
11:53:42 But, but, is that true or, or what what are your thoughts about that a little bit critical of one core microbiota, but I'd be okay with the notion of having three or four core microbiota that you know not every, not everybody converges on on one core.
11:54:01 I think there are some core functions, but different configurations that give that core function, I add that's how I would put it.
11:54:12 So then, like you would say like some first approaches, where we start with 10 microbial strains. That's still meaningful right to do.
11:54:24 I think we learn an awful lot from that. Yeah, yeah. Absolutely, absolutely.
11:54:31 Right. 10 is already pretty complicated to try to figure out so
11:54:36 it's meeting was asking a question um she was surprised that there was no hydrogen sulfide in the gas, you want to comment on that.
11:54:46 Sure.
11:54:48 And it is detectable in some people and Sophie producers are present in the gut, they
11:54:58 install fate is a component of Newsome, so it's it's generally considered a pathological when sulfate reduces get very abundant.
11:55:14 But yeah, I saw I don't know why they didn't detect it. I would I would agree with you, I'd expect a low level to be there.
11:55:22 Good point.
11:55:25 I was surprised about is the very high content of nitrogen gas.
11:55:31 Where does that come from two ways, smaller gulp it down.
11:55:36 Yeah, yes.
11:55:46 There's not a lot of denied verification or so we don't eat that much nitrate usually so well should it come from. Yeah.
11:55:48 Mostly we swallow it. Yep.
11:55:52 And, yeah, you're right I don't, I don't see any evidence for D night certification to end to or head to toe in the gut. There is in the mouth but but but not in the gut.
11:56:05 So, the nitrate reduction that happens there is discriminatory nitrate reduction to ammonia, so.
11:56:20 Okay.
11:56:23 I'll go ahead and, again, is Alfred suggested feel, feel free to interrupt at any at any point.
11:56:32 So, not now, I'd like to focus our conversation a little bit on the Carrick acid and graft versus host disease.
11:56:43 So, our target for engineering in this project that I'll tell you about as be Carrick acid, and we're specifically trying to influence be Terek acid production to, to prevent the development of graft versus host disease.
11:57:00 So I'll tell you about both of those.
11:57:02 So right they go back to the very beginning, there are hundreds of metabolites in the blood. Humans that are attributed to the gut microbiome, and people like Michael fish baguette.
11:57:34 UC San Francisco are identifying these different metabolites.
11:57:26 The one that we've been focusing on is a common fermentation product from the Firmicutes in the godson and that's beauty Eric acid.
11:57:39 We people need beauty Eric acid to be healthy.
11:57:45 And we don't make it. So this is a.
11:57:49 We've turned this over this requirement for be tear gas and we've turned it over to our gut microbes, but without the check acid our guts are not healthy.
11:58:02 Let me tell you about the tear gas and in particular, in the context of graft versus host disease. So this is a common it's a life threatening complications that follows bone marrow transplant.
11:58:16 So, some leukemias.
11:58:19 The treatment includes the destruction of the bone marrow, often a radiation and bone marrow is where, you know, much of your immune system is coming.
11:58:37 And so the bone marrow can be restored and the way it's restored is with a transplant from a match donor.
11:58:38 So, Again following irradiation to kill leukemia bone marrow.
11:59:03 The bone marrow is restored with a transplant, they try to match the donor as closely as possible. But that doesn't mean you can get close. It's not always identical.
11:58:54 And so the donors bone marrow, which is generating immune response can attack the recipients body as foreign.
11:59:08 And that's a graft versus host disease.
11:59:12 It's kind of the opposite of a typical transplant, you think of a transplant as the, what's being transplanted being rejected that Oregon being rejected a liver transplant the livers rejected or a heart transplant or long.
11:59:26 This is the opposite the graft the bone marrow is rejecting the host that it goes into an accomplice, the consequences are are not are not good.
11:59:40 It's maybe a third to half of the time it's fatal condition
11:59:48 gvhd typically starts in the gut.
11:59:56 There is some disability AOSIS a term that we heard last week that I'm using here to talk about the gut microbiome not providing the services that the host needs.
12:00:11 And as a result of that being a leaky gut and so you see microbes leaking from the lumen into the host tissue and starting an immune response. And this is common, Lee the starting point for graft versus host disease is this immune response.
12:00:33 Beauty rate is a compound that we know of.
12:00:37 It's actually the preferred energy source for mitochondria in the in these epithelial cells. So, mitochondria in energy production and epithelium release driven preferentially by beauty Right.
12:00:58 Yeah, I just said it's a preferred energy source for mitochondria lining the colon.
12:01:08 Oh, sorry.
12:01:11 I'm not gonna really talk about but there's a decrease likelihood of colon cancer is associated with a strong viewed right production.
12:01:20 Even regulation of satiety when you know your full and quit eating is related to beat right but the point that the focus that I want to take is the reduced incidents and severity of graft versus host disease.
12:01:35 And we know that from an animal model.
12:01:43 This is Pavin readies a colleague of mine here at the University of Michigan. He has an animal model for graft versus host disease.
12:01:50 And in this article. He looked at the impact of beauty rate on survival from bone marrow transplant in mice.
12:01:58 So, on the y axis here we're looking at percent survival.
12:02:03 And on the x axis is weeks after a bone marrow transplant.
12:02:10 The blue line at the top is a Isagenix transplant. That is, they, the mice go through the same procedure but they're getting back their own bone marrow.
12:02:24 It's Isagenix, this is just to show that the process of going through the radiation, and treatment and bone marrow transplant by itself is not lethal to mice.
12:02:55 interesting part here is in red and green. And so, in green is where solution of beauty rate was devised into the large intestine, every few days. And here we're looking at the survival of my so after 50 weeks, you know, about half of the mice are still
12:03:03 alive, as compared to mice that rather than getting a beauty right solution just got a sailing treatment.
12:03:12 So, there is the most. The strongest evidence that production of beauty rate in the intestine.
12:03:24 Large Intestine in this case of mice reduces the reduces death from bone marrow transplants.
12:03:34 So, by the way, I'm not going to go into it but the the mechanism is well understood. Viewed right, by the way, is not only a energy source for the mitochondria.
12:03:45 It's also a potent
12:03:48 regulator of host cell gene expression. And so, Pavin has stepped through and so this isn't, this isn't just an observational study, he goes through mechanistic Lee and shows the changes that are initiated by beauty right.
12:04:05 We won't bother with that.
12:04:07 So, When I came to the University of Michigan.
12:04:12 I wanted to not only do experiments in the laboratory with the microbes that we had isolated. I wanted to work with a human cohort so to get some bring some.
12:04:25 Bring that dimension to the research and so you know I asked whether or not fermentation from the gut microbiome can be enhanced by supplementing with dietary fibers.
12:04:35 I mean with everything that we've discussed over last couple hours I mean it would seem like of course that would work but, you know, we needed some evidence for that and so I wanted to work with a healthy cohort, and I you know I'm at a university and
12:04:50 it's like a lot of students around and so I developed the introductory microbiology introductory biology course is the first biology course that students take at the university.
12:05:03 And I focused the lab course on the gut microbiome, and I invited people to participate in this study so they were consented. They didn't need to consent they could take the course whether without consenting but most people can send it to being involved
12:05:23 in being subjects. In this study,
12:05:30 a little bit more background information.
12:05:32 Most of us, regardless of age, regardless of sex. Most of us don't consume the recommended amount of dietary fiber. So the recommended amount from the
12:05:50 FDA is here in grey, the actual amounts that's consumed is in black. So most of us get about, hey you know what about half of the recommended amount of dietary fiber.
12:06:06 And this, um, how do you quantify it I mean how do you quantify dietary fiber in this chart.
12:06:14 Yep.
12:06:15 So, nutrition science has worked hard to determine how much fibers in in Brussels sprouts or in brown rice or white rice.
12:06:31 And so they've.
12:06:33 I mean there's a national database on the fiber content of foods, and that fiber, by the way, includes for mental fiber, that's what we're talking about, but it also includes fiber that is not broken down.
12:06:53 So, I mean, lots of the cellulose that you eat isn't broken down, we don't have the microbes a break it down, we can't break it down so that fiber includes both formidable fiber and bulking fiber that passes through the system, and not degraded.
12:07:14 I don't know the debt that I'm just curious, what do they like what's the definition of fiber right like when you see fiber exactly what do they need.
12:07:25 Fiber is that component of food, mostly from plants. That is not metabolized by human enzymes, it makes it to the large intestine, where it can be degraded by microbes but not necessarily.
12:07:46 So, my definition would be some, something like that. So, so like the carbon equivalent, because somebody will be very have very diverse calculations, this is grams.
12:07:58 So, okay, grams Okay, yeah, great grams per day. So the recommended intake for, you know, males that are 20 to 50 is about 40 grams per day, you know about 25 grams per day for females in that age group.
12:08:16 So that'd be grams per day and you can look at the side of anything you bind the gross in a supermarket and it'll tell you how many grams of dietary fiber in that,
12:08:27 in that food.
12:08:30 So, the point I want to make is our microbiome are not. There's room here, there's room to add fiber, and we're tested the hypothesis that if we, if we add this amount of fiber that we would see increased production of short chain fatty acids.
12:09:01 Be iterating particular account. Yeah, boy you go out with a question.
12:09:00 Again, something, never understood so we made a statement that Oh, we don't we don't have a Microsoft degrees cellos.
12:09:11 And what I mean we.
12:09:13 So we have microbes that degree lots of things but what is it that is it because I would die It's not have enough.
12:09:20 So loss of control my house microbes and cellulose, but what yet is a typical that no humans containers just what when I keep on hearing statements like that yeah so what what is behind this elephant, people have tried and I mean occasionally you get
12:09:38 a cellulose the greater but they're never very abundant and so you laces.
12:09:45 Sell them find those in shotgun meta genomes.
12:09:51 You know, very good question. I don't why aren't they, there is this is, is it just a matter of time if we start eating enough Barnsley you know Daya will start to house a little problem and it just said, How is my clothes I can be great.
12:10:10 I think we I think we probably get lots of cellulose in our diet.
12:10:15 I don't know, hey, Bernard, can you answer that question, if you're on Can you answer that question for us.
12:10:28 Maybe he's not here. Yeah.
12:10:32 That's something we said that the residents my time might be too short.
12:10:37 Oh, interesting.
12:10:39 Yeah, I was just saying that because I mean I think there are other people that know more about this than me but cows, for example, where do you do have similar civilization.
12:10:49 They have a real long residence time. And then you can have room in a Coco's, the gross and produce the hydrogen, I mean rabbinical because the great syllabus for example then produces hydrogen and methanogens remove it.
12:11:01 You can have the Center for going on. And I suppose that in the human. God is not possible because there's too much flow, yeah yeah wow I like that I like that a possible explanation now.
12:11:14 Terry you got your bike. I was trying to turn up somebody.
12:11:22 Right, so that resonance time of that the shallowness of moving too fast or residing No.
12:11:27 Okay, so there's still a dilution. That's the suggestion. Yeah, that it moves through too fast we just don't microbes that the gradient grow too slowly, don't have enough so I'm so I guess So ultimately, it means that, just the biochemistry of degrading
12:11:44 Santa Claus is a slow compared to typical transit time, because that's it, that's a statement.
12:11:51 But what I'm still in a wise salary and everything is moving at the same rate, why is it that, why is this the shadows that requires more longer resonance time.
12:12:05 Yeah, I don't know, and it is, you know, it is tied up with lignans and.
12:12:09 I mean, it may not be accessible because it's in the plant in a, you know, part of the plant cell wall so there might be an accessibility issue there to don't know.
12:12:20 Don't know.
12:12:27 Okay so several people are responding to okay just just difficult to break down so look, this is what is probably the offering right probiotics and that's the delusion is probably not the complete answer because the regurgitation time the room and have
12:12:42 cow is like four hours for five hours. Right. And in this in this time, there is cellulose degradation.
12:12:45 Right. So, it is my kinesthetically possible but apparently not happening in the gut.
12:12:50 Yeah.
12:12:54 Very good, good, good, good question. Sorry. Yeah, no, no I hadn't thought about it.
12:13:01 So I'm going to show you some results for this experiment that we did.
12:13:07 By adding fiber to the diet of undergraduates at the University of Michigan who consented to participate in this study. So the experimental design is like this there's, there's one week before we started any dietary modification and participants collected
12:13:26 for samples. They measured Ph.
12:13:30 They took a sample that we extracted the DNA of to get a 16 s analysis and shotgun message you know for sun.
12:13:42 They also took breath measurements of hydrogen and methane.
12:13:47 Again, these are microbial products from the gut microbiome we don't make either these, and they also took samples for short chain fatty acids.
12:13:57 There was a one week transition where they ramped up consumption of one of several dietary fibers. So, the fibers we use were extracted from plants, they're commercially available, and people ramped up to 40 grams per day.
12:14:20 And then during the third week.
12:14:24 They continued to take whatever supplement they were taken, and they collected for more samples.
12:14:30 So, in general, the comparisons that we make are an average, so like would take an average of these pH measurements in week three and compare them to the average in week one.
12:14:43 So for each person we're trying to collect multiple samples just to get some of the capture some of the day to day variability. But in the end, we're looking at what we're asking about before, consuming a prebiotic the during consuming a prebiotic.
12:15:01 Yeah. And again this sort of.
12:15:07 This was really a quick turnaround time, lots of these dietary supplementation studies go for 12 weeks or more.
12:15:19 We're trying to do it in within a semester and get data back for the students to work with. But I also thought about the ecology of the system it's like hey that system is turning over quickly.
12:15:31 People are losing half of their microbiome every day so we should be able in a week's time to see differences.
12:15:39 So, it turns out to be true. This is the very first semester where we did this supplementation. And this was, we added resistant starch resistant resistant to human amylase.
12:15:57 It's from potatoes.
12:16:00 And we asked, and we looked at be right production.
12:16:06 And I'm showing the first semester so I think there are 20 people that were compliant with the protocol again on the y axis we have beauty rate concentrations.
12:16:22 And on the x axis each of the individuals so here's the first individual blue is the average for week one red is the average for week three.
12:16:27 And they're just arrange here based on their incoming viewed right concentrations.
12:16:32 Here is the population of 20 people, here's the average incoming view iterate and here's the average blu ray concentration. During consumption of the resistant potato starch, and we increased it no question the strong statistical significance.
12:16:54 And so, yes we could increase the rate production.
12:16:59 But we also noted that the individual variation is striking. I mean look at this here three people that came in with about the same level of beauty right this is physical beauty right extracted from a fecal sample.
12:17:15 This person didn't respond at all kind of want a dramatic response here and you know something intermediate here. And so, I mean, with this is what we'd like to understand the hypothesis is that that variable responses reduce due to some competence some
12:17:36 combination composition of the microbiome or other, the environment of the microbiome in one possibility or gat gases hydrogen in particular in the environment.
12:17:54 So,
12:17:54 this is what we want to try to address, and we want to understand is because we've just started an NIH funded study, to try to prevent graft versus host disease by providing resistant starch to individuals so individuals who are admitted to the University
12:18:13 of Michigan hospitals for a bone marrow transplant, have an option. Based on this study of the healthy undergraduate students they have the option to enroll in a study where their diet is going to be modified by adding resistant starch done.
12:18:30 By the way, I have to say.
12:18:34 I couldn't believe that we got this result.
12:18:36 The first time out of the gate.
12:18:39 We didn't do anything that control diets of undergraduates who participated. We didn't ask them to do anything to change anything about their diet.
12:18:49 They did record it.
12:18:51 But other than that, there's incredible variability and diet in lifestyles for all these people and yet we saw a difference.
12:19:05 How much of a pathetic, they have to consume to get this result in 40 Grand 40 grand, not much. Yeah. So, twice a day so we did, we did 20 grams twice a day.
12:19:18 So, you know, like three tablespoons in the morning three tablespoons in the afternoon.
12:19:25 I've been taking this resistant potato starch for the last seven years.
12:19:29 Still haven't killed me but that that's just an end of one.
12:19:34 So, so it's not difficult to consume and how man's good question on the result back, please. So, it's a nice result I wanted to ask about the three points that actually.
12:19:59 Before, and all of those seems to have a significant decrease Do you have any idea why this could happen in the in the right side of the blood. Yeah.
12:20:02 event, very observant is a good observation and I can tell you this, we've observed that every time we've done this every time we've repeated this.
12:20:13 I don't, I don't know.
12:20:17 I don't know what the reason is we are getting to a.
12:20:24 I'll show you a little bit we now have had 800 people go through with different supplements and all.
12:20:30 What seems to be the case is that during week three, the range has decreased. People have generally moved to a smaller variation in Abuja right concentration between people.
12:20:45 I understand mechanisms for how can increase, I don't know, I really don't know why that's decreasing.
12:20:56 Reading different things. I actually have a weird question, Is this like always a first semester class or is it something that you do throughout the year.
12:21:10 I'll answer that. But before I do, Shana white Why are you asking that. I'm wondering if the students diet changes from that first week to week three depending on their habits and also how much they're exploring their, their environment at that point.
12:21:28 Yeah, yeah, yeah. Interesting.
12:21:31 Yes, we've repeated it, both in both semesters.
12:21:36 And it doesn't seem to be I mean another consideration would be well Are these all freshmen, are they just coming to the university and so, but we have repeated it, it's not dependent on the semester.
12:21:53 And it's not, if you say, well let's just look at freshmen versus sophomores, those are the majority of the students that are enrolled.
12:22:02 We don't see a difference there so we haven't been able to trace the difference to to any of those factors but interesting question.
12:22:17 Okay, so, by the way, just a little bit about that path from dietary fiber resistant starch to beauty rate.
12:22:29 In general, there's one exception that we we've only seen a couple of times, the bacteria that the grade resistant starch. Don't make beauty right.
12:22:40 So the two most common responders are befuddle bacterium for Kelly and ruminate caucus bro me I.
12:22:48 They responding a majority of people that respond to resistant starch.
12:22:54 I'm now going to talk to us about resistant starch, but their products. None of them make beauty right.
12:23:02 So there's at least a two step anaerobic food chain where intermediate products from that breakdown the acetate lactate model we're all ago sack rides that are released from the resistant starch breakdown.
12:23:19 feed the secondary firm enters the beauty right producers. So these are organisms that are common in most, most people have one of the one or multiple typically multiple of these beautiful eight producers.
12:23:34 So it's not just like one organism one resistant Polly sack right there at least two step food chain, and if hydrogen is important if hydrogens important.
12:23:46 There might be a third, a third step with the seat engines and nothing antigens influencing this.
12:23:56 So, we've now had for the time I made this slide we had 800 participants who shared their data.
12:24:06 Pretty good compliance amongst those who agreed to participate.
12:24:13 Females and male averages representative of what the breakdown is in an introductory biology courses and age range is pretty restricted.
12:24:26 But
12:24:30 what one thing that you might ask, I mean how many kinds of bacteria are in a fecal sample. So we now had a total of 6000 samples from hundreds of participants.
12:24:42 And so what we did was this is based on the V for region of the 16 has gene. And we didn't do any clustering of those sequences, we used applicants sequence variants, as VCs.
12:24:58 So, if a sequence is different in that region by one base. We said that's a different ample con, and we're not going to cluster them together.
12:25:10 This result really stuns me.
12:25:14 So, first in the top the number of sequences per sample.
12:25:18 In general we had, you know, 10,000 to 30,016 sequences for each sample so each of these points is a sample. And this is just reporting the number of sequences per sample.
12:25:33 So, you know there's there's not a huge variation or. Yeah, we have we have a similar number of samples, and we generally don't recover more diversity with more samples we're sampling this community.
12:26:04 Complete.
12:25:57 We're nearly completely for this definition of a different kind of bacteria. But here's the result that stunned me that, on average, you know, there are 60 to 80, different kinds of bacteria in a sample.
12:26:13 So, by the way, I did a survey around the floor.
12:26:18 And everybody on the floor that I'm on works on the gut microbiome. Typically people suggested 1000 to 10,000.
12:26:28 This just floored me So this says at any one point in time.
12:26:32 And they're, they're more like 60 or 80 things that you have to think about, not 1000 or 10,000. So, this kind of gets back to a question somebody asked earlier well.
12:26:45 How many can you put together some synthetic communities and put them in mice, it's like, yes and maybe the numbers that you need to do that are lower than some of us are expected.
12:27:01 Anyhow, I'd rather think about engineering a system that has 60 to 80, different components, rather than 6000 8000.
12:27:11 So what we did is we looked for correlations between some of these primary to graders of resistance starch and beauty rate producers.
12:27:21 And, you know, we started to get patterns. So, the befuddle bacterium seem to correlate with these two beautiful regimens read is a positive relationship, and the Asterix are indicating statistical significance.
12:27:44 Our bro me I, one of the graders seems to have a preferential partner as he wrecked Tally. So, I'm not gonna make any major conclusions from this but just to give you an idea of.
12:27:58 Now that we've got hundreds of samples samples from hundreds of people we can begin looking for correlations. In this case we're looking for correlation between primary to graders, and the secondary for mentors have viewed great producers.
12:28:15 And we can see patterns, beginning to emerge. So, when the dietary supplement is resistant starch from potatoes.
12:28:24 If room no caucus is present.
12:28:27 There was a statistically higher production and beauty rate.
12:28:32 When the supplement was taken. Then when room no caucus was not present.
12:28:38 We see that pattern with potatoes, we see with insulin, and even a hint of it but not statistically significant. With accessible starch. So, again, increasing our bromine AI is associated with higher view right here with all fibers and with significant
12:29:00 values and in just a couple of those. So, just to give you a hint of, you know what we're what we're starting to do.
12:29:09 I won't bore you with all the data but what we're trying to put together is an anaerobic food web from from from fiber to beauty, right.
12:29:19 So, we got resistant starch from corn resistance session potatoes insulin from chicory root, we've tracked that through different primary to graders.
12:29:32 We see different secondary to graders here and again we're trying, we're trying to my model.
12:29:42 These organisms to be able to predict which fiber to use with which type of microbiome that's present.
12:29:53 And again we have some support for some of these summer hypothetical just want to what we know about with the, with the organisms.
12:30:15 So, for, for these first and second graders. Is there a reason why so you bacterium actually produces beauty Right. I mean, and and the first graders can use resistant starch but don't produce booty rate, right.
12:30:23 So, is there is there an underlying reason known for why that is
12:30:32 why it no first grade as taking in releasing booty right.
12:30:39 Excellent question.
12:30:40 Anybody want to offer an answer i mean i don't i don't have one.
12:30:45 I don't know why that is typically broken down into into two organisms.
12:30:53 Anybody want to offer a speculation on that.
12:30:59 I want to mention that this is also the kind of the, one of the most interesting questions that was a raising that bonus session so it's definitely a question of a common theme.
12:31:11 Yeah.
12:31:14 So, room in a caucus is not really producing be iterate and it's kind of a tautology because it's not there but it's not.
12:31:27 Right here. Right, right, right. It's, it's not really in the business metabolic business plan to produce speed right it's more like an acetate and ethanol producing hydrogen producing organism.
12:31:40 And so, so the question is why is this nice not occupied by the iterate producer.
12:32:04 That could be energetic reasons that the yield might be lower, for producing beauty rate as opposed to producing acetate and hydrogen, that's certainly true.
12:32:00 It could be also question about uptake because these iterate produces in the end produce be iterate from carbohydrates so the four monomers and sort of dissect rights and not apparently from the resistance starch so the room in a caucus probably has some
12:32:19 different enzymes to access that resource that might be different from from the other direct produces. Hey, Alfred Can I jump in just for a second, right at that point because that's a critical one that you're making the resistant starch, doesn't enter
12:32:39 the cell. It has to be broken down with with enzymes that are on the cell surface. So, rumor Cockers bromine is difficult bacterium for calorie they both have the enzymes or degradation of resistant starch, out of the cell surface.
12:32:56 And when those when that resistant starch is broken down, it releases all comers.
12:33:06 It releases glucose molto, molto try iOS and bigger all comers inside what do you think that those things that are released, are what the secondary for mentors are consuming.
12:33:18 Right.
12:33:20 So I want to inject one thought, I don't know how, how much how much credence to that may be too. So this is a theme that started already.
12:33:34 It was a really solid talk that not there. There may be organism that are more predisposed for one type of metabolism versus, let's say, calculated metabolism versus Coco's agenda metabolism, different type of things.
12:33:48 And, and I noticed that.
12:33:50 Yeah. So you mentioned before that the beauty, the beauty producer tend to be Firmicutes and. And then we also know independently, somehow permit us somehow more resistant to a Ph.
12:34:08 that sort of thing. So, could there be some link there, that these, because they have to make return we have to take acetate, and we'll have to work with us.
12:34:24 Whereas, maybe the first layer guys are more into. Not in sort of the upper half of the damage and what sort of in getting rid of acid rather than making use of se Terry.
12:34:46 so these befuddle bacterium for Cali Adela sentence and some other species, their central metabolism.
12:34:44 From glucose produces acetate and lactate and lactate has a compared to the other organic acid fermentation products. It has a low pKa. So when befuddle bacterium is there, the pH is lower.
12:35:03 We know that.
12:35:05 So, yeah, I was in your description you asked about PPPH maybe having an influence and I think it does and I think it does especially when befuddle back to him as a primary to greater.
12:35:21 But then maybe there was another.
12:35:23 I got sidetracked on that that wasn't the main point of your comment.
12:35:32 I got sidetracked on that that wasn't the main point of your comment, but pH is OPHO acetate, the need to make use of acetate actually produce, to put it together to make reiterate, you at least need to be able to work with acetate I mean the.
12:35:51 filmmakers do tend to do better at the lower pH, what was what was the higher acetate by, by the way, it kind of rookies at this modeling thing if, if people have ideas about
12:36:00 how to work with different kinds of data to come up with a predictive model I'd be delighted to talk with you.
12:36:09 Let me show some of the people probably interested in you beating them some problems to work.
12:36:17 Great. We have accumulated now a pretty good data set.
12:36:23 to be able to do this kind of thing.
12:36:26 Let me show you some of the microbiology experiments that that we do. So we were looking for preferential relationships between these primary graders of resistant starch and abuser a producers and so did a very simple experiment using resistant starch
12:36:42 as the sole carbon and energy source. We either use befuddle back channel for Cali as the primary integrator or room no caucus bro me I.
12:36:53 And then in the same test tube. We also put two of the, the two most abundant viewed right producers in this cohort of people for Kelly bacterium president ci and you back to and wreck Tally.
12:37:07 So this replicates of this tube had befuddle bacterium.
12:37:13 And these two organisms replicates of this dude had our bro me I in these two organisms and so we're really looking at a competition between Iraq tally and half presidency I win resistant starches degraded by one or the other.
12:37:27 And the results of it have been reproducible, and in my mind spectacular. So, when befuddle bacterium for Kelly's degrading for Cali back chain pause let's see I outcompete direct Tally.
12:37:44 And the opposite is true when our bro me eyes that the greater iraq tally now competes for Kelly bacterium presidency Hi, so. This to me is the, this was our first evidence of preferential relationships between primary graders and beauty right producers.
12:38:07 Tom Can you describe a little bit more about this experiment is this letter repeated that gross dilution psychosis is one shot experiment, what, what yeah this is a incredibly we didn't have to do any, we didn't have to do multiple transfers so we started
12:38:25 the back, we started the experiment with Naka alum that is as close as we could get to being equal for all three organisms. and we let it grow for 48 hours
12:38:42 of pregnancy I need vitality can't grow on resistant starch that was a control that was not showing you the results from the control. And so their growth is dependent on before Kelly breaking down a resistant starch.
12:38:54 And so, The first experiment we did we just had triplicate samples of each of the each of them at the end of the experiment we played it out the bacteria, and just based on colony morphology, you can distinguish all three organisms.
12:39:15 Yeah.
12:39:16 But the, the density that's reaches not very high. But what did you put on only a little bit of a stretch, but what what.
12:39:27 Well, the, what I'm not showing you is the is the abundance of difficult bacterium for Kelly or are bro me I, you know, they would they would be on another log scale.
12:39:38 Right, so, so they're the primary graders and they're growing, they're getting the majority of the energy out of it. So, this is just looking at the at the second secondary fermented.
12:39:52 Yeah, so it's, I guess it's at the 1% level, but compared to the primary.
12:39:59 Yeah, it's a good, it's a good point I should I should include those numbers in here.
12:40:07 Yeah I include include those in here.
12:40:12 I mean, there is some competition I mean befuddle big period for Kelly when it breaks down and releases some of those multiple ago Sacra rides. If there's no other organism the US on it, it will eventually use those.
12:40:26 So before Bactrian grows more dance when nobody else is around.
12:40:31 Yeah, yeah, yeah, that point started being made here, but I agree with you tonight it'd be a good one to include. Anyhow, the, what I wanted to point out was.
12:40:44 It looks like they're preferential interactions between these organisms.
12:40:49 Anybody want to offer suggestions for what they think is driving this difference Why does for Kelly bacterium do better with difficult bacterium and why does iraq Kelly do better when our bromine breaks down.
12:41:03 The resistant starch. I've got ideas but I don't have the answers so anybody want to offer some speculation, I mean I'd appreciate it because it give us some ideas.
12:41:14 I actually have a question to both of these primary starch the greatest have the same fermentation pattern. In other words, do they pronounce the same and products, and now as you mentioned earlier.
12:41:40 Our bro me I produces acetate co2 and hydrogen and befuddle bacterium produces
12:41:37 lactate acetate and co2.
12:41:40 So then if you take the fermented medium.
12:41:46 I'm just with the primary for mentors, spin out the cells, and then ask, what is the growth rates of these strains in this precondition medium on let's say glucose.
12:41:59 So, what would you get
12:42:03 other words.
12:42:13 After I understood everything except your last comment about on glucose. Oh, well, that at the end. Or you may not even have to add a substrate but the question is, is there anything in this precondition medium that comes from the metabolism of this primaries,
12:42:23 that simply inhibit or reduces the growth rate of these of one of the other audiences, as opposed to making different substrates available. Yeah, great.
12:42:36 I like that a lot.
12:42:38 Good good experiment we haven't done that that's a good that's a great idea.
12:42:43 So, in so you're, you're looking at it from the potential of an inhibitor.
12:42:52 I mean, he can be an unpopular ethanol can be as sort of a solvent. Yeah, right, right, right, you're sticking them together and then ask the question Who's fitter.
12:43:05 Yeah. Right, right.
12:43:07 Yeah, I like it.
12:43:10 By the way, we just.
12:43:13 I met earlier this morning with the master student who is doing this.
12:43:18 She.
12:43:20 I didn't want to show it because I haven't been been through it but she showed me data from the human cohort that supports this pattern.
12:43:30 So that is when before Cali blooms FCI does in our Bromyard direct tally so we've got some indication that whatever the mechanism is which we don't know.
12:43:46 It seems to be happening in people as well. So, I'm just saying that I think we can with a setup like this we can start to understand the interactions.
12:43:56 We need to understand the interactions to be able to engineer the system. Well, Tom, so I have a comment as well to your previous slide. So I think that gets back to the original question right what is what is fiber like the many different types of fibers,
12:44:09 and maybe these, these different primary graders will degrade them in different ways, this you know the mixture of this resistant starch in different ways.
12:44:18 And because of this, usable carbohydrates right would allow one species like the FP to grow slower or faster than er, so right. I can think of the problems I can think of many hypothesis that can explain the data.
12:44:34 Yeah, yeah. Well that's kind of fun right to have multiple possibilities.
12:44:41 That's right, you're right so resistant starches right just that's just glucose. Paul it's a polymer of glucose, not nothing else is oh it's just a polymer of glucose.
12:44:51 Yes. Oh, it's cold.
12:44:58 Oh okay I guess and by the way it's resistant to human amylase is because of the crystalline structure.
12:45:04 Oh ok, ok. So, the human amylase is can't break into the crystalline structure. If you take resistant starch and heat it human amylase is it that breaks up that melts the crystals human Emily's is cannot attack that easily.
12:45:18 So this is just a physical confirmation of the starch, that is inaccessible it naturally occurring in potatoes and most.
12:45:30 I see.
12:45:31 But that would be FNRB have different efficacy of the degrading that's resistant starch and then maybe because of the.
12:45:41 Yeah. Hey, another good point. FPNER can't grow on resistance, neither of them can grow on resistant starch.
12:45:50 I've simplified this term that I've simplified this figure too much I say, I should have had FP and er, no I understood the primary to greater if there's no primary to agree to this I was just curious the other way the bf the primary traders with affinity
12:46:10 different efficacy or different you know breakdown product over this.
12:46:14 Yep. All pot all good possibilities in it they're releasing multiple trials and multiple Tetris or gluten in it that explains this.
12:46:27 Yes. And it could be that in combination with what Alfred suggested it's, you know, the dominant position some stimulation. So
12:46:39 here's the one slide that I have to go back to the, to the, to the local environment.
12:46:47 So right you remember mythos antigens consume hydrogen.
12:46:52 Reduce co2 to methane.
12:46:55 So, we, we just had people we collected breast samples and identified a person has nothing antigenic or not nothing energetic their microbiome is pathetic authentic or not.
12:47:06 And, hey there's an awful lot of variability here, but there is less beauty rate.
12:47:16 The concentration of physical beauty rate is lower in people who are both antigenic.
12:47:26 So, you know, a strong significance. So again, I mean it's it's consistent with this model that when hydrogen is being removed, less bude rate is being made.
12:47:38 It's consistent with that but you could also think of a lot of other explanations so this isn't a causal relationship, it's just an early look at the human data.
12:47:51 And I found that to be intriguing.
12:47:55 So.
12:47:59 Yep, we're, we're getting we're putting together a more specific model to look at differences in the composition. It includes preferential interactions.
12:48:15 We continue to think about gases we're also thinking about pH a lot as a possibility of what drives this variation.
12:48:33 And as I mentioned, we want to solve that because we're in a clinical trial now and if we could understand how, which fiber to use, which probiotics to use in case we need to do that as a next step will be able to target this beautiful a production More
12:48:46 precisely, so.
12:48:52 Yep.
12:48:51 This is incorrect it's 40 grams per day.
12:48:56 When we supplement diet diet with fibers.
12:48:59 More than half the individuals have an increase in beauty rate.
12:49:04 We look it looks like Brooke Cochise bro me as a keystone species although.
12:49:11 Yeah, which it is, but there may be others.
12:49:15 We know that hydrogen impacts of fermentation product of beauty origins, don't know whether that's happening in people yet or not but it's kind of intriguing possibility.
12:49:27 And based on. Well, mythos antigens are, I shouldn't say impact but they are related to view the right production.
12:49:35 So, I've got a great group of people that are contributed that, as well as funding from these sources.
12:49:49 And I'll just leave you with monument to the water closet that I photographed in Santiago when I was there for a meeting and suggest to you. Hey, how many of these lead with a suggestion to take care of your microbial garden.
12:50:08 Eat more fiber. So I'll in there.
12:50:15 Thank you so much time for this very exciting and very engaging talk this stipulated a lot of discussions on sort of key elements that have been coming back over all the talks more or less.
12:50:29 There was one question just in the context of the the the correlation with lower, view the rate at methane. And could you then potentially and hand speed right production by feeding people mF energetic inhibitor like ES.
12:50:48 Yeah, I mean, we're talking about engineering now.
12:50:51 Yeah, interesting possibility. I mean, If this models right bs would would have that impact.
12:51:00 By the way, Stanton's that people take for regulating cholesterol. Those also inhibit with antigens.
12:51:09 We have the same pathway as the archaea do for cholesterol synthesis. And so, status.
12:51:17 That might be a natural that might be an experiment that's being done naturally, and that would be yes but with Stanton's to see if that influences it.
12:51:29 The. The only problem I have with that suggestion is that when you look to indigenous peoples and when you look across the tree of life it for mammals.
12:51:37 Most of them are mythos antigenic. So, I'm not.
12:51:42 I'm a little reluctant to try to wipe out them with antigens.
12:51:47 I think they're playing an important role there.
12:52:10 Please, you know, have more questions.
12:52:00 So, I.
12:52:10 So Tom I go back to one of your slides right it says we were commanded a fiber I'm just curious, How to the dietitian, you know, the people who are commanded diet so how do they decide how do they decide like what is the recommended fiber content, what
12:52:18 is the criteria behind this kind of decision.
12:52:22 I wish I knew the answer to that. I've talked to a number of dietitians and I've never got an answer that I could understand.
12:52:33 So I put that slide up there and you know say hey we're not getting enough fiber, but people have people said, I guess experiment could be done so just like experiment you have done with your students.
12:52:45 So have, like, maybe half of the Healthy People have dietary supplements within fiber pills right and then the other half not and so I'm just wondering whether people have compared the two cohorts and the decided that this supplement is like a boost to
12:53:00 help you don't you're not aware of such studies, I don't think they've done that they have done these studies to look at can help, whether fiber, or not helps control type two diabetes, the answer is yes.
12:53:13 So there are studies like that, but I don't understand where the original recommendation came from, which was your first question. Thank you. Yeah.
12:53:30 I may ask my other question about you that so I wonder if you are aware, if there is a range of you today that is normally, on, on the Honor Guard, because I saw, for example you on the students that you did experiment with it was between five and 20
12:53:49 con, and concentration don't remember the thing. I wonder if there is.
12:53:54 This is kind of a range on a broader population, or even if it's a bit broader the distribution itself concentration. In what way to extend it goes, and then back to the question back to the observation with you, we discuss about the high.
12:54:12 Yeah.
12:54:14 Because the threshold if actually, if it cannot go above, kind of negative effect if you take two months fibers.
12:54:24 Right, so we haven't been able, so we there does seem to be an upper limit.
12:54:29 But I have no idea about mechanistic Lee, how that might come about. I also don't have any idea and I don't think anybody else does, what the desired concentration of beauty rate is.
12:54:45 It's right so I mean you can look at those experiments at Pavin ready did and, you know, he can he can prevent prevent graft versus host disease with it.
12:54:58 You can starve mice for fiber, and hence beauty rate and see lots of inflammation in the gut and leak in the development of a leaky gut.
12:55:11 But, but we don't have I don't know of any estimate of what what's healthy what's, what's the range that you want to get to.
12:55:20 And that's.
12:55:22 Yeah, that'd be most useful to know that.
12:55:33 Tommy those sample was increased betrayal levels. What happened to the other short chain fatty acids.
12:55:40 Yep. So in general, we, we stimulated all of the short chain. We stimulated acetate we stimulated beauty rate on a population average appropriate decreased.
12:56:00 And what.
12:56:03 But I'm a little hesitant about that because that population averages, you know, condensing.
12:56:09 It doesn't that doesn't happen in every in every person but in general acetate and be right go up the total goes up appropriate goes down and it's with statistically significant
12:56:24 bit rate went up a lot, the units was something about minimal and went from almost double right i mean the the from from 510 to I mean it's a decent number.
12:56:39 These are very decent increase. Yeah. What about I think was more people were, were down now to more like a 25% increases.
12:56:45 But these are solid, the really.
12:56:49 Yeah, yeah, yeah, despite what about,
12:56:58 oh no I acetate.
12:56:54 It's already very high, a little bit.
12:57:01 Well no proportionate so the proportions don't change much. As you know that 60 2020 ratio proportion does not change. so everything.
12:57:13 Mostly, but, but the appropriate is is down, statistically, right now, but but because I a similar increasing acetate would mean would, would mean a lot because actually natural is already high.
12:57:31 And then that know in terms of effect on pH and for solar sending percentage wise it's similar Yeah, yeah, okay, but it's an absolute number that counts in terms of a Ph.
12:57:43 Yeah right here I'd be, I'd be glad to share those data with yeah I don't know the numbers aren't off my head right off in.
12:57:51 Okay.
12:57:54 And maybe related to this was the Stanley, you may only at A.
12:58:01 I did not ask them was a, you know, you said okay for me to stand to make, make a beautiful from acetate and and it is that, yeah, I tend to make.
12:58:28 I am a.
12:58:19 Yes. Um, so, again, I guess a broader question. So, what does it mean when I hear this kind of statements are not this type of a this final time to do this this file attention is so special about making butare versus making papaya night that it really
12:58:43 isn't that different. They organized at a final level.
12:58:45 Yep. What is so special about it.
12:58:55 Alfred What's so special about it, so deeply. It's the final level. Yeah, it's the sticky geometry of stimulating electron acceptor so to be rate reduction Janine sort of two pairs of f and g h for populate only one.
12:59:10 So it depends what the substrate is and the oxidative pathway.
12:59:15 What how the end product of an oxidative pathway is converted into an electron acceptor. In the case of appropriate, they are two strategies, actually.
12:59:27 So when the appropriate a probiotic acid bacteria grows slowly. They ferment glucose to procreate if they're growing fast, actually, you have lactic acid bacteria that use glucose to produce lactate, and then the niche of the provisioning acid bacteria
12:59:45 is on the lactate that is produced from these primary for mentors to produce putrid, but it's essentially a question of steak Yama tree. how many electron accepting reactions didn't need to promote substrate oxidized.
13:00:00 I put in this case, I think, it isn't a major carbon source acetate football.
13:00:07 No acetate is not a great source to make theater right it's it's it's it's still it's okay. Yes, it's so and and and the pathway to from.
13:00:20 So, if you produce acetate from glucose that's a very short pathway and depend, but it depends on the hydrogen partial pressure, the longer pathway is essentially the bit rate pathways so this is essentially a radio trade of thing that select for sort
13:00:38 of for from organisms with more shorter pathways that that's my thinking about that. Yeah, yeah. Likewise.
13:00:48 And so, Going back to the question or the fire.
13:00:52 And so you so is it is a known for these fire or just primarily organized, like, like that.
13:01:06 Yes, I mean that it has been mapped to the genomes.
13:01:10 So, yes, it's just that, like, what's the exclusion of okay so you take this populated list is that possible why not connect both pathway and express the genes on the way you need it.
13:01:30 That's a, that's a big question, Terry.
13:01:33 I mean, and you could say, well, they should carry the genes for resistant starch degradation to and just expressing when they need it so you kind of get another issue to me you need to you need to collect so many highlights incentives to to do things
13:01:47 but.
13:01:49 But the lower part I thought it would be easier to to collect the different.
13:01:53 Yeah, yeah, I don't, I don't know, I don't know what the best way is to think about that,
13:02:02 just just just one one perspective, which is sort of going back to the business plan metabolic business plan of the organism, which is reflected into sort of the file and why the genome probably more accurately which is, you know, a distinction of sort
13:02:18 of core metabolism which might consist of how an organism deals with Pirate Bay, do you have a pirate dehydrogenase or pirate production oxidizer abductees makes a huge impact for the stock geometry.
13:02:33 The question whether you have a venue or the organisms have bifurcating electron systems are not makes a huge impact what end products, produce. So, so my thinking is that if the core metabolism and then again the genome is constrained g sort of these
13:02:52 organisms in these high flex environments, typically need specialized so there is a core core metabolic core, and depending on you know what these core enzymes are, they are sort of a limited number of options metabolically what end products can be used,
13:03:09 and what can be funneled into the upstream part, based on accessing resources.
13:03:16 And that defines as I the way I think about it, and metabolic core and the business plan of an organism.
13:03:25 So, I have no problem with taking business plan and the organism okay this organization had this business plan that organism has bad business plan, I guess my problem is this business plan seem to be kind of a very restricted in its in changing as far
13:03:43 as a way to a tree.
13:03:46 And that's my ended Tom is the expert in that, that's fine the business plan of soil organisms is totally different than I've got microbes, because the flexes of substrates, both rate as well.
13:04:05 The type of compounds is so different in soil, and then in the gut inside you have low flux environments so therefore it has been pages for organisms to have a yield strategy which means long pathways, with low flux whereas in the gut.
13:04:19 Typically, you have high flux environments which selects for short pathways
13:04:29 me so.
13:04:31 Now go ahead.
13:04:40 Speaking Can you speak out loud. And my name is so I would like to ask about this soil, God difference so and and relate with a Titan is that we see a microscope he was at the start.
13:04:50 So, if I understood correctly in the gut to have this tight community why in the solemn is not this case.
13:05:04 No, so
13:05:04 I think that the flux of resources in soil typically doesn't provide doesn't produce that density of microbes.
13:05:10 But there are lots more surfaces. So, what would the micro graphs I've seen of so microbes as they're spread out on surfaces and less so like that ball of organisms I showed the to begin today.
13:05:27 But, in opposition is it fun biofilms that also they in this way that can also be close to each other, or they are more sparse.
13:05:40 Um, I mean I think a biofilms is more important in the soil.
13:05:58 Then, then the gut. I mean we don't have the surfaces so much in the gut for biofilms to form, but I'm not sure that's your question.
13:05:56 Yeah, some.
13:06:15 Thanks.
13:06:06 Well,
13:06:10 fellow metabolism aficionados unless there's some. Any other questions, please let's thank Tom again for this great stimulating talk, which tied in a lot of things together, so thanks Tom right thank you.
13:06:26 Thanks and happy to be here. Thanks for the invitation to you to come and see you next week. Good.