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The microbiome is a population of bacteria, fungi, protists and viruses that inhabit a specific environment. There are different microbiomes found throughout the animal digestive tract, each with important roles in animal digestion, feed conversion, overall health. Dr. Mallory Embree is the co-founder and CSO of Native Microbials. Her company has explored relationships between microbial populations and important animal production metrics. They have devised custom mixtures to supplement the diet, with positive results for animals, farmer profit, and enhanced sustainability.
Talking Biotech is a weekly podcast that uncovers the stories, ideas and research of people at the frontier of biology and engineering.
Each episode explores how science and technology will transform agriculture, protect the environment, and feed 10 billion people by 2050.
Interviews are led by Dr. Kevin Folta, a professor of molecular biology and genomics.
357 Optimizing Animal MIcrobiomes for Sustainable Production
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Kevin Folta: [00:00:00] Hi everybody. And welcome to this. Week's talking biotech podcast by collabora. Now the term microbiome's almost become a household word. It's this concept that you are more not you than you are. You that you're just simply a vessel for trillions of microbes that flourish in the rich diverse ecosystems of your.
so places like the mouth, skin, intestines, everything else, they all Harbor specific bacterial and fungal species that work with us. I guess sometimes against us in aspects of metabolism and sometimes pathogen suppression. Now microbial communities are complex and they're really coming into focus, uh, with new genomics tools.
So they're frequently the target of misinformation and even products that claim to affect the micro communities, uh, in order to affect aspects of health or function, or even seen ads for [00:01:00] mental acuity. So what's real and what's not. And I think today's guest gives us an outstanding look into how this can be used in really productive ways.
So today's guest founded a company to understand the microbiomes of animals and draw associations between population structure and animal health. With real hard data from those data, her company was able to identify specific microbes that aid in aspects of different parts of animal health, uh, maybe even increasing feed efficiency or even suppressing greenhouse gas in mission today, our guest is Dr.
Mallory Emry she's the co-founder in CSO of native microbials. Welcome to the podcast Dr. Em. Thank
Mallory Embree: you for having me.
Kevin Folta: Well, it really is a pleasure because I've wanted to have somebody on for a long time to talk about microbiomes, especially treatments, or I guess you would say supplements that are considered as probiotics and the products that [00:02:00] native microbials makes it makes intuitive sense to me, but it almost seems like a solution looking for a problem.
I mean, dairy production is doing great beef, swine poultry, breeders. The genetics are so good at getting animals to market weight fast. So. Do we have a problem that a probiotic can fix or maybe enhance the production in, uh, livestock?
Mallory Embree: Oh yeah, definitely. Uh, but that problem actually tends to vary a lot by animal species.
So some livestock animals, um, are very, very efficient, like you're alluding to right. Uh, chickens, especially the, uh, meat kind that are called broilers actually have a super insane feed conversion ratio. Right? Uh, we actually ran a study once where we just had regular co five hundreds, which is one of the, um, kind of industry standard, uh, bird species.
And they were just in a pen with no pathogen challenge, clean litter. Um, and the birds had a 1.2 FCR after 40. So that means [00:03:00] that they put on 1.2 pounds of weight for every pound of food that they ate, which is totally crazy. But that said, if you start to look at some of the bigger animals, especially the ruminants, they actually aren't that efficient with their feet.
So if you look at beef feed, lot animals, for example, they're at an average of six to one. So they'll need to eat six pounds of feed to put on about one pound of. Dairy cows on the other hand are measured a little bit differently. Uh, you actually look at pounds of milk produced per pound of feed, and they tend to be around 1.3 on the low end, up to about 1.7 to 1.8 on the high end.
Um, that doesn't sound like that big of a difference, but when you actually extrapolate those numbers out, Based on how much a dairy cow eats per day. It ends up being about 20 to 30 pounds difference in milk production between the lowest producers and the highest producers. So there's still a lot of room for improvement, um, in terms of feed efficiency for ruminants.
So if you look back at the animals that are [00:04:00] more efficient, right? Like chickens, uh, we're looking more at health and. So even though those animals have really good feed efficiencies, they generally don't achieve those numbers in the real world. Um, so genetics certainly plays a part in performance, but it turns out that the environment has an impact on performance as well.
Some people say it's up to 50%. Right. And so the microbes that we tend to look at for birds that are already very efficient are ones that help basically make the existing microbiome a lot more resilient so that the birds don't get as sick as often, which helps them actually achieve their genetic potential.
So
Kevin Folta: is that mostly for birds that are in these large? I don't wanna say feed a lot, but these large coop environments where they're raising broilers from chicks to full size birds in a, in a bio secure, um, barn, basically. Um, a hundred thousand birds at a time, or is this something that even, uh, that you may see some effect for someone who raises, you know, chickens or turkeys in a, in a small farm environment, it can
Mallory Embree: happen [00:05:00] to both honestly, right?
Because birds, um, they tend to pick up a lot from the environment as the microbiome establishes. And so it can happen in both environments. Uh, the one that we tend to focus on though, is that bigger, complex, right? With the tens of thousands of birds. Just because there seems to be a lot more disease challenge.
And
Kevin Folta: is it really just a question of disease or is it response to other types of stresses that can affect either growth or in the cases of layers? Um, egg laying that kind
Mallory Embree: of thing. It tends to be more disease, like, especially the GI diseases and, um, necrotic enteritis. In particular.
Kevin Folta: Okay. Yeah. And this makes a lot of sense in, in a way.
So you're talking about, because a lot of people don't know and I raise chickens, ducks, uh, turkeys and geese. So I'm a, I'm a poultry guy, um, at, at home, there's all kinds of, uh, complex microbiome that happens in the crop and in the gizzard and the different compartments that chickens. Many different, uh, birds use in processing their food.[00:06:00]
And so it kind of makes sense that each one of these would've a microbial community because we see chickens that get disorders of the crop and you can smell them and you can, you know, know something isn't quite right there, yeast, overgrowth, all kinds of stuff. So this is making good, intuitive sense to me.
Are there any other effects in things like ruminants, um, beyond feed
Mallory Embree: convers. So I think feed conversion is the big one. Uh, just because it's making more energy for the cow. And then once the cow has more energy that can then go have different effects, right? Like the big one that we're looking at obviously is milk production.
So can we help cows be more efficient with their feeds so that they ultimately make more milk and milk fat and milk protein, but we're seeing some other benefits in some of our studies as well. Like for example, we found that cows that were fed in the closeup period actually had better. Better quality colostrum as well, which was interesting.
And
Kevin Folta: colostrum being the first milk that's produced during lactation, uh, that primarily is used to feed the developing cabs, [00:07:00] right? The first things. Yep. It's just for the cab. And so here's the question I always have when we discuss this kind of technology, we're talking about microbiomes and, and, uh, your company being able to, I guess, breed specific types of bacteria and maybe other, uh, microbes that are supplemented with feed to aid in the conversion or the resistance to disease in the case of poultry.
But how do you know. What works, I mean, is it stuff that is supposed to be there and isn't because of the environment by which they're, you know, raised or is it something that you just thought was, okay, this would maybe make sense if we add it to what's already there,
Mallory Embree: dude. That's like the million dollar question in microbiome, right?
Like that's what everybody wants to know. And so our take on it. Like, yeah, we weren't animal scientists. Um, yeah, my background, I never studied dairy cows before. And so we like going into it didn't necessarily know what microbes were the most important [00:08:00] in a room, for example. And I guess to back up even further, like, I guess the entire hypothesis that our company was built on, right.
Was that basically, if you look at dairy cows, right? Like you have populations within a herd that are more efficient and less efficient with. Right. And gosh, cows have been bred to just be more and more productive over time. And so their genetic background is pretty homogeneous, like, especially compared to humans.
Right. And so we were hypothesizing that this. Difference in production was coming from differences in the microbiome. Um, and so what we ended up doing there is we actually went out and collected Ru samples from lots of cows. So we went to commercial herds. We went to universities, we worked with, um, contract research organizations and we basically collected room samples from cows so that we could actually try and figure out what microbes were the most.
I. . Um, and so in the da, in the case of dairy cows, it [00:09:00] wasn't necessarily that the cows were deficient in a particular microbe, right? Like cows are super dependent on their room and microbiomes to give them the energy that they need. Like, you actually can't make a germ-free cow. Like a cow would just not exist without its room and microbes.
And so there's some base functionality that always exists within the microbiome. So what we were looking for there was actually, um, just what. Microbial differences existed between the more efficient and less efficient cows. Um, and so we decided to choose the microbes that appeared in the more efficient animals to then turn into a product.
Um, in the case of some of our more health oriented products, like we talked about chicken, but we're also developing probiotics for dogs, as well as. And so there, the microbes for our dog product are, um, intended to treat and prevent chronic uropathy, um, and bad bouts of diarrhea for equine. It's all about colic.
So treatment and [00:10:00] prevention of colic in horses. And we took a similar approach there as well, where we actually surveyed, um, the Fe season intestinal content of animals to kind of get an idea of what healthy looked like. And it turns out in those cases. Basically generally adult microbiomes are very, very stable, right?
And this is kind of true across all animals, including humans. And typically you'll get this major dysbiosis that happens if there's like a major diet change, or if the animal goes through some sort of disease and ends up taking some me. So in the case of companion animals, we found that animals that tended to have these kind of more severe chronic GI issues just couldn't rebuild their microbiomes.
So it was more of a deficiency in that case. So we kind of found these microbes that were lacking, that were preventing unhealthy animals from getting back to that healthy state. And we decided to turn that into a [00:11:00] product so we could kind of help. I guess achieve the healthier microbiome.
Kevin Folta: Okay. So then here's the other million dollar question is the deficiency in the microbiome because the animal's sick and then you, you have a screwed up microbiome or is it that you have a deficiency in the microbiome that leads to the illness?
Mallory Embree: I think it kind depends. Um, I think was,
Kevin Folta: is it totally chicken or the
Mallory Embree: egg yeah, it's totally chicken and egg. It really, really depends. It's hard to say, like, if you just kind of look at how. Microbiomes develop. Right? Like having these successions of different microbial communities is totally normal. Like you expect some change, um, like let's say for example, there's a dog it's totally healthy and then gets on antibiotics.
Right? Like that's certainly something that can impact the microbiome and have like a permanent change that kind of sets the animal's health on a downward trajectory. Right. So, so it really just depend.
Kevin Folta: That's a [00:12:00] really interesting question. Now, when you, when let's go back to ruminants, because we're talking about, uh, cow Rus, uh, could you describe what that Ruen is just for people who maybe aren't familiar with, how livestock digest.
Mallory Embree: Yeah, totally. So dairy cows and beef feed, lot animals, and even like goats, for example, uh, they're all considered ruminants because they have a specialized stomach called the Ru. So this stomach is pretty much the first one in the GI tract, and that's where all of the microbes live, the ones that actually enable them to break down, um, their feed into usable energy for the animal.
So it's just this specialized organ. Um, yeah. Where all of the microbial diversity tends to live.
Kevin Folta: Yeah. And, and this isn't nearly as harsh of an environment as the stomach itself, right? This is actually a place that, um, where a lot of the digestion of things like fibrous, grasses and stuff really starts to occur in that room.
Mallory Embree: Exactly. Yeah. The pH is a lot higher. [00:13:00] Um, Yeah. And if you actually look at room content, like it's still a very, very grassy looking like it looks like feed that's being broken down.
Kevin Folta: it's smelly too. I've actually gotten to look at one of those cows that has the hole in the inside of it. Oh, nice. Like a
Mallory Embree: cannulate animal.
Kevin Folta: Yeah. Is that what they call it? cannulate. It sounds so much better than with the window in the side.
Mallory Embree: you get to your entire arm?
Kevin Folta: Um, I, I didn't take the opportunity to do that, but, um, I, I, I did, uh, get to see what was in there and smell what was in there. And, um, it, it really is amazing that there's this entire supp chamber that evolved inside ruminants that really provides this first step that allows them to really start to break down these more harsh, uh, feeds that they, that they consume.
And how do you, are there any real similarities across species or are they all really D. Uh, in terms, in terms of the microbes that are present.
Mallory Embree: Oh, I see. Yeah. [00:14:00] So if you look at ruminants, right, if you just kind of group all ruminants together, there are certain similarities in particular kingdoms. Like the Ruen fungi actually tend to be very, very similar.
Um, you'll see the same species like popping up in all ruminants, for example. Don't believe we know if they're truly different though, just because not all of them have actually been isolated and genetically sequenced. Right. So we can't compare them on the genome level quite yet, but there's certainly similarities just because the room, like, whether it be in a goat or a dairy cow, right.
Ultimately has the same function. Right. So it still needs this, uh, microbial population that can actually break down feed. So there's certain similarities that they must have. Um, if you were to compare like the Ru of a dairy cow to the small intestine of a chicken, it's totally D.
Kevin Folta: Yeah. So how do you know what's right though?
And this is like the question you have these different compartments in different [00:15:00] animals, different maybe developmental stages of life, um, maybe, you know, ill or not ill, whatever, but how do you know you have the right combination of microbes? Is it really just a bunch of tests to see who does best in the presence of specific introduced, uh, bacteria or fungi microorganisms?
I should.
Mallory Embree: I mean, ultimately that's what you have to do, right? Like you have to do some sort of animal study to actually corroborate this effectiveness that you're saying that these microbes actually have, but we try to improve our chances of that by actually doing that initial survey experiment, where we actually go out and sequence a bunch of, um, microbiomes from animals, just to give us a better shot at coming up with the right combin.
Kevin Folta: Yeah, so you're, so it is really intriguing to me. So you're going on your you're looking to see who's there, uh, in terms of microorganisms, in terms of the animals that are high performers and the ones who are low performers for specific trait, and then, um, assuming causality that the [00:16:00] microbiomes are, what's making the animal, not the other way around.
So you're going into an animal's, uh, digestive tract and kind of sequencing what's present in different chambers in high performers and low performers and kind of making inferences to which species of microorganisms are most beneficial in these different compartments. And I, I guess I'm kind of starting to see how this, this could work.
You said we've been going with the term microorganisms. Are these just bacteria? Are they bacteria? And you mentioned fungi before, but what kind of mix is. Oh man.
Mallory Embree: So when you say microbiome broadly, that's gonna include bacteria, fungi produce viruses, right? Like basically every kind of microorganism. Um, if you look at the actual research though, it's definitely biased towards bacteria.
When we study microbiomes, we tend to look at bacteria and fungi just because there's a lot more, um, I guess, manufacturability there, like those have the most, uh, [00:17:00] they're the most feasible for us to actually create and turn into a product.
Kevin Folta: and how did you end up going down this path? I mean, it seems like a, in a way, an obvious one, but also a really risky one because it, it, it seems like, you know, maybe you get a little bit of a change here and there, but it does, you know, maybe wouldn't be like a, you know, profound difference to start a company on how did you get there?
Mallory Embree: Yeah. Um, so I guess it was kind of a gamble for us, right? Cause you never really truly know if a product's gonna take off. I think for us what we did. Me and my co-founder Mike, right. We kind of looked at the industry like the dairy industry in particular. And one really interesting thing that we noticed was that dairy farmers today actually feed a lot of microbes.
Like they feed a lot of Sacra SIA, for example, and some of the other kind of generic grass microorganisms that you'll find in your yogurt. Hmm. Um, and I guess me coming from an anaerobic microbiology [00:18:00] background, right. The scientific community already knows that the room is super important for digestion in cows.
Right. So we just wanted to see if we could find better microbes that would help the cows more than some of these more traditional direct fed microbials.
Kevin Folta: Yeah. When you say grass microbes, you mean GS, right? Yes. Like the general
Mallory Embree: nicer face.
Kevin Folta: Yes. Yeah. I just wanted to make sure, cause we're talking cows and they eat grass and the other beautiful part about this and you, and that really, you can.
Maybe appreciate as a listener, uh, to the podcast is that, uh, the cost of feeding animals is getting excessively high. And if you could save a, a farmer or rancher, 5% mm-hmm , it would be a big score. So what kind of, uh, Changes. Do you see
Mallory Embree: we had no idea what to expect, right? Like when we were first starting the company and when we first did our trials, we weren't even sure if it was gonna work honestly.
Um, but today we have a product that [00:19:00] we're commercializing. So we've done a number of animals studies with academics, and we have one product that we're currently selling. That's just comprised of four native room and microbes, uh, that we had to isolate in our labs. And we're finding that when. Dairy farmers feed it to lactating dairy cows.
The cows end up making about six pounds more energy, correct. And milk per cow per day. So it's pretty significant.
Kevin Folta: No, that that's really impressive. So we're speaking with Dr. Mallory Emry, she's the co-founder and chief science officer at native microbials. And we're talking about probiotic, bacteria, and fungi and microorganisms that can be introduced into feed, to influence different traits in livestock.
This is the talking biotech podcast by collabora, and we'll be back in just a moment. Now we're back on, Cora's talking biotech podcast. We're speaking with Dr. Mallory Emry, she's the co-founder and chief science officer at native [00:20:00] microbials. And we're talking about probiotic supplements that are available now for helping livestock.
And now it turns out. As you say, companion animals, your dogs at home to aid in digestion and digestion translates into feed, conversion and health and, uh, larger animals. And then, uh, maybe some benefits to our dogs at home as well. So I'll play devil's advocate. Um, a lot of people would look at. Uh, this as, um, tinkering with nature.
And, and I hear it every day that we talk about anything from chemistry to genetic engineering. People don't like it because you are, you know, you're intervening in a place that you just let it go, let nature sort it out. So how do you convince the average consumer that this is a good idea. Mm-hmm, ,
Mallory Embree: it's actually not that hard.
So over like the past 10 years or so. Right? Like once we really understood how good microbiomes. right. Like, there's been all this data just showing how important all these microbes living in us are to health. Um, it [00:21:00] already has this really positive connotation, right? Like it's really easy for consumers to kind of understand that what we're doing right.
Is just looking at what a healthy microbiome looks like. We then go into the microbiome and actually isolate out the strains in our products. Right. Because you can't actually buy these microbes. I don't know, like some sort of culture collection, right? Like they just don't exist there. Um, and then we just feed it back to the animal.
Right. So we don't do any sort of genetic modification. We're not evolving the strains in a way. We're literally just isolating them from the animal and then growing them up and then feeding it back to the animal.
Kevin Folta: Is that the toughest part? I mean, isolating it and figuring out how to make it grow.
Optimally.
Mallory Embree: Absolutely. So it. Like microbiome. I feel like the there's so much focus just on doing the sequencing and understanding the microbes and looking at mechanism, but it turns out [00:22:00] that most of the microbes that actually live in microbiomes are considered uncultured. So this means that there is no isolated representative of that species.
Right. And this kind of happened just because, um, like when sequencing really took off, right. Uh, scientists just started sequencing every sort of sample just to see what microbes were there. And eventually the sequencing data just completely outpaced the microbiology mm-hmm . So we knew all these microbes were there, but that's kind of where microbiome stopped.
Just because there wasn't anything that you could do past that because there was no microbe to actually do experiments with. Um, so for us, like once we did these survey experiments, right? Like once. Sequenced all of these room samples from dairy cows. We knew what microbes that we wanted. Right. But we just had to go in and isolate them ourselves, which is a lot easier said than done.
Um, and so we have some proprietary methods that we [00:23:00] use to actually get out the microbes that we want. Um, and then from there we have to do a lot of fancy formulation to actually ensure they can be delivered back to the. As you can imagine. A lot of the microbes that we work with are actually Aros. So they don't like being in the atmosphere.
Right. Like oxygen kills them and so we have to build in some protections for them to make sure that they actually have a shelf life.
Kevin Folta: Yeah, that's something that I don't think the average person listening might appreciate is, you know, you're taking something that really loves to live in the toasty, warm gut lining of, of, of a, of a mammal or a bird.
And now you're asking it to grow in a Petri dish or, you know, a culture vessel yes.
Mallory Embree: Grow in the steel tank. Do great. yeah,
Kevin Folta: it. It's really true. I mean, it's really is a challenge to this entire thing. . And I guess when I, when I, when I think about that, I start to think, you know, how do you, how do you know you get the right [00:24:00] one?
I mean, there's so many thousands of things that are present there. How do you, you know, is, I mean, I guess you just have to keep sequencing and isolating, right?
Mallory Embree: Yep. That's exactly what it is. So usually when you're looking at bacteria, you'll sequence, a gene called the 16 S R RNA gene. It's one that, um, is basically used to identify bacteria.
On the fungi side, you use a gene called the its gene. And so you'll use any sort of sequence similarity there to actually assign taxonomy and confirm that it's the microbe that you're actually looking for.
Kevin Folta: Yeah, that's the, the, its the internal transcribed space or the ribosomal repeats. Right. And so you're, this is what's so funny back in, I think 2008, 2009, we sequenced J we did a really comprehensive sequencing of, um, some plant material and.
We found this mountain of 16 acid bacterial genes. Um, and the guy who was working with our bioinformatics at the time said, we're gonna throw all those out. Just filter that stuff out. I said, no, you keep that stuff. because [00:25:00] it doesn't just tell us about the plant. It tells us who's living on the plant.
Yeah, exactly. And well, we, we ended up publishing a, uh, it was like the last figure in the paper, a total throwaway. Of these are the pathogens that are resident and the things that are resident on this plant. Even though we weren't having seen disease, we had evidence of the pathogens being there. And it probably was the, I don't know if it was one of the first microbiome papers in plants or, or figures, but for us, it was just a total afterthought and I could have made a career out of it.
totally swung and missed. . Well, um, one of the things that we see, um, in your literature is this idea of founder effect. And what is that when we speak of microbial supplementation?
Mallory Embree: Yeah. So when you're looking at the founder effect, um, this is more relevant for chickens, right? Just because, um, basically chicken farming is kind of an assembly line, right?
Like you'll have eggs, they all hatch it. Once the birds kind of go down. Almost car wash, where they're sprayed with a bunch [00:26:00] of different additives. Um, and then they're transported to the complex, right? And so since they're kind of not in their natural environment, right, they're not able to pick up some of these more maternal microbes.
And so this founder effect becomes a lot more relevant. Uh, it basically means that the first microbes that kind of get into the GI system, those are the ones that colonize and kind of set the trajectory of the microbiome develop.
Kevin Folta: Yeah. And I guess this is important, as you mentioned in this kind of a pipeline, because it's a sterile operation where they basically are sexed and then, uh, usually sexed and then, um, vaccinated and then go through this process where they get to a very highly bio secure environment.
That's probably relatively devoid of. Uh, bacterial or microbes that they naturally would encounter when hatching under mom. Mm-hmm exactly. Yeah. So, I mean, it's, it's, it's a really interesting thing. So do you have, uh, or is it a target to start to think about ways to develop that [00:27:00] foundational microbiome in, uh, developing chicks?
Mallory Embree: Absolutely. Cause we're finding that has one of the biggest impacts on the final microbiome. You kind of have to think about it as a path, right? Like the animal's gonna go through all these major successions throughout its life, especially at feed changes in the case of chickens. And so the more that you can do to kind of influence the starting spot of the microbiome, the more control you're gonna have over where it ends up.
And so that's absolutely one strategy we're taking there. Um, another thing that we're actually looking at is calves. So baby cows, um, and trying to figure out what microbes are important for room
Kevin Folta: development. Yeah. And, and most of those are coming from the mother in colostrum and milk. Right. So is that something that you look at, or is it strictly, uh, you looking at the animal itself rather than the, uh, feed?
Mallory Embree: Yeah, we're absolutely looking at feed. So. [00:28:00] The calves are supposed to get colostrum. Right. But not all of them do. Some of them will actually get a colostrum replacement. Right. Which is kind of more like a synthetic milk. Um, the important process that we're really focusing on though is actually weaning.
So once the calve starts receiving grain, there's a lot of changes in the room in that, um, seem to really impact health outcomes of the.
Kevin Folta: No really good. And so, so what other, uh, animals are you working on? I know that I look at your website and I saw things on they're like salmon and like, how, how broad does your company's targets go?
And can you give us a little sense of a pipeline?
Mallory Embree: Yeah, so ultimately like our goal is to get onto all relevant livestock and companion. So, of course we have a dairy product we're working on beef feed, lot animals as well. Uh, we have the chicken product that we're working on. It's primarily for broilers today, but we're also looking at layer applications.
So the [00:29:00] egg-laying chickens, uh, products that we're working on, um, for the future includes swine products. We've done a little bit in salmon and I'll tell you right now that the ocean scares me. the ocean introduces a lot of weird things into the microbiome. Are hard to control. Um, and then again, on the companion side, we're looking at X, Y, and N dog products.
Kevin Folta: Yeah. I guess in, uh, salmon farming, the big one is your SEIA. Like you actually, the microbe that leads to the PLA uh, plague, right? That you use a significant amount of antibiotics to control. Uh, some of these potential really, uh, um, potentially dangerous pathogens in fish.
Mallory Embree: Exactly. So again, there'd kind of be more of a health play to see what sorts of microbes we can find to make the animal microbiome more resilient.
Kevin Folta: Yeah. And I, I get the idea of this founder effect too, in that the founder effect, if you have something that colonizes a specific niche of the, of the. Uh, digestive system or [00:30:00] skin or leaves or whatever, you find a microbiome, you have something that's there and taking up space and growing and, and competing for resources.
It's less likely that something is detrimental can come along and colonize. Is, is that true?
Mallory Embree: Yes. No, completely true. And you can think of it too. Like it's important to have the founder. Microbes there just because when the microbiome does go through a, a big dysbiosis, right? Like maybe you get sick and you have to take a bound of antibiotics.
These are the microbes that are basically gonna rebuild the microbiome after that. So it's important that they're there.
Kevin Folta: Well, how are, and I, and I know that you have a couple of, of. Products that are already available. Um, I think one for one for, uh, cattle and one for dogs maybe is, and, and how are those, I guess what's the consumer response so far or the industry response?
Mallory Embree: Yeah, no. So it's been very, very positive so far. And so we work pretty closely with the dairy farms that are on our product, just to show that the product's actually working, [00:31:00] um, that they have improved digestability, which of course is really important now with feed costs, um, on the dog side, where. Doing really, uh, controlled case studies in individual dogs and basically seeing how Archis helps them rebuild the microbiome.
So it's pretty
Kevin Folta: cool. Yeah. Archis is the, or what, that's the name of the, of the product, right? Of the product. Yes. Yeah. The micro blend. Yeah. That's and you also have one for chickens, correct? Yeah. So these things are available and people are using them and farmers and ranchers are tough customers that are cheap and very, um, Careful.
And so if you're selling these products, they must be doing okay. And what are some of the biggest changes that you're seeing from the field in terms of, is it feed conversion and disease resistance as before?
Mallory Embree: Yeah, so it's on the milk production side basically on the, and yeah, so it's. It's one of those things where like, yeah, farmers can be cheap, but they're all very much driven by data.[00:32:00]
Right? Like they understand the numbers. And so as long as we can kind of go back and show them like, Hey, you are making more money because you're making this much more milk on. This much less feed. Um, everybody seems to be happy with that.
Kevin Folta: Yeah. I shouldn't have said cheap. I should have said shrewd investors.
right. Because they'll spend money. If they know they're gonna get value for it, if they're gonna get return on that investment, I'm married one. So I know how it rolls. Um, but, uh, what about the idea of, you know, the outside looking in the farmer and the end consumer is great, but you have to have social license to be able to operate, take it from any of the companies that have done genetic engineer.
How can you up appeal to ideas of sustainability and, and the ways that these products can enhance sustainability on the farm
Mallory Embree: mm-hmm right. So especially on the cattle side, right? Like they get a lot of attention from methane, right. Because there's these big populations of meth antigens that actually live in the room in, and as the [00:33:00] cow is digesting her feed, right?
Like she'll just be making more met. Um, and so one of the things that we're actually doing is we are testing for emissions on our products. There's this pretty cool methane measurement system called the green feed system where like, basically you'll put cow cookies in it and the cow will go stick her head in this machine.
And you can actually measure all of the different gases that are produced. Um, we've actually run a study like that for our beef feed lot product. And we found that emissions are reduced anywhere from 20 to 30%, which is pretty. um, On the dairy side, we are actually running that study right now, but we have sequenced the meth Angen populations in cows that are on our product, and we are seeing a reduction in the metogenic population.
So we're hoping that translates to a reduction in the missions
Kevin Folta: as well. Wow. That's really cool because you can, so many people have pointed a finger at cattle farming and said, you know, or ranching, uh, or cattle raising and have said, you know, this [00:34:00] is a huge place of greenhouse gases. So if you can cut it by 20%, but the number of cows that are around the world, that's pretty huge.
Absolutely. So tell me more about that pipeline. We touched on it briefly. What, what are some of the things that the future holds.
Mallory Embree: Um, so I guess one cool thing that we're actually developing is actually the next iteration of the dairy product. Um, so if you kind of look at the life of the company, right?
Like we started like seven and a half years ago. Right. And everything was still a hypothesis. We were developing our platform and we're trying to see if we could even create. Like this advanced probiotic, basically. Right? And so the first iteration of our dairy product was just two microbes. They were the ones that we had isolated that, um, seemed to be the most manufacturable.
So there, we were able to kind of advance them to that manufacturing stage pretty quickly. And so that kind of became the first iteration of the product. [00:35:00] Uh, while we were working on that product, we were trying to get additional microbes through that manufacturing pipeline, just to figure out how to scale them.
Um, eventually we got two more and so that's the current product that we're selling now, GLS frontier. And that's the one that's improving milk production by about six pounds. Um, now that we've been around for a while, right? Like we've carried many more microorganisms through this manufacturing pipeline and we're coming out with the third version of the product , which now has seven microbes in it.
And, um, I'm hoping that there's gonna be a fill of inches fungus, which happens to be like one of my favorite. Microbes that we're handling. And, uh, yeah, we're actually gonna put that one into trial next year. So we'll see how it does.
Kevin Folta: Oh, I hope your favorite works out for
Mallory Embree: you're so weird. Like these Phil OUS fungi are totally crazy.
They only live in Rus, like, first of all. Right. So they're this very, very [00:36:00] niche species and they're pretty understudied. Like, honestly, there's only three labs in the world that even study these microbes and. It's kind of funny because like they're starting to isolate them and genome sequence them. Right.
Like, along with all the other microbes in the microbiome. Right. But, uh, it's kind of like they're having a taxonomy dual like, everybody wants to name it first. So I feel like every time I pull up a image is fungus paper. Like someone's reassigned the microbes to a totally different gen that they've made up.
um, so it's like the wild west right now. It's pretty cool. Yeah. I don't even know what to call my favorite pH images, fungus. So ,
Kevin Folta: what are the odds that there's something out there that's yet to be discovered that could be a real benefit yet, you know, or you know, something that maybe would never naturally occur inside the digestive system, uh, from the animal itself, maybe something that comes from the plant, you know, it's is there still exploration [00:37:00] going kind of laterally that way?
Mallory Embree: Oh, absolutely. No, there's so much exploration going on in the microbiome. Like there's so many uncultured microbes that have never been studied that yeah, that that's absolutely something that could happen. It's totally feasible.
Kevin Folta: Well, this has really been interesting. I, I guess maybe the other question that, um, before we wrap up is one of the big criticisms back when we talked about, um, like yogurt or, uh, human microbiome supplements, these things that they would sell.
And a lot of people were very critical saying, well, we know that these bacteria, um, even though they're being delivered, maybe in spore form, they never di they never survived the digestion of the. We talked about Rus and crops and how these are all upstream of the real harsh environments. But how do you get something into say a small intestine?
Mallory Embree: Yeah, definitely. No, it requires specialized formulation. Like you, like, I feel like it's [00:38:00] an area that's kind of. Underdeveloped right. Just because maybe it's not as sexy as sequencing microbiomes. Right. But it's absolutely something that's relevant. Um, you have to make sure that the microbes have some sort of wax protection around them in order to actually make it through the stomach.
Right. Like, cuz as you're saying, like the pH of the stomach is so low to kind of stop pathogens from getting in. Right. Um, so it requires a lot of formulation. To actually, uh, get to the intended
Kevin Folta: target. Yeah, that's the question that always comes up for me is, is how do you get it? Where it belongs mm-hmm
And so that one, you know, seems really obvious, but maybe something a little less obvious would be how are microbiomes different between two very similar types of organisms. So we talked about dairy cattle versus beef cattle, and it would seem like. You know, these two would probably be almost identical, but is really that the case.
Mallory Embree: And so one of the things that we've actually discovered, that's super [00:39:00] interesting. So dairy cows, um, like they typically live for several years, right? Like they go through several lactation cycles. And so the diets that they're on tend to kind of reflect that. So they have a lot more forage in it. There's still some grains so that they get a lot of energy, but it tends to be very.
So now, if you look at their counterpart in beef feed, lot, for example, like they're still ultimately the same animal species, but they're managed in a completely different way. You'll on a beef feed lot. You're basically finishing the animal and bringing them up to their final weight. And so farming their involves basically feeding them a lot of grain.
So these animals will be on 90% concentrate diets, which is, uh, what people call hot diets. Right. Just because they're so highly ferment. And the interesting thing that we found there is that the microbiome completely gets flipped on its head. So instead of kind of being this nice balanced ecosystem where there's a lot of [00:40:00] forages being digested that then get fermented into different volatile fatty acids, it's completely skewed towards the VFA direction, right.
Just cause there there's no fiber for the microbes to the gray. And so because of. There tends to be some weird biochemistry that happens. And, um, I guess if you look this up in literature, right? Like this over fermentation of grain, all these hot diets is usually called acidosis, right? Just because the room will basically drop in pH right.
To a point where the microbes actually stopped functioning. And traditionally this, this disease was believed to be brought about by an accumulation of LACT. The idea being that black kid accumulates, and it just drops pH faster. When we did our research, we found that that might not be the only thing that's actually happening.
So we think that as the microbes are fermenting, all of the highly fermentable grains in the [00:41:00] diet they're of course making all these volatile fatty acids, but they're also making carbon dioxide. And so in the room in, um, basically it's buffered by. Right, which also involves CO2. And so as more and more CO2 accumulates, it basically ruins the buffering ability of the Ruen, which then makes the entire system even worse.
Right? Like, it's kind of like this hill that just keeps getting worse and worse. And I guess what I'm trying to say is like, ultimately like. There's this cascade that starts to happen where the pH is. Totally. I balanced the microbes are basically swimming an acid, and I have this hypothesis that they're actually starting to go into solve pathogenesis.
Like they're actually flipping over and making ethanol. Cause they're trying to find some way to actually kind of offload all these electrons that are being generated in their metabolism. And this is actually something that we just started to kind of delve into and we have some compelling data. That shows that there actually isn't an [00:42:00] ethanol accumulation.
Um, I guess my pet project is, I think this is actually happening in humans, too, right? Like with a Western diet, it's, it's kind of the same idea, right? Like it's obviously different because we're mono, gastrics compared to a ruminant, but on Western diets, you're kind of eating these rapidly fermentable diets.
And I have a suspicion that it's going down the same path and ultimately ending up in salve.
Kevin Folta: Well, very, very interesting stuff though. I mean, it's really interesting because here you're looking at essentially animals that are highly related yet have two very different sets of microbiomes that really are shaping to fit the diet they're given.
Mallory Embree: Yeah, exactly. And ultimately, right. Like it's not just about the microbes. It's more important. Like the chemistry that they're actually doing. Right. and then how that chemistry intern impacts the. um, so it's kind of looking into those sorts of weird relationships. Um, [00:43:00] and I think the one thing that's actually overlooked a lot is that livestock's actually a pretty good model system.
People that study microbiome of humans tend to struggle a lot just because humans have this diverse genetic background, we eat different things every single day. And all of these things will impact the microbiome composition, which makes it an absolute nightmare to study sometimes. Um, like I think, uh, what's his name?
I think Dan Knights actually did this study where he was just trying to track all of the D. Human parameters like blood measurements, metabolism, measurements, everything. Right. And he wanted to see how the microbiome was related to these things. And in this study he actually had some soil controls. So there's some poor student that had to go and only eat soil
Yeah. And there were a couple of them and they found that even the soiling controls had different microbiomes. Right. Which is [00:44:00] crazy. But, um, If you look at livestock though, they actually have very homogeneous genetic backgrounds, right. Because of breeding. Like chickens are literally just like a clone army and they eat the same thing every single day.
So the microbiome data is actually very, very clean and relatively
Kevin Folta: stable. No, that's really, it is really interesting. And I'm really appreciate you kind of enlightening me on the topic a lot because I. Never really knew much about it. And I always kind of never wanted to dig in because it seems like a tremendous rabbit hole that once I start going into microbiomes, I'll never come out and it just seems like that to me.
So so Dr. Mallory Emry, uh, thank you very much for your time today. And if, oh, do you have a, uh, website or place you could direct people if they wanna learn more about your product?
Mallory Embree: So our website is www.nativemicrobials.com. And, um, yeah, anybody can go visit that website to kind of see what products that we're putting together.
[00:45:00] Um, the email for us, if they wanna get more information is info@nativemicrobials.com.
Kevin Folta: Very good. Well, thank you very much for joining me today. I really appreciate it. And I hope as things go on you keep us in mind and come back and talk about the next big breakthrough. Cool. Thank you. And as always, thank you for listening to another week of the talking biotech podcast.
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