The Bat Microbiome: Part of the Bacterial Ecology Puzzle with Dr. Jack Gilbert

Richard Jacobs: Hello. This is Richard Jacobs with the Finding Genius podcast, the health, medicine, and bioscience edition. My guest today is Professor Jack Gilbert at the University of California, San Diego. As part of the Scripps Institution of oceanography, we’re going to be talking about bats and their microbiome and that is a very, very diverse organism and more species of them than maybe all other organisms. I don’t know. But we tend to Harbor a lot of nasty viruses whenever and I guess there are microbiomes that are super interesting. So that’s all we’ll talk about. So, Jack, thanks for coming.

Jack Gilbert: My pleasure. Great to be here.

Richard Jacobs: So why do you study bats?

Jack Gilbert: Well so this is work that came out of one of my postdoctoral fellowship incumbents called Holly Lutz. And Dr. Lutz was a Ph.D. who is interested in exploring the association between microbes and host conditions in various environments. And one of the things she was most interested in was bats in Africa. And the basic paradigm was to try and understand what was really going on between bat health. The ability of bat to survive and whether the microbes that lived in and on them could be playing a role in. And so the, it’s of interest because, you know, bats as you say, are a hotbed for viruses, but they’re also under a huge amount of pressure in various parts of the world due to encroaching human activities. The reason we see them as a reservoirs potential disease. So we were interested to understand if the microbes present inside bats played any role at all and the physiological lifestyle and how they survive.

Richard Jacobs: So what’s interesting and unique about the microbiome of bats?

Jack Gilbert: What’s fascinating from our viewpoint is that led to an entire, another suite of work, which was published again just recently that allowed us to see that bats and other flying animals such as birds or bats as one of the few flying mammals had a very specific adaptation that potentially was uniquely positioned for flight. A lot of this could be seen physiologically. You know, bats and birds are very short guts. We have a very long gut. It goes, you know, has a very convoluted intestinal length, right? Whereas they’ve got some very short and it looks like they haven’t evolved very, very tight associations between their bacteria and their bodies. We have very tight associations. Bacteria in our bodies provide a huge amount of nutrients and services to our body that can be fundamental to maintaining health or fundamental to recovering from the disease. Whereas in the bats, they have definitely impacted by the types of environments they did. But we think that might be more due to the fact that whatever they’re exposed to, whatever place they live in has different types of bacteria. If you live in a dry environment versus a wet environment, different species of bacteria are going to thrive. And that it’s that environmental contamination of their bodies, which shapes what kind of bacteria live on them. Now our bodies are, many mammals and many other species of animals are much more prescriptive in what they allow to live inside them, whereas bats and birds appear to be much less prescriptive.

Richard Jacobs: Well, when you say that they’ve short gut, does that mean transit time is shorter or the number of processes that the food they eat goes through is less?

Jack Gilbert: Yeah, it’s mean both of them really, I mean, it’s just shorter generally. So physiologically if you compare the length of our gut to our size mass and you did the same for a bird and a bat their guts would be significantly shorter. It’d be like if we were missing about 75% of our intestine. So, they have a very, very short gut physiologically, physically that it’s very short, but that leads to the food having a very short retention time. So it’s consumed and then heads out and it’s differentially absorbed. So they are getting a lot of their calories from rapid absorption of that food energy very early on and they’re relying a lot less on the bacteria in the colon to break it down and ferment it, which makes sense if you think about what they eat, they eat a lot of highly sugary or high fat and protein-rich foodstuffs, right. Insects or fruits. And so those sources of food have a huge calorific energy value, but they’re also able to be processed by the host without much need of further processing by bacteria to really gain much out of it. So there are multiple stages.

Richard Jacobs: What about the environment that bats are in? I mean in their cage or wherever they hang out and she needs to be in close contact with all their feces. That creates one environment and then when they venture out and now they’re in a completely different environment, its air currents and fresh air and every day they’re exposed to those two extremes, at least. Does that affect how their microbes interact with them?

Jack Gilbert: Potentially? We literally don’t know the answer to that. I mean it’s an interesting suggestion that microbes might go very rapid turnover in these animals. It’s very difficult to capture the same animal that multiple times in the day and determine what its microbiome might look like. One would assume that once all organisms have colonized it in the environment in which you grew up they will maintain their position. So it’s not like the organisms are likely being flushed out. A new one’s turning up all that. It’s just more likely that whatever environment they grow up in which shape or what organisms can colonize and live on them. But once those organisms colonize the bat it’s more likely that they’ll stay there. Even if they’re not necessarily physiologically advantageous for the bat. However, we don’t know. We don’t know if they are physiologically advantageous to the bat. And there’s some work that Holly Lutz is working on right now, which may suggest that the bacteria that live on the skin of the bat can change whether it’s susceptible to ectoparasites. And obviously, if you have more ectoparasites, parasites living on the outside of your body you are Morris sicker, right? You have more disease. So it’s possible that the bacteria on the skin of the animal may be playing a role in that relationship.

Again, a lot more work is needed to understand that.

Richard Jacobs: The echolocation, tissue organ on a bat, has anyone looked there to sample and see if there are microbes associated with it? Cause it’s just an unusual organ. I wonder if it attracts unusual bacteria.

Jack Gilbert: Maybe we don’t have any information on that at all. But yeah, those are the kinds of questions which are very interesting to me.

Richard Jacobs: So what sort of the studies that you conducted to observe that really informed you a lot about curiosities and bad places to look at?

Jack Gilbert: Well this is our first foray into bats. We’ve done a lot of work or most of our work is in humans and the environments that humans interact with. We’ve also done working Komodo dragons and in different animal and plant species around the world. And in fact, the world itself, the largest survey of microbial diversity on the planet, the earth microbiome project. So, you know we investigate microbes and how they interact with each other and how that interaction shapes the environments around them. Whether the environment is the ocean or a human intestine or the skin of a bat, it makes no difference to us. We are interested in how those microbes are playing a role in shaping their world.

Richard Jacobs: Well. What are some of the commonalities and how microbes interact that you think are really informative for people?

Jack Gilbert: I think for people generally, I think the biggest commonality is probably how they respond to environmental nutrients. What is the potential for us to be able to shape microbes in any environment by altering the availability of their food. You could say this is the same for the soils of a corn crop as it would be for our intestine by understanding how we can selectively promote the growth of specific organisms. We could change the productivity or disease resistance of a crop of corn or maize. Just as we could change the ability of a human to survive infection by promoting the growth of bacteria, which would make them less susceptible. Microbes play a huge role in human health, crop health, animal health, and we’re just starting to uncover ways that, whereby we can manipulate that microbiome in order to have the biggest impact upon human health.

Richard Jacobs: You mentioned that the microbes and bats are in a tiny bound is in humans, for instance. What does that mean?

Jack Gilbert: Well, that means in humans, certain bacteria have almost evolved to live inside us. The environment they are most adapted to is our gastrointestinal tract. Whereas in bats and birds, the same does not appear to be true. They do not peer to have bacteria that have evolved to live inside their bodies. And so it’s part of our eco-evolutionary relationship with the world. That shapes the kind of organisms that have grown up alongside us as a species. And you know, many other mammals and other species. So it’s an interesting potential adaptation to the flight that birds and bats have reduced their reliance upon bacterial symbiosis in order to have this special magic trick up their sleeve of being able to hop on the wing and fly away.

Richard Jacobs: How do you know when evaluating a bacteria, whether it’s been, it’s only able to live in this creature that doesn’t exist in other places?

Jack Gilbert: Right. I think the opportunity for organisms to play a role in shaping the ecological health of any kind of community and the environment around them and the role that plays in the health of the animal is a cornerstone of most of our understanding. However, there are lots of lots of different animals and species out there and we are only just starting to understand the potential implications of microbial exposure and microbial ecology inside these animals and their role in helping those animals to survive.

Richard Jacobs: Can you tell that a certain bacteria has altered itself to live in one midst of one creature versus being able to live in many?

Jack Gilbert: No, not always. No. I mean the adaptation of a particular organism to an environment is shaped by a myriad of factors. But there are certain species of bacteria that we’ve observed in the human intestine, for example, or in the Ruman of a cow or even a termite that is highly selected for survival in that environment. And also those many of the adaptations of the host seemingly tied towards being able to manage and manipulate the microbes that interact with the host. Good case is our immune system. We think of more of as an army out to wipe out the bugs. But there’s definitely a suggestion that it’s probably more like a national park or a ranger or a gardener. It’s there to manipulate and manage the garden of bacteria that live in and on an organism like us. So when you look at the whole organism, the host and his microbiome, we can start to see traits that are evident that help us to see that there was co-evolution, that the organisms in our body have evolved alongside us and that both our species and then adapted to each other.

Richard Jacobs: So what kind of commonalities have you seen? You said you looked at Komodo dragons, bats and people and cows. What are some of the big similarities?

Jack Gilbert: Well, big similarities. The fermentation of plant products is the biggest similarity in most mammals. You know, mammals, on the whole, aren’t very good at degrading plants and we don’t really have enzymes, proteins that munch up of the proteins that are capable of degrading plant man. So our bodies are the same as a cow or a chimpanzee or even a termite, have adapted to have an evolutionary relationship with the bacteria or series of bacteria, which can degrade plant. So we can actually get nutritional ad fund advantage out of that plant.

Richard Jacobs: Okay. So the degradation of plants. Any other commonalities that are surprising?

Jack Gilbert: Well, there are many different ones. A more specific than that. So certain vitamins like vitamin B12 can be synthesized by certain bacteria and that appears to have a commonality in lots of different ones. We could be here all day if we started to get into the potential commonalities of the mammalian gut microbiome.

Richard Jacobs: Well, the reason I ask is I always hear about people’s gut bacteria very rarely than other animals. So since you look there, you know, what else have you learned? I mean, what are some of the really surprising differences?

Jack Gilbert: Oh well, the differences are really akin to the physiology of the gut system. You know, remember from biology that cows have four stomachs for example. And you know, we don’t have, we have one stomach and then a long complex gut. The relationship between the different types of bacteria that survived and those different animal species and ourselves are more akin to what we are evolved, what we have evolved or adapted to consume. We’re on the bowls. If you look at the guts of cats for example, who are carnivals, their microbiota are very different from ours and so is their gut physiology. The microbiota are more revolved to ferment protein, whereas ours are more evolved to be able to ferment fiber from plants. And the same for cows and termites for example. So it’s a, yes. Pretty broad.
Richard Jacobs: Okay. so bats, is that a new focus for you and then is it a big focus or is it just, you know, they’re interesting and we’re looking at them as well.

Jack Gilbert: We’ve published two papers on it. One ourselves and one in collaboration with someone else. It’s a small focus for our lab. I’m really driven by Holly. She’s the primary lead PI behind that program. But our lab deals who say with microbes and virtually every environment on earth. So, it’s pretty diverse.

Richard Jacobs: So when a creature eats another creature, you know, a bat eats an insect, or if I eat, you know, a piece of meat or something, you know, if it’s cooked, probably there’s most of the microbes that were associated with it are gone. But, you know, animals don’t eat cooked food for the most part. So like when a bat eats an insect, what do you think happens with the insect’s microbiome versus the bats when it eats it? Or maybe another creature that doesn’t have a very short gut, a longer one. What do you think is happening? What kind of interaction is there?

Jack Gilbert: Well, for the most part, the number of microorganisms present in the food would be so tiny compared to the number of microorganisms already present in the guts of the animal that was during the consuming. It would be like dropping a potted plant in the Amazon rain forest and hoping for it to survive, thrive and take over. It’s not ecologically or competitively adapted to that environment. So it’s very unlikely it will have much of an effect at all. The same is true for things like probiotics and the majority of the time where we take a probiotic when you’re healthy. It excretes quite rapidly. For the most part. We don’t see colonization by the probiotic. So yeah, I mean, it’s unlikely that when we consume the microbiome of another animal that it will play much of a role in shaping our own. But there could be examples or exceptions to that rule that we haven’t yet understood. We’ll see.

Richard Jacobs: You know, the food itself, if you eat a certain diet, it can dramatically change your appearance and maybe cause dysbiosis, et cetera. I guess it’s the food itself doing it, not the microbes in it, but I just wondered how much the effect of microbes have if they have any,

Jack Gilbert: I mean, you remember the food is shaping what bacteria live inside you, right? So not necessarily which ones are inside you right now, but the proportions of the different species which are already inside you. So if you fed your garden different type of fertilizer, you might get different types of plants becoming more dominant over time. The same is true for your gut. So if you eat different types of food over time, it will change the types of microbes that dominate. But on the whole, the organisms which live inside you colonize you very early on. And realistically you’ve just been changing the proportions of the membership, not necessarily the composition of the membership. Right. And that’s an important thing to understand. Yeah. The food is definitely playing a role in your physiology because you absorb the nutrients and that plays a role. But how microbes interact with the food also plays a role in your BCT and potentially depression and anxiety and immune state and many other even cardiometabolic disease states. So we have to consider not the separation of the host and the microbiome, but its response in combination.

Richard Jacobs: Makes sense. Any other learnings that you’ve gotten from, you know, it’s a good thing you’ve studied the microbiome of so many different animals and different scenarios. I mean, how do you feel like you’re bringing those learnings to play now and looking at-bats?

Jack Gilbert: Well, I guess that’s just another part of the puzzle. I mean the second paper that we published recently was designed explicitly to come to try and understand why we saw such differentiation in bats. Bats appeared to be different. So we compared them to the microbiomes of ground-based and other flying animals and found that indeed there are more commonalities in the differences between flying animals and grounded animals than there are necessarily between the different species. And that’s interesting. That helps us to do meta-analysis or comparative analysis, which can shape our understanding of how microbes have adapted to living to multicellular organisms that live around them. Remember, this is a microbial world for the first year to 3 billion years. So only really in the last 500,000 to 500 million years, sorry, that the multicellular life has taken off and is having such a big impact. So, you know, microbes have adapted to using us as a resource and, and there’s been a lot of co-evolution so it’s interesting to be able to do those kinds of comparisons.

Richard Jacobs: So what’s the best way for people to see what you’re doing and if they can read the papers, but at least you know, see what your research is about? Where can they find you?

Jack Gilbert: Oh, I’m all over the place. Really. You’re talking to my name on Google. I’m not the dead poet. But the best place to find out literature is Google scholar. But we also have a website gilbertlaboratory.com which has some information about the people that work in the lab and the kind of work we do.

Richard Jacobs: Well, Jack, thanks for coming on the podcast. I appreciate it.

Jack Gilbert: My pleasure. I have a lovely time. Thank you very much.