protist fermentation:
an interview with eli gerrick
recorded december 2021Elisa:
I’m really excited to talk to you Eli, because you are introducing us to a
definition of fermentation that is not often discussed– usually when we talk
about fermentation it is in the context of food. But I’ll let you start. What
is fermentation?
Eli: Yeah, thanks! I’m sure there are a lot of definitions of fermentation depending on what you are talking about. But the one I am going to be focusing on is that fermentation is just the production of energy from carbohydrates in the absence of oxygen. When we are talking about fermented food, we are forcing the microbe to eat carbohydrates in the absence of oxygen, which is why we ferment things in an anaerobic environment. Then the microbes generate all these waste products because fermentation is an inefficient process, and that is what is creating all the fun things in out fermented foods like alcohol.
Usually when we think of fermentation we are talking predominantly about fungi and bacteria. What I want to talk about today is a different type of fermentation because it is not happening to food outside of the body that we then eat, and it is not done by yeast or bacteria. I want to talk about is fermentation by a different group of organisms called protists, and it is going to be fermentation that is done inside of the body, of food that has already been ingested.
E: Cool! So what are protists? Tell us a little bit about these guys.
Eli: I guess the scientific-y definition would be single-celled eukaryotes. But an easier to digest definition would be (it’s going to be a longer definition too) unlike humans, unlike plants, every single entity is a single cell, so in a lot of ways people tend to think of them almost like bacteria, because bacteria are also unicellular organisms. But protists are actually more closely related to humans than they are to bacteria, so super super different from bacteria. They are an entirely separate part of the tree of life. Protists are also super diverse, so it is hard to have one definition for them, because there is a ton of different lineages of protists, they are all over the world, they are inside of organisms, and they live free in the environment.
Most people have probably heard about protists but don’t know they have. A lot of infectious diseases are caused by protists, but a lot of people think it is just bacteria. For example, Plasmodium falciparum, the pathogen that causes malaria, one of the most deadly infectious diseases, is a protist. There is also sexually transmitted diseases that are caused by protists like Trichomonas vaginalis. A lot of diarrhea is caused by protists. Most people have heard of Giardia, which is why you don’t drink stream water when you go hiking. That’s also a protist. So protists are super important for our lives and people hear about them all the time but don’t realize that they are so different from all these other organisms that we talk about like bacteria and yeast.
E: Interesting. So if we want to picture a protists, what do they look like? And how big are they compared to bacteria and yeast?
Eli: Good question. So protists are a lot bigger than bacteria. I read somewhere that for scale purposes, if a bacterium has human sized, protists would essentially be the size of an elephant. So they are a lot bigger, which also makes it really exciting that they have been largely ignored in a lot of ways in parts of the scientific sphere. In terms of what they look like there is a lot of variability. Some of them are the most boring things I have ever looked at, where it is just a ball. Microscopially speaking it’s a big ball but still microscopic and it’s just a sphere. And then other ones, particularly the ones that I like to study, are very cool, they look like little aliens. They are essentially these teardrop shaped things that have a dorsal fin going along one ridge of their body, and they have these little spindly arm that they use to swim in a breaststroke style to get where they want to go. So they are very cool alien looking things. But some of them are also very boring. So lots of diversity in what they look like [laughs]
E: Maybe I’ll find a link that I can add so people can check out what they look like if there are photos out there.
Eli: Yeah, because describing it is hard and insufficient
E: It just sounds like an alien...
Eli: The link will probably look like that too...
As I mentioned a second ago, protists are typically thought of as parasites, as bad. They cause disease in humans. And honestly there is a good reason for that: most of the ones that people studied initially were parasites. So people discovered that there are these diseases causing protists like Plasmodium and Trichomonas and Giardia, and all of these cause infectious diseases. Then people started identifying other protists, and they were trying to figure out what disease they caused and they couldn’t. So people stopped studying them at all. It turned out that the reason nobody could figure out what disease they caused was because they were actually commensals, or members of the microbiome that don’t cause disease. They can actually be beneficial for the health of the host, and that’s only recently coming to light. That’s the paradigm the lab I’m in, Dr. Howitt’s lab, is trying to push and what I am really interested in.
E: Are there additional limitations as well? Culturing them is really hard, sequencing, et cetera. Why did it take so long to identify protists?
Eli: In terms of identifying them, it is both harder and easier than bacteria I would say. The way that most people look at identifying new bacteria at this point is by sequencing, where they will sequence a part of DNA that all bacteria have. The part of the DNA that is used for that type of sequencing doesn’t exist in protists, and so all these all these techniques that we use to find new species of bacteria are completely blind to protists. In that way protists are harder to look at. But you can see them really easily under a microscope whereas bacteria you can’t. That’s something we learned to do in our lab: whenever you are looking at a mouse (which is the model we use) you always just check it to see if it has protists, which is a lot easier than if you had to find a specific kind of bacteria.
But I think this lack of sequencing approaches makes it much more difficult to look at protists. And as you mentioned, growing them is also insanely difficult and so that also makes it a lot harder. The field is definitely behind in terms of comparing it to a lot of bacterial studies.
E: So you mentioned it is part of the human microbiome, but it’s also part of the gut of other species, right?
Eli: Yes, yes. So, it’s funny. I love how scientists always do this, but I just mentioned that nobody studies protists as part of the gut microbiome, everyone was just like ‘they are either parasites or nothing,’ and that’s how people looked at them. But actually protists are found in the microbiome all over the animal kingdom now. Where they were originally really studied as members of the gut microbiome was in termites. People studying termites have known that protists are members of the microbiome of termites for like 40 years, and it was only in 2016 that people studying mammals were like “Oh, it’s part of the microbiome.” And so we are all saying this is a new idea but it’s totally now, we just don’t listen to the entomologists!
[laughs]
But the protists in the microbiome of termites is really interesting because they serve a super critical role in the microbiome of termites. Fermentation by these protists is incredibly important for these termites, and also for earth in general because termites are really important for the carbon cycle, which is where animals like us make carbon dioxide when we breathe, and then plants like trees take that carbon dioxide from the air and turn it into sugars through photosynthesis and then when the plant dies, the carbon dioxide needs to be released. Trees are notoriously hard to digest. If you eat bark you cannot digest it, and that is true for most animals. What’s really interesting is that termites are one of the few animals that can digest wood and break down trees, but the termite itself can’t do that. Termites don’t encode all of the genes required to break down wood. It’s actually the protists in the microbiome of the termite that can break down the wood and turn it into energy. Basically, if you have a termite that doesn’t have protists in its microbiome, that’s a dead termite because it can’t eat.
The way that protists are breaking down all this wood is actually through fermentation, fermenting the wood into something the protists can eat, and also making something that the termite can eat. So it is this symbiosis where the termite gives wood to the protist, and the protist turns the wood into energy for both of them.
E: Interesting! That’s super cool. It’s crazy how termites are know for breaking down wood, but they are actually dependent on another organism that lives in their gut to do that. And how co-dependent these species are. What is a termite without a protist?
Eli: Yeah, exactly. I think that’s a super interesting framework to look at. For better or for worse that is not the case in humans. Most people in industrialized countries do not have protists, so we obviously aren’t as co-dependent on these organisms as termites are. But it is still really interesting to think about just how important protists can be for the life of animal hosts in both a parasitic sense where they can kill you if they cause disease, but also in a symbiotic sense where they are helping you live. Termites are definitely the most reliant on their protists of any animal in the animal kingdom that we know about. But protists are also super widespread in microbiomes. It’s something that I think is super interesting, that these fermentative protists are everywhere... people have looked in birds and they are in birds, people have looked in mammals and they are in all types of mammals, people have looked in mice, humans, cats, dogs, and all these have protists.
Something that I am studying, which other people are looking at too, is that protists are even widespread in reptiles. Just to get an idea as to how diverse and widespread protists are we have a collaborator, this awesome scientist named Tim Colston, who goes around the world and swabs the cloaca of reptiles. The cloaca is the universal hole in reptiles that serves lots of reproductive and waste excreting functions.
This project actually started in my living room because I have a tortoise and she had protists in her microbiome. Now we are looking at reptiles from the Steinhart Aquarium in San Francisco, reptiles in Ethiopia, reptiles from Columbia, and trying to see whether or not they have protists and see what type. What is really exciting is that most reptiles we see seem to have protists in their microbiome. It seems to be almost a universal fact of life on earth is that you have protists in your microbiome, which is exciting because people (unless you’re a termite person) didn’t realize that until recently, and even a lot of scientists and microbiome scientists still don’t appreciate the importance of protists in the microbiome.
E: Have you been looking more at identification and characterization of these novel protists, or have you also been looking at function?
Eli: Yeah, great question. First we are just looking at the identification, diversity and prevenance of them. It’s unfortunately really hard to look at function of protists and reptiles because we don’t have a good model system. There is no reptile version of a mouse that we can stick them into and study the effects on the immune system. We are trying to do some functional studies on a couple of protists that we found in reptiles to understand more about their biology and the effects they might have on the host, and we have already found some interesting things. For example, as we mentioned, fermentation is the breakdown of carbohydrates in an anaerobic environment to create energy, and so you would usually think that herbivores, which eat lots of carbohydrates, would be the main ones that would have these protists or fermentative organisms in their guts. What is weird is that we are finding the same species of protists in my tortoise that lives in my living room as a carnivorous snake that comes from the jungle in Columbia. It’s just sort of highlighting what we know about what these things are doing, what they are eating, what they are fermenting. You wouldn’t assume that snakes and tortoises have similar nutritional inputs, and so we don’t know what these protists are eating and what they might be doing to the host. But we are hoping to potentially shed some light on that.
E: Right. Protists are also found in the environment, so I would assume that given how ubiquitous and diverse protists are, there would be greater protist diversity between the tortoise in your living room and an Amazonian snake? Are there core prostist microbiome species that are found across all guts?
Eli: Yeah, yeah, absolutely. There must be something about these that makes them well adapted to live in the gut microbiomes in general, regardless of what the host is doing or the lifestyle of the host. And that’s of course something we still don’t know, but it’s a really interesting question.
E: And have you done any comparisons of gut protists across different host species? So protists found in the gut microbiome of mice, birds or reptiles. Are they all within the same order, genus... what is the taxonomic grouping?
Eli: Oh! Yeah so they are in the same… they are definitely in the same phylum. The group of protists that I study are all in the same phylum or sort of evolutionary lineage. There are certain lineages that are found in mice versus humans versus reptiles. But that same lineage of protists is found in microbiomes all across the tree of life, which is particularly exciting.
E: Interesting. To get back to humans, you mentioned they are mostly gone in the western gut? What do you think that says about gut microbiome research? We are mostly focused on bacteria in the gut microbiome and how it’s different between industrialized and indigenous populations, but what about protists? What is the impact of protists on gut health?
Eli: Yeah, I think it’s a super interesting questions. Something that is always talked about in terms of the rising incidence of these inflammatory diseases like inflammatory bowel disease, allergies, asthma and stuff like that is lack of diversity in microbes that we are exposed to in the western world, and how that might be partially explaining the rising instance of these diseases. Bacteria is always focused on because there is a huge decrease in diversity between members of the microbiome between someone from the western world compared to someone with a more traditional lifestyle. But there is a difference between the types of bacteria and the species and maybe the number of those bacteria, but for protists it’s more of a binary answer. Most people in the western world just don’t have any protists. It’s not “Oh, we have less diversity of protists, we have fewer numbers of them.” No, it’s more like “We don’t have any.” And so, the potential impacts that those could have on our immune system development or predisposition to inflammatory diseases could be pretty huge. It also could obviously be nothing [laughs], we don’t know yet. I think there is definitely potential for it to be a factor.
One of the things I think is really interesting about that, or that sort of lends credence to that, is some of the work that was done by my advisor on this one species of protists in mice called Tritrichomonas muris. This protist is a very common member of the mouse microbiome, and as it’s fermenting the fiber that the mouse eats it creates a waste product that then signals to the mouse’s immune system to start prepping for fighting a worm. Even though the protist is not a worm, and the anti-worm immune response from the mouse does not harm the protist at all, it’s still this signaling back and forth between the two that causes the development of an anti-worm immune response.
The reason this is super interesting in terms of thinking about the microbiome and the development of all these diseases like allergy and asthma in westernized populations is that one of the prominent ideas as to why these diseases are occurring is that there is a lack of natural stimulators of the allergic immune response. In immunological terms, the allergic immune response is the same as the worm fighting immune response. People think that lack of exposure to parasitic worms is what is causing a lot of these diseases, and in fact some experimental therapies for inflammatory diseases like types of inflammatory bowel disease is to give people parasitic worms to try to trat the disease. What might be really interesting is instead of giving you a parasitic worm, you could just have a protist in your microbiome, so you wouldn’t be having diarrhea, growth stunting and everything that comes with having a worm. Also it’s gross. Instead, maybe just having a more diverse microbiome, especially with protists, that could help prevent the onset or the predisposition of people to these diseases in these countries.
“This protist is a very common member of the mouse microbiome, and as it’s fermenting the fiber that the mouse eats it creates a waste product that then signals to the mouse’s immune system...this signaling back and forth between the two that causes the development of an anti-worm immune response.”
E: Do you know if whether in countries that have higher rates of parasitic worm infections there are also higher rates of protists commensals in the gut microbial community?
Eli: That is a great questions and one I wish we knew the answer to, but not yet. It’s something that I think a lot of people are interested in—or “a lot” [laughs] in my small sphere of science a lot of people are interested in, so I think I will be answered before too long. Right now we have no idea because as we mentioned earlier the types of sequencing approaches we use to look at protists are so different from what we use to look at bacteria, and so it’s just been sort of a blind spot up until this point.
E: In your experimental models, how easy is it to successfully have protists become part of the gut microbiome community? I guess what I’m getting at is how easy would it be for someone to start a protist probiotic company? [laughs]
Eli: No, I think that’s a really good question and something that I think is so exciting about protists as members of the gut microbiome. There is this thing in microbiome research called ‘colonization resistance,’ where let’s say you have a microbe you want to put into a gut microbiome, there is a good chance if you try to put it in it won’t be able to establish itself as a member or a long term member of the microbiome, because there are already all these microbes in the gut microbiome that outcompete it. And so that can be true for a lot of bacteria and stuff, if there is already a microbiome in, let’s say, a mouse which is where people usually look at this. But what is exciting about these protists is that this is not the case. If we take mice that we breed ourselves or order from the vendor and we try to put one of our protists in, 100% of the time the protists easily just become a long-term member of the gut microbiome. And so because there doesn’t seem to be this colonization resistance it could potentially be relatively easy to put protists in mice or people for therapeutic purposes.
What we don’t know yet is whether the reason that we can so easily put these protists in mice is because they don’t have any other protists, and so maybe if you already have a protist that would prevent you from having another one. But since most people in western countries don’t have any, that shouldn’t be a problem. You know, for example I’ve screened my whole lab including myself and my wife for protists and all of us are negative, so they are very, very uncommon.
E: Interesting. Do you think part of that is just a sampling issue, since you are using stool as a screen? That if you were to take a sample from the small intestine directly, you would see protists? Since in mice you use the cecum to check for protists, not the stool…
Eli: Yeah, yeah, the stool is usually not a good indicator of what the composition of the small intestine is because there is so much of the downstream colon that’s there. But, if there is something that only lives in the small intestine you’ll still pick it up in the stool because in this case, shit literally flows downhill, so everything from the small intestine makes it into the stool. So I wish there was a caveat that said I still had a protist because I obviously really wanted one, but I’m pretty sure that I don’t [laughs]
E: That’s really interesting. I’m also assuming no one screens for protists when doing fecal transplants? So there could be a super protist donor out there?
Eli: I don’t think so. But I wouldn’t be surprised if someone had accidentally transferred protists through a fecal transplant, just by chance.
E: What is the treatment for pathogenic protists in humans?
Eli: Oh great question! A lot of them are treated with this drug called metronidazole, which essentially just kills anaerobic organisms, which are organisms that don’t use oxygen for energy production, so, ones that ferment things. These drugs will kill parasitic protists like Giardia, but they will also kill the commensal protist in the gut microbiome. A lot of things could have contributed and likely contribute to the fact that humans in western countries don’t have protists. One of them is obviously hygiene because most of these things are fecal-oral transmission, but one of them could also just be that we have used drugs to kill all of them and never got them back.
E: Are they also transmitted in the same way as the gut microbiome through vaginal birth and skin contact?
Eli: Probably, yeah. Hard to say for sure with the protists, but since they do go fecal-oral it wouldn’t be surprising. In mice it’s a large way in which they transmit it. Mice eat their own poop, or the poop of their friends, the original fermented food. That’s not a great model, but presumably [in humans] it’s vaginal birth and just breaks in hygiene that would cause transmission.
“Mice eat their own poop, or the poop of their friends, the original fermented food”
E: Cool! What do you think are the changes that there are protists that play a role in food fermentation?
Eli: I looked this up before the interview! I was pretty sure there were no protists involved in fermenting foods, and it looks like no. I did find one thing saying that seaweed is a protist, but then again the definition of protists keep changing. Some website (that I don’t remember how reputable it was) was saying seaweed is technically a fermented food because it’s used in fermentation a lot. But I think that it’s more that you are fermenting protists and eating them, and not the other way around. So I don’t think there are any protists involved in actually doing [food] fermentation.
E: I was wondering since they are so common in water that maybe you get some when you are making a brine or something...
Eli: Yeah, so I guess what I’ll say is that it is unlikely that current fermented foods use protists, but I bet we can do it if you want to…
E: Use some stream water to ferment some foraged greens from the side of a river...
Eli: Yeah, we can do something like that. Make some protist kombucha or something…
E: Interesting... protist kombucha...that would be cool. That’s just a cool name, protist is a cool word...
Eli: It is a cool word, it would definitely be a good marketing ploy.
E: Definitely great marketing! Is there anything else you want to share?
Eli: I don’t think so.
E: Well, thank you so much Eli, it was great chatting with you!
Eli: Yeah, thanks! I’m sure there are a lot of definitions of fermentation depending on what you are talking about. But the one I am going to be focusing on is that fermentation is just the production of energy from carbohydrates in the absence of oxygen. When we are talking about fermented food, we are forcing the microbe to eat carbohydrates in the absence of oxygen, which is why we ferment things in an anaerobic environment. Then the microbes generate all these waste products because fermentation is an inefficient process, and that is what is creating all the fun things in out fermented foods like alcohol.
Usually when we think of fermentation we are talking predominantly about fungi and bacteria. What I want to talk about today is a different type of fermentation because it is not happening to food outside of the body that we then eat, and it is not done by yeast or bacteria. I want to talk about is fermentation by a different group of organisms called protists, and it is going to be fermentation that is done inside of the body, of food that has already been ingested.
E: Cool! So what are protists? Tell us a little bit about these guys.
Eli: I guess the scientific-y definition would be single-celled eukaryotes. But an easier to digest definition would be (it’s going to be a longer definition too) unlike humans, unlike plants, every single entity is a single cell, so in a lot of ways people tend to think of them almost like bacteria, because bacteria are also unicellular organisms. But protists are actually more closely related to humans than they are to bacteria, so super super different from bacteria. They are an entirely separate part of the tree of life. Protists are also super diverse, so it is hard to have one definition for them, because there is a ton of different lineages of protists, they are all over the world, they are inside of organisms, and they live free in the environment.
Most people have probably heard about protists but don’t know they have. A lot of infectious diseases are caused by protists, but a lot of people think it is just bacteria. For example, Plasmodium falciparum, the pathogen that causes malaria, one of the most deadly infectious diseases, is a protist. There is also sexually transmitted diseases that are caused by protists like Trichomonas vaginalis. A lot of diarrhea is caused by protists. Most people have heard of Giardia, which is why you don’t drink stream water when you go hiking. That’s also a protist. So protists are super important for our lives and people hear about them all the time but don’t realize that they are so different from all these other organisms that we talk about like bacteria and yeast.
“Protists are also super diverse, so it is hard to have one definition for them, because there is a ton of different lineages of protists, they are all over the world, they are inside of organisms, they live free in the environment”
E: Interesting. So if we want to picture a protists, what do they look like? And how big are they compared to bacteria and yeast?
Eli: Good question. So protists are a lot bigger than bacteria. I read somewhere that for scale purposes, if a bacterium has human sized, protists would essentially be the size of an elephant. So they are a lot bigger, which also makes it really exciting that they have been largely ignored in a lot of ways in parts of the scientific sphere. In terms of what they look like there is a lot of variability. Some of them are the most boring things I have ever looked at, where it is just a ball. Microscopially speaking it’s a big ball but still microscopic and it’s just a sphere. And then other ones, particularly the ones that I like to study, are very cool, they look like little aliens. They are essentially these teardrop shaped things that have a dorsal fin going along one ridge of their body, and they have these little spindly arm that they use to swim in a breaststroke style to get where they want to go. So they are very cool alien looking things. But some of them are also very boring. So lots of diversity in what they look like [laughs]
E: Maybe I’ll find a link that I can add so people can check out what they look like if there are photos out there.
Eli: Yeah, because describing it is hard and insufficient
E: It just sounds like an alien...
Eli: The link will probably look like that too...
As I mentioned a second ago, protists are typically thought of as parasites, as bad. They cause disease in humans. And honestly there is a good reason for that: most of the ones that people studied initially were parasites. So people discovered that there are these diseases causing protists like Plasmodium and Trichomonas and Giardia, and all of these cause infectious diseases. Then people started identifying other protists, and they were trying to figure out what disease they caused and they couldn’t. So people stopped studying them at all. It turned out that the reason nobody could figure out what disease they caused was because they were actually commensals, or members of the microbiome that don’t cause disease. They can actually be beneficial for the health of the host, and that’s only recently coming to light. That’s the paradigm the lab I’m in, Dr. Howitt’s lab, is trying to push and what I am really interested in.
E: Are there additional limitations as well? Culturing them is really hard, sequencing, et cetera. Why did it take so long to identify protists?
Eli: In terms of identifying them, it is both harder and easier than bacteria I would say. The way that most people look at identifying new bacteria at this point is by sequencing, where they will sequence a part of DNA that all bacteria have. The part of the DNA that is used for that type of sequencing doesn’t exist in protists, and so all these all these techniques that we use to find new species of bacteria are completely blind to protists. In that way protists are harder to look at. But you can see them really easily under a microscope whereas bacteria you can’t. That’s something we learned to do in our lab: whenever you are looking at a mouse (which is the model we use) you always just check it to see if it has protists, which is a lot easier than if you had to find a specific kind of bacteria.
But I think this lack of sequencing approaches makes it much more difficult to look at protists. And as you mentioned, growing them is also insanely difficult and so that also makes it a lot harder. The field is definitely behind in terms of comparing it to a lot of bacterial studies.
E: So you mentioned it is part of the human microbiome, but it’s also part of the gut of other species, right?
Eli: Yes, yes. So, it’s funny. I love how scientists always do this, but I just mentioned that nobody studies protists as part of the gut microbiome, everyone was just like ‘they are either parasites or nothing,’ and that’s how people looked at them. But actually protists are found in the microbiome all over the animal kingdom now. Where they were originally really studied as members of the gut microbiome was in termites. People studying termites have known that protists are members of the microbiome of termites for like 40 years, and it was only in 2016 that people studying mammals were like “Oh, it’s part of the microbiome.” And so we are all saying this is a new idea but it’s totally now, we just don’t listen to the entomologists!
[laughs]
But the protists in the microbiome of termites is really interesting because they serve a super critical role in the microbiome of termites. Fermentation by these protists is incredibly important for these termites, and also for earth in general because termites are really important for the carbon cycle, which is where animals like us make carbon dioxide when we breathe, and then plants like trees take that carbon dioxide from the air and turn it into sugars through photosynthesis and then when the plant dies, the carbon dioxide needs to be released. Trees are notoriously hard to digest. If you eat bark you cannot digest it, and that is true for most animals. What’s really interesting is that termites are one of the few animals that can digest wood and break down trees, but the termite itself can’t do that. Termites don’t encode all of the genes required to break down wood. It’s actually the protists in the microbiome of the termite that can break down the wood and turn it into energy. Basically, if you have a termite that doesn’t have protists in its microbiome, that’s a dead termite because it can’t eat.
“Basically, if you have a termite that doesn’t have protists in its microbiome, that’s a dead termite.”
The way that protists are breaking down all this wood is actually through fermentation, fermenting the wood into something the protists can eat, and also making something that the termite can eat. So it is this symbiosis where the termite gives wood to the protist, and the protist turns the wood into energy for both of them.
E: Interesting! That’s super cool. It’s crazy how termites are know for breaking down wood, but they are actually dependent on another organism that lives in their gut to do that. And how co-dependent these species are. What is a termite without a protist?
Eli: Yeah, exactly. I think that’s a super interesting framework to look at. For better or for worse that is not the case in humans. Most people in industrialized countries do not have protists, so we obviously aren’t as co-dependent on these organisms as termites are. But it is still really interesting to think about just how important protists can be for the life of animal hosts in both a parasitic sense where they can kill you if they cause disease, but also in a symbiotic sense where they are helping you live. Termites are definitely the most reliant on their protists of any animal in the animal kingdom that we know about. But protists are also super widespread in microbiomes. It’s something that I think is super interesting, that these fermentative protists are everywhere... people have looked in birds and they are in birds, people have looked in mammals and they are in all types of mammals, people have looked in mice, humans, cats, dogs, and all these have protists.
Something that I am studying, which other people are looking at too, is that protists are even widespread in reptiles. Just to get an idea as to how diverse and widespread protists are we have a collaborator, this awesome scientist named Tim Colston, who goes around the world and swabs the cloaca of reptiles. The cloaca is the universal hole in reptiles that serves lots of reproductive and waste excreting functions.
This project actually started in my living room because I have a tortoise and she had protists in her microbiome. Now we are looking at reptiles from the Steinhart Aquarium in San Francisco, reptiles in Ethiopia, reptiles from Columbia, and trying to see whether or not they have protists and see what type. What is really exciting is that most reptiles we see seem to have protists in their microbiome. It seems to be almost a universal fact of life on earth is that you have protists in your microbiome, which is exciting because people (unless you’re a termite person) didn’t realize that until recently, and even a lot of scientists and microbiome scientists still don’t appreciate the importance of protists in the microbiome.
E: Have you been looking more at identification and characterization of these novel protists, or have you also been looking at function?
Eli: Yeah, great question. First we are just looking at the identification, diversity and prevenance of them. It’s unfortunately really hard to look at function of protists and reptiles because we don’t have a good model system. There is no reptile version of a mouse that we can stick them into and study the effects on the immune system. We are trying to do some functional studies on a couple of protists that we found in reptiles to understand more about their biology and the effects they might have on the host, and we have already found some interesting things. For example, as we mentioned, fermentation is the breakdown of carbohydrates in an anaerobic environment to create energy, and so you would usually think that herbivores, which eat lots of carbohydrates, would be the main ones that would have these protists or fermentative organisms in their guts. What is weird is that we are finding the same species of protists in my tortoise that lives in my living room as a carnivorous snake that comes from the jungle in Columbia. It’s just sort of highlighting what we know about what these things are doing, what they are eating, what they are fermenting. You wouldn’t assume that snakes and tortoises have similar nutritional inputs, and so we don’t know what these protists are eating and what they might be doing to the host. But we are hoping to potentially shed some light on that.
E: Right. Protists are also found in the environment, so I would assume that given how ubiquitous and diverse protists are, there would be greater protist diversity between the tortoise in your living room and an Amazonian snake? Are there core prostist microbiome species that are found across all guts?
Eli: Yeah, yeah, absolutely. There must be something about these that makes them well adapted to live in the gut microbiomes in general, regardless of what the host is doing or the lifestyle of the host. And that’s of course something we still don’t know, but it’s a really interesting question.
E: And have you done any comparisons of gut protists across different host species? So protists found in the gut microbiome of mice, birds or reptiles. Are they all within the same order, genus... what is the taxonomic grouping?
Eli: Oh! Yeah so they are in the same… they are definitely in the same phylum. The group of protists that I study are all in the same phylum or sort of evolutionary lineage. There are certain lineages that are found in mice versus humans versus reptiles. But that same lineage of protists is found in microbiomes all across the tree of life, which is particularly exciting.
E: Interesting. To get back to humans, you mentioned they are mostly gone in the western gut? What do you think that says about gut microbiome research? We are mostly focused on bacteria in the gut microbiome and how it’s different between industrialized and indigenous populations, but what about protists? What is the impact of protists on gut health?
Eli: Yeah, I think it’s a super interesting questions. Something that is always talked about in terms of the rising incidence of these inflammatory diseases like inflammatory bowel disease, allergies, asthma and stuff like that is lack of diversity in microbes that we are exposed to in the western world, and how that might be partially explaining the rising instance of these diseases. Bacteria is always focused on because there is a huge decrease in diversity between members of the microbiome between someone from the western world compared to someone with a more traditional lifestyle. But there is a difference between the types of bacteria and the species and maybe the number of those bacteria, but for protists it’s more of a binary answer. Most people in the western world just don’t have any protists. It’s not “Oh, we have less diversity of protists, we have fewer numbers of them.” No, it’s more like “We don’t have any.” And so, the potential impacts that those could have on our immune system development or predisposition to inflammatory diseases could be pretty huge. It also could obviously be nothing [laughs], we don’t know yet. I think there is definitely potential for it to be a factor.
One of the things I think is really interesting about that, or that sort of lends credence to that, is some of the work that was done by my advisor on this one species of protists in mice called Tritrichomonas muris. This protist is a very common member of the mouse microbiome, and as it’s fermenting the fiber that the mouse eats it creates a waste product that then signals to the mouse’s immune system to start prepping for fighting a worm. Even though the protist is not a worm, and the anti-worm immune response from the mouse does not harm the protist at all, it’s still this signaling back and forth between the two that causes the development of an anti-worm immune response.
The reason this is super interesting in terms of thinking about the microbiome and the development of all these diseases like allergy and asthma in westernized populations is that one of the prominent ideas as to why these diseases are occurring is that there is a lack of natural stimulators of the allergic immune response. In immunological terms, the allergic immune response is the same as the worm fighting immune response. People think that lack of exposure to parasitic worms is what is causing a lot of these diseases, and in fact some experimental therapies for inflammatory diseases like types of inflammatory bowel disease is to give people parasitic worms to try to trat the disease. What might be really interesting is instead of giving you a parasitic worm, you could just have a protist in your microbiome, so you wouldn’t be having diarrhea, growth stunting and everything that comes with having a worm. Also it’s gross. Instead, maybe just having a more diverse microbiome, especially with protists, that could help prevent the onset or the predisposition of people to these diseases in these countries.
“This protist is a very common member of the mouse microbiome, and as it’s fermenting the fiber that the mouse eats it creates a waste product that then signals to the mouse’s immune system...this signaling back and forth between the two that causes the development of an anti-worm immune response.”
E: Do you know if whether in countries that have higher rates of parasitic worm infections there are also higher rates of protists commensals in the gut microbial community?
Eli: That is a great questions and one I wish we knew the answer to, but not yet. It’s something that I think a lot of people are interested in—or “a lot” [laughs] in my small sphere of science a lot of people are interested in, so I think I will be answered before too long. Right now we have no idea because as we mentioned earlier the types of sequencing approaches we use to look at protists are so different from what we use to look at bacteria, and so it’s just been sort of a blind spot up until this point.
E: In your experimental models, how easy is it to successfully have protists become part of the gut microbiome community? I guess what I’m getting at is how easy would it be for someone to start a protist probiotic company? [laughs]
Eli: No, I think that’s a really good question and something that I think is so exciting about protists as members of the gut microbiome. There is this thing in microbiome research called ‘colonization resistance,’ where let’s say you have a microbe you want to put into a gut microbiome, there is a good chance if you try to put it in it won’t be able to establish itself as a member or a long term member of the microbiome, because there are already all these microbes in the gut microbiome that outcompete it. And so that can be true for a lot of bacteria and stuff, if there is already a microbiome in, let’s say, a mouse which is where people usually look at this. But what is exciting about these protists is that this is not the case. If we take mice that we breed ourselves or order from the vendor and we try to put one of our protists in, 100% of the time the protists easily just become a long-term member of the gut microbiome. And so because there doesn’t seem to be this colonization resistance it could potentially be relatively easy to put protists in mice or people for therapeutic purposes.
What we don’t know yet is whether the reason that we can so easily put these protists in mice is because they don’t have any other protists, and so maybe if you already have a protist that would prevent you from having another one. But since most people in western countries don’t have any, that shouldn’t be a problem. You know, for example I’ve screened my whole lab including myself and my wife for protists and all of us are negative, so they are very, very uncommon.
E: Interesting. Do you think part of that is just a sampling issue, since you are using stool as a screen? That if you were to take a sample from the small intestine directly, you would see protists? Since in mice you use the cecum to check for protists, not the stool…
Eli: Yeah, yeah, the stool is usually not a good indicator of what the composition of the small intestine is because there is so much of the downstream colon that’s there. But, if there is something that only lives in the small intestine you’ll still pick it up in the stool because in this case, shit literally flows downhill, so everything from the small intestine makes it into the stool. So I wish there was a caveat that said I still had a protist because I obviously really wanted one, but I’m pretty sure that I don’t [laughs]
E: That’s really interesting. I’m also assuming no one screens for protists when doing fecal transplants? So there could be a super protist donor out there?
Eli: I don’t think so. But I wouldn’t be surprised if someone had accidentally transferred protists through a fecal transplant, just by chance.
E: What is the treatment for pathogenic protists in humans?
Eli: Oh great question! A lot of them are treated with this drug called metronidazole, which essentially just kills anaerobic organisms, which are organisms that don’t use oxygen for energy production, so, ones that ferment things. These drugs will kill parasitic protists like Giardia, but they will also kill the commensal protist in the gut microbiome. A lot of things could have contributed and likely contribute to the fact that humans in western countries don’t have protists. One of them is obviously hygiene because most of these things are fecal-oral transmission, but one of them could also just be that we have used drugs to kill all of them and never got them back.
E: Are they also transmitted in the same way as the gut microbiome through vaginal birth and skin contact?
Eli: Probably, yeah. Hard to say for sure with the protists, but since they do go fecal-oral it wouldn’t be surprising. In mice it’s a large way in which they transmit it. Mice eat their own poop, or the poop of their friends, the original fermented food. That’s not a great model, but presumably [in humans] it’s vaginal birth and just breaks in hygiene that would cause transmission.
“Mice eat their own poop, or the poop of their friends, the original fermented food”
E: Cool! What do you think are the changes that there are protists that play a role in food fermentation?
Eli: I looked this up before the interview! I was pretty sure there were no protists involved in fermenting foods, and it looks like no. I did find one thing saying that seaweed is a protist, but then again the definition of protists keep changing. Some website (that I don’t remember how reputable it was) was saying seaweed is technically a fermented food because it’s used in fermentation a lot. But I think that it’s more that you are fermenting protists and eating them, and not the other way around. So I don’t think there are any protists involved in actually doing [food] fermentation.
E: I was wondering since they are so common in water that maybe you get some when you are making a brine or something...
Eli: Yeah, so I guess what I’ll say is that it is unlikely that current fermented foods use protists, but I bet we can do it if you want to…
E: Use some stream water to ferment some foraged greens from the side of a river...
Eli: Yeah, we can do something like that. Make some protist kombucha or something…
E: Interesting... protist kombucha...that would be cool. That’s just a cool name, protist is a cool word...
Eli: It is a cool word, it would definitely be a good marketing ploy.
E: Definitely great marketing! Is there anything else you want to share?
Eli: I don’t think so.
E: Well, thank you so much Eli, it was great chatting with you!
Eli Gerrick
completed his doctoral work at Harvard University, where he studied the pathogenic bacterium Mycobacterium tuberculosis. He is now a postdoctoral scientist in the Howitt lab at Stanford Medical School, where he discovered his true scientific love: symbiotic protists in the microbiome and how they affect the health of their hosts.