"The Gut Microbiome: How the Host and Microbial Communities Influence Each Other" SwatTalk
with Amy Vollmer, Isaac H. Clothier Jr. Professor of Biology
Recorded on Wednesday, April 22, 2020
TRANSCRIPT
Amy Cheng Vollmer:
It's really nice to be with you online, when I was asked to give a SwatTalk last fall I was surprised to learn that I was not going to be speaking in front of a live audience, I had never done that before in my career at Swarthmore. I've given lots of talks to alums, but they've always been at alumni gatherings. And so when Lisa Schaefer who was coordinating this event was talking to me about it, she said, "Well, don't worry, Amy, it's all electronic, we do it on this thing called Zoom." And I thought, okay, that's one more thing I'm going to have to stress about before I get this talk.
Amy Cheng Vollmer:
Well, it turns out I've been teaching on Zoom for several weeks now and I'm quite comfortable with it. And so I'm delighted instead of dreading learning new technology and trying to give a talk, I'm delighted to be here.
Amy Cheng Vollmer:
So the topic I'm going to tell you about is an area of microbiology that's really exciting and that is that the good bacteria that we host all over our body, but especially in our guts influence our physiology and actually our behavior. I won't talk very much about our behavior, that would have to be a separate talk. But this is the lecture in my microbiology class that gets the most sums up.
Amy Cheng Vollmer:
And in fact, I expanded it to two lectures in my syllabus because the second talk is actually about the gut microbiome and the brain. But tonight we're going to talk about the gut microbiome and what I'm hoping to do is to tell you about some really exciting advances that have been going on in the field in particular in humans and their gut microbes. And then also I'm going to touch a little bit on some research that is the result of a collaboration between my lab and that of Sara Hiebert Burch.
Amy Cheng Vollmer:
Sara just retired last December. She's an animal physiologist and she is an expert on hummingbirds and other small mammals, other small mammals that she housed in the vivarium at Swarthmore. And so I'll tell you a little bit about our kind of dipping our big toe into the big pool of the gut microbiome.
Amy Cheng Vollmer:
So I want to clarify some terms. So microbiota is the modern term, it used to be called flora in your gut because we thought bacteria were more like plants. But it turns out that the microbiota encompass bacteria and related microbes called archaea, as well as fungi, and viruses that infect those organisms. And so we call all of those things in this case, in our gut, the microbiota.
Amy Cheng Vollmer:
When we talk about the microbiome, we're also including the genes inside those organisms. And when I say the word microbiome, I'm kind of referring to all of that, the organisms and their genes and what their genes do for us. When you look around the human body, we're not one ecosystem, we're a whole series of ecosystems. And you know that your skin is rather dry, you know that the inside of your ear is kind of a waxy or really different place than your skin, that your nasal passage and your armpits and all these places on your body have very specialized conditions.
Amy Cheng Vollmer:
And not surprisingly, those different zip codes on our body, if you will, have different residents that are specialized for those conditions. The microbiomes in and on us are quite dynamic in their composition and they respond to us and to the environment in which we live.
Amy Cheng Vollmer:
So a little bit about the gut. So right after fertilization, the human embryo is just a big ball of cells and yet somehow that ball of cells starts to be able to be differentiated. And one of the things that happens is it organizes itself into three layers and very quickly those three layers form a cylinder. And the middle of the cylinder is kind of hollow. And so the outer layer is the ectoderm, and the ectodermal cells basically form our skin and our nervous system.
Amy Cheng Vollmer:
The mesoderm basically forms all our important internal organs, the heart, the lungs as well as the skeletal system and the muscular system. And the endoderm, this tube that goes down the middle of us forms the gut, and the gut starts out as a very simple tube, in panel B here in the second frame here. And that tube begins to invaginate and make little pouches.
Amy Cheng Vollmer:
And the pouches are then held together by connective tissue. And pretty soon you see a big bulge that's going to come the stomach, and then these loops keep looping around and they get all held together by connective tissue. All right. And if you look at these various kind of outcroppings, you'll see the beginnings of the liver, the gallbladder, the lower part of the intestine, the pancreas actually has two parts that join together, and then the rest of the small and the large intestine. So that tube becomes highly differentiated depending on what part of the body it's going through.
Amy Cheng Vollmer:
All right, so more a little intestinal loops, this focuses on how the small intestine becomes this stack set of loops and then the large intestine, the ascending, the transverse and the descending colon. Oftentimes in some diagrams, they'll cut away the transverse colon so that you can actually see what's behind it.
Amy Cheng Vollmer:
And so everything that's shown in this large diagram here basically started out as that endodermal tube. And so it's pretty remarkable how specialized each region is, and it shouldn't surprise you that each of these regions has its own special chemical and physical characteristics. And because of that, different resonant microbes.
Amy Cheng Vollmer:
Now if we take a cutaway of the small intestine, you can see the inside is hollow, that hollow part is called the lumen, that's where everything you eat will pass through. And if you look at the interior of this tissue, you will see these sinker like projections, a fold of the intestinal lining. And then the folds have other folds called villi, little sinker like projections. And when you look at the individual villi, they're made up of these stacks of cells, almost like bricks, one right next to the other.
Amy Cheng Vollmer:
And when you see one of these cells, you can see that it has even more invaginations of its membrane. So in biology we often say that the structure of something tells you a lot about its function. This is a tissue where the surface area has expanded massively and that's because its function is to absorb nutrients.
Amy Cheng Vollmer:
What's remarkable is that in experimental animal systems where the animals are raised in the absence of microbes, in the absence of their commensal microbes, these villi don't form, and the cells in them do not form microvilli. So that the development and differentiation of host cells does so in response to commensal stimulation. Here's a closeup of those microvilli, they're attached to the cytoskeletal structures in the underlying cell to keep them upright and they're going to sway in the waves of Paracelsus that move the food matter through the intestine.
Amy Cheng Vollmer:
These cells that aren't on the surface of the intestinal lining actually will be sloughed off and replaced from below because there's mechanical wear and tear. This increased surface area is how we are able to maximally absorb nutrients from what we eat. All right, so there's a little cartoon of these cells in the small intestine and I want to contrast the small intestine with the large intestine.
Amy Cheng Vollmer:
So this is where we absorb nutrients that we've been able to break down, and then what flows further into the large intestine are the indigestible foods, the fibers, the fibers food for us is not digestible. And the microbial population in the large intestine then break down those fibrous foods, they absorb nutrients, they also give us some extra nutrients from that.
Amy Cheng Vollmer:
And then there are no villi in the large intestine, they have these large invaginations, but they don't have any of the extra surface area modifications, because the large intestine's job is to absorb water back into the body. And you have a problem eliminating if you don't take in enough water because then your body tries to take up water and then you have a hard time eliminating, and that's not a good thing.
Amy Cheng Vollmer:
The small intestine tends to have fewer numbers of bacteria than the large intestine and I'll show you some numbers in a second. When there is a case where the small intestine is overtaken by more bacteria that can actually cause problems, so irritable bowel syndrome and Crohn's disease tend to be inflammations where there are too many bacteria that make their way upstream where they should be staying downstream. In healthy hosts, Paracelsus and the flow of nutrients keeps this differentiation intact.
Amy Cheng Vollmer:
So how do you get your microbiome? Where does it come from? You don't buy it at the store, you get it from mom. I always tell my students, this is why more people call home on Mother's Day than Father's Day, because mom's started you out with this amazing gift when babies are born and if they're born naturally, the head comes out first and the baby's face actually faces mom's anus.
Amy Cheng Vollmer:
Now, usually in a birthing situation the mother's bowels have been cleared but as she exerts herself vapors from her bowels and counter the baby's head and the baby's first breaths often will absorb some of those vapors. So the baby is inoculated with mom's microbes at birth. Now, if a baby is delivered by C-section, that inoculation is delayed.
Amy Cheng Vollmer:
But that's not the only way you get microbes. After babies are born, they're held, they're cuddled, they're passed around to all the aunts and uncles and grandmas and grandpas and siblings and maybe the family dog gives it a lick. And so you will obtain all of these microbes from your family very shortly after birth.
Amy Cheng Vollmer:
Now, something that used to happen a generation or two ago is that on what mothers gave birth to babies that were going to be given up for adoption, those babies were put in a separate part of the nursery and the end, the mothers were not allowed to see them and nobody really held these babies. And oftentimes the babies would not thrive, in fact, there was a term called failure to thrive.
Amy Cheng Vollmer:
And we now know that the main reason for this failure to thrive condition was because even when the babies were fed formula, they didn't maximally absorb the nutrients in the formula because their microbiomes and their guts had not been properly inoculated. In modern times when babies are given up for adoption, there are volunteers in the hospital, nurseries called coddlers, and they come in and they hold the babies and they cuddle them just as much as birth mothers would do in their hospital rooms.
Amy Cheng Vollmer:
And the failure to thrive notation in the nurseries basically has gone away. Excuse me. The other thing that mom does for you is in her breast milk. Initially breast milk doesn't actually contain very much milk, the milk proteins and the milk sugars don't come in for about three days. So what is that stuff that the baby is drinking than during those early three days?
Amy Cheng Vollmer:
Well, one of the things the baby is getting in what's called the colostrum is antibodies, whatever mom has encountered in her environment, she is passing those antibodies to the baby. This is important because the baby's own immune system won't mature for several months after birth. And so this passive immunity is really important for the baby. But really remarkably is that in the first few days, mom is giving the baby bacteria.
Amy Cheng Vollmer:
In particular bifidobacteria, these are exactly the bacteria that the baby needs to digest the sugars in mother's milk and to extract nutrients from them. So before mom feeds you her milk, she actually inoculate your guts with the bacteria that are going to help you get the most out of those meals, so that's pretty remarkable. So after birth, baby gets inoculated, and then pretty soon they start to extract nutrients. And as the baby is put on solid foods, the complexity of the microbiome increases.
Amy Cheng Vollmer:
In the baby's guts and in a child's guts, what happens is they begin to house bacteria that will digest what the host cannot break down. This is an anaerobic environment, there's no oxygen. And so a process called fermentation goes on and short chain fatty acids as well as some chemicals called aldehydes and a few alcohols are made. And those are what the bacteria produce, and often the host can absorb those and utilize those.
Amy Cheng Vollmer:
The composition of the gut microbiome is absolutely affected by what the host eats, not only food but also any antibiotics they might encounter. So in the GI tract, there's different genre of bacteria living in different areas and these are just names of different groups of bacteria. And here are the bifidobacteria that help you digest milk.
Amy Cheng Vollmer:
The stomach is not a terribly hospitable place, and so there are not a lot of bacteria per cubic centimeter, the duodenum, a little bit more populated. And as you move down, the jejunum is still not such a hospitable place, but as you move down into the colon, and here's where the transverse colon has gotten cut so you can see everything. Now you're talking about 10 of the 11th or 10th to the 12th, and the kind of wonderful, usual suspects that I'll be talking about in a little bit.
Amy Cheng Vollmer:
So in the human gut, there are two major phyla of bacteria that predominate, the bacteroidetes shown in blue here, and the firmicutes shown in red. When you're on a high fiber diet and the environment in your gut is very acid, the predominant members are firmicutes. And there are almost no detectable proteobacteria.
Amy Cheng Vollmer:
If you're going to get food poisoning, the proteobacteria are the usual suspects. And so this healthy gut prevents the colonization of your gut by possible pathogenic bacteria. In a no fiber or low fiber diet when someone eats highly processed foods, I always say to students, "If you're eating really processed foods, you should probably eat the cardboard box that it came in because you're actually going to get more benefit out of that."
Amy Cheng Vollmer:
Now, you see the bacteroidetes dominating, the firmicutes making a smaller portion and now you see a much more evidence of those proteobacteria that can be problematic, not all of them are, but some of them are. This data come from a kind of little experiment that a journalist engaged in and left his kind of salad eating life behind and went somewhere in the world where he couldn't get a lot of fiber. And this was the change in his own microbiome. Going feral, my one-year journey to acquire the healthiest gut microbiome in the world. He went unhealthy first and then went healthy.
Amy Cheng Vollmer:
These distributions also are affected by fat. So here, we're dealing with a low-fat diet and a high-fat diet. And so one of the things that they're measuring is the predominance of a particular type of bacterium which produces butyrate. So butyrate is a short chain fatty acid, and it actually is very protective, it's an anti-inflammatory. And so those little brick like cells that are in your intestine, they are held together by mortar, that's very important. And if you have inflammatory problems in your gut, that mortar disintegrates and now you have what's called leaky gut. And then you have a lot of problems when that happens.
Amy Cheng Vollmer:
So butyrate producing bacteria decrease when you're on a high fat diet. And so that's one of the problems with our modern lifestyle when we eat a lot of French fries and fried foods is that those butyrate producing bacteria decrease. And in some individuals they're quite low and in those cases we have conditions like obesity and irritable bowel syndrome.
Amy Cheng Vollmer:
All right, so the firmicutes are associated or they're called gram positive bacteria putting the two big groups. And so half of them are gram positive, half of them are gram negative. Firmicutes are pro-inflammatory and pro BC and bacteriodetes, the opposite.
Amy Cheng Vollmer:
And so we need both for balance and you can see that the balance changes over time. Babies have a fairly simple diet and so they have equal amounts of bacteroidetes, firmicutes and other. And then as kids grow up and have a more complex diet, things get much more interesting. Pregnant women have their own unique microbiome which shifts back shortly after birth.
Amy Cheng Vollmer:
And then as an adult hopefully you maintain a good balance. And as one gets older, sometimes that balance shifts a little bit. So the microbiome it turns out is affected by lots of things including invasion by parasites. And so just to sums our blood flukes and they invade the bladders and intestines and lay their eggs, and then the eggs compete with the host for food. And these are data that simply show that these are days after infection 28 days and 50 days after infection in the small intestine on the top, and then the large intestine, the bottom on the left are the infected hosts and on the right or the non-infected hosts, you can see that 50 days after infection, the distribution of things in the microbiome really change.
Amy Cheng Vollmer:
And there's an appearance of new groups of phyla that are normally not abundant, and this happens both in the small and the large intestine compared to the controls. So we're learning all kinds of things about what can upset the balance of the microbiome and thereby upsetting the physiology of the host.
Amy Cheng Vollmer:
There's been a lot of study of obesity and how the microbiome proportions change, but it also is the case with undernutrition, so we look at the other end of the spectrum. And what we can see is that I have to keep moving the participants box around so I can see my data. But basically the ratio of firmicutes to bacteroidetes varies between the control group, the undernourished children and the children who have a tendency for obesity.
Amy Cheng Vollmer:
And so it's not just who's there but in what proportion. And so it might be kind of antithetical to think, "Well, these two ratios are more comparable, but when you actually look at the distribution, you see that the proteobacteria, which are not shown in this ratio really dominate in the obese children and are not as abundant in the undernourished kids."
Amy Cheng Vollmer:
So I want to highlight some work done by some Swarthmore alums because this is an alumni talk, and because we have some really accomplished alums out there. One being Mike Mahowald who audited my microbiology class in the late '90s. He went on to study with Jeff Gordon, who in many people's minds is kind of the father of the study of the mouse microbiome. And one of the things that Mike did was to establish a model system.
Amy Cheng Vollmer:
So in Jeff Gordon's lab, they raised germ-free mice, these mice are bred and housed in germ-free sterile boxes, and all their food is sterilized. And then what they can do with the germ-free mice is they can humanize their guts by giving them the inocula from human patients and they've created this simplified model of the human gut and then can look at the impact of food and distribution of the different phyla and look at what happens to the mouse.
Amy Cheng Vollmer:
And so these are data that you don't need to pay that much attention to, but there are different ways to measure the health of the gut, this is one way to do it. And so these abbreviation stand for a bacteroidetes, BT, a firmicute ER, and then when you have both of them present.
Amy Cheng Vollmer:
And so the gut is very healthy when both of them are present. The higher this bar is, the healthier the gut environment for everybody. Acetate, butyrate and propionate are three short chain fatty acids. And so what we can see here is in germ-free mice we have very little acetate produced when we give it BT, these bacteria are the major acetate producers.
Amy Cheng Vollmer:
And the amount of acetate is diminished when we have a mixture of the two kinds of bacteria. In contrast, the butyrate producers are the other type of bacteria, the firmicute and they tend to dominate producing butyrate even when the other BT bacteria there.
Amy Cheng Vollmer:
And remember butyrate is that wonderful anti-inflammatory. Propionate is mainly the product of the BTs, and even when the firmicutes are there, propionate levels are still pretty high. So there's a balance in the gut of the various chemicals that are produced and it takes both BT and the ER representatives to make things happen.
Amy Cheng Vollmer:
This MCT is just a transporter, so it's another way to measure kind of the metabolism in the gut. And in this case it's really having both bacteria present that allows for maximum transport. This is not a paper by a Swarthmore alum, but I was introduced to Sydney Finegold by one of our very distinguished alumni, many of you know him Bennett Lorber.
Amy Cheng Vollmer:
And I got to meet Dr. Finegold at a meeting in Toronto. He was in his '80s, he brought his girlfriend and we met at the bar in the hotel and he was telling me about this study and he said, "Amy, I have found that in late onset autism, particular combinations of bacteria that are not found in match siblings and in age matched controls."
Amy Cheng Vollmer:
And I was just fascinated by this. He said, "The problem is nobody will fund my research. Nobody really believes this." And so finally, finally he had a trial and he wiped out the guts of these kids with antibiotics and then fed them a lot of probiotics and many of their most severe symptoms were mitigated. But this is what he found in the guts of the autistic boys.
Amy Cheng Vollmer:
So we have predominating bacteroidetes and a smaller lower number of firmicutes, right? These are their siblings, so similar, but a little bit more equal distribution between these two major phyla. But look at the controls, this is the dominating firmicutes here. And so this was one of the studies that got people thinking about what is happening in the gut might be affecting chemistry in the brain.
Amy Cheng Vollmer:
As people started studying this, they looked at germ-free mice and they looked at what was happening with their behavior. So here's the first place I ever read about the gut brain axis, the conclusion they make in their abstract is we conclude that the presence or absence of conventional intestinal microbiota influences the development of behavior, and as a company by neurochemical changes in the brain.
Amy Cheng Vollmer:
This was just really astounding in this particular model system that they had created. So this opened up a whole field, normally neuroscientists don't even talk to microbiologists because they're studying this amazing brain and we studied things like, "poop" but it turns out the stuff that's making your poop is affecting what's in your brain, and that was pretty amazing.
Amy Cheng Vollmer:
There have been studies that talk about anxiety like behavior and how it's correlated with gut inflammation. But this particular study talks about how the arrows go both ways, in other words, the behavior of the host can affect the physiology of the gut and vice versa. So that was another really interesting window on processes that we had never thought might be related.
Amy Cheng Vollmer:
And in fact, there are a couple of different ways you can look at inflammation. So our control organisms have no inflammation or very little inflammation. And when we give them this bacterium that we called TM, they have inflammation measured in two different ways. One by a particular enzyme, and one by the infiltration of white blood cells that are trying to deal with the inflammation.
Amy Cheng Vollmer:
All right, so we can see that that's high in both cases. The red boxes are treatment with known anti-inflammatory drugs, and both of these drugs have some side effects and have some variable efficacy in different kinds of patients. But it turns out that if you give, instead of the prescription drugs, if you give particular species of bacterium, bacteria, and this B stands for bifidobacterium by the way.
Amy Cheng Vollmer:
They have the same anti-inflammatory effects without any of the side effects that the prescription drugs are known to display. So boy, if you could control some of this just by diet, that would be so much easier. This is another amazing paper by Renuka Nayak who is now at UCSF in the lab of Peter Turnbaugh. And Renuka has been investigating something that physicians have seen for a long time, that patients respond very differently to medication, even if they have identical symptoms. If they weigh the same, if they're the same gender and everything else is the same, people have completely different outcomes and it turns out it depends on their microbiota.
Amy Cheng Vollmer:
And so Renuka is now trying to figure out if the best thing we could do for patients is first figure out what's in their guts after we've diagnosed an illness, figure out what's in their guts and have a plan as to what treatment is going to be the most effective. She's working in rodent systems right now, but ultimately because of her role as a physician scientist she's in rheumatology, and so she's hoping to think about how she can help human patients.
Amy Cheng Vollmer:
Another alumna, Lea Guthrie who is now a postdoc at Stanford, has been looking in particular at chemotherapy in colorectal cancer and how patients with nearly identical disease progression and in nearly identical places in their intestine respond vastly differently to particular kinds of chemotherapy. And again, personalized medicine takes on a new kind of dimension when we think that maybe before you're treated for your colon cancer, we need to look at your microbiome signatures first and figure out what's the best course of treatment.
Amy Cheng Vollmer:
It's a shame to waste treatment of a patient with a chemical that's probably not going to work in them instead generating toxic intermediates and side effects and all of that. And so Leah's working very hard to figure out what the best path forward is and looking at what markers in the microbiome are the most important ones to look at.
Amy Cheng Vollmer:
And it turns out your gut health can affect your heart health. Wow. It's not just the gut and the brain, it turns out it's gut and the heart. And so I have to tell you my inbox is so full these days, it's a little overwhelming. And no wonder I've expanded my kind of half a lecture to a whole lecture.
Amy Cheng Vollmer:
But heart health, but also chronic kidney disease, atherosclerosis and hypertension. And we've just heard that some of these factors are complicating issues in our current pandemic. And this was a highlight basically of an extension of some of Leah's work, not only does your microbiome affect how you deal with chemotherapeutics, but actually particular balances of the microbiota may actually help the immune system be better in the terms of surveillance for tumors.
Amy Cheng Vollmer:
And so many doctors who are treating cancer now are having patients also keep dietary notes about what they've taken in and whether they feel better when they eat certain foods or other foods. And in dealing with malnourishment, I already showed you the one study from Mexico, but sometimes when you put kids into feeding programs and they don't seem to be gaining weight, it's because they actually don't have the right microbes in their guts to help them absorb.
Amy Cheng Vollmer:
And so now pre-treating or co-treating these individuals with probiotics seems to really increase the probability that the treatment for malnutrition will take. This is fairly new study from last year.
Amy Cheng Vollmer:
So in the middle of all of this microbiome stuff and I definitely didn't study this as a graduate student, there were some students at Swarthmore, Corey Benjamin, Barry Zee, and then later Tristan Bice and Doug Gilchrist-Scott who convinced Sara Hiebert Burch and myself to do some of this microbiome stuff. And Sara looked at me and we rolled our eyes and what, sure, why not.
Amy Cheng Vollmer:
And so we started out with the Siberian hamsters that Sara has, hence had it downstairs in the vivarium, as well as the mice. And we didn't take enough samples for us to do anything really rigorous, but basically we showed that changes in fatty acids and the diets of these organisms seem to affect their microbiota.
Amy Cheng Vollmer:
It was enough to peer reviewed abstracts, presented at a national meeting and put Swarthmore on the map. People didn't really realize that we could do this kind of stuff and Sara and I had a really great time collaborating. And again, when I was hired in 1989 you told me I was going to be doing this, I would have rolled my eyes at you.
Amy Cheng Vollmer:
And then a really remarkable pair of students, Tianyu Liu and Helen Hougen decided to do a more comprehensive study. And so they fed mice different amounts of saturated fatty acids and they wanted to look at the kind of before and after of that feeding. And what they concluded was saturated fatty acids had a much more profound effect in shifting the profile of the microbiome than two different regimes of polyunsaturated fatty acids.
Amy Cheng Vollmer:
And the shift was toward profiles that were more typical of obese individuals. And so here are their data, these are two top is before treatment, bottom is after treatment, there are two different regimes of polyunsaturated fatty acid treatment, those two changes were not significant but what was significant was when a 14-week treatment of saturated fatty acids did lead to a shift.
Amy Cheng Vollmer:
And here the bacteroidetes are the bottom gray bars and the firmicutes are the white bars. So this paper came out the week that Tom graduated from Swarthmore, Helen had graduated the year before. And it was published in Anaerobe Magazine. Anaerobe Magazine had never, ever published a paper where the first author was an undergraduate student, they kept moving my name up to the front and I kept saying, "No, the first author is the person who did the majority of the work and wrote the majority of the paper." And that is Tom and you need to keep him first.
Amy Cheng Vollmer:
And the editors of Anaerobe told me that it was the first paper that they had published where the lead author was an undergraduate student, and he wasn't undergraduate because he didn't graduate until the end of that week.
Amy Cheng Vollmer:
So this leads us to hummingbirds. So Sara's actual favorite study organism isn't a mouse or a Siberian hamster. Those are just convenient organisms to have in teaching labs. Sara is an expert in the physiology of hummingbirds, and hummingbirds in contrast, all the other studies that I've presented so far are not domesticated laboratory animals, they are wild, they are exquisitely diverse.
Amy Cheng Vollmer:
And some of them migrate hundreds and hundreds of miles and others have them just stay put in the same area, so those are a couple of variables that we can measure. And they represent the most extreme form of physiology, they have to consume so many calories because their wings beat so fast. Here's some data, thousands of times per minute, or they can slow them down at night. And their body temperature goes for about a hundred degrees Fahrenheit, a little bit warmer than hours down to 50 degrees Fahrenheit, we can do this.
Amy Cheng Vollmer:
So this is a little bit like hibernation but it's called torpor because instead of overwintering the way bears do, torpor is just every night. So 12 hours at 38 degrees Celsius, 12 hours at 10 degrees Celsius. And so one of the questions we had, what bacteria are going to oscillate like this? And so I want to tell you a little story about that.
Amy Cheng Vollmer:
So the two species that we are studying are the Anna's hummingbird and the Rufus hummingbird. Anna's a resident in the Pacific Northwest near San Juan Island where Sara now lives in her retirement, but she would summer there when she was still working at Swarthmore. And then the Rufus that migrate all the way up from Mexico along the California coast.
Amy Cheng Vollmer:
This is a picture of the students in my research group from last summer. The last time I hosted students in my lab, and this is the same group with one edition, they dressed up for a miniature golf tournament and they dressed up as hummingbirds and they were all holding flowers. Not only did they win the tournament, I think they came in second place for their costumes. I have no idea who won first place in the costumes, I rather like these. But among this group are Ryan Stanton, Calla Bush St. George, and JB Robert, and some of their work is what I'm going to show you next. I'm going to show you a lot of data, but I'm just going to summarize it for you.
Amy Cheng Vollmer:
So Calla wanted to ask about the difference or the distribution of phyla in the gut microbiome between hummingbirds that were fattening and hummingbirds that were not fattening. So the ones that need to fatten are the ones that are going to migrate and the ones that are not fattening are the ones that are just resonant. She was also looking at differences between hatch year hummingbirds, the ones still fed by their parents and after hatch year who were feeding themselves.
Amy Cheng Vollmer:
And these are a lot of data, but basically the one significant thing she found was that the firmicute percentage really differed between the lean and the fat Rufus hummingbirds, she's got a lot more data in her thesis but I'm just going to concentrate on that. Ryan Stanton looked at several different hypotheses about the weather when you're about ready to lay an egg, if your physiology is really different than a male, my guess would be yes. But is that reflected in the microbiota?
Amy Cheng Vollmer:
What about the impacts of molting on a hummingbird, are they going to need more protein and more bacteria that help you make protein when you have to make more feathers? Some of the birds carry a lot of eggs from ectoparasites and he wondered whether that might affect the microbiota. And then he was looking at combinations of all three.
Amy Cheng Vollmer:
And so one of the significant things he found was that in fact the Rufus female that was about to lay an egg or had just laid an egg has much lower numbers of a particular group of bacteria that you haven't heard about before, the actinobacteria as compared to the male of the same species. But he didn't see any difference in microbiota abundances between Anna's hummingbirds that were carrying parasites or not.
Amy Cheng Vollmer:
And so his conclusion there is maybe carrying that parasite eggs isn't a burden, it would be interesting to look at those that are occupied by the adult parasites, that's a little bit harder to suss out. So I also want to go back to some preliminary studies done by Isabella Erickson that was really showed us something really unusual. We're not looking at a lot of firmicutes or bacteroidetes. The predominant phylum in these birds are actinobacteria. They are barely on the map in any of the mammals that we've looked at.
Amy Cheng Vollmer:
And in fact the majority of the actinobacteria can be accounted for by a single genus, the genus corynebacteria. And so JB wanted to study that observation and he went deep into the literature and ran into my office and said, "Amy, Amy, Corynebacteria make extra cold shock proteins," and cold shock proteins are what you're going to need to come out of torpor.
Amy Cheng Vollmer:
I want to do this experiment, I want to set up artificial torpor. And so he took all the different bacterial species that I have in my freezer, he got them out, he put them on liquid culture, and then he sent one directly through 37 degrees for 72 hours straight. And then he cycled the other set, set of triplicates through torpor. And then he played it at every 12 hour point and then he did a final plating.
Amy Cheng Vollmer:
So I only have one species of corynebacteria in my freezer, but JB managed to track down somebody in Germany who sent us two dozen species of corynebacteria. And JB was so busy last fall, I gave him permission to hire a volunteer to help him because he just couldn't do everything and still pass all of his other classes.
Amy Cheng Vollmer:
And so what he did was he cycled the bacteria through these two temperatures, and then he did serial dilutions and plated to figure out how when we ran out of bacteria in these various samples. And so I'm sorry that I don't have better looking data, JB has lots of data, but this is the best I could do.
Amy Cheng Vollmer:
And basically what he's showing is the ones that are cycled, so this is 10 to the minus one, 10 to the minus two, 10 to the minus three. When do we run out of bacteria? Well, in this case, we don't run out of bacteria until the 10 to the minus six plating. The control group that's been at 37 degrees, we pretty much run out here, we have a few colonies here. And so we're at least an order of magnitude better survival after the temperature cycling, no other bacteria that we studied did this.
Amy Cheng Vollmer:
And he was looking here at three different species of corynebacteria. Here's one where you see them surviving for a couple of dilutions and nobody's alive on the plates that were kept at 37 degrees. So to summarize what our lab has found in the last few years is that actinobacteria actually dominate what are the usual suspects in everybody else's gut that we've studied so far, they are not affected by molting or body fat. And they are not as dominant in egg-bearing females as they are in the rufus.
Amy Cheng Vollmer:
And probably because the egg-bearing females actually don't go through torpor that wouldn't be good for the eggs. Many, many species of the corynebacteria survive better in a torpor regime than a constant 37 degrees. We've seen that firmicutes are more abundant in lean versus fat juvenile rufus, but not in adults but this capitulate some of the things we've seen in mice. And the ectoparasite eggs don't seem to be a particular burden, but we'd love to know what the adult parasites do.
Amy Cheng Vollmer:
So that's our excitement about the hummingbird microbiome, all of these students plus a couple more were going to go to a national meeting to present their work, but unfortunately that national meeting got canceled. So I want to sum up by telling you a little bit more about our own microbiomes and are thinking about the fact that we have as many as 10 times more microbes in and on us than our own cells makes you really wonder who we are.
Amy Cheng Vollmer:
That the microbiome affects how we digest and what we absorb but also is now clearly going to be affecting our brain chemistry and also very much a part of our immune response, keeping our immune response tuned up properly. And so how can we maintain healthy microbiomes in us? I'm going to tell you about pre and probiotics in a little bit.
Amy Cheng Vollmer:
We might want to think about our eating habits, but I also want to emphasize there are other things that absolutely affect our microbiomes. One is hydration and the health of your colon, it depends on how well hydrated you are and how much sleep. If you don't sleep, your body doesn't do maintenance and repair very well, and those maintenance and repair operations compete with your normal daytime activities.
Amy Cheng Vollmer:
And so sleep turns out to really affect the distribution in your microbiome. And finally, with the gut brain access, we now know there's a two way street between what we eat and how our brains are responding and that would be the subject of another talk.
Amy Cheng Vollmer:
So prebiotics, prebiotics are fiber filled foods that will promote a healthy balance of bacteria in your gut, these are all kinds of things that are good for you. And when we talk about fruits like apples, we talk about eating the peels and many people also eat the core. The less processed the better. And probably some of you see foods on here when you know, when you consume these foods or you just feel great.
Amy Cheng Vollmer:
Probiotics are anything that will give you an inoculum of good bacteria. And when you look at yogurt containers, not frozen yogurt but refrigerated yogurt, you will see that they contain active live yogurt cultures, they don't say live bacteria because then probably nobody would buy them but that's in fact what you're eating. Spoons full of yummy, healthy bacteria.
Amy Cheng Vollmer:
But anything that you eat is fermented it's going to contain good bacteria, and every culture has fermented foods and drinks that make you feel better when you eat them. And so eat as many fermented things as you possibly can. Eat more like a gatherer than a hunter. When I talk to students, I say in the hunter gatherer days it wasn't like there was a woolly mammoth kill every Friday afternoon and everybody got to eat woolly mammoth steak all weekend.
Amy Cheng Vollmer:
And when you gathered, you're gathering a handful of nuts, not a bushel full of nuts. And so the idea that we need to eat more like gatherers in small quantities, natural foods that are not processed is probably the way to go.
Amy Cheng Vollmer:
This caveman says, "I'm tired of hunting and gathering," but nobody's invented grocery stores yet. When you Google the gut microbiome, one of the amazing things that you see is that mood disorders are linked to what is in your gut. If you think about it, why do we call comfort food, comfort food? They're heavy and starch and they probably allow the microbiome to make fermentation products that comfort our brain.
Amy Cheng Vollmer:
If you want to do some more reading, I have two general books, fantastic books written for general audiences "Good Germs, Bad Germs" is by Jessica Snyder Sachs, a really talented science writer who first broached this whole idea of the fact that we really have healthy bacteria in and on us.
Amy Cheng Vollmer:
"Why We Get Sick" is an older book, but that came out that really launched the field of Darwinian Medicine, thinking about the illness and symptoms in the context of evolution. And finally the gut microbiome itself, I recommend three fantastic books. One, a very popular one by Ed Yong, a very gifted young writer talks about rifts off of Walt Whitman, and talks about how he got interested in biology because he likes zoos and now realizes that we are walking zoos with all of the microbes in and on us.
Amy Cheng Vollmer:
Martin Blaser has written this book about "Missing Microbes", saying that as we become more civilized and eat more processed food that we are becoming less diverse in our microbial diversity and how that advent of antibiotics has limited the diversity in our guts and that's not a good thing.
Amy Cheng Vollmer:
And this book called "Gut" by Giulia Enders and illustrated by her sister is a little tongue in cheek but very, very informative about how the gut itself works and then how it is a host and ecosystem for diverse bacteria. So that's the end of my formal remarks and I've been watching the chat box flashing and I'm happy for Dina to send me some questions.
Amy Cheng Vollmer:
I also want to qualify and say I'm not a physician, I'm not an immunologist, so there's a bunch of things you're going to ask me where I'm going to make a pretty generalized statement and usually end with a term that says something like, and it's rather complicated, but I'm happy to take questions.
Dina:
Great, thank you so much. That was incredibly informative. I learned a lot and I'm sure everyone else did as well. We don't have too much time left but there are a couple of questions I want to make sure that we can get to. One of them comes from Eric [inaudible 00:53:31], I'm sorry [inaudible 00:53:34].
Amy Cheng Vollmer:
Oh, yes. Hi, Eric.
Dina:
So his question is [inaudible 00:53:39] the microbiome influences behavior is acting on the nervous system through nerves in the gut, or our metabolic traveling all the way to the brain to cause the changes?
Amy Cheng Vollmer:
Eric, the answer is both. So the vagus nerve connects the gut and all the major organs all the way up to the brain, and we used to think the vagus nerve was just a conduit but it turns out the vagus nerve has on its surface. The vagus nerve is actually a pair of nerves that goes all the way up the body has receptors on it for antidepressants.
Amy Cheng Vollmer:
In addition, those short chain fatty acids and all the other metabolites that are made to get absorbed into our bloodstream and do get carried and pass the blood brain barrier. And so at low concentrations, those metabolites are not going to affect brain activity, but if the concentrations are high enough, they will antagonize and affect regular neurotransmitter couplings in the brain, so both
Dina:
I see a couple of questions coming in about COVID, so I want to make sure we ask one about the virus. So one question from Dimitri Nadat from 2002. He said, "What types of viruses, bacteria and pathogens can gut flora help with examples, respiratory or COVID-19?"
Amy Cheng Vollmer:
I don't know the answer to that directly, the viruses that we find in the gut are viruses that affect bacteria, so that is about that ecosystem. I am not sure how the lung itself is affected by anything in the gut and so I really can't answer that, but I think your overall immune readiness may be influenced by what's in your gut, and of course your overall immune readiness is important no matter what kind of infection you're fighting.
Dina:
This is an interesting one for Mark Rubinstein of 81. Sorry, the chat is going so quickly, I don't want to lose track of that question, "Is there evidence that current climate change has affected the gut microbiome in humans or other species?"
Amy Cheng Vollmer:
I don't know if I would say it would be direct or indirect, but climate change itself is changing the kinds of animals we interact with, and the kinds of food that we might have access to, and so that may overall affect the dynamics of the microbiome. I will say I did see real quickly, how do you collect hummingbird poop? All right, so Sara Hiebert Burch is the hummingbird whisperer, she has hummingbird feeders everywhere, she has mist nets, she will capture hummingbird in a miss net, she will have a purge on a small centrifuge tube as it purchased there it voids into the centrifuge tube and it has bottom, the cloaca and pee and poop all come down.
Amy Cheng Vollmer:
She looks at its fat content through pushing part, it's chest feathers, she weighs it, she looks at parasite load, she does everything four minutes later and they banned them and then they let them go. So she does the heavy lifting, then she puts all those... then we have barcodes and we put the tubes on dry ice and they're shipped back to us and we have a huge system in the lab of separating the pee and the poop and keeping everything cold and then putting everything away in a freezer that's backed up by the generator.
Amy Cheng Vollmer:
So we have pictures of hummingbirds perched on a little tube and then we collect. And how many bird poop is the size of a human eyelash? So yeah. But the molecular techniques now can amplify the DNA in those samples. I can see a lot of names in the chat and I'm just waving at all kinds of former students, so it's just nice to see all of your names.
Dina:
Chris Roger from 1997. He asked, "Given that every person's Michael brought by almost a different, how complex is the process of mapping it out so that doctors can better prescribed medications to help with issues or individuals?"
Amy Cheng Vollmer:
This is a great question and the secret is it's not who is in your microbiome, it's what are they capable of doing metabolically. So the best metaphor I can use is, you have a piece of music you would like it played by a full orchestra, but all you have is the marching band. So now you're going to parse out the treble stuff to the flutes because you don't have violins and the stuff that the cellos would play you give to the trumpets and trombones, right? And you're still able to play that piece.
Amy Cheng Vollmer:
So it's not just who's there, it's what their role is given everybody else in the microbiome. And that means that we have to look one level down from who's there to the metabolome, which is what are the molecules there and who has been responsible for making them. And it's really the composition of the molecules that is going to be telling us how drugs are going to be metabolized and things like that. So that's called metabolomics.
Amy Cheng Vollmer:
And if I were getting into science now, that's what I'd be doing.
Dina:
From Karen Cervanos, "When people use over the counter probiotics, do they need to continue taking them indefinitely? Do the bacteria not establish themselves in the gut?"
Amy Cheng Vollmer:
You need to take probiotics, I just eat yogurt and then keep them happy by eating high fiber foods. So it's pro and pre together. If you eat probiotics in the morning and then all you eat is Twinkies and moon pies, they're going to go out, they're not going to want to hang around because you're not very happy place to be, you're not feeding them.
Amy Cheng Vollmer:
That's why I say to my students, eat the box, at least eat the box of the two-piece caveman, they're survivor. So it's a combination of pre and pro. And if you're eating yogurt and you eat some fermented foods, you don't have to take the probiotic pills. But Karen, feeding of your gut microbes requires fiber.
Dina:
This is a great one that just came in from Eric Schnadig, "What do we know about the relationship between the occurrence of allergies in the state of an individual's microbiome?"
Amy Cheng Vollmer:
Well, allergies are a hyper reactivity of your immune system, and so we didn't have time to talk about the immune system, but it definitely is the case that the health of your microbiome in your gut affects the set point of your immune readiness and your immune health. And I can't get into it too much more than that, but if you have allergies and you start keeping a food diary, you start to see some correlations.
Amy Cheng Vollmer:
I used to get migraines, those aren't allergies, but those are a whole other extreme condition. And I figured out the foods that I needed to avoid and it was so simple, I was shocked. And you know there are certain things when you eat them, you say, "I'm going to pay for this tomorrow, I know I'm not going to feel good, but you know I'm going to eat it anyway."
Amy Cheng Vollmer:
For me, my magic food is artichokes, when I eat artichokes, man, I feel great. And I'm sure it's because all that fiber microbes just love. And so I think if you're aware of that you can try to do that, and when you do that, I think your word is how good you're feeling. And I'm hoping that how good I'm feeling gives me some little indicator of how ready my immune system is to protect.
Dina:
Karama Neil from class of 1993 asks.
Amy Cheng Vollmer:
Hi, Karama.
Dina:
"Are there connections between certain genotypes and certain microorganisms?"
Amy Cheng Vollmer:
Probably, and again, it's not just who's there but what role are they serving? So a particular genus that's in your microbiome might be playing the melody in the symphony, but that genus in somebody else's microbiome maybe playing the harmony. So it's not genetic, certainly as a part of this, but this is one of those areas where nature and nurture really work in concert to create what's in you.
Amy Cheng Vollmer:
So I think I'll just stop there. I'm not surprised Karama asked that question, but I really can't go any further.
Dina:
From Warati Morris of 04 asks, "Is there research that evaluates healthy fat diets and their effect of microbiome? Are those effects different than the high fat affects you showed earlier?"
Amy Cheng Vollmer:
Sure, yes. And so the saturated versus polyunsaturated kind of feeding regimes have been studied in the mouse model systems and to the extent that they can be parlayed into human health. So you've heard about kind of good fats like avocado and olive oil and those kinds of things versus animal fats and things like that. So there's definitely correlative studies, pretty strong studies. I didn't really talk about many of those.
Dina:
Another question comes from Olivia Perez of 2015.
Amy Cheng Vollmer:
Hi, Olivia.
Dina:
Who I was going to say, I think she's in STEM. She asks, "In the gut microbiome studies, how do scientists design experiments to establish directionality in the relationships they observed, does health produce a particular microbiome signature or does a healthy gut be get a healthy individual?"
Amy Cheng Vollmer:
So those experiments are difficult to do with human subjects because you would really want to kind of clear out the microbiome using kind of heavy antibiotics. And there are some issues that we worry about with that. Certainly the gnotobiotic mouse studies and the humanized mouse studies have given us a sense of direction.
Amy Cheng Vollmer:
Sometimes we're presented with opportunities because individuals have had heavy courses of antibiotics or had surgery or after a colonoscopy where they're cleared out we can start to look. That's why causality is very difficult, it's correlation. And now that we know that the arrow is kind of a double ended arrow, that's what makes things both interesting and complicated.
Dina:
We have one from a current student, Eva Carolzach of 22. She has a personal interest in studying the biological basis of eating disorders. And I know one of your slides addressed under nutrition, but I just want to emphasize her question was, "How my dietary changes, especially restriction negatively impact your microbiome, are there specific things that are affected?"
Amy Cheng Vollmer:
I'm sure there are with extremely restricted diets. One of the things that happens is you usually are limited for vitamins that we can't make and that our gut microbiomes deliver for us. And micronutrients, zinc and magnesium and vanadium and those things on the periodic chart that nobody pays attention to that are actually pretty important. Those are often missing or lacking, and that can cause severe issues. One of the first places that shows up in individuals with eating disorders is in their skin because your skin turns over very rapidly and it's so visible.
Amy Cheng Vollmer:
And so people look like they have beri beri or scurvy which are vitamin deficiencies. So when that happens, there's probably a limit, a bottleneck in who's left in your microbiome and the balance of chemicals that are made between the butyrates and the acetates and the propionates and all the short chain fatty acids probably changes that may affect the physiology of the host, which then could feedback into behavior that restricts even more.
Amy Cheng Vollmer:
So breaking that cycle at some point is really important but it's very delicate because at the point where someone has an extreme eating disorder you have to very careful about how you ramp back up.
Dina:
Thank you. I wish I could ask more questions because there are so many that came in, but there's so much praise that's coming for your presentation, Dr. Vollmer. So thank you so much and thank you for so much of your time tonight.
Amy Cheng Vollmer:
Well, I have to say I'm seeing names kind of as people are adding to the chat, many of whom I recognize some from my microbiology classes. A few names from introbio have crept in there. The good news is I don't remember how anybody did in anything, that's not how I can remember any of my students. I'm pleased that this forum has allowed such great interactions, I'm happy to take your email questions, if you want to send me email, I might not answer right away. I've got a week and a half of classes left but I'm happy to hear from you. As always, it's great to be involved with Swarthmore alumni, even if it's not in person, and I really appreciate being able to participate in SwatTalk.
Dina:
Thank you so much. I feel like I returned back to campus for a class. So thank you again.
Amy Cheng Vollmer:
Oh, let me wish [crosstalk 01:07:51].
Dina:
Yeah.
Amy Cheng Vollmer:
Take care everyone and please be safe.
Dina:
Stay well everyone. Bye.
Amy Cheng Vollmer:
Bye.
Amy Cheng Vollmer:
The recording will be available in a week or so. Bye now...
