Revealing the twenty most important species living in your body

What lives in you? It is a simple enough question. Yet, for most of history, it has been unanswerable. Finally, in just the last few years, we have begun to get a picture of the creatures on which you depend for existence, the creatures that constitute, literally, the majority of your cells, the creatures being dragged around as you cook breakfast, drive your car, shower or do anything else. It is a fuzzy picture, seen through the lenses of genes rather than through a microscope, and yet it is the best we have ever had.

What exactly do we see? One of the first things is simply which species are common and which are rare. These simple data, cloaked in technology, are a kind of breakthrough. They represent a first step into a new land, a step in which what we are able to appraise is akin to what tropical discoverers encountered in the 1800s.

Here, I am reminded of Henry Walter Bates, that explorer-scientist who embedded himself in the Amazon for several decades. While there, Bates found roughly 14,000 species of animals, of which roughly 9,000 were new to science. Bates wrote back to his colleagues in Europe about the birds, bees and especially the beetles. Every log he turned revealed to him something new and so he turned and turned, losing himself in the search to lay hold of the simplest features of the unknown, an unknown that he came to believe was everywhere, eating, mating and calling to him, leading him further down each path.

The explorers who are now revealing your body, all of our bodies, are superficially different than Bates. They wear lab coats. They do not need to go outside. They deal neither in the glamour of flittering wings nor of shimmering elytra but instead with fecal samples on toilet paper shoved into envelopes and sent to labs to be processed. One man’s feces, as they say, is another man’s rare butterfly. OK, probably no one says that, but it is true that it is just such samples through which the wildernesses of our guts are beginning to be discovered.

Recently, The American Gut project (on which, in full disclosure, I am a collaborator) revealed the results of samples of gut microbes from 1268 people.  As far as I know, this is the largest human microbiome study to date, far larger than that of the Human Microbiome Project itself. In as much, it will provide a window into a variety of phenomena taking place in guts across America, including which species are common and which are rare (and hopefully, eventually, why). These scientists have come back from the jungles and announced their finds; or at least come back from the computer to announce the availability of the data. What does this look like to those of us more distant from the action, those of us waiting for a letter from the far reaches of our inner jungles? I’ll tell you. Adam Robbins-Pianka, a graduate student in Rob Knight’s lab, just sent me an email. His equivalent of Bates’ letter about the Amazon was, the more modern, “Sorry this took so long. Here they are.” I think I responded with the elegiac, “Cool.” It seems OK at this point to long for the days of Bates.

But back to the microbes. What was in there, in the email, was a list of the bacteria species found in human guts, beneficial bacteria (or at least on a species by species basis, bacteria that are best thought of as beneficial until proven otherwise). There were a total of just over 1000 species, fewer species than I would have expected and yet more species, for example, than there are species of mammals in the Americas. For these species, Adam tallied for me two types of commonness, how many of the 1268 people they were found in and, when in those people, a crude measure of their relative abundance (for those in the know, the proportion of reads which they constitute). As I’ve said elsewhere, in considering another habitat, belly buttons, these kinds of commonness relate to those we think of in rain forests or other macro ecosystems. In macro-ecosystems, the purview of our ordinary daily experience, species that are both frequent, and when present, abundant play a disproportionate role in ecosystem process—if they are trees, they make the most leaves, if they are termites they decompose the most matter, if they are ants they eat the most termites. It is reasonable to believe the same is likely to be true of bacteria. If they are the most common bacteria on our skin or in our guts, well, they are the most likely to benefit or cost us, to do something of consequence one way or another. We can’t rule out that rare species also matter. Some definitely do. An initially rare pathogen, for example, can prove deadly. But we know that the common species matter and if they are both common and frequent, they matter on nearly all of us; they should be the ones we all know. But they are not.

Abundance freq microbes

Figure 1. The first thing one sees in looking at these data is that those species found on many people (to the right on the panel above) tend to be the same ones that are abundant when present (higher values on the y-axis), which is to say, with a few interesting exceptions, there are true oligarchs in the gut, species that dominate human guts, species that are undoubtedly among the most common on Earth, species that number in the trillions in every room you have ever gone into, because you bring them with you.

As revealed by the American Gut data, the very most common bacterium in the human gut is a rod-shaped species of the genus Bacteroides (in the family Bacteroidaceae). It appears in nearly all adults. It is also one of the best-studied species in the gut and yet, by any realistic reckoning, it is more poorly known than the rarest bird species of the Galapagos. What we do know, is that when present, this species is abundant, the white oak of the intestines. And when abundant, this microscopic oak benefits you everyday. Conversely, where it is rare, problems seem to arise, obesity, inflammation, diarrhea. You can take the girl out of the city, in other words, but you shouldn’t take the Bacteroides out of the girl.

(Rarer species of Bacteroides, of which there are many, possess their own superpowers, such as the ability to digest sushi seaweed, an ability discovered in a Bacteroides species found, so far, only in Japanese guts. What specialties lurk in the other strains found here one can only speculate).

Whereas Bacteroides is common in essentially everyone, one of its cousins, a species of Prevotella, the seventh most common species in the American Gut samples, becomes more common in vegetarians.  Meanwhile, a species of the related Parabacteroides is also very common, but all we know about it is what we can infer about its biology based on its relatives.  “If Parabacteroides is like Bacteroides,” the sentence begins, it is likely to be similar. But then again, just as when someone makes the same assertion about you and your kin, such assertions are not always true.

Most common gut species

The second most common bacterial species in the gut, a species found in all but one hundred of the twelve hundred people who sampled themselves, does not yet have a name. Neither does the genus to which it belongs. All we know is that it is very common and is a member of the family Ruminococcaeae. Yes, the second most common species in human guts does not even correspond to a named genus. Yes, this species is probably helping to sustain your life and lifestyle, even though it has no name. Yes, naming and better understanding this species seems very important, but no one has gotten to it yet. I suspect no one will for a while. Such are the realities in a new land. The mapmakers are few relative to the dimensions of the terra incognita, the miles of hills and valleys of our inner continents.

Another unnamed species of the genus Faecalibacterium in the same family is the third most common species. Both this and the Ruminococcaceae species are members of the bacterial order Clostridiales which also includes the fourth most common species of bacteria in guts, a species of the family Lachnospiraceae, and the fifth most common species, a Streptococcus. Streptococcus species are most often found in the mouth and stomach where they can be mild pathogens; just what they are doing in the gut (= large+ small intestines) is less clear. As for species of Lachnospiraceae,they are fiber specialists. They need the stringy, hard to digest stuff to thrive. In the absence of fiber, they grow rare. When they go rare, our risk of certain cancers may go up.

The Clostridiales also contain the thirteenth (Ruminococcus), sixteenth (Veilonella), eighteenth (Coprococcus), and nineteenth (Clostridium) most common species. The very worst species of Clostridium, “C. diff.,” can be deadly, but most are not. Just what turns a good Clostridium bad, we don’t know. Could we use good Clostridium to fight bad?

The fourteenth most common bacteria in fecal samples, a species of the genus Akkermansia (in the family Verrucomicorbiaceae) may actually be more common than it seems from these samples. It is so intimately associated with the gut lining that it may “wash out” in fecal samples less often than other species. Species of Akkermansia seem to be tightly linked to obesity and inflammatory disorders. Treat them poorly, at the expense of both, it seems, your slender figure and your health.

Also on the list of the top twenty bacteria in your gut are three species that while present in many studies, usually don’t get mentioned. They are listed in the tables of who was present without comment. Could they be incredibly important? Maybe. Probably. Maybe not. At number 9, Neisseria is very abundant when it is present. Interestingly, it is absent in about half of those people sampled. What does that mean? We don’t know. Also, a species in the family Planococcaceae (that could not readily be assigned to a genus) is the tenth most common and a species of the genus Rothia is twelve most common. That is all I can tell you. Frankly, how little we know about these common species is scandalous and, as a biologist, thrilling.

The twentieth most common microbial species in human guts is actually the result of a bit of evolutionary chicanery. As is now well-documented and was originally advocated by Lynn Margulis, the chloroplasts in plants, those power centers in which sunlight is converted into sugars, are actually the descendants of cyanobacteria that were ingested by the species from which the rest of the plant cells descend. It is, in other words, a bacterium inside a plant. As a result of this history, when someone has plant material in their gut we see the evidence in the form of chloroplast-bacterial DNA.

Of course, among a thousand species, there are also many others that are sometimes common or interesting in other ways. With the help of some talented science writers, we’re trying to share many of these species’ stories with you via essays contributed to our Invisible Life Project. For example, a species of Bifidobacterium commonly found in breast milk was found in 881 people (though it was rarely abundant even though often present). Florence Williams writes about this species and breast milk more generally. It turns out breast milk is a smorgasbord of microbial goodness, a goodness lost on a generation of formula-feeders.

A species of Corynebacterium was very frequent, but this is likely an artifact of sampling in as much as Corynebacterium, as Veronique Greenwood describes, is usually a skin bacterium, one which might have been rubbed onto toilet paper samples by overly eager participants. Staphylococcus skin bacteria were also common, presumably for the same reason.

A species of Lactobacillus was found in 661 participants. This species is probably one of the same ones found in yogurt, as Christina Agapakis expounds. Perhaps it is more common in those who consume yogurt with active cultures. A large industry is predicated on this idea; it would be nice to test this assumption.

Two hundred and seven people housed methanogens, microbes that produce methane. Those individuals, as Gilberto Flores points out, may actually be contributing to global warming one fart at a time.

Five hundred and sixty six people supported populations of a species of PseudomonasPseudomonas species can, as Gaddy Bergmann points out, go bad, though they usually don’t.

And all of this is just a glimmer of what is really going on, a measure of what we see leaving the gut. We are, in a way, earlier in the story of the discovery of what is going on in our guts than Bates was in the Amazon. At least he could chase the birds and insects that fascinated him. Our ability to chase is limited. We use tools through which we see the microbes indirectly. We fumble with colons filled with species on which we clearly depend shining the diffuse but weak light of our modern techniques. Upon noting what it has revealed, we send emails to each other saying, “Look what I have found, pretty cool.” And then we get back to looking, scribbling away with the ones and zeros of our modern notebooks with an eagerness Bates would have recognized, an eagerness to lay hold of what is ever more obviously mostly unknown.

Header image credit: Proceedings of the National Academy of Sciences, March 11, 2008: Bacteroides fragilis surface capsule expression.

By | 2016-11-22T13:47:16+00:00 December 10th, 2013|

About the Author:

Rob Dunn
Rob Dunn is a biologist and writer in the Department of Applied Ecology at North Carolina State University. Central to all of his work is the sense that big discoveries lurk not only in faraway tropical forests, but also in our backyards and even bedrooms. The unknown is large and wonderful and Dunn and his collaborators, students, and postdocs love to spend their days in it.

12 Comments

  1. Jay December 11, 2013 at 1:12 pm - Reply

    Great post! Seems like there are huge health implications and a lot of analysis left here to do. Is there a similar project for the bladder?

  2. Mike Crowl December 12, 2013 at 5:21 pm - Reply

    Apart from the silly throwaway line about farts contributing to Global Warming (what? we’re gonna put a tax on humans farting next?) this is a great article. Incidentally, though it seems from your paragraph about methane and farts that Gilberto Flores makes a connection between certain people’s farts and global warming, in fact he never mentions the latter in the article you’ve linked to.

  3. Gilles Arbour December 14, 2013 at 2:39 pm - Reply

    Thanks Rob for this fascinating article. My understanding is that in total around 1,000 different microbe species have been identified so far in all of the 1,268 individuals tested. Some microbes are present in almost everyone’s gut while others are only present in some people. What I would like to know is the number of species in individual guts. For example: Do 70% of the people tested have over 500 species in their guts? Or 300? Do 5% of the people tested have less than 100 species? Are there some people with more than 1,000 species? What was the smallest and largest number of species found in in anyone’s gut? That kind of information.

    I am thinking about ecosystems in general. There are various types of healthy ecosystems. They don’t have the same species but they have a certain number of species that keeps them strong and provides the ability to perpetuate itself. I am wondering if the same idea applies in the guts. If one has a long term antibiotic treatment that decreases the number of species wouldn’t that person become more susceptible to some disease?

    I am reminded of a high school biology project where each of the students would gather water, soil and plants from a thriving river besides our college. Enough to fill up a good size aquarium. Then, week after week, we had to identify and quantify the observed species, make graphs etc. Just a simple high school project. Within months, in every single aquarium, the biodiversity would dwindle down to very few species, mostly cyanobacteria. In other words each aquarium had such a limited ecosystem that it was not sustainable. The whole biota became very unhealthy and weak. Are we doing the same thing within our guts?

  4. […] word on turd. The most abundant species in human faeces. Fascinating finds, shared by Rob Dunn. Read of the […]

  5. Rita Sewell December 15, 2013 at 10:57 pm - Reply

    Who would have believed that the human gut would be our next amazing frontier. The potential wisdom we can gain from this adventure could change much of our understanding of disease and health. I changed my eating habits 7 years ago. As a result I have not had a sick day since, I heal quickly and I have no significant mood swings any longer. I believe my gut flora are thrilled with my decision and have rewarded me… perhaps.

  6. bernie cullen December 17, 2013 at 12:54 pm - Reply

    You say the choloroplast-bacteria found in some people’s guts are just the remains of the vegetables they ate for lunch–could any of the other bacteria found in very small amounts in some people’s guts just be from food they had recently eaten? Intentionally (yoghurt, probiotics) or unintentionally (spoiled meat, unwashed vegetables/fruit from garden)? Probably the number of chloroplasts is far greater than any bacteria most people eat, but maybe some other bacteria are more resistant to getting from the mouth to the stomach and surviving intact enough to be detected.

  7. Annamaria Talas December 24, 2013 at 4:22 pm - Reply

    Hats off to the explorers of the vast ecosystems inside our body. Gargantuan task to tease apart the connections of our microbial residents with one another and with our cells. Could network science fast track the work?

    If I’d need to single out one species, I’d be interested in B.fragilis. First I’d like to know if there is an association between the health of the immune system of the volunteers and the presence of B.fragilis in individual guts. I’d also like to eavesdrop any conversation that might be going on between them and our immune cells. What’s the message?

    Keep the flag flying, many congratulations!

  8. JohnR January 6, 2014 at 4:33 pm - Reply

    I’m a lot more interested than I otherwise would have been since I found I had a bad case of SIBO (which seems to be a rather diffuse and squabbling sort of diagnosis, but judging from my outcome, a very real one). Changing my diet to one less rich in complex carbohydrates (ie almost everything that gives life meaning and pleasure), I dropped over 40 pounds in less than a year and find myself in dramatically better health, including far lower methane production. No more intolerable gastric distress (so far, anyway) and my wife thanks the doctor every day with tears in her eyes. God only knows what the little buggers are doing to us and each other in the jungles of our guts, but reading about the various forms and effects of “mind-controlling” parasites, it gives one to pause and ruminate on the possibilities..

  9. Around the web January 24, 2014 at 3:13 am - Reply

    […] YourWildLife.org recently published an article where they “revealed” the twenty most common species living in the human body. […]

  10. […] also interesting to note that while the most dominant group of bacteria in the American Gut is the genus Bacteroides – by a country mile – this group of bacteria is a minor, minor player in the Hadza gut. Almost […]

  11. […] also interesting to note that while the most dominant group of bacteria in the American Gut is thegenus Bacteroides – by a country mile – this group of bacteria is a minor, minor player in the Hadza gut. Almost […]

  12. […] a side note, the most abundant genera or group of bacteria in the American Gut Project is Bacteroides of the phylum Bacteroidetes.  In […]

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