Gut bacteria recap the evolution of apes

By Ed Yong | November 16, 2010 5:00 pm

Gorilla

Welcome to Humanville, a lively metropolis of over a hundred trillion bacteria living in and around your body. Like many cities, most of Humanville’s denizens live in its centre – the bowels – although a sizeable population have set up shop in the surrounding suburbs of the skin. The residents of Humanville, collectively known as the microbiome, are model citizens. They’re the unseen force that processes much of the city’s food supply, regulates its defences against invaders, and keeps it working like a healthy, well-oiled machine.

Humanville isn’t alone. It is one of many similar bacterial conurbations, each thriving in the body of a different animal. Those that live in humans have understandably received the most scientific attention. But Howard Ochman from the University of Arizona wanted to go further afield to study at the locals who live in neighbouring cities – Gorillaville, Chimpville, Bonoboville and so on.

He found that the evolution of these microbes mirrors those of their hosts to a remarkable degree. As an example, the bacteria found in two species of gorilla are more closely related to each other than either one is to the inhabitants of Humanville. The bottom line: you could reconstruct the evolution of the apes, simply by comparing the bacteria in their bowels (provided you used the right methods; more on this later).

In some ways, this isn’t surprising. In the womb, Humanville is empty. It receives its first batch of bacterial migrants at the moment of birth, when they flood in from mum’s vaginal tract. If this was all there was to it, you would naturally expect the bacteria to evolve in the same trajectory as their hosts. But the environment can also change this microscopic community.

As we get older, the bacteria of Humanville change to cope with different sources of food, from the milky diets of babies to the complex carbohydrates of adulthood. As adults, our diet also affects our bowel buddies. In African villages where high-fibre diets are the norm, Humanville is populated by plant-digesting microbes that are relatively rarer in the guts of fat-guzzling Europeans. Diseases, courses of antibiotics, and changes in body weight can also shift the balance of the microbiome, causing some members to move in and others to leave.

But Ochman’s work suggests that these individual variations obscure a broader pattern. Geography, diet and disease aside, the main thing that influences the members of these bacterial cities is the species of the host. There may be millions of variations on the Humanville theme, but as a whole, these communities share common traits that distinguish them from the bacteria in Gorillaville, Chimpville and so on.

Two years ago, Ruth Ley also found that communities of gut bacteria are mainly influenced by the species of their host. By sampling the dung of over 60 species of mammals, including 17 primates, she found that even zoo animals from separate continents had similar microbes in their stools.

However, she also found that the evolutionary relationships between these communities were odd, and certainly nothing like the family trees that link their hosts. Instead, the bacterial tree seemed to be defined by diet. For example, there was a ‘generalist’ branch that included bacteria from humans, gorillas, bonobos, lemurs, elephants and armadillos. The microbes from chimps, orang-utans and flying foxes clustered on a different part of the tree entirely.

But Ley’s study, large though it was, involved a lot of captive animals that were raised in zoos. To get a more realistic perspective on the gut bacteria of wild apes, Ochman relied on a massive bank of ape poo, collected by experienced trackers from remote sites across central Africa. All in all, he analysed 26 samples taken from two species of gorilla (western lowland and eastern lowland), bonobos, three subspecies of chimps, and humans.

These samples, combined with a far more detailed look at the genes of the bacteria within, gave Ochman a family tree that mirrors the relationships between the host species. The three versions of Chimpville – one for each subspecies – all clustered together on a tight branch, as did the two Gorillavilles. The host species completely overwhelms the influence of things like geography. For example, one of the chimp groups lives in the same area as one of the gorillas, but their gut bacteria are only distantly related.

The two diagrams below highlight this match – the one on the left is built using the apes’ own DNA, and the one on the right comes from the DNA of their bacterial tenants. The odds of randomly getting such a close match are just one in two million.

Ape_trees

Of course, it could be the case that the apes all eat unique diets, and that it’s this that determines in the bacteria in their bowels. But Ochman ruled out that explanation. In his stool samples, he also sequenced genes from chloroplasts, small compartments inside every plant cell that carry their own small genomes. These genes tell us about the types of plants that the apes were eating, and Ochman couldn’t find any clear differences between the veggie diets of the different species. As he concludes, “It seems after all that you are not what you eat.”

NB: I use “bacteria” in this story as an unfortunate shorthand. Alongside bacteria, gut communities also contain archaea – a group of microbes that look superficially similar to bacteria but are vastly different in terms of their biochemistry and evolutionary history.

Reference: PloS Biology http://dx.doi.org/10.1371/journal.pbio.1000546

Image: by me

More on microbiomes:

If the citation link isn’t working, read why here
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An introduction to the microbiome


Comments (9)

  1. Nathan Myers

    “Gut bugs” might be a better choice of term than “gut bacteria”.

    This is a really interesting report. Now we need to understand how each species succeeds in favoring its characteristic flora and keeping the rest out.

  2. Guy Plunkett

    Fascinating.

    RE: “I use ‘bacteria’ in this story as an unfortunate shorthand.” This is why retaining the term “prokaryotes” is useful; we often need a shorthand for “archaea and/or bacteria.”

  3. @Guy – But prokaryotes is completely useless when talking to a general audience, which is the level I’m aiming at. Try asking how many people on the street know what it means.

  4. Shade

    Just make the word a link to wikipedia or other site, and if they can’t be bothered to read what a prokaryote is that is their loss.

  5. Are you being serious? While I’m at it, why bother writing papers up at all? I could just put the entire text up and then put links from any technical term across to the relevant Wikipedia page. I could probably write a script to do that for me and get some sleep.

  6. natselrox

    Great writeup as usual, Ed!

    I posted this story on the RatSkep forum and Calilasseia pointed out a research about a similar study with regards to lice and how the lice in humans, chimps and gorillas mirror the phylogenetic tree of hominids. For those interested, the article can be read here: http://www.rationalskepticism.org/evolution/evolution-of-hominids-mirrored-by-gut-microbiota-t15973.html#p582411

  7. Nice write-up Ed. And I back your decision not to use the term prokaryote — unless you want to spend a paragraph defining it for the lay audience (which is the audience for this blog). After all, what you’re writing is “Not Exactly Rocket Science.” I also agree that linking to Wikipedia would be hazardous at best, given the unpredictable nature of its entries. Cheers!

  8. @ Matt – Thanks. And of course, I have used the term prokaryote before on this blog – twice – but only when the story absolutely required it and only after careful definition.

    This is all Writing 101 stuff. If you make your audience do extra work to understand what you’ve written and that audience goes somewhere else, it’s not because they’re lazy, it’s because you’re a rubbish communicator.

    @Natselrox – Awesome link. Thanks for that.

  9. Sums it up perfectly: “If [your] audience goes somewhere else, it’s not because they’re lazy, it’s because you’re a rubbish communicator.”

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