Some Microbes Have Been With Us Since Before We Existed

Certain gut bacteria have evolved in parallel with apes, so that their family tree perfectly mirrors our own.

Around 10 million years ago, a population of African apes diverged down two paths. One lineage gave rise to gorillas. The other eventually split again, producing one branch that led to humans and another that forked into chimpanzees and bonobos. This is the story of our recent evolutionary past. It’s also the story of some of the microbes in our guts.

We have tens of trillions of bacteria and other microbes in our guts—at least one for each of our own human cells. Some species within this microbiome are passers-by, which we pick up from our food and our environments. But others are much older companions.

Andrew Moeller from the University of California, Berkeley, has found that there are a few groups of human gut bacteria whose history pre-dates humanity. Their ancestors lived in the guts of ancestral apes, and as those ancient animals diverged into modern species, the microbes did, too. In technical terms, they co-speciated. In simpler ones, if you drew out their family tree, you’d get ours for free; you could reconstruct the evolution of apes simply by comparing the right bacteria in their bowels.

“Some of the bacteria in our gut are derived from very ancient lineages that have been passed down through the primates for millions of years,” says Moeller. “They’re like our genes in that sense.”

Co-speciation between animals and microbes is fairly common. Aphids, those sap-sucking banes of gardeners, carry a bacterium called Buchnera which provides them with essential nutrients that are missing from their meals. Their alliance was formed between 200 and 250 million years ago, when the dinosaurs were just starting out, and their fates have been entwined ever since. The family trees of aphids and Buchnera strains are also perfect matches.

That’s kind of a special case, though. Buchnera lives inside the cells of its host, and nowhere else. It’s also strictly passed from mother to offspring via egg cells. Co-speciation was almost a foregone conclusion. Our gut bacteria have no such constraints. They live freely within the ecosystem of our bowels. They can move vertically from parent to child, but also horizontally from peer to peer. It’s much less obvious that they should have co-speciated with us at all.

In 2010, Howard Ochman found hints that they might. He was the first to show that a family tree constructed using the microbiomes of apes mirrored the one drawn from their own DNA. So, for example, the microbiomes of three chimp subspecies were more similar to each other than to bonobo microbiomes, and more similar to bonobo microbiomes than to human ones.

But Ochman just looked at microbiomes as a whole. Moeller, his graduate student at the time, decided to look for particular species and strains of bacteria whose histories match our own.  Moeller relied on a large bank of stool samples, collected from wild apes in Cameroon, Tanzania, and the Democratic Republic of the Congo, and from wild humans living in Connecticut.

He found many examples of co-speciation within two families of bacteria that are common in our guts—the Bacteroidaceae (“BACK-tuh-roy-DAY-see-ay”) and the Bifidobacteriaceae (“BIH-fih-doh-BACK-tee-ree-AY-see-ay”). Some of the co-speciating microbes, like Bacteroides vulgatus, are familiar to researchers; others are a mystery, and haven’t even been named yet.

But it’s not as if the entire microbiome is co-speciating neatly, or even most of it. “There are some bacteria that seem to track their host lineage perfectly and others that don’t seem to care which host they’re in—they’re just jumping around,” says Moeller. For example, one lineage had jumped from chimps to gorillas, and another recently moved from humans to chimps.

One entire family—the Lachnospiraceae (“LACK-no-spih-RAY-see-ay”)—is especially prone to such jumps, perhaps because they can form hardy spores that allow them to survive outside the gut. Many gut bacteria can also form spores, which means that these horizontal jumps may be the rule rather than the exceptions.

Still, this study “shows clear potential for the co-evolution between humans and their gut microbiome,” says Britt Koskella, an evolutionary biologist at the University of California, Berkeley, who was not involved in the study. “It also raises interesting questions about how modern human behavior, such as cleanliness and changes in diet, might be altering those tight associations and leading to increased health problems.”

She’s talking about the hypothesis, popularized by Martin Blaser, that we are inadvertently evicting longstanding bacterial partners from our bodies. Moeller certainly found some evidence for this. He showed that some lineages of co-speciating bacteria are present in gorillas, chimps, and bonobos, but their counterparts are missing from Western guts (although some still exist within people living in rural Malawi).

That raises two important questions. First, why are these microbes disappearing? Blaser and others have blamed the trappings of modern life, including wanton use of antibiotics and an obsession with sanitation. That’s possible, but in a previous study, Moeller showed that the diversity of the human gut microbiome has been falling for a very long time; it’s lower among human hunter-gatherers than chimps or gorillas, and then lower still among Western city-dwellers. “I think it probably started when humans started cooking our food,” he says. “Immediately, you’re going to lose some ability to host a complex consortium of bacteria, because you don’t need them anymore.”

Which brings us to the second question: “Are these lost groups doing important things in chimps and bonobos, which we’re not getting?” Moeller asks. Some would argue that these microbes must have be doing something important, given their long history with us. Perhaps they helped to digest our food or calibrate our immune system, and perhaps their absence partly explains why inflammatory and autoimmune diseases are on the rise.

It’s a compelling idea, but a speculative one. We still don’t really know how these ancient microbes are affecting us, or vice versa. Which means, according to Katherine Amato, from Northwestern University, that we can’t strictly claim that we’re co-evolving with them. “Do these patterns of co-speciation matter to us in the grand scheme of natural selection?” she asks. “Does having the wrong strain make individuals less reproductively successful?” Jessica Metcalf, from the University of Colorado in Boulder, has similar questions. “What do bacteria that co-diversified with their hosts have in common?” she asks. “And are they more important to their hosts than ones that were acquired through the environment?”

“When we start to be able to answer these questions is when things will really get exciting,” says Amato. To do that, she thinks researchers will need to look at the entire genomes, to see if changes in the microbes correlate with new traits or abilities in their hosts. They’ll also need to move outside the apes and think about monkeys, lemurs, and other primates. “Searching for patterns among only four host species may be over-simplifying aspects of the story,” she says.