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.”