Gut Bacteria Predates Humanity, Study Finds

(CN) — The history of the bacteria in our guts predates our species, evolving in parallel with our ape relatives over millions of years, according to a new study.

Researchers detailed how microbes in our ancestors' intestines split as humans continued to evolve and split in the ape family tree, beginning with ancestral African apes.

Scientists had thought that our gut bacteria were largely derived from where we live, our diet and the kind of medicine we take. However, those factors may be less important than evolutionary history.

"It's surprising that our gut microbes, which we could get from many sources in the environment, have actually been co-evolving inside us for such a long time," said Howard Ochman, a professor of integrative biology at the University of Texas.

The findings, which were published Thursday in the journal Science, demonstrate that several lineages of the most common bacterial taxa — a group of one or more populations of an organism or organisms — in the human gut are the results of cospeciation.

Cospeciation occurs when two or more lineages of organs or organisms that are ecologically associated differentiate into new biological species. Cospeciation is fairly uncommon.

The researchers say that cospeciation with chimpanzees, bonobos, humans, and gorillas over the last 15 million years has led to the current bacteria taxa in our guts.

"Divergence times of these cospeciating gut bacteria are congruent with those of hominids, indicating that nuclear, mitochondrial and gut bacterial genomes diversified in concert during hominid evolution," the study says.

The team analyzed modern species by digging through feces samples from Cameroonian gorillas, Tanzanian chimps, Congolese bonobos and humans from Connecticut. To demonstrate any potential evolutionary relations between gut bacteria, the scientists then ran genetics tests on three different groups of bacteria, which account for roughly 20 percent of the human gut bacteria in total.

Observations of a gene called gyrase B led scientists to determine that when a common ancestor became two new species, at least two of the groups of gut bacteria appear to have done so as well.

"I think it's really interesting, because it's been difficult to find signatures of cospeciation," Ran Blekhman, an assistant professor in human genomics at the University of Minnesota, told the Guardian. Blekhman was not involved in the study.

The study referenced two situations where bacteria split into distinct strains at roughly the same time as their hosts were splitting into distinct species. The team explained that one such bacterial split occurred about 15.6 million years ago, as the gorilla lineage diverged from the other hominids. The other bacterial split began about 5.3 million years ago, as the human lineage separated from the lineage leading to chimps and bonobos.

Among the three families of bacteria that the researchers analyzed — Lachnospiraceae, Bacteriodaceae and Bifidobaceriaceae — the latter two had evolutionary trees that closely resemble the hominid evolutionary tree, with some minor differences.

The Lachnospiraceae group of bacteria was apparently transferred at least four times between different host species, according to the researchers. They speculate that since bacteria form spores and can therefore survive outside their hosts for extended periods of time, they should be able to pass between different species easily.

"We've known for a long time that humans and our closest relatives, the great apes, harbor these bacteria in our guts," said Andrew Moeller, a postdoctoral researcher at the University of California, Berkeley. "And the biggest question we wanted to answer is, where did these bacteria come from? Did we get them from our environment or from our evolutionary history? And how long have they persisted in host lineages?"

The team also mentioned several potential applications for their research, including fecal transplants for patients whose gut bacteria have been suppressed by antibiotics, tracing migration patterns over millions of years, and establishing a more nuanced understanding of all species.

"What's most exciting to me is the possibility that this codiversification between bacteria and hosts could extend much further back in time," Moeller said. "Maybe we can trace our gut microbes back to our common ancestors with all mammals, all reptiles, all amphibians, maybe even all vertebrates. If that's true, it's amazing."

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