Our gut microbes have lived with us since before we were human

In the dark, oxygen-free zone of your large intestine there is a community of microbes that help you digest food, fight off harmful pathogens, and which may even affect your mood and emotions.

Now, a new study suggests that this intimate relationship between our microbes and ourselves is older than the human species itself.

In a paper published Thursday in Science, researchers provide evidence that our gut microbes have been passed down from generation to generation over millions of years, evolving right alongside us in a process called cospeciation.

Before launching this study, the research team, led by Andrew Moeller, a post-doctoral researcher at UC Berkeley, and his former advisor, Howard Ochman, professor of integrative biology at the University of Texas, already knew that humans and their closest living relatives — chimps, bonobos and gorillas — all had a distinct microbial fingerprint that made it easy to distinguish one species from another. But whether those communities shared a single common ancestral community, or if it is just that different animals pick up different microbes from their environment, was up for debate.

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In their earlier work, the authors relied on a type of genetic analysis that allowed them to see what major groups of bacteria were in the guts of each of the animals they studied, but this technique could not differentiate between different strains of the microorganisms.

“If you think of the microbial community as a garden, previous methods could tell us if there were trees, shrubs or flowers, but not if they were dogwoods, roses or hibernums,” Moeller said.

In this paper, the authors used a new type of analysis that allowed them to take a more detailed look at the types of bacteria in fecal samples from wild chimps, bonobos, gorillas and humans.

When they compared the data, they found that the microbial population of the human gut is most similar to the population living in the guts of bonobos and chimpanzees — which are closer to humans on the evolutionary tree than the great apes.

The authors also found evidence that bacteria in the guts of humans and chimps split into different strains 5.3 million years ago — about the same time that humans and chimps first split into different species. The split between the gorilla microbes and human microbes went even further back to 15.6 million years ago, the same time that the gorilla lineage diverged from the other hominids.

“The only explanation from this very non-random pattern is that the bacteria has diversified along with the humans and the apes,” Moeller said.

In other words, as our ancient relatives separated into different species over time, their microbes did too.

As often happens in science, the new findings suggest a whole pack of new questions. For example, how far back does this primordial gut microbial community go? Can it be traced back to the first ancestral mammal? Does it go even further back to the first vertebrate to live on land? And did the genetic changes in the microbes lead them to perform different functions in the guts of different animals, or were the changes simply neutral?

“This is all something we are looking into,” Moeller said.

But one thing he can say for sure is that despite major changes in lifestyle and diet, there is a direct line of descent between the microbes of ancient hominids and those that live in our guts today.

“There is no question that what you eat and what medicine you take can affect the overall composition of your microbiome, but this study adds a new dimension to that,” Moeller said. “Even though we have totally changed our lifestyles, there are some bacteria that have persisted over millions of years.”

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