Researchers: Gut microbes evolved with humans

In the dark, oxygen-free zone of your large intestine is a community of microbes that help you digest food, fight off harmful pathogens, and 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 gut microbes have been passed down from generation to generation over millions of years, evolving alongside us in a process called cospeciation.

Before launching this study, the research team, led by Andrew Moeller, a postdoctoral researcher at UC Berkeley, and his former adviser, Howard Ochman, an integrative biology professor 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 whether different animals just pick up different microbes from their environment, was up for debate.

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 the 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 are.

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 human and chimp ancestors 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.

The new findings raise new questions — for example, how far back does this primordial gut microbial community go? Can it be traced to the first ancestral mammal, or 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.

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.”

Scientists say microbes may also influence our emotions. There are more than 100 trillion microbes living in our intestines, and gathered together, they would weigh more than our brains.

In his new book, “The Mind-Gut Connection,” Dr. Emeran Mayer explains how these organisms insert themselves into the running dialogue between the brain and the gut. In the process, he says, they help determine how stressed out we get, when we get sick and how quickly we recover.

Mayer is the director of the UCLA Oppenheimer Family Center for Neurobiology of Stress and co-director of the CURE Digestive Diseases Research Center. He has been studying interactions between the gut and the mind for 30 years.