Gut microbes less diverse in humans than in apes

Humans have evolved a less diverse mix of gut microbes than great apes have.

Compositions of microbial communities in the gut steadily changed as African apes evolved, but in humans such shifts have reached a frenzied pace with most alterations weeding out microbe diversity, Andrew Moeller, an evolutionary biologist at Yale University, and colleagues report November 3 in the Proceedings of the National Academy of Sciences.

Great apes and humans share a common set of intestinal microbes, the researchers concluded after examining fecal samples from wild chimpanzees, bonobos and gorillas and from people living in the United States, Malawi, Tanzania, Venezuela and Europe. Moeller and colleagues traced how each species’ microbes changed as the human and ape branches of the primate family tree split from each other. In the time since the last human-ape common ancestor, between 8 million and 19 million years ago, the relative microbial mix has undergone 35 major shifts. Half of those have occurred in the human lineage, the researchers found. Those shifts left humans with a few types of bacteria dominating the gut as well as some rare varieties mixed in. Apes’ guts still contain a wider variety of bacterial types, but with each type in fairly low abundance.

Bacteroides bacteria, which are associated with eating meat, increased in abundance in human guts to five times the level found in apes. Another microorganism called Methanobrevibacter, which helps break down complex carbohydrates from plants, decreased by a similar amount in humans compared with apes.

Human microbiomes have continued to change rapidly. People living in rural Malawi had gut microbe communities more similar to bonobos than people in the United States did.

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Moeller says environmental differences between humans and apes may account for many of the changes. “Gorillas, chimps and bonobos spend a lot of time rolling around in the dirt and grooming each other,” he says. They probably encounter a wider array of microbes than do humans, who live indoors, use antibiotics and eat more meat and less fruit and leaves than apes do.

Cooking may have lessened humans’ reliance on gut microbes, says Rebecca Stumpf, a biological anthropologist at the University of Illinois at Urbana-Champaign. Cooking breaks down nutrients into easily digestible forms, potentially taking jobs from microbes that would otherwise perform that duty.

Less diversity in gut microbes might reflect poor habitat and dietary quality, Stumpf says. In people, low microbe diversity has been linked to obesity, gastrointestinal diseases and immune system problems. Comparative studies such as this one may help researchers learn what makes humans unique and contribute insights into human health and disease, she says.

Everyone’s exact microbial mix differs somewhat. And no one gut combination is probably right for everyone, says Ran Blekhman, a computational geneticist at the University of Minnesota in St. Paul.

It is still unclear how much of a role genetics might play in determining a species’ or an individual’s microbial mix. Moeller and colleagues hypothesize that different diets account for most of the diversity changes seen between species and between the different human populations in the study. The researchers are searching for genetic changes that might also contribute to the microbe shifts.

Genetics might also play a role in the dichotomy between human groups, Blekhman says. Researchers already know that people who live in areas where pathogens such as malaria are prevalent often have genetic variants that make people resistant to infection. He speculates that some people might have variants that favor friendly microbes, which help to digest local foods.

Editor’s note: This article was updated on November 24, 2014, to reflect changes made to the study manuscript between an early release version and the final version. The study populations were updated to include Tanzania, and “hunter-gatherers” was removed from a sentence on gut microbe communities that were similar to those in bonobos.