Evolutionary Relationships Hold, Even in Our Guts

It's all relative. The bacteria in this gorilla's gut
are similar to those of another gorilla species.

The human body is coated with bacterial cells. They live on our skin and between our teeth. They particularly like our warm, nutrient-filled gut, where they help digest food, make vitamins, and produce some seriously smelly gas. But when it comes to these gut bacteria, we are not what we eat. A new analysis of feces from humans and several other primates finds that evolutionary history, not diet, determines the makeup of our intestinal bugs.

Babies are born sterile, then they start picking up bacteria from their mothers. These microbes multiply and fill the intestines; one adult's gut can hold a thousand species. But it's not clear what exactly influences the makeup of that community—that is, what particular species of bacteria, in what quantities, hang out in our guts. It could depend mainly on what we get from our mothers, on what we eat, or on some other factor. Scientists have started using new genetic techniques to work out whether different species of animals have different communities; some studies in recent years have concluded that animals with similar diets have similar microbial communities.

To find out if diet was really key, Yale University evolutionary biologist Howard Ochman gathered samples of feces from 26 animals in the wild, representing three subspecies of chimpanzees, two species of gorillas, and two humans—one from Arizona and one from the Central African Republic, whose poop had originally been misidentified as belonging to an ape. Ochman didn't go out in the field for these samples; most were in freezers of colleagues who had collected them for other studies. "Basically, you get them by telephone," he says.

Ochman and colleagues sequenced the bacterial DNA in each sample and focused on a particular gene whose sequence varies from species to species. The primates varied in both the types of bacteria their guts contained and the number of bacteria of each type. The team used this data to construct a tree of the bacterial relationships among the primates. Primates with many of the same number and kind of gut bacteria were placed close together on the tree, and vice versa.

To Ochman's surprise, the tree matched the evolutionary relationship of the primates. The gut bacteria of the humans more closely resembled those of the two chimp subspecies, for example, than they did those of the gorilla species. "We were just amazed," Ochman says. Diet probably isn't a factor, because the two humans shared the same gut bacteria even though they lived in vastly different parts of the world.

Ochman doesn't know why our microbial communities are so similar to our evolutionary relationships, but he suspects there may something about a species' gut physiology that makes it welcoming to a particular community of microorganisms. His team reports its findings online today in PLoS Biology.

"I like their approach" of building a tree based on comparing the makeup of microbial communities in different animals' guts, says microbiologist and infectious disease specialist David Relman of Stanford University in Palo Alto, California. He agrees that these data suggest that evolutionary relationships are more important than diet, but without knowing the animals' diet, he says, "it's hard to know how strong a statement one can make about the role of diet."