From Science:
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.
More here.