UC Berkeley biologist helps discover evolutionary links between gut bacteria of humans, hominids

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Microbes in the stomachs of humans and modern apes have evolved from ancient bacteria of their common ancestors, according to a study published by a multi-institution research team Friday.

The study — co-authored by UC Berkeley postdoctoral scholar Andrew Moeller — compared the gut microbiomes of humans with those of chimpanzees, bonobos and gorillas. The comparison revealed that some human gut bacteria are the direct descendants of gut bacteria that lived within the common ancestor of humans and apes, and it showed that they evolved over the course of 15 million years.

According to Moeller, the evolution of gut bacteria in humans, chimpanzees and gorillas diverged at the same time as the species diverged from their common ancestor. The team concluded from this discovery that gut bacteria have co-evolved with hominid evolution to “shape modern human immune systems and development.”

“Our results may eventually lead to a better understanding of how we have co-evolved, (or) co-adapted, with bacteria,” Moeller said.

The team — which included researchers from campus as well as from Duke University, University of Pennsylvania and the University of New Mexico — conducted its experiments by collecting feces samples from 24 gorillas living in Cameroon, 47 chimpanzees from Gombe National Park in Tanzania, 24 wild bonobos from the Democratic Republic of the Congo and 16 people from Connecticut.

The team’s analysis of the DNA from the feces samples dated the split of human and chimpanzee gut bacteria at about 5.3 million years ago and dated the split of human and gorilla bacteria at about 15.6 million years ago. This finding roughly coincides with the dates when these species diverged, according to Moeller.

The team then analyzed the samples’ bacterial DNA to create a microbiome family tree for three families of bacteria — Bacteroidaceae, Bifidobacteriaceae and Lachnospiraceae — that together make up about 20 percent of all the microbes in the human gut. Of these families, Bacteroidaceae and Bifidobacteriaceae directly correlated with the calculated date of human divergence from their ape ancestors.

Much of endemic bacteria in humans comes from their environment and shifts with diet and lifestyle. Research in mouse models has shown that gut bacteria are involved with the development of blood vessels in the large intestine, according to Moeller, and gut microbes also train immune systems to fight pathogens.

Researchers do not yet know if bacteria in parts of the body other than the gut have co-speciated with hominids, according to Moeller, who added that determining when these bacteria began their partnerships with the human lineage will require studying the gut microbes of more distantly related mammals.

“I am interested in asking how far back in time our relationships with gut bacteria extend,” Moeller said. “We now know that some bacterial lineages have been intimately associated with us for at least 15 million years, but it’s possible that the relationships are even more ancient.”

Contact Jessie Qian at [email protected] and follow her on Twitter at @jessieq96.