Researchers look at paleo gut for clues to human evolutionary history

A comparison of the gut microbiomes of humans, chimps, bonobos and gorillas shows that the evolution of two of the major families of bacteria in these apes' guts exactly parallels the evolution of their hosts.

Findings from the study, by an international team of researchers and published in the latest issue of the journal Science, may help calm some of the anxiety today about the bacteria in our gut being under constant assault by antibiotics, stress and bad diets.

This shows that the microbes in our guts are determined in part by our evolutionary history, not just external factors like diet, medicine and geography. Obesity, cancer and some inflammatory diseases have been linked to imbalances in the mix of microbes in our stomach and intestines.

"We are showing that some human gut bacteria are the direct descendents of gut bacteria that lived within our common ancestors with apes," said lead researcher Andrew Moeller, of Museum of Vertebrate Zoology at University of California, Berkeley. "It shows there has been an unbroken line of inheritance or transfer from one generation to another for millions of years, since the dawn of African apes."

The importance of the human microbiome has become evident over the past decade as scientists have sequenced the microbial populations from healthy and unhealthy people, from newborns to seniors, and of peoples around the world. There are about as many microbial cells in our body as our own cells, and they appear to be transmitted from mother to child during birth and continually altered by the home environment, type of diet, medications and even the family pet.

Gut bacteria, in particular, guide the early development of our intestines, train our immune systems to fight pathogens and may even affect our moods and behavior. "We know that gut bacteria are really integrated with our biology, and this research gives us a framework for investigating how that has come to be," Moeller said.

Moeller and his colleagues obtained feces 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 United States, then isolated bacterial DNA from these samples, amplified the DNA of the gyrase B genes present and catalogued the variations within three major bacterial families to create a microbiome family tree for three families of bacteria - Bacteroidaceae, Bifidobacteriaceae and Lachnospiraceae - that together comprise about 20 percent of all the microbes in the human gut.

Only bacteria in the Bacteroidaceae and Bifidobacteriaceae families showed cospeciation with their ape hosts, with gut microbial diversity lowest in humans and highest in gorillas.

"Once we calibrated the molecular clock, we were able to date the split of human and chimp bacteria at around 5.3 million years ago, and the human-gorilla gut bacteria split at around 15.6 million years ago, which are roughly in line with what we know from fossil and genomic data of the hosts," Moeller said. "It is one more line of evidence that gut bacteria have cospeciated with humans."

"In a way, host speciation is like continental drift: When two continents drift apart, whole biotas begin to diverge," he was quoted as saying in a release from UC Berkeley. "Here, as the hosts are splitting, a good chunk of their microbiota is also splitting and diversifying."

The third bacterial family tree, the Lachnospiraceae, was more complicated. There were apparently at least four times when these bacteria were transferred between different host species. The researchers speculate that because these bacteria form spores and can thus survive outside their hosts for long periods, they were easily passed between species.

"We have shown that the microbiome is a composite of microbial lineages, some that have cospeciated with us, and some that have been passed around from one host species to another," said Moeller, who is beginning to assemble a snapshot of the microbes in the guts of our ancient ape ancestor, a paleo gut that fit our paleo diet, hoping to go further back in time if all mammals have evolved their microbiota from a common ancestral population.

"It's surprising that our gut microbes, which we could get from many sources in the environment, have actually been co-evolving inside us for such a long time," said corresponding author Howard Ochman at the University of Texas at Austin, who noted that the microbes were passed down over hundreds of thousands of host generations. Endit