"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 Ochman, also noting that the bacterial flora have been propagated over hundreds of thousands of generations of hosts.
To carry out this study, Moeller and colleagues used a new approach. Typically, analysis of the microbiome takes advantage of a particular piece of a bacteria’s genome, the 16S ribosomal subunit. That specific part of bacterial DNA doesn’t change much and as such easily indicates the identity of the bacteria in the community when it’s sequenced. Because of that lack of change, the team switched to a gene that has a higher rate of evolution, called gyrase B (it encodes for DNA gyrase - a protein that helps DNA uncoil and coil).
The investigators found that only the Bacteroidaceae and Bifidobacteriaceae families showed cospeciation with their ape hosts; gut microbial diversity was highest in gorillas but lowest in humans.
"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 explained. "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," Moeller continued. "Here, as the hosts are splitting, a good chunk of their microbiota is also splitting and diversifying."
Other findings show that the Lachnospiraceae tree was more complicated. There were propbably at least four times when bacteria in this family got transferred to a different host species, something the team suggests was easy for these bacteria since they form spores.
"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," explained Moeller.
A comparison of the microbial flora of Africans from Malawi to the U.S. human microbiota showed distinct differences, with some lineages apparently lost by Americans.
"It will be interesting in the future to do a full study of human populations using this strain-level method to see whether we can use bacteria to reconstruct the history of human migrations,” said Moeller. “What's most exciting to me is the possibility that this codiversification between bacteria and hosts could extend much further back in time. Maybe we can trace our gut microbes back to our common ancestors with all mammals, all reptiles, all amphibians, maybe even all vertebrates. If that's true, it's amazing," he concluded.
Sources: Science Daily via University of California, Berkeley, Science