Gut microbiome plays role in evolution

By using a novel system of taxonomy a team has made a key advance toward understanding which of the trillions of gut microbes may play important roles in how humans evolve.

The international collaboration led by scientists from Oregon State University in the US came up with a novel way of classifying the microbes – a taxonomy based on their ancestry and common distribution across mammals. Known as ClaaTU – short for cladal taxonomic units – the new algorithm and corresponding software help clarify potential ecological or evolutionary mechanisms.

“The gut microbiome matters to the health of mammals like humans and mice, so perhaps it also affects a mammal's ability to survive and reproduce in nature,” said lead author Christopher Gaulke, a postdoctoral scholar in the College of Science at Oregon. “If so, then the gut microbiome may influence how animals evolve such that individuals that carry the proper set of gut microbes are more likely to thrive.”

ClaaTU identifies microbial clades ­ – a group of organisms thought to have descended from a common ancestor – that manifest across multiple sets of mammal communities more frequently than expected by chance. Those that do – the ones that are “conserved” in the mammalian microbiome – possibly played and continue to play important roles for their hosts.

“Identifying gut microbes that link to mammalian evolution is the first step toward evaluating this bold idea that gut microbes influence evolution,” Thomas Sharpton, a microbiology and statistics researcher at OSU’s, said. “We were able to uncover an expansive array of such microbes by using our new approach to compare microbiomes across mammalian species.”

The team also found Humans living “Western lifestyles” – those eating diets high in fat and low in fiber – tend strongly away from gut microbiome clade diversity when compared with non-Western humans and non-human primates. That suggests changes in lifestyle, environment and/or genetics that go along with Westernization are connected with the conservation of gut bacterial clades. “It’s an observation that elevates concern that industrialization may have impacted the gut microbiome that our human ancestors evolved to harbor,” Sharpton said.

The work is published in mBio.