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Gut microbes followed migrating humans across continents, new study suggests
A Tsimane extended family gets ready for the morning, while a large pot of manioc roots cooks in preparation to make shocdye, a local fermented brew.
Michael Gurvenhide caption
Michael Gurven
The Hadza people are hunter-gatherers who have roamed northern Tanzania for thousands of years
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The indigenous Tsimane people forage, fish and hunt in the Boli
These two rural communities, separated by an ocean, may appear to have little in common. But a new study shows that they share remarkable similarities when it comes to the bacteria in their guts
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Experts say the new paper in the journalNature suggests this microbial kinship may have taken shape long ago, before human migration split these groups’ ancestors apart
The study, which relied on stool samples from both groups, also showed that both the Hadza and Tsimane microbiomes were markedly different from city folk, even those living nearby
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The findings suggest that some strains of gut bacteria have long coexisted with humans, possibly to their mutual benefit. It’s an idea that some scientists say raises questions about the impacts of losing those microbes to modern lifestyles
“If we were inhabited by very similar microbes over a long period of time, it suggests that our human genomes may have come to expect a certain set of microbes and functions,” says Justin Sonnenburg, a professor of microbiology and immunology at Stanford University and the study’s senior author. “When you start to lose biodiversity in your gut, there may be big issues for your human biology to adjust to and accommodate.”
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Other researchers not affiliated with the paper say the hypothesis is intriguing, but not yet proven — and that perhaps there’s a reason these microbes tend not to appear in city dwellers’ guts
“Another alternative is that the industrialized microbiome profile may actually be adapted to an industrialized lifestyle,” says Andrew Moeller, an associate professor of evolutionary biology at Princeton University. “From a health perspective, is it good or deleterious that industrialized humans have lost a lot of ancestral microbial taxa [groups]? We actually don’t know.”
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Documenting what’s been kept and lost is a step towards figuring that out, he says
Microbes hitchhiked on migrating humans
Sonnenburg has previously contrasted the microbiomes of the Hadza with those of industrialized people. He and his colleagues wanted to compare these two communities with one another. “They’re living a lifestyle that’s much more similar to the lifestyle our ancestors lived, and so therefore is more hospitable to microbes that were handed down through many generations over the course of human evolution,” Sonnenburg says.
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Still, the major overlap was “startling,” he says. In comparing the genetic material in stool samples from dozens of individuals collected by the Tsimane Health and Life History Project, with previous analysis from the Hadza community, Sonnenburg and his colleagues found they had around 1,200 of the same bacterial species living in their guts — a near-90% overlap
In a typical gut microbiome, hundreds to thousands of species interact with each other — mostly bacteria, along with some fungi and viruses. “The microbes are helping us digest foods in our gut, secreting molecules that get absorbed into the bloodstream,” Sonnenburg says. “And our blood, of course, circulates throughout our bodies.”
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The gut bacteria can influence moods, behavior, and the body’s response to infections, affecting fundamental parts of biology and health, he adds
Microbiomes are dynamic — which means they can also change quickly, depending on what foods we eat and what medicines we take
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So it’s remarkable that the Hadza and the Tsimane — isolated communities living very far apart, eating different vegetables, fish and meats — have gut bacteria that are much the same, Sonnenburg says
He and his colleagues think Hadza and Tsimane peoples’ shared microbial profile goes back to their common ancestors in Africa, before some of those humans left the continent, passed through Eurasia and crossed a land-bridge that once connected Russia with Alaska, and eventually settled in the Boliared
“Once the land bridge went away, we had a clear picture that it was going to be very hard for them to exchange gut bacteria through traditional human contact means,” says Ben Good, a theoretical biophysicist at Stanford and a study co-author
Using dating techniques based on the rates at which bacteria change, they determined that on average, the microbial strains likely shared a common ancestor about 17,000 years ago — with some dating much further back. “That is consistent with the idea that these populations in South America, Africa and probably in other parts of the world are not just acquiring microbes from their environment that match their lifestyle, so much as transmitting microbes over generations,” Sonnenburg says.
Other researchers agree that the findings support the concept that large swaths of the gut microbiome migrated with humans — and likely evolved with them, too
“If the bacteria and the humans had a shared history for many, many generations, there are more opportunities for selection,” says Taichi Suzuki, an assistant professor at Arizona State University not affiliated with this paper, who conducts microbiome research. “We would expect more potential dependencies between [the co-evolved] gut microbes and our own genome, basically.”
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Babies are born with a blank slate microbiome, and start acquiring gut bacteria right away
“We first get our microbes from our mother’s vaginal canal, mother’s skin,” says Suzuki at Arizona State, “Then as we develop, we get microbes mostly from other individuals in the household and the community.”
This human-to-human transmission occurs through the fecal-oral route — ingesting microscopic particles of poo in the air and dust — and serves the important function of passing along microbes that are specific to humans, says Moeller at Princeton. “Something that might make that less disgusting is realizing how tiny these things are,” he says, “They’re a micron or less in length, and in principle, you just need one cell to found a new population.”
The gut also picks up generalist microbes that exist in the environment by ingesting food, soil and water, Moeller says. For instance, E. coli — a bacteria that’s found in many places, and thrives in the bodies of humans and many animals
Some researchers hypothesize that the microbes that have co-evolved with humans may help protect human health — or at least do less harm. For instance, in a case study, those with African ancestry have been found to have a far lower risk of getting seriously ill from an African strain of H. pylori, presumably because their genomes developed alongside the bacteria, compared with those of other ancestries who are susceptible to developing a deadly stomach cancer. It’s an example that shows the potential harms of a mismatch between gut microbes and the human genome, Suzuki says.
Around 60% of the gut microbes the Hadza and Tsimane people share are rare or absent from the guts of people who live modern, industrialized lives, according to the paper. “The microbes that inhabit my gut are very unlikely to be the microbes that were handed down through the generations from my great great grandparents,” Sonnenburg, the Stanford co-author, says. “They are much more likely to be a product of my current lifestyle and the people that I’ve interacted with locally.”
He thinks losing these ancestral microbes may be harming human health. While proving causation is tricky, “a lot of the arrows are pointing in the same direction, that our modern microbiome has changed in ways that may be propagating inflammation, may be unhealthy for us and leading to inflammatory diseases,” Sonnenburg says
Much scientific work will be needed to prove or disprove the theory. “With regards to the evolutionary questions like, which of [these] microbes have we co-evolved with? Which ones have we lost that would be beneficial to regain? It’s still early days for that line of questioning,” Moeller at Princeton says
Still, he adds, determining which gut bacteria have been with humans for a long time helps move the field forward
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