Most of us have heard that gut bacteria matter for digestion, mood and immunity.
The usual advice tends to stop at yogurt or a probiotic pill. New research zooms out to a far longer timeline.
Researchers at Stanford University have found that gut microbes shared by two indigenous populations on opposite sides of the globe are rare or missing in people in industrialized countries.
The findings were published October 7, 2026, in Nature.
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The team sequenced stool samples from the Hadza, hunter-gatherers in Tanzania, and the Tsimane, foragers and farmers in the Bolivian Amazon.
The two groups share more than 1,200 bacterial species. Nearly 90 percent of the Tsimane's microbes also showed up in the Hadza.
About 60 percent of those shared species are rare or absent in the gut of people living in industrialized countries.
The average Hadza individual carries roughly 750 bacterial species. The average Californian carries about 250.
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Justin Sonnenburg, professor of microbiology and immunology at Stanford, is the study's senior author.
He said the shared species look like ancient companions passed down from generation to generation for millennia as humans spread across the globe.
What modern lifestyles appear to strip from the gut
The paper does not pin the depletion on a single cause. Earlier work by Sonnenburg's lab points to a familiar set of suspects.
Low-fiber diets, antibiotics, more cesarean births and less breastfeeding have all tracked with lower microbial diversity in industrialized populations.
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In mouse studies, a low-fiber diet depleted gut diversity within three or four generations. The lost species did not come back on their own, even when fiber was reintroduced.
Benjamin Good, assistant professor of applied physics at Stanford, is a co-senior author.
He said the DNA signatures point to bacteria that were already present in the common ancestors of both groups, and presumably in our ancestors too.
How diet appears to shift the microbes you still have
Diet also seems to work the other way. In a 10-week trial published in Cell in 2021, the same Stanford lab asked 36 healthy adults to add fermented foods to their meals.
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The list included yogurt with live cultures, kefir, fermented cottage cheese, kimchi, sauerkraut, vegetable brine drinks and kombucha.
According to a release from Stanford Medicine, microbial diversity in the fermented-food group went up and markers of inflammation in the blood, including interleukin-6, went down.
A separate high-fiber arm of the same trial did not shift diversity in that short window, though it did change how existing microbes behaved.
The new Nature paper is observational. It cannot prove that any one food brings a lost species back, and the researchers do not claim it does.
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Sonnenburg has argued that these microbes may be part of our evolutionary biology.
If so, people in industrialized countries may be missing a huge part of what the human genome adapted to over tens of thousands of years.
The two dietary levers best documented in the Stanford group's own trials remain the same.
Plenty of plant fiber from vegetables, legumes, whole grains, nuts and seeds, and a regular rotation of traditionally fermented foods on the plate.
This article is made and published by Ida-Marie Palm Varbæk, who may have used AI in the preparation.