Thousands of miles and an ocean separate the Tsimané of lowland Bolivia from the Hadza of Tanzania. Their ancestors split tens of thousands of years ago. Their diets look nothing alike. Yet their gut microbiomes are strikingly similar, according to a study in Nature from researchers at UC Santa Barbara and Stanford University.
Left: A group of Hadza people. Credit: Idobi, CC BY-SA 3.0. Right: Tsimané people. Photo from The Swedish Expedition to Bolivia (1913-1914). Credit: The National Museums of World Culture. Colorized by Archaeology News Online Magazine. Public domain
The Hadza are one of the last hunter-gatherer groups on Earth. They hunt impala and kudu, catch birds and fish, and gather tubers and berries. The Tsimané are Indigenous forager-farmers in the Bolivian Amazon. They grow plantains, rice, manioc and corn, and eat lean meat from fish, peccary and other forest animals. Both groups live with little industrial influence.
The team ran the first deep sequencing of Tsimané stool samples. Earlier work had only sequenced them at low resolution. Deep metagenomic sequencing reads all the DNA in a sample. It breaks the DNA into millions of short pieces, lines up the overlaps, and matches the longer stretches against databases of known microbial genomes. This method picks up rare, low-abundance species that other tools miss.
The Tsimané carry about 1,400 gut species in total. They share 1,231 of them with the Hadza, which is roughly 90 percent. About 60 percent of those shared species are rare or missing in people from industrialized societies. Earlier research found the average Hadza person hosts around 750 species. The average Californian hosts about 250.
A group of Hadza hunters. Credit: Eid John, CC BY-SA 4.0
So why do two groups with different food and homes share so much? Not because both live in rural areas with limited antibiotics, says UCSB anthropologist Michael Gurven. His point is that people have carried these bacteria for hundreds of generations.
Stanford’s Benjamin Good and his group tested that idea on 636 of the shared species. The work was tricky. Microbes evolve fast. They also swap DNA with other strains, a process called horizontal gene transfer. That swapping blurs family trees. Good’s team looked for several independent genetic signs to separate deep shared ancestry from recent exchange. They also tracked mutations in inherited DNA, which build up at a steady pace like a clock, to estimate when species split.
The results lined up with human history. Split times for many species matched the migration out of Africa and the later move into the Americas. Senior author Justin Sonnenburg, a Stanford microbiologist, said the findings show these microbes traveled with people around the globe and passed from parent to child for thousands of years.
A group of Tsimané people. Photo from The Swedish Expedition to Bolivia (1913-1914). Credit: The National Museums of World Culture. Public domain
The gut microbiome digests fibrous food, makes vitamins and trains the immune system. People in industrialized countries have far less microbial diversity. They also face more autoimmune disease, Type 2 diabetes and obesity. These conditions are rare in nonindustrialized groups. The new study can’t prove the loss causes the illness. It does show that industrial life erased species people kept for tens of thousands of years, and it did so in only a few generations. Antibiotics, processed diets low in fiber and high in fat and sugar, and highly sanitized homes all play a part.
What this loss does to human health is still unclear. Researchers say it’s the next big question.
The risk isn’t limited to city dwellers. Diet and access to medicine are changing fast in Tsimané communities. Gurven warns that their microbiomes could soon lose diversity, and that the loss could hurt their immunity and health.
Publication: Carter, M. M., Liu, Z., Olm, M. R., Martin, M., Sprockett, D. D., Ghadermazi, P., … Sonnenburg, J. L. (2026). Prehistoric global migration of vanishing gut microbes with humans. Nature. doi:10.1038/s41586-026-11106-1