Hadza and Tsimané Share Ancient Gut Microbiome Heritage

The Tsimané of Bolivia and Hadza of Tanzania share more than 1,200 bacterial species in their gut microbiomes. More than 60 percent of these shared species are rare or absent in industrialized populations, pointing to a deep ancestral microbial heritage. This near-90% overlap suggests a core set of gut microbes traveled with human ancestors before major migrations out of Africa split these groups apart tens of thousands of years ago.

Researchers from UC Santa Barbara and Stanford University conducted the first deep comparison of the two groups' microbiomes using deep metagenomic sequencing of stool samples. The Tsimané shared 1,231 of approximately 1,400 species identified with the Hadza. This diversity starkly contrasts with industrialized guts. The average Hadza individual hosts about 750 microbial species, while the average Californian has only about 250.

Microbial divergence dates align with prehistoric human migrations

Scientists used mutation rates in bacterial DNA as a molecular clock to estimate when shared microbial strains diverged. For many species, divergence estimates correspond to the timeframe of major prehistoric human migrations. Genetic isolation analyses produced time estimates consistent with these ancient dispersals. Using these dating techniques, the microbial strains likely shared a common ancestor about 17,000 years ago on average. Some strains date much further back.

The researchers employed population genetics analysis to estimate when microbial strains separated. They looked for independent genomic signatures to distinguish deep shared ancestry from recent microbial exchange, a process complicated by horizontal gene transfer between bacteria. The study indicates many microbial lineages in these populations have deep evolutionary roots extending back through ancient human migrations.

Traditional diets and lifestyles preserve ancestral microbiome diversity

The high microbiome diversity in both groups is tied to their subsistence practices and limited exposure to industrialization. The Hadza are hunter-gatherers who have roamed northern Tanzania for thousands of years. Their diet includes hunting mammals like impala and kudu, birds, fish, and foraging for fruits, tubers, and berries.

The Tsimané are Indigenous forager-farmers living in the Bolivian Amazon. Their diet includes plantains, rice, manioc root, corn, and lean meat from fish, peccary, and other forest animals. Industrialization is associated with antibiotic exposure, low-fiber high-fat high-sugar processed diets, and sanitized living conditions. Previous work links such microbiome changes to autoimmune diseases, Type 2 diabetes, obesity, and other chronic conditions.

The gut microbiomes of both groups were markedly different from those of city folk, even those living nearby. The industrialized microbiome profile may be adapted to an industrialized lifestyle. Losing ancestral microbes may be harming human health and could be linked to inflammation and inflammatory diseases.

Research confirms deep co-evolution of humans and gut microbes

The study used deep sequencing and genetic isolation analyses to support long-term host-microbe co-evolution. Justin Sonnenburg, a professor of microbiology and immunology at Stanford University and the study's senior author, oversaw the research. The Tsimané Health and Life History Project team, co-directed by UCSB anthropologist Michael Gurven, collected voluntary stool samples.

Michael Gurven said: "The analysis shows strong evidence that their ancestors, and presumably all of us, had these same bacteria long ago." Benjamin Good, a theoretical biophysicist at Stanford and senior co-author, made a statement about the core set of bacterial species traveling with ancestors. The researchers identified genetic signatures in bacterial DNA of both populations.

Loss of ancestral microbes risks health of Indigenous groups

Researchers warn that changing diets and medicine access threaten Tsimané microbiome diversity, with potential consequences for immunity and health. They warn that Tsimané microbiomes could lose diversity due to rapid changes in diet and access to medicines. Such loss could harm Tsimané immunity and health. The study suggests that some strains of gut bacteria have long coexisted with humans, possibly to mutual benefit.