Prehistoric global migration of vanishing gut microbes with humans

Researchers used deep, strain-resolved metagenomics to trace long-term associations between humans and their gut microbes by comparing faecal microbiomes from Tsimane horticulturalists in Bolivia and Hadza hunter-gatherers in Tanzania. From 133 Tsimane samples they reconstructed 12,746 metagenome-assembled genomes (MAGs) representing 1,408 species and compared these with 32,034 MAGs from 137 Hadza individuals. Despite geographic separation and no recent contact, 1,231 species overlapped between the two populations (87.4% of Tsimane species), and 60.2% of those shared species (848 taxa) are rare or absent in industrialized populations. This large shared set implies an ancestral gut microbiome component that persists in non-industrialized humans.

Population-genetic analyses that account for high recombination rates at the strain level examined 636 species with sufficient genomes and found typical pairwise average nucleotide identity around 98%, implying common ancestors roughly 100,000-200,000 years ago - timescales consistent with human migrations out of Africa and into the Americas. The analyses revealed stronger strain-level reproductive isolation between these non-industrialized cohorts than seen in industrialized groups, consistent with prehistoric co-migration and long-term maintenance of gut lineages. Many of those long-standing microbial partners are disappearing from industrialized populations, and the downstream effects on human health remain unresolved.