Transitions in human gut viral communities from ancient to industrialized societies

The composition and function of the human gut microbial community (the microbiome) have changed substantially over millennia, with implications for human health. While microbiome research has focused primarily on bacterial dynamics, the long-term history of gut viral communities (the virome) remains largely unexplored, despite their crucial role in shaping bacterial populations. We analyzed gut viromes from 13 pre-modern human coprolites (21 BCE–1500 CE), as well as 371 non-industrialized and 417 industrialized contemporary human fecal samples. We found that, over time and with industrialization, gut viral communities have become functionally homogenized, increasingly dominated by temperate lifestyles, less likely to infect problematic bacteria, more supportive of bacterial pathogenicity, and depleted in genes that help bacteria combat stress and toxicity. These synergistic ecological shifts suggest that long-term changes, especially with industrialization, have fundamentally altered the gut virome, likely affecting human health. These insights into historical shifts in gut viral community and function open potential avenues for ecologically grounded therapeutics to enhance gut microbiome resilience.