An integrated gut phage catalogue of nonhuman primates reveals functional adaptation to host ecology and evolutionary link to humans

Abstract Nonhuman primates (NHPs), the closest evolutionary relatives of humans, are pivotal models for biomedical and ecological research. Gut phage are recognized as critical modulators of gut microbial communities; however, comprehensive insight into gut phage of NHPs is lacking. We used gut metagenomes spanning 25 NHP species and constructed an integrated gut phage catalogue (IGPC) comprising 11 389 nonredundant phage genomes. Our results revealed that the composition and function of NHP gut phage were significantly influenced by host clade, dietary niche and lifestyle. Host clade exerted a stronger influence than dietary niche on gut phage diversity. The lifestyle of NHPs influenced gut phage diversity and altered auxiliary metabolic gene profiles for different NHP species. Comparatively, 78.5% of IGPC phages were detected in human guts, with higher prevalence in nonindustrialized human guts. crAss-like phage—the most prevalent human-associated phage—were abundant in NHP guts, while exhibiting distinct evolutionary differences from crAss-like phage of humans. These findings comprehensively characterize the gut phageome of NHPs, revealing NHP host-driven and environment-driven functional adaptations, and provide an evolutionary understanding of the gut phageome between NHPs and humans.