Gut Phage Biobank: a collection of bacteriophages targeting human commensal bacteria

Abstract

The scarcity of cultivated gut bacteriophages hinders gut microbial research and application. Here we report the establishment and characterization of a Gut Phage Biobank (GPB) (https://db.cngb.org/genomics/datasets/GDS0000055) through a systematic isolation workflow and containing 104 isolates that target abundant or disease-associated gut bacteria. Genomic analysis reveals high diversity among these phages, and key genes of phage-bacteria interactions. The infection matrix demonstrates high host-specificity and varying infectivity of these phages under different conditions, unveiling phage-bacteria interaction mechanisms. In-depth characterization of the phages targeting obligate anaerobes uncovers a previously undescribed family and four previously undescribed genera, one of which is more prevalent than the well-known crAss-like phages globally except in Eurafrica. Cohort analysis reveals a higher prevalence of Mediterraneibacter and Dorea and a lower prevalence of Mediterraneibacter phages in Asian disease population. In vitro and in vivo evidence of phage inhibiting Dorea highlight the potential of phages in disease intervention. This biobank represents a valuable resource for advancing gut microbial research and holds promise for manipulating microbiomes.