Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort

Abstract

Indigenous bacteriophage communities (virome) in the human gut have a huge impact on the gut bacterial communities (bacteriome), but virome variation at a population scale is not fully investigated yet. Here, we analyse the gut virome in a population-level cohort of 4,198 deeply phenotyped individuals. We discovered thousands of high-quality phage genomes including previously uncharacterized ones with different bacterial hosts than known major phage clades. The distribution of host bacteria was a strong determinant for the distribution of phages, and virome diversity was highly correlated with anti-viral defence mechanisms of the bacteriome, such as CRISPR-Cas and restriction-modification systems. We identified 97 various intrinsic/extrinsic factors that significantly affect the virome, including age, sex, lifestyle, and diet, most of which showed consistent associations with both phages and their predicted bacterial hosts. Among the metadata categories, disease and medication had the strongest effects on the virome structure. Overall, these results present a basis to understand the symbiotic communities of bacteria and their viruses in the human gut, which will facilitate the medical and industrial applications of indigenous viruses.

Lytic bacteriophage vB_KmiS-Kmi2C disrupts biofilms formed by members of theKlebsiella oxytocacomplex, and represents a novel virus family and genus

“…Analysis using NCBI BLASTN showed the genome of vB_KmiS-Kmi2C shared 85.6 % identity (80 % query coverage) with a phage metagenome-assembled genome (accession OP072809) recovered from human faeces in Japan [42]. Preliminary analysis of the genome sequence using the online version of ViPTree suggested the phage was novel (not shown).…”

“…Analysis using NCBI BLASTN showed the genome of vB_KmiS-Kmi2C shared 85.6 % identity (80 % query coverage) with a phage metagenome-assembled genome (accession OP072809) recovered from human faeces in Japan [42].…”

Signals triggering prophage induction in the gut microbiota

“…In comparison, the characterisation of the viral fraction is much more recent and virome deep sequencing revealed the striking diversity of these viruses, largely dominated by bacteriophages (phages). The recent years have seen a bloom of gut phage catalogues, each collecting up to 50,000 different phage species (Nayfach et al, 2021 ; Nishijima et al, 2022 ; Shah et al, 2021 ; Tisza & Buck, 2021 ; Townsend et al, 2021 ; Zuppi et al, 2021 ).…”