Long-read metagenomics reveals phage dynamics in the human gut microbiome.

ABSTRACT: Gut bacteriophages profoundly impact microbial ecology and health^1-3; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations⁴. We identified multiple instances of integration of the same phage into bacteri

SUBMITTER: Wirbel J 

PROVIDER: S-EPMC12823448 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature