Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.

ABSTRACT: Horizontal gene transfer (HGT) is a major driver of bacterial evolution, but its role in shaping the human gut microbiome over time remains poorly understood. Here, we present a longitudinal metagenomic analysis of 676 fecal samples from 338 individuals in the Lifelines-DEEP study collected ~4 years apart, using a newly developed workflow to detect recent HGT events from metagenome-assembled genomes. We identified 5,644 high-confidence HGT events occurring within the past ~10,000 years across 116 gut bacterial species. We find that species pairs with an HGT relationship were significantly more likely to maintain stable co-abundance relationships over the 4-year period, suggesting that gene exchange contributes to community stability. Notably, HGT and strain replacement act together to diss

SUBMITTER: Peng H 

PROVIDER: S-EPMC12749903 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature