Short‐term probiotic supplementation affects the diversity, genetics, growth, and interactions of the native gut microbiome

The precise mechanisms through which probiotics interact with and reshape the native gut microbiota, especially at the species and genetic levels, remain underexplored. This study employed a high-dose probiotic regimen of <i>Bifidobacterium animalis</i> subsp. <i>lactis</i> [200 billion colony forming units (CFU)/day] over 7 days among healthy participants. Weekly fecal samples were collected for metagenomic sequencing analysis. We found that probiotic intake can significantly enhance the diversity of the gut microbiome and impact single nucleotide variations, growth rates, and network interactions of the resident intestinal bacteria. These adaptive changes in the gut microbiota indicate the swift evolutionary responses of native bacteria to the ecological disturbance presented by probiotic supplementation. Notably, the microbial community appears to undergo rapid and multifaceted ecological adjustments, potentially preceding longer-term evolutionary changes. This knowledge lays the groundwork for further exploration into the mechanisms underlying probiotic-mediated modulation of the gut microbiome, highlighting the necessity of encompassing ecological and evolutionary perspectives in the design and optimization of probiotic applications.