Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature

"The diverse species that make up the human gut microbiome evolve throughout the lifetimes of individual hosts and over longer timescales across many host colonization cycles. Recent work has shown that rapid evolution within hosts is common among commensal gut bacteria, with new mutations often arising and sweeping to high frequency in healthy adults over the course of days to months even in the absence of obvious perturbations such as antibiotics1,2,3,4,5."

"A new adaptation first appearing in one host's microbiome may potentially spread to many hosts through strain transmission and subsequent horizontal gene transfer (HGT). The human gut microbiome is known to be a hotspot for HGT6,7,8, allowing adaptive alleles to be recombined easily onto new genetic backgrounds. HGT has been shown to play a crucial role in the transmission of some genes, such as antibiotic resistance genes9, especially across species boundaries."

"When an adaptive allele spreads in a population by means of a 'gene-specific' selective sweep, other nearby 'hitchhiking' variants, which may be neutral or even deleterious, will be transferred together with the adaptive variant. As a result, the same genomic sequence bearing both the adaptive allele and the hitchhikers will appear in otherwise distantly related strains present in different host microbiomes6,10,11."

The human gut microbiome contains diverse bacteria that evolve within hosts and across colonization cycles. Rapid within-host evolution often produces mutations that sweep to high frequency in healthy adults over days to months without obvious perturbations. Adaptive alleles emerging in one host can spread to others via strain transmission and horizontal gene transfer (HGT). The gut microbiome is a hotspot for HGT, enabling recombination of adaptive alleles onto new genetic backgrounds and facilitating transmission of genes such as antibiotic resistance. The role of HGT, particularly homologous recombination, in spreading adaptive alleles among strains of the same species remains unclear. Gene-specific selective sweeps transfer nearby hitchhiking variants, producing local sequence sharing and elevated linkage disequilibrium near adaptive alleles.

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