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

Area of Science:

• Microbiology
• Evolutionary Biology
• Genomics

Background:

• The human gut microbiome comprises diverse, evolving species influenced by host interactions.
• Understanding shared adaptations is key to identifying selection pressures and functional microbiome differentiation.
• The spread of adaptations across human gut microbiomes remains largely unexplored.

Purpose of the Study:

• To develop a novel statistical method for detecting adaptive allele sweeps in microbial populations.
• To investigate the extent and nature of adaptive evolution in commensal human gut bacteria across global populations.

Main Methods:

• Developed the integrated linkage disequilibrium score (iLDS), a selection scan statistic.
• Applied iLDS to analyze around 30 prevalent commensal gut species from 24 human populations.
• Leveraged hitchhiking signals of deleterious variants with beneficial variants to detect selective sweeps.

Main Results:

• Identified over 300 selective sweeps across the analyzed gut bacterial species.
• Found an enrichment of sweeps in carbohydrate metabolism loci, suggesting dietary adaptation.
• Observed significant differences in selection targets between industrialized and non-industrialized populations.

Conclusions:

• Recombination fuels pervasive adaptive evolution in human gut commensal bacteria.
• Host diet and lifestyle are critical selection pressures shaping the gut microbiome.
• Specific adaptations, like maltodextrin metabolism, reflect recent dietary shifts in industrialized societies.