Mobile Gene Sequence Evolution within Individual Human Gut Microbiomes Is Better Explained by Gene-Specific Than...

Area of Science:

• Microbial genomics
• Evolutionary biology
• Human microbiome research

Background:

• Pangenomes, the total gene pool of a species, are shaped by horizontal gene transfer, drift, and selection.
• Previous studies on ancient evolutionary scales suggest pangenomes confer niche adaptation to bacteria.
• The evolutionary dynamics of mobile genes on shorter timescales remain less understood.

Purpose of the Study:

• To investigate the selective pressures on mobile genes within individual human microbiomes.
• To understand pangenome evolution on shorter, within-lifetime evolutionary scales.
• To differentiate between gene-family specific and host-specific selective pressures.

Main Methods:

• Inferred selective pressures on mobile genes in 176 Fijian individuals' microbiomes.
• Mapped metagenomic reads to identify single nucleotide variants (SNVs) in mobile genes.
• Calculated population genetic metrics to assess deviations from neutral evolution models.

Main Results:

• Mobile gene evolution varied more by gene family than by human social attributes (household, village).
• Evolutionary simulations reproduced observed patterns without assuming adaptive value for hosts.
• Highly mobile genes showed rapid spread signatures; a subset involved in defense/metabolism exhibited species-specific selection.

Conclusions:

• Gene-specific selective pressures are dominant over host-specific pressures for mobile genes in the human microbiome over short evolutionary timescales.
• Mobile gene evolution is influenced by intrinsic gene properties and interactions rather than broad host factors.
• Findings contrast with longer-term evolutionary perspectives on pangenome adaptation.