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Pervasive selective sweeps across human gut microbiomes.

Richard Wolff1, Nandita R Garud1,2

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|January 8, 2024
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Scientists identified over 300 instances of adaptation in the human gut microbiome, revealing how diet shapes microbial evolution. This study highlights selective sweeps in carbohydrate metabolism, particularly maltodextrin utilization in Westernized populations.

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Area of Science:

  • Microbial evolution
  • Human microbiome research
  • Population genetics

Background:

  • The human gut microbiome comprises diverse, evolving species influenced by host selection pressures.
  • Understanding common adaptations reveals key drivers of microbiome function and host traits.
  • A systematic scan for widespread microbiome adaptations has been lacking.

Purpose of the Study:

  • To systematically identify adaptations that have spread across human gut microbiomes.
  • To develop a novel statistical method for detecting adaptive haplotype spread.
  • To investigate the role of diet in driving microbiome evolution.

Main Methods:

  • Developed the integrated Linkage Disequilibrium Score (iLDS) to detect adaptive haplotype spread.
  • Applied iLDS to ~30 prevalent commensal gut species from 24 global populations.
  • Analyzed selective sweeps, focusing on carbohydrate metabolism and population-specific differences.

Main Results:

  • Identified over 300 selective sweeps across various gut species.
  • Found enrichment of sweeps in carbohydrate metabolism loci, suggesting dietary adaptation.
  • Observed significant differences in selection targets between Westernized and non-Westernized populations.
  • Discovered a maltodextrin metabolism sweep unique to Westernized populations.

Conclusions:

  • Selective sweeps are common in human gut microbiome evolution.
  • Host diet significantly impacts the targets of microbial selection.
  • Microbial adaptations reflect responses to dietary components, such as maltodextrin in Western diets.