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Published on: April 28, 2022
Genome-wide sweeps create ecological units in the human gut microbiome.
Xiaoqian Annie Yu1, Cameron R Strachan2,3, Craig W Herbold1,4
1Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
Nature
|May 6, 2026
Summary
Genome-wide selective sweeps shape the human gut microbiome, creating distinct bacterial populations similar to global epidemics. These sweeps, driven by adaptation, influence various host conditions and have occurred throughout human history.
Area of Science:
- Microbiome research
- Evolutionary biology
- Genomics
Background:
- The human gut microbiome is influenced by host and environmental factors, impacting health and disease.
- While microbial associations with health conditions are known, the adaptive mechanisms driving population structure are unclear.
Purpose of the Study:
- To investigate the role of unifying adaptive mechanisms in differentiating microbial populations within the human gut.
- To understand the evolutionary processes shaping bacterial lineages in the microbiome.
Main Methods:
- Analysis of genome-wide selective sweeps in bacterial populations.
- Phylogenetic tree construction, excluding recombination events to reveal clonal descent.
- Dating divergence events to estimate the spread of sweep clusters.
Main Results:
- Genome-wide selective sweeps are a common mechanism differentiating gut bacteria, creating epidemic-like population structures.
- These sweeps occur across diverse human populations and are found in at least 66 bacterial taxa.
- Sweep clusters can spread globally within decades and are linked to various host conditions, including colorectal cancer and type 2 diabetes.
Conclusions:
- Selective sweeps provide an evolutionary explanation for stably inherited bacterial strains with differential host associations.
- This mechanism offers a theoretical framework for analyzing microbial adaptation and population dynamics in the gut microbiome.
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