ArticlePLoS biology2019
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.
Article in PLoS biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 216 papers, 1 of them a synthesis that pooled it.
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Who cites it
216 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster.BMC microbiology · 2021Pooled it
- Eukaryotic and bacterial gut communities vary along a lifestyle-associated urbanization gradient: comparative analysis of Germany and Madagascar.Gut microbes · 2026Article
- Precise probiotic therapy: Advances, bottlenecks, and the road to microbiome-informed nutrition.Gut microbes · 2026Review
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- Gut Microbiome Disruption in Shelter Cats with Feline Panleukopenia: Virome Co-Detection and Enteric Dysbiosis.Biology · 2026Review
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- Select microbial metabolites promote tau aggregation in a murine tauopathy model.Nature communications · 2026Article
- Complex adaptive architectures constrain the pace of adaptations sweeping across human gut microbiomes.bioRxiv : the preprint server for biology · 2026Article
- MetaStrainer: accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.Bioinformatics (Oxford, England) · 2026Article
- Linkage of nucleotide and functional diversity varies across gut bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Immune surveillance and microbial escape in the aging host: Why does the microbiome lose its balance?PLoS biology · 2026Review
- Modulating microbial intake helps to maintain the gut microbiome diversity.Communications biology · 2026Article
- Uniform bacterial genetic diversity along the gut.Nature communications · 2026Article
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- Recent Microbial Evolutionary Insights From Metagenomics.Genome biology and evolution · 2026Review
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- Priority effects drive strain-level community composition of honeybee gut microbiota.The ISME journal · 2026Article
- Experimental evolution in an era of molecular manipulation.Nature reviews. Genetics · 2026Review
- Glyphosate-based herbicide exposure triggers genetic adaptation but not diversity collapse within bacterioplankton species.ISME communications · 2026Article
156 more citing papers are in PubMed but not listed here.
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Abstract
Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here, we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in approximately 40 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over 6-month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps may be seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts.
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