ReviewPhilosophical transactions of the Royal Society of London. Series B, Biological sciences2022
Detecting bacterial adaptation within individual microbiomes.
Review in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed.
- Complex adaptive architectures constrain the pace of adaptations sweeping across human gut microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Studying adaptation at the invisible scale.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Novel genes arise from genomic deletions across the bacterial tree of life.bioRxiv : the preprint server for biology · 2026Article
- De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen.Nature communications · 2025Article
- A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections.Nature communications · 2025Article
- Intraspecies dynamics underlie the apparent stability of two important skin microbiome species.Cell host & microbe · 2025Article
- Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.mSystems · 2025Review
- Previously hidden intraspecies dynamics underlie the apparent stability of two important skin microbiome species.bioRxiv : the preprint server for biology · 2025Article
- Land conversion to cropland homogenizes variation in soil biota, gene assemblages, and ecological strategies on local and regional scales.The ISME journal · 2025Article
- Distinguishing among evolutionary and ecological processes shaping microbiome dynamics.The ISME journal · 2025Review
- Selenium alters the gene content but not the taxonomic composition of the soil microbiome.Environmental microbiome · 2024Article
- Article
- Reversions mask the contribution of adaptive evolution in microbiomes.bioRxiv : the preprint server for biology · 2024Article
- Regulatory fine-tuning of mcr-1 increases bacterial fitness and stabilises antibiotic resistance in agricultural settings.The ISME journal · 2023Article
- Seminars in immunology special issue: Nutrition, microbiota and immunity The unexplored microbes in health and disease.Seminars in immunology · 2023Review
- Article
- Gut immune responses and evolution of the gut microbiome-a hypothesis.Discovery immunology · 2023Review
- Genomic population structures of microbial pathogens.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
The human microbiome harbours a large capacity for within-person adaptive mutations. Commensal bacterial strains can stably colonize a person for decades, and billions of mutations are generated daily within each person's microbiome. Adaptive mutations emerging during health might be driven by selective forces that vary across individuals, vary within an individual, or are completely novel to the human population. Mutations emerging within individual microbiomes might impact the immune system, the metabolism of nutrients or drugs, and the stability of the community to perturbations. Despite this potential, relatively little attention has been paid to the possibility of adaptive evolution within complex human-associated microbiomes. This review discusses the promise of studying within-microbiome adaptation, the conceptual and technical limitations that may have contributed to an underappreciation of adaptive
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.