ArticleNature communications2024
Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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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
15 citing papers in PubMed.
- Host-Microbiome Immune Interaction Networks: A Comparative Evolutionary Perspective Across Worms, Mice, and Humans.Pathogens (Basel, Switzerland) · 2026Review
- Select microbial metabolites promote tau aggregation in a murine tauopathy model.Nature communications · 2026Article
- Uniform bacterial genetic diversity along the gut.Nature communications · 2026Article
- Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments.PLoS biology · 2026Article
- Article
- Experimental evolution in an era of molecular manipulation.Nature reviews. Genetics · 2026Review
- A machine learning-derived genomic dataset from bacteria frequently reported as probiotics.Frontiers in bioinformatics · 2026Article
- Community coalescence reveals strong selection and coexistence within species in complex microbial communities.bioRxiv : the preprint server for biology · 2025Article
- Quantifying the intra- and inter-species community interactions in microbiomes by dynamic covariance mapping.Nature communications · 2025Article
- Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History.Molecular biology and evolution · 2025Article
- Distinguishing among evolutionary and ecological processes shaping microbiome dynamics.The ISME journal · 2025Review
- Predicting the first steps of evolution in randomly assembled communities.Nature communications · 2024Article
- Predicting the First Steps of Evolution in Randomly Assembled Communities.bioRxiv : the preprint server for biology · 2024Article
- Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history.bioRxiv : the preprint server for biology · 2023Article
- Within-host evolution of the gut microbiome.Current opinion in microbiology · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Gut microbiota can adapt to their host environment by rapidly acquiring new mutations. However, the dynamics of this process are difficult to characterize in dominant gut species in their complex in vivo environment. Here we show that the fine-scale dynamics of genome-wide transposon libraries can enable quantitative inferences of these in vivo evolutionary forces. By analyzing >400,000 lineages across four human Bacteroides strains in gnotobiotic mice, we observed positive selection on thousands of cryptic variants - most of which were unrelated to their original gene knockouts. The spectrum of fitness benefits varied between species, and displayed diverse tradeoffs over time and in different dietary conditions, enabling inferences of their underlying function. These results suggest that within-host adaptations arise from an intense competition between numerous contending variants, which can strongly influence their emergent evolutionary tradeoffs.
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Registered trials
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.