ArticleCell host & microbe2021
Quantifying rapid bacterial evolution and transmission within the mouse intestine.
Article in Cell host & microbe, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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.
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Who cites it
38 citing papers in PubMed, 51 citations in OpenAlex.
- Community-wide adaptive evolution of gut bacteria during dietary transitions.bioRxiv : the preprint server for biology · 2026Article
- Simulating the host niche: balancing complexity and control in the experimental evolution of antibiotic resistance and pathoadaptation.Microbiology (Reading, England) · 2026Review
- Bi-directional highways and super-seeder tissues underpin parasite dissemination in experimental Leishmania donovani infection.Nature communications · 2026Article
- Metabolic strategies of Enterobacteriaceae gut colonization.Nature reviews. Microbiology · 2026Review
- Toward a Functional Genetics of Adaptation: Insights From Microbial Experimental Evolution.Genome biology and evolution · 2026Review
- Modelling the role of the microbiome in antimicrobial resistance across scales.Nature microbiology · 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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- Quantifying host-microbe interactions with bacterial lineage tracing.Science (New York, N.Y.) · 2026Review
- Fecal metagenomic profiling in patients with colorectal adenomas to characterize gut microbial composition and functional potential.Frontiers in microbiology · 2026Article
- Experimental evolution in an era of molecular manipulation.Nature reviews. Genetics · 2026Review
- Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series.Bioinformatics (Oxford, England) · 2025Article
- Within-host bacterial evolution and the emergence of pathogenicity.Nature microbiology · 2025Review
- Quantifying the intra- and inter-species community interactions in microbiomes by dynamic covariance mapping.Nature communications · 2025Article
- Evolutionary adaptation of probiotics in the gut: selection pressures, optimization strategies, and regulatory challenges.NPJ biofilms and microbiomes · 2025Review
- Article
- Article
- Evolution of Escherichia coli strains under competent or compromised adaptive immunity.PLoS pathogens · 2025Article
- Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions.Current protocols · 2024Article
Corrections and comments
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Authors and funding
16 authors at 3 institutions in 2 countries.
Funding
Abstract
Due to limitations on high-resolution strain tracking, selection dynamics during gut microbiota colonization and transmission between hosts remain mostly mysterious. Here, we introduced hundreds of barcoded Escherichia coli strains into germ-free mice and quantified strain-level dynamics and metagenomic changes. Mutations in genes involved in motility and metabolite utilization are reproducibly selected within days. Even with rapid selection, coprophagy enforced similar barcode distributions across co-housed mice. Whole-genome sequencing of hundreds of isolates revealed linked alleles that demonstrate between-host transmission. A population-genetics model predicts substantial fitness advantages for certain mutants and that migration accounted for ∼10% of the resident microbiota each day. Treatment with ciprofloxacin suggests interplay between selection and transmission. While initial colonization was mostly uniform, in two mice a bottleneck reduced diversity and selected for ciprofloxacin resistance in the absence of drug. These findings highlight the interplay between environmental transmission and rapid, deterministic selection during evolution of the intestinal microbiota.
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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.