ArticleScience (New York, N.Y.)2019
Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut.
Article in Science (New York, N.Y.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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Who cites it
96 citing papers in PubMed, 143 citations in OpenAlex.
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- TPMM: three-component posterior mixture model enables robust inverton detection in low-depth metagenomes and suggests potential viral invertons.Bioinformatics (Oxford, England) · 2026Article
- Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Long-read metagenomics and methylation-based binning support the discovery of antibiotic resistance gene-host associations in complex communities.Genome biology · 2026Article
- A phase-variable capsule facilitatesmBio · 2026Article
- Heterogeneity in microbial antibiotic responses: genetic basis and within-host evolution.Trends in genetics : TIG · 2026Review
- Temperate phages enhance bacterial host fitness via RNA-guided flagellar remodelling.Nature microbiology · 2026Article
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- Complex adaptive architectures constrain the pace of adaptations sweeping across human gut microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.Cell host & microbe · 2026Article
- Isolation of novel phages from a resistant Dorea longicatena strain reveals genes associated with phage resistance.Npj viruses · 2026Article
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- Gut Phage Biobank: a collection of bacteriophages targeting human commensal bacteria.Nature communications · 2025Article
- Cell-to-Cell and Patient-to-Patient Variability in Antimicrobial Resistance.Microorganisms · 2025Review
- Bacteriophage-driven DNA inversions shape bacterial functionality and long-term co-existence inGut microbes · 2025Article
- Maximizing bacterial survival: integrating sense-and-respond and bet-hedging mechanisms.Trends in microbiology · 2025Review
- Dynamics of dN/dS within recombining bacterial populations.bioRxiv : the preprint server for biology · 2025Article
36 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
Phase variation, the reversible alternation between genetic states, enables infection by pathogens and colonization by commensals. However, the diversity of phase variation remains underexplored. We developed the PhaseFinder algorithm to quantify DNA inversion-mediated phase variation. A systematic search of 54,875 bacterial genomes identified 4686 intergenic invertible DNA regions (invertons), revealing an enrichment in host-associated bacteria. Invertons containing promoters often regulate extracellular products, underscoring the importance of surface diversity for gut colonization. We found invertons containing promoters regulating antibiotic resistance genes that shift to the ON orientation after antibiotic treatment in human metagenomic data and in vitro, thereby mitigating the cost of antibiotic resistance. We observed that the orientations of some invertons diverge after fecal microbiota transplant, potentially as a result of individual-specific selective forces.
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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.