ArticleNature genetics2025
A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen.
Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
16 citing papers in PubMed.
- Dual screen for gut metabolites suppressing enterobacterial growth and invasiveness reveals structure-activity relationships among anti-infective indoles.Gut microbes · 2026Article
- Review
- Compendium of RNA modifications for bacterial stress adaptation.Microbiology and molecular biology reviews : MMBR · 2026Review
- Article
- Simulating the host niche: balancing complexity and control in the experimental evolution of antibiotic resistance and pathoadaptation.Microbiology (Reading, England) · 2026Review
- Locus of Adhesion and Autoaggregation (LAA) pathogenicity island genesMicrobiology spectrum · 2026Article
- Article
- Organoids: generation strategies, applications, and future challenges.Stem cell research & therapy · 2026Review
- Growth-dependent tRNA Reprogramming and Codon Bias Link Translation to Metabolic State inbioRxiv : the preprint server for biology · 2026Article
- Adaptation ofmSystems · 2026Article
- Engineering Organoid Platforms for Pathogenesis Research.Research (Washington, D.C.) · 2026Review
- Gut microbiota in Henoch-Schönlein purpura: from pathogenesis to therapeutic strategies.Frontiers in immunology · 2026Review
- Beyond antibiotic resistance: evidence for resistance-nodulation-division (RND) efflux pumps as virulence determinants.Microbiology and molecular biology reviews : MMBR · 2025Review
- The pcnB gene sustains Shigella flexneri virulence.PLoS pathogens · 2025Article
- tRNA-modifying enzymes in bacterial stress adaptation.Open biology · 2025Review
- Organoid models advance dysentery control.Nature genetics · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
Studying the pathogenesis of human-adapted microorganisms is challenging, since small animal models often fail to recapitulate human physiology. Hence, the comprehensive genetic and regulatory circuits driving the infection process of principal human pathogens such as Shigella flexneri remain to be defined. We combined large-scale Shigella infections of enteroids and colonoids with transposon-directed insertion sequencing and Bayesian statistical modeling to address infection bottlenecks, thereby establishing the comprehensive genome-wide map of Shigella genes required to infect human intestinal epithelium. This revealed the Shigella virulence effectors essential for epithelial cell colonization across geometries and intestinal segments, identified over 100 chromosomal genes involved in the process and uncovered a post-transcriptional mechanism whereby tRNA-modification enzymes and differential codon usage exert global control of a bacterial virulence program. Our findings provide a broadly applicable framework for combining advanced organotypic tissue culture with functional genomics and computational tools to map human-microorganism interactions at scale.
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What Socratic holds
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 Socratic graph.