ArticleNature microbiology2020
Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice.
Article in Nature microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 1 of them a synthesis that pooled it.
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
67 citing papers in PubMed, 1 synthesis or guideline pooled it, 96 citations in OpenAlex.
- Dynamic Distribution of Gut Microbiota in Pigs at Different Growth Stages: Composition and Contribution.Microbiology spectrum · 2022Pooled it
- Animal gut microbes and microbiomes in the 21st century and beyond.Science China. Life sciences · 2026Review
- Antisense transcription reveals disease-associated adaptations in the human gut microbiome.Nature microbiology · 2026Article
- An atlas of colonization factors in the human gut microbiome reveals ecological strategies and inflammatory bowel disease signatures.Nature communications · 2026Article
- Single-bacterium RNA-seq protocol to uncover heterogeneous expression of coding and noncoding genes in Bacteroides thetaiotaomicron.STAR protocols · 2026Article
- An anaerobic pathogen rewires host metabolism to fuel oxidative growth in the inflamed gut.Cell · 2026Article
- Enriching Bacteria-Specific RNA From Host Samples Before NGS With Transcript-Capture.Bio-protocol · 2026Article
- Spatial distribution: Effect of oxygen availability on gut microbiota adhesion and colonization.Journal of food and drug analysis · 2026Article
- Intestinal fungi shape the biology of the mammalian gut.PLoS pathogens · 2026Article
- Enteric nervous system in exercise physiology: a microbiota-neural interface.npj metabolic health and disease · 2026Review
- CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.Nature communications · 2026Article
- Striking a balance: how the gut microbiome shapes the fate of intestinal CD4+ T cells.Discovery immunology · 2026Review
- Transcript-Capture sequencing enriches mRNA ofNAR molecular medicine · 2026Article
- Factors influencing gut microbial colonization: A host-microbe-environment interaction perspective.Current research in food science · 2026Review
- Bacteroides fragilis colonization induces protective systemic IgA.Microbiome · 2025Article
- A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.Scientific data · 2025Article
- Interbacterial warfare in the human gut: insights from Bacteroidales' perspective.Gut microbes · 2025Review
- Hydrogel-based experimental models of the gastrointestinal tract.Microbiome · 2025Review
- Transcript-Capture sequencing enriches mRNA ofbioRxiv : the preprint server for biology · 2025Article
- Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 3 institutions in 2 countries.
Funding
Abstract
A complex microbiota inhabits various microenvironments of the gut, with some symbiotic bacteria having evolved traits to invade the epithelial mucus layer and reside deep within the intestinal tissue of animals. Whether these distinct bacterial communities across gut biogeographies exhibit divergent behaviours is largely unknown. Global transcriptomic analysis to investigate microbial physiology in specific mucosal niches has been hampered technically by an overabundance of host RNA. Here, we employed hybrid selection RNA sequencing (hsRNA-Seq) to enable detailed spatial transcriptomic profiling of a prominent human commensal as it colonizes the colonic lumen, mucus or epithelial tissue of mice. Compared to conventional RNA-Seq, hsRNA-Seq increased reads mapping to the Bacteroides fragilis genome by 48- and 154-fold in mucus and tissue, respectively, allowing for high-fidelity comparisons across biogeographic sites. Near the epithelium, B. fragilis upregulated numerous genes involved in protein synthesis, indicating that bacteria inhabiting the mucosal niche are metabolically active. Further, a specific sulfatase (BF3086) and glycosyl hydrolase (BF3134) were highly induced in mucus and tissue compared to bacteria in the lumen. In-frame deletion of these genes impaired in vitro growth on mucus as a carbon source, as well as mucosal colonization of mice. Mutants in either B. fragilis gene displayed a fitness defect in competing for colonization against bacterial challenge, revealing the importance of site-specific gene expression for robust host-microbial symbiosis. As a versatile tool, hsRNA-Seq can be deployed to explore the in vivo spatial physiology of numerous bacterial pathogens or commensals.
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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.