ArticleGut microbes
A single cell survey of the microbial impacts on the mouse small intestinal epithelium.
Article in Gut microbes. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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
27 citing papers in PubMed, 43 citations in OpenAlex.
- Developmental factors drive the compartmentalized and discontinuous maturation of the small intestinal epithelium during the early postnatal period.PLoS biology · 2026Article
- Omics-based decoding of molecular and metabolic crosstalk in the skin barrier ecosystem.Cell death and differentiation · 2026Review
- Dietary capsaicin attenuates type 2 diabetes via gut microbiota and bile acid metabolic pathways.iScience · 2026Article
- Weaning drives microbiome-mediated epigenetic regulation to shape immune memory in mice.Nature microbiology · 2026Article
- Article
- An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut.Cell host & microbe · 2026Article
- Epithelial sensing of vitamin A shapes intestinal antimicrobial defense.bioRxiv : the preprint server for biology · 2026Article
- Host response to bacteria induces a shift towards the enteroendocrine cell lineage in the murine enteroid model.PLoS pathogens · 2026Article
- FUT2-mediated intestinal fucosylation: a master regulator of host-microbiota symbiosis in health and disease.Frontiers in microbiology · 2026Review
- Microbiota shape the colon epithelium controlling inter-crypt absorptive goblet cells via butyrate-GP R109A signalling.Gut microbes · 2025Article
- Intestinal stem and progenitor cells exhibit distinct adaptive responses to inflammatory stress in IBD.Stem cell research & therapy · 2025Article
- Adiponectin Regulated by Indole-3-Acetic Acid in Paneth Cells Controls Renewal and Differentiation of Gut Stem Cells.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025Article
- Sex-specific programming of the gastric and duodenal mitochondrial biogenesis by early-life stress.Genes & genomics · 2025Article
- The IL-18 receptor is expressed on murine small-intestinal enterochromaffin cells and executes a recovery program upon injury.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Article
- Chinese Sausage Simulates High Calorie-Induced Obesity In Vivo, Identifying the Potential Benefits of Weight Loss and Metabolic Syndrome of Resveratrol Butyrate Monomer Derivatives.Journal of nutrition and metabolism · 2025Article
- Article
- Single Cell Analysis of Human Colonoids Exposed to Uranium-Bearing Dust.Environmental health perspectives · 2024Article
- BEST4American journal of physiology. Cell physiology · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 2 institutions in 2 countries.
Funding
Abstract
The small intestinal epithelial barrier inputs signals from the gut microbiota in order to balance physiological inflammation and tolerance, and to promote homeostasis. Understanding the dynamic relationship between microbes and intestinal epithelial cells has been a challenge given the cellular heterogeneity associated with the epithelium and the inherent difficulty of isolating and identifying individual cell types. Here, we used single-cell RNA sequencing of small intestinal epithelial cells from germ-free and specific pathogen-free mice to study microbe-epithelium crosstalk at the single-cell resolution. The presence of microbiota did not impact overall cellular composition of the epithelium, except for an increase in Paneth cell numbers. Contrary to expectations, pattern recognition receptors and their adaptors were not induced by the microbiota but showed concentrated expression in a small proportion of epithelial cell subsets. The presence of the microbiota induced the expression of host defense- and glycosylation-associated genes in distinct epithelial cell compartments. Moreover, the microbiota altered the metabolic gene expression profile of epithelial cells, consequently inducing mTOR signaling thereby suggesting microbe-derived metabolites directly activate and regulate mTOR signaling. Altogether, these findings present a resource of the homeostatic transcriptional and cellular impact of the microbiota on the small intestinal epithelium.
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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.