ArticleCellular microbiology2020
Germ-free and microbiota-associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes.
Article in Cellular microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Equine endometrial organoids preserve tissue structure and cycle-stage transcriptional identity†.Biology of reproduction · 2026Article
- The microbial metabolite desaminotyrosine protects against graft-versus-host disease via mTORC1 and STING-dependent intestinal regeneration.Nature communications · 2025Article
- Determinants of divergentmBio · 2025Article
- FGF receptor kinase inhibitors exhibit broad antiviral activity by targeting Src family kinases.Cellular and molecular life sciences : CMLS · 2024Article
- Direct Salmonella injection into enteroid cells allows the study of host-pathogen interactions in the cytosol with high spatiotemporal resolution.PLoS biology · 2024Article
- LNCGM1082 in Gut Epithelial Cells Promotes Expulsion of Infected Epithelial Cells and Release of IL-18.ImmunoHorizons · 2024Article
- Organoids capture tissue-specific innate lymphoid cell development in mice and humans.Cell reports · 2022Article
- A motile doublet form of Salmonella Typhimurium diversifies target search behavior at the epithelial surface.Molecular microbiology · 2022Article
- Assessment of source material for human intestinal organoid culture for research and clinical use.BMC research notes · 2022Article
- The role of intestinal stem cell within gut homeostasis: Focusing on its interplay with gut microbiota and the regulating pathways.International journal of biological sciences · 2022Review
- The phenotype of the gut region is more stably retained than developmental stage in piglet intestinal organoids.Frontiers in cell and developmental biology · 2022Article
- Intercrypt sentinel macrophages tune antibacterial NF-κB responses in gut epithelial cells via TNF.The Journal of experimental medicine · 2021Article
- Comparative transcriptional profiling of the early host response to infection by typhoidal and non-typhoidal Salmonella serovars in human intestinal organoids.PLoS pathogens · 2021Article
- Epithelium-autonomous NAIP/NLRC4 prevents TNF-driven inflammatory destruction of the gut epithelial barrier in Salmonella-infected mice.Mucosal immunology · 2021Article
- Bacterial detection by NAIP/NLRC4 elicits prompt contractions of intestinal epithelial cell layers.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Gastrointestinal epithelial innate immunity-regionalization and organoids as new model.Journal of molecular medicine (Berlin, Germany) · 2021Review
- Article
- Salmonella enterica Infection of Murine and Human Enteroid-Derived Monolayers Elicits Differential Activation of Epithelium-Intrinsic Inflammasomes.Infection and immunity · 2020Article
- Germ-free and microbiota-associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes.Cellular microbiology · 2020Article
- Intestinal restriction of Salmonella Typhimurium requires caspase-1 and caspase-11 epithelial intrinsic inflammasomes.PLoS pathogens · 2020Article
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Authors and funding
9 authors.
Funding
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Abstract
Intestinal epithelial organoids established from gut tissue have become a widely used research tool. However, it remains unclear how environmental cues, divergent microbiota composition and other sources of variation before, during and after establishment confound organoid properties, and how these properties relate to the original tissue. While environmental influences cannot be easily addressed in human organoids, mice offer a controlled assay-system. Here, we probed the effect of donor microbiota differences, previously identified as a confounding factor in murine in vivo studies, on organoids. We analysed the proteomes and transcriptomes of primary organoid cultures established from two colonised and one germ-free mouse colony of C57BL/6J genetic background, and compared them to their tissue of origin and commonly used cell lines. While an imprint of microbiota-exposure was observed on the proteome of epithelial samples, the long-term global impact of donor microbiota on organoid expression patterns was negligible. Instead, stochastic culture-to-culture differences accounted for a moderate variability between independently established organoids. Integration of transcriptome and proteome datasets revealed an organoid-typic expression signature comprising 14 transcripts and 10 proteins that distinguished organoids across all donors from murine epithelial cell lines and fibroblasts and closely mimicked expression patterns in the gut epithelium. This included the inflammasome components ASC, Naip1-6, Nlrc4 and Caspase-1, which were highly expressed in all organoids compared to the reference cell line m-IC
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