Mus musculus
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ABSTRACT:
PROVIDER: PRJNA357823 | ENA |
REPOSITORIES: ENA
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Project description:We analyzed the transcriptional profile of colon and small-intestinal (SI) tissues in response to ex-vivo colonization with members of the gut microbiota. Tissues were dissected from SPF or GF mice, and connected to the ex-vivo gut organ culture system. Then, microbial cultures or fecal samples were infused into the lumen, and tissues were processed in different time points, as indicated below.
2016-12-17 | GSE92471 | GEO
Project description:Transcriptional responses of colon tissues following ex-vivo colonization with human microbiome
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Project description:The intestinal microbiota fundamentally influences the development of a normal intestinal physiology and education and functioning of the mucosal immune system. The goal of this study is to analyze how the transcriptional profile of the murine colon can be influence by colonization of gnotobiotic mice with specific bacterial strains .
2021-08-09 | GSE181502 | GEO
Project description:The GeneChip Porcine Genome Array was used to identify the transcriptional response upon Salmonella typhimurium infection in three porcine intestinal sections (jejumun, ileum and colon) along a time course of 1,2 and 6 days post infection. The objetives in this study were i) characterize transcriptional changes upon S. typhimurium infection in the intestinal mucosa; ii) identify differences among porcine intestinal sections in inmune resposes against S. typhimurium; iii) identify change that could be associated to salmonellosis pathogenesis and symtomatology; and finally, iv) identify transcriptional changes that could be induced by S. typhimurium in order to get bacterial survival and successful colonization.
2012-06-20 | GSE22596 | GEO
Project description:Transcriptional response of small-intestinal lamina propria CD4+ T cells to bacterial colonization
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Project description:Epithelial cells of the mammalian intestine are covered with a mucus layer that prevents direct contact with intestinal microbes but also constitutes a substrate for mucus-degrading bacteria. To study the effect of mucus degradation on the host response, germ-free mice were colonized with Akkermansia muciniphila. This anaerobic bacterium belonging to the Verrucomicrobia is specialized in the degradation of mucin, the glycoprotein present in mucus, and found in high numbers in the intestinal tract of human and other mammalian species. Efficient colonization of A. muciniphila was observed with highest numbers in the cecum, where most mucin is produced. In contrast, following colonization by Lactobacillus plantarum, a facultative anaerobe belonging to the Firmicutes that ferments carbohydrates, similar cell-numbers were found at all intestinal sites. Whereas A. muciniphila was located closely associated with the intestinal cells, L. plantarum was exclusively found in the lumen. The global transcriptional host response was determined in intestinal biopsies and revealed a consistent, site-specific, and unique modulation of about 750 genes in mice colonized by A. muciniphila and over 1500 genes after colonization by L. plantarum. Pathway reconstructions showed that colonization by A. muciniphila altered mucosal gene expression profiles toward increased expression of genes involved in immune responses and cell fate determination, while colonization by L. plantarum led to up-regulation of lipid metabolism. These indicate that the colonizers induce host responses that are specific per intestinal location. In conclusion, we propose that A. muciniphila modulates pathways involved in establishing homeostasis for basal metabolism and immune tolerance toward commensal microbiota. Keywords: Analysis of target gene regulation by using microarrays Adult germ-free female NMRI-KI mice (45 – 65 days) were used for bacterial mono-association. Two bacterial strains were used in this study, A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826). A. muciniphila was grown anaerobically in a basal mucin based medium and L. plantarum was grown anaerobically at 37°C in Man-Rogosa-Sharpe broth (MRS; Le Pont de Claix, France). After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.
2011-09-20 | E-GEOD-18587 | biostudies-arrayexpress
Project description:Group B Streptococcus (GBS) is a leading cause of infant sepsis worldwide. Colonization of the gastrointestinal tract is a critical precursor to late-onset disease in exposed newborns. Neonatal susceptibility to GBS intestinal translocation stems from intestinal immaturity; however, the mechanisms by which GBS exploits the immature host remain unclear. β-hemolysin/cytolysin (βH/C) is a highly conserved toxin produced by GBS capable of disrupting epithelial barriers. However, its role in the pathogenesis of late-onset GBS disease is unknown. Our aim was to determine the contribution of βH/C to intestinal colonization and translocation to extraintestinal tissues. Using our established mouse model of late-onset GBS disease, we exposed animals to GBS COH-1 (WT), a βH/C-deficient mutant (KO), or vehicle control (PBS) via gavage. Blood, spleen, brain, and intestines were harvested 4 days post-exposure for determination of bacterial burden and isolation of intestinal epithelial cells. We used RNA-sequencing to examine the transcriptomes and performed gene ontology enrichment and KEGG pathway analysis. A separate cohort of animals were followed longitudinally to compare colonization kinetics and mortality between WT and KO groups. We demonstrate that disseminated to extraintestinal tissues occurred only in the WT exposed animals. We observed major transcriptomic changes in the colon of colonized animals, but not in the small intestine. We noted differential expression of genes among WT and KO exposed mice indicating that βH/C contributes to alterations in epithelial barrier structure and immune response signaling. Overall, our results demonstrate an important role for βH/C in the pathogenesis of late-onset GBS disease.
2023-05-31 | GSE230856 | GEO
Project description:The intestinal microbiota influences the development of a normal intestinal physiology, education and functioning of the mucosal immune system. The goal of this study is to analyze how the transcriptional profile of the colonic endothelial cells is influence by colonization of gnotobiotic mice with specific bacterial strains . The goal of this study is to analyze how the transcriptional profile of the colonic endothelial cells is influence by colonization of gnotobiotic mice with specific bacterial strains .
2022-10-05 | GSE180907 | GEO
Project description:Background & Aims: We have recently established long-term culture conditions under which single crypts or stem cells derived from murine small intestine expand over long periods of time. Growing crypts undergo multiple crypt fission events, whilst simultaneously generating villus-like epithelial domains in which all differentiated cell types are present. We have now adapted the culture conditions to grow similar epithelial organoids from mouse colon and human small intestine and colon. Methods: Based on the murine small intestinal culture system, we optimized the murine and human colon culture system. Results: Addition of Wnt3A to the growth factor cocktail allowed mouse colon crypts to expand indefinitely. Further addition of nicotinamide, a small molecule Alk inhibitor and a p38 inhibitor was essential for long-term human small intestine and colon culture. The culture system also allowed growth of murine Apcmin adenomas, human colorectal cancer and human esophageal metaplastic Barrett’s epithelium. Conclusion: The culture technology should be widely applicable as a research tool for infectious, inflammatory and neoplastic pathologies of the human gastrointestinal tract. Moreover, regenerative applications may become feasible with ex vivo expanded intestinal epithelia. Human organoids were grown embedded in Matrigel in HISC (Human intestinal stem cell culture) medium. Additionally, human small intestinal crypts and villi were isolated independently from a freshly operated sample. RNA was isolated using the RNeasy Micro kit (Qiagen). Samples were labled according to Agilent guidelines with Cy3, whereas human reference RNA (Stratagene) was labeled in Cy5. Feature Extraction Software was used to extract and normalize data.
2011-12-07 | E-GEOD-28907 | biostudies-arrayexpress
Project description:Background & Aims: We have recently established long-term culture conditions under which single crypts or stem cells derived from murine small intestine expand over long periods of time. Growing crypts undergo multiple crypt fission events, whilst simultaneously generating villus-like epithelial domains in which all differentiated cell types are present. We have now adapted the culture conditions to grow similar epithelial organoids from mouse colon and human small intestine and colon. Methods: Based on the murine small intestinal culture system, we optimized the murine and human colon culture system. Results: Addition of Wnt3A to the growth factor cocktail allowed mouse colon crypts to expand indefinitely. Further addition of nicotinamide, a small molecule Alk inhibitor and a p38 inhibitor was essential for long-term human small intestine and colon culture. The culture system also allowed growth of murine Apcmin adenomas, human colorectal cancer and human esophageal metaplastic Barrett’s epithelium. Conclusion: The culture technology should be widely applicable as a research tool for infectious, inflammatory and neoplastic pathologies of the human gastrointestinal tract. Moreover, regenerative applications may become feasible with ex vivo expanded intestinal epithelia.
2011-12-07 | GSE28907 | GEO