E. coli expression data from gnotobiotic ceca 14d post-inoculation
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli K-12 Escherichia coli
PROVIDER: GSE6426 | GEO | 2007/02/02
SECONDARY ACCESSION(S): PRJNA99501
REPOSITORIES: GEO
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Project description:Transcriptional expression of MG1655 and UTI89 harvested from monoassociated gnotobiotic mouse ceca (female C57Bl/6) Experiment Overall Design: Transcriptional profiling of genes shared between two different E. coli strains (after application of electronic probe mask on raw data)
2008-06-14 | E-GEOD-6426 | biostudies-arrayexpress
Project description:Transcriptional profiling of Salmonella typhimurium in the ceca of germ-free and Bacteroides thetaiotaomicron-monoassociated gnotobiotic mice. Comparison with response in MM-Glucose.
2013-07-23 | GSE49076 | GEO
Project description:Transcriptional profiling of Salmonella typhimurium in the ceca of germ-free and Bacteroides thetaiotaomicron-monoassociated gnotobiotic mice. Comparison with response in MM-Glucose. In vivo transcriptional profiles of Salmonella typhimurium obtained from biological triplicate samples taken from cecal contents of germ-free and Bacteroides thetaiotaomicron-monoassociated mice 5 days post-infection with S. typhimurium. Biological duplicate samples from in vitro culture of S. typhimurium in MM-Glucose used for comparision.
2013-07-23 | E-GEOD-49076 | biostudies-arrayexpress
Project description:Transcriptional expression of MG1655 and UTI89 harvested from various time points during aerobic or anaerobic growth in Luria-Bertani medium Keywords: time course analyses (aerobic and anaerobic)
2007-02-02 | GSE6425 | GEO
Project description:Transcriptional expression of MG1655 and UTI89 harvested from various time points during aerobic or anaerobic growth in Luria-Bertani medium Experiment Overall Design: Transcriptional profiling time course analysis of genes shared between two different E. coli strains (after application of electronic probe mask on raw data)
2008-06-14 | E-GEOD-6425 | biostudies-arrayexpress
Project description:Transcriptional profiling of Bacteroides thetaiotaomicron was performed on samples taken from (i) chemostat cultures (in vitro) and (ii) from the ceca of gnotobiotic monoassociated NMRI mice (in vivo). In vitro profiles were obtained from biological duplicate cultures taken at five timepoints from log to stationary phase in three types of media: (i) minimal media glucose (MM-G), (ii) minimal media maltotriose (MM-M), and (iii) rich media (TYG). In vivo profiling was performed on 12 mice, each colonized with B. thetaiotaomicron for ten days. The in vivo profiling was conducted in two separate experiments: (i) 6 male NMRI mice fed standard polysaccharide rich mouse chow and (ii) 3 male NMRI mice fed standard polysaccharide rich mouse chow and 3 male NMRI mice fed a simple sugar diet containing glucose and sucrose but deficient in polysaccharides. Keywords: other
2005-03-30 | GSE2231 | GEO
Project description:E. coli expression data from gnotobiotic ceca 14d post-inoculation
| PRJNA99501 | ENA
Project description:We compare the transcriptome of gnotobiotic Ae. aegypti generated by contaminating axenic (bacteria-free) larvae with bacterial isolates found in natural mosquito breeding sites. We focused on four bacterial isolates (Lysobacter, Flavobacterium, Paenibacillus and Enterobacteriaceae) and found that different gnotobiotic treatments resulted in massive transcriptomic changes throughout the mosquito development.
2021-12-15 | GSE173472 | GEO
Project description:We illustrate an approach for integrating preclinical gnotobiotic animal models with human studies to understand the contributions of perturbed gut microbiota development to childhood undernutrition, and to identify new microbiota-directed therapeutic concepts/leads. Combining metabolomic and proteomic analyses of serially collected plasma samples with metagenomic analyses of serially collected fecal samples, we characterized the biological state of Bangladeshi children with severe acute malnutrition (SAM) as they transitioned to moderate acute malnutrition (MAM) after standard treatment. Gnotobiotic mice were subsequently colonized with a defined consortium of bacterial strains representing different stages of microbiota development in healthy children from Bangladesh. Administering different combinations of Bangladeshi complementary food ingredients to colonized mice and germ-free controls revealed diet-dependent changes in representation and metabolism of targeted weaning-phase strains, including accompanying increases in branched-chain amino acids, plus diet- and colonization-dependent augmentation of IGF-1/mTOR signaling. Host and microbial effects of microbiota-directed complementary food (MDCF) prototypes were subsequently examined in gnotobiotic mice colonized with post-SAM MAM microbiota and in gnotobiotic piglets colonized with a defined consortium of targeted age- and growth-discriminatory bacteria. Finally, ar andomized, double-blind study revealed a lead MDCF that affected the representation of targeted bacterial taxa and increased levels of biomarkers and mediators of growth, bone formation, neurodevelopment, and immune function.
2019-08-20 | GSE119641 | GEO
Project description:Background: Inflammatory bowel diseases (IBD) may be caused in part by aberrant immune responses to commensal intestinal microbes including Bacteroides thetaiotaomicron (B.theta). Healthy, germ-free HLA-B27 transgenic (Tg) rats develop chronic colitis when colonized with complex gut commensal bacteria whereas non-transgenic (nTg) rats remain disease-free. However, the role of B.theta, a well-characterized anaerobic commensal bacterium, in causing disease in Tg rats is unknown nor is much known about how microbes respond to host inflammation. Methods: Tg and nTg rats were monoassociated with a human isolate of B.theta. Colonic inflammation was quantified by blinded histological scoring and real-time RT-PCR assays of pro-inflammatory cytokines. Cecal bacterial concentrations were measured by quantitative plating. Whole genome transcriptional profiling of B.theta recovered from ceca was performed using custom GeneChips and data analyzed using dChip, Significance Analysis of Microarrays, and Gene Set Enrichment Analysis (GSEA) software. Results: B.theta monoassociated Tg rats had significantly more colonic inflammation and increased colonic levels of pro-inflammatory cytokine mRNAs compared to nTg controls. Transcriptional profiles of cecal B.theta were significantly different in Tg vs. nTg rats. GSEA revealed that the Gene Ontology molecular function of receptor activity, which is comprised mainly of genes that encode nutrient binding proteins, was significantly enriched with genes upregulated in B.theta from Tg rats. KEGG canonical pathways of ribosome, oxidative phosphorylation, pyrimidine metabolism, purine metabolism, peptidoglycan biosynthesis, and metabolism were significantly enriched with genes downregulated in B.theta from Tg rats. Numbers of viable bacteria/gram cecal contents in Tg vs. nTg rats were not significantly different. Conclusions: B.theta induces mild colitis in HLA-B27 Tg rats, which is associated with changes in the expression of microbial metabolic and nutrient binding pathways, but no difference in concentrations of luminal bacteria. Mechanistic studies of differentially expressed B.theta genes may reveal novel pathways that contribute to IBD. The fully-sequenced human fecal isolate of B.theta (VPI-5482) was grown on Brain-Heart Infusion (BHI) agar and in BHI broth under strict anaerobic conditions using pre-reduced media. Adult germ-free HLA-B27/b2 microglobulin transgenic rats and adult germ-free non-transgenic littermate were monoassociated with B.theta for six weeks in gnotobiotic isolators at the National Gnotobiotic Rodent Resource Center at UNC Chapel Hill. Bacterial RNA was isolated from rat cecal contents and hybridized on Affymetrix human gut microbiota community GeneChip.
2012-01-11 | E-GEOD-34966 | biostudies-arrayexpress