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Bacteroides thetaiotaomicron ameliorates colon inflammation in preclinical models of Crohn’s Disease [Bacteroides]

ABSTRACT: Analysis of the Bacteroides thetaiotaomicron(BT) transcriptome during co-culture with Caco-2 intestinal epithelial cells To identify potential bacterial protein(s) involved in the anti-inflammatory effect of BT in colitis, BT was incubated with Caco-2 human intestinal epithelial cells for 2 hours, and bacterial gene expression was assessed on a Bacteroides thetaiotaomicron VPI-5482 specific microarray. Forty-three BT genes were up-regulated by five-fold or more and of these, twenty genes encoded hypothetical proteins.

ORGANISM(S): Bacteroides thetaiotaomicron VPI-5482

PROVIDER: GSE118525 | GEO | 2019/03/06

REPOSITORIES: GEO

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Gene expression of Bacteroides thetaiotaomicron, in vivo with and without IgA 225.4

Project description:Rag1-/- C57BL/6 or Rag1-/- C57BL/6 injected with the IgA producing hybridoma producing 225.4 anti- Bacteroides thetaiotaomicron (Capsular polysaccharide 4 dependent carbohydrate epitope specific epitope) mice were colonized with B. thetaiotaomicron wildtype strain VPI-5482 for 10 days. Cecal bacteria were harvested and snap frozen and RNA isolated. Keywords: Single time point, experimental and control groups.

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Characterizing the interactions between a naturally-primed IgA (mAb 260.8) and its conserved Bacteroides thetaiotaomicron species-specific epitope in gnotobiotic mice [array]

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Genome-wide RNA-seq of Bacteroides thetaiotaomicron VPI-5482 with Bacteroides phage challenge

Project description:Purpose: Examining the transcriptome of Bacteroides thetaiotaomicron VPI-5482 challenged with Bacteroides phage to assess surface molecule expression changes Methods: Bacteroides thetaiotaomicron was grown in BPRM in vitro or Germ-Free mice were monocolonized with Bacteroides thetaiotaomicron and gavaged with ARB25 phage. Fold change was calculated as live phage versus heat-killed phage treated samples with n=3 biological replicates. Once cells reached an optical density corresponding to mid-log phase growth (absorbance between 0.4-0.5), RNA was isolated and rRNA depleted. Samples were multiplexed for sequencing on the Illumina HiSeq platform at the University of Michigan Sequencing Core. Data was analyzed using Arraystar software (DNASTAR, Inc.) using DEseq2 normalization with default parameters. Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >5-fold and with at least 2/3 biological replicates with a normalized expression level >1% of the overall average, and a p-value < 0.05 (t test with Benjamini-Hochberg correction) Results: Specific capsule expression was increased in wild-type B. thetaiotaomicron during phage infection in vitro and in vivo. Many corresponding in vivo genes were upregulated as well as other surface layer proteins.

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Bacteroides thetaiotaomicron VPI-5482

Project description:Bacteroides thetaiotaomicron VPI-5482 Raw sequence reads

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Bacteroides thetaiotaomicron VPI-5482

Project description:Bacteroides thetaiotaomicron VPI-5482 Transcriptome or Gene expression

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Analysis of the transcriptome of Bacteroides thetaiotaomicron during growth on complex N-glycan as the sole carbon source

Project description:The goal of this project was to sequence the transcriptome of wild type Bacteroides thetaiotaomicron VPI-5482 grown in minimal media with either glucose or bovine alpha 1 acid glycoprotein (AAGP) as the sole carbon source. Using these data we could then compare relative gene expression levels under each condition and identify genes specifically upregulated during growth on AAGP. Analysis of the spent media indicated that only the N-glycan component of the AAGP had been used by the cells to support growth.

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Bacteroides thetaiotaomicron ameliorates colon inflammation in preclinical models of Crohn’s Disease [mouse colon]

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2019-03-06 | GSE118524 | GEO

Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats

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2014-01-01 | E-GEOD-38534 | biostudies-arrayexpress

Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats

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Genome-wide RNA-seq of Bacteroides thetaiotaomicron VPI-5482 grown on ribose

Project description:Purpose: Examining the transcriptome of Bacteroides thetaiotaomicron VPI-5482 grown on ribose to look at global changes in regulation in vitro on the defined monosaccharide, ribose as a sole carbon source. Methods: Bacteroides thetaiotaomicron was grown on 5 mg/ml ribose or glucose as a sole carbon source in vitro. Fold change was calculated as ribose over glucose with n=3 biological replicates. Once cells reached an optical density corresponding to mid-log phase growth (absorbance between 0.6-0.8), RNA was isolated and rRNA depleted. Samples were multiplexed for sequencing on the Illumina HiSeq platform at the University of Michigan Sequencing Core. Data was analyzed using Arraystar software (DNASTAR, Inc.) using RPKM normalization with default parameters. Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >5-fold and with at least 2/3 biological replicates with a normalized expression level >1% of the overall average RPKM expression level in either glucose or ribose, and a p-value < 0.05 (t test with Benjamini-Hochberg correction) Results: We identified 81 genes differentially expressed at a 5-fold cutoff when grown in ribose over the reference glucose condition, many of which are involved in other metabolic processes important for seemingly unrealted nutrients.

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