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
Project description:This SuperSeries is composed of the following subset Series: GSE5865: B.thetaiotaomicron or B. longum mono-association versus B. thetaiotaomicron/B. longum co-colonization, PR chow, NMRI GSE5866: B.thetaiotaomicron mono-association versus B. thetaiotaomicron co-colonization with B. longum, PR chow, B6 GSE5867: B.thetaiotaomicron mono-association versus B. thetaiotaomicron co-colonization with B. animalis or L. casei, PR chow, B6 Refer to individual Series
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.
Project description:Gnotobiotic NMRI mice were colonized at birth with B. thetaiotaomicron. Mice were sacrificed at P17 or P30, cecal contents were harvested and used for transcriptional profiling. Keywords: developmental timepoints, in vivo
