ABSTRACT: The genome sequencing of Bacteroides sedimenti sp. nov., isolated from a chloroethenes-dechlorinating consortium enriched from river sediment
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:Purpose: Examining the transcriptome of human gut bacteria (Bacteroides xylanisolvens/Bacteroides ovatus) that grow on mucin O-linked glycans as a sole carbon source Methods: Strains were grown on 10 mg/ml mucin O-linked glycans (MOG) or 5 mg/ml glucose as a sole carbon source in vitro. Fold change was calculated as MOG over glucose. Once cells reached an optical density corresponding to mid-log phase growth, 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.) Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and biological replicates with a normalized expression level >1% of the overall average RPKM expression level. Results: We identified genes activated in response to mucin O-linked glycans from Bacteroides xylanisolvens/Bacteroides ovatus strains
Project description:<p>Malaria, caused by <em>Plasmodium</em> species, remains a significant cause of morbidity and mortality globally. Gut bacteria can influence the severity of malaria, but the contribution of specific bacteria to the risk of severe malaria is unknown. Here, multiomics approaches demonstrate specific species of <em>Bacteroides</em> are causally linked to the risk of severe malaria. <em>Plasmodium yoelii</em> hyperparasitemia-resistant mice gavaged with murine-isolated <em>Bacteroides fragilis</em> develop <em>P. yoelii</em> hyperparasitemia. Moreover, <em>Bacteroides</em> are significantly more abundant in Ugandan children with severe malarial anemia than with asymptomatic <em>P. falciparum</em> infection. Human isolates of <em>Bacteroides caccae</em>, <em>Bacteroides uniformis</em>, and <em>Bacteroides ovatus</em> but not <em>Bacteroides thetaiotaomicron</em> caused susceptibility to severe malaria in mice. However, the pathogenic potential of gut <em>Bacteroides</em> towards susceptibility to severe malaria is dependent on additional gut microbiota, indicating a consortium effect in severe malaria. Approaches that target gut <em>Bacteroides</em> may present an opportunity to prevent severe malaria and associated deaths.</p>
Project description: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.
Project description:Analysis of colonic epithelial cell gene expression in germ-free, Bacteroides uniformis-colonized, and Clostridia-colonized gnotobiotic mice. Bacteria were isolated from our SPF mouse facility and were used to selectively colonize germ-free mice. Germ free mice were left germ free or were colonized with Bacteroides uniformis or a consortium of Clostridia. Total RNA was extraced from colonic epithelial cells.
