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Bacteroides thetaiotaomicron VPI-5482

ABSTRACT: Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization

PROVIDER: PRJNA797447 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17994100.fastq.gz	Fastqsanger.gz
	SRR17994200.fastq.gz	Fastqsanger.gz
	SRR17994101.fastq.gz	Fastqsanger.gz
	SRR17994201.fastq.gz	Fastqsanger.gz
	SRR17994102.fastq.gz	Fastqsanger.gz

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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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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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Expression data of Enterohemorrhagic E. coli O157:H7 (EHEC) strain 86-24 when cultured with Bacteroides thetaiotaomicron VPI-5482

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Expression data of Enterohemorrhagic E. coli O157:H7 (EHEC) strain 86-24 when cultured with Bacteroides thetaiotaomicron VPI-5482

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