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Transcriptional profiles underlying morphological heterogeneity in Bacteroides thetaiotaomicron

ABSTRACT: Transcriptional profiles underlying morphological heterogeneity in Bacteroides thetaiotaomicron

PROVIDER: PRJNA1222394 | ENA |

REPOSITORIES: ENA

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Transcriptional profiles underlying morphological heterogeneity in Bacteroides thetaiotaomicron

Project description:Genetically identical bacteria can be phenotypically diverse. This is exemplified in the Bacteroidota, a predominant bacterial phylum of the human gut microbiota. However, the molecular basis of morphological heterogeneity in Bacteroidota species and potential functional consequences thereof are poorly understood. Here, we systematically characterize the cell morphology of Bacteroides thetaiotaomicron during its growth in laboratory culture and upon isolation from different host niches. We then develop a sensitive ‘mini-bulk’ transcriptomics approach to chart cell size-related gene expression patterns. The protocol builds on the MATQ-seq method that we here optimize for B. thetaiotaomicron, combined with CRISPR/Cas-based depletion of ribosomal sequences. We demonstrate that our transcriptomic pipeline accurately quantifies gene expression on a genomic scale. Its application to sort-collected B. thetaiotaomicron cells of different size enables us to derive morphological marker genes whose expression is enriched in bacterial cells of defined sizes. These morphological marker genes—encoding e.g. proteins involved in cell cycle, primary and secondary metabolism, and membrane-associated processes—are validated using single-molecule fluorescence in-situ hybridization. As microbial heterogeneity has become an emergent theme in microbiota research, this study may serve as a blueprint to link different phenotypes with functions in ever-increasing resolution.

2025-02-28 | GSE289312 | GEO

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

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.

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Bacteroides thetaiotaomicron OMV proteomics

Project description:Comparative proteomics of Bacteroides thetaiotaomicron samples comparing the total membrane (TM) and outer membrane vesicles (OMV) of WT B. thetaiotaomicron and delta 4364

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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.

2020-05-01 | GSE147071 | GEO

Role of OxyR and iron in gene regulation in Bacteroides thetaiotaomicron

Project description:Role of OxyR and iron in gene regulation in Bacteroides thetaiotaomicron

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In vitro transcriptional profiling of Bacteroides thetaiotaomicron in lactose, galactose and human milk oligosaccharides

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In vitro transcriptional profiling of Bacteroides thetaiotaomicron in lactose, galactose and human milk oligosaccharides

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