Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Clostridioides difficile R20291 Toxin Mutants

PROVIDER: PRJNA762329 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR15841251_1.fastq.gz	Fastqsanger.gz
	SRR15841251_2.fastq.gz	Fastqsanger.gz
	SRR15841252_1.fastq.gz	Fastqsanger.gz
	SRR15841252_2.fastq.gz	Fastqsanger.gz
	SRR15841253_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Clostridioides difficile: R20291_pMTL84151 transconjugant (C) vs. R20291_pMTL84151-03890 (T1)

Project description:Gene expression level of Clostridioides difficile (C. difficile) strain R20291 comparing control C. difficile carring pMTL84151 as vector plasmid with C. difficile conjugated with a pMTL84151-03890 gene. Goal was to determine the effects of 03890 gene conjugation on C. difficile strain R20291 gene expression.

2023-11-30 | GSE219066 | GEO

Jenior2021 - Clostridium difficile 630 model

Project description:The pathogen Clostridioides difficile causes toxin-mediated diarrhea and is the leading cause of hospital-acquired infection in the United States. Due to growing antibiotic resistance and recurrent infection, targeting C. difficile metabolism presents a new approach to combat this infection. Genome-scale metabolic network reconstructions (GENREs) have been used to identify therapeutic targets and uncover properties that determine cellular behaviors. Thus, we constructed C. difficile GENREs for a hypervirulent isolate (strain [str.] R20291) and a historic strain (str. 630), validating both with in vitro and in vivo data sets. Growth simulations revealed significant correlations with measured carbon source usage (positive predictive value [PPV] ≥ 92.7%), and single-gene deletion analysis showed >89.0% accuracy. Next, we utilized each GENRE to identify metabolic drivers of both sporulation and biofilm formation. Through contextualization of each model using transcriptomes generated from in vitro and infection conditions, we discovered reliance on the pentose phosphate pathway as well as increased usage of cytidine and N-acetylneuraminate when virulence expression is reduced, which was subsequently supported experimentally. Our results highlight the ability of GENREs to identify novel metabolite signals in higher-order phenotypes like bacterial pathogenesis.

2023-11-27 | MODEL2205060002 | BioModels

Effect of tcdR mutation in Clostridium difficile sporulation

Project description:Clostridium difficile is an important nosocomial pathogen and the leading cause of hospital-acquired diarrhea. Antibiotic use is the primary risk factor for the development of C. difficile-associated disease because it disrupts normal protective gut flora and enables C. difficile to colonize the colon. C. difficile damages host tissue by secreting toxins and disseminates by forming spores. The toxin-encoding genes, tcdA and tcdB are part of a pathogenicity locus, which also encodes the gene tcdR that codes for the toxin genes positive regulator. TcdR is an alternate sigma factor that initiates transcription of tcdA and tcdB at their promoters. Alternative sigma factors are known to regulate virulence and virulence associated genes in many pathogenic bacteria. We created a tcdR mutant in the epidemic-type C. difficile R20291 strain in an attempt to identify the global role of tcdR. A site-directed mutation in tcdR affected both toxin production and sporulation in C. difficile R20291. Spores derived from the tcdR mutant were found to be mildly temperature sensitive. Moreover, nearly two fold more taurocholate was needed to germinate spores from the tcdR mutant than the spores prepared from the wild-type parent strain. Comparison of the tcdR mutant transcriptome with the parent strain revealed many differentially expressed late sporulation genes in the tcdR mutant. These data suggests that gene regulatory networks of toxin production and sporulation in Clostridium difficile are linked with each other.

2017-03-07 | GSE85395 | GEO

Transcriptomic profile of a Clostridioides difficile rsbW deletion mutant compared to parental R20291 strain

Project description:RNA-seq was conducted to uncover the regulatory roles of RsbW in the lifestyle of Clostridioides difficile strain R20291. RNA were extracted from planktonic cultures, which were grown in BHI-S (Sigma-Aldrich, USA) to early stationary phase (10h). The cells were re-suspended in LETS buffer and lysed using Fast-prep 24 instrument (MP Bioscience) and RNA was extracted using 1 ml Trizol (Ambion, USA). Samples were cleaned and sequenced by Novogene Company Limited, PE150 with approximately 10 million reads per sample. After QC, reads were aligned to R20291 (NC_013316.1) with Bowtie2 and readcounts were generated with Samtools and Bedtools. Differential gene expression analysis was conducted with DESeq2 with a p-value of 0.05, differential gene expression was determined with ± -2 logFC.

2022-08-22 | E-MTAB-12114 | biostudies-arrayexpress

L-lactate supplementation influences toxin production of Clostridioides difficile via energy metabolism

Project description:Metabolomic and transcriptomic analysis of changes in the exponential and stationary phase of Clostridioides difficile after cultivation in casamino acids medium (reference) and supplemented with L-lactate and the connection to toxin production.

2021-01-31 | GSE139354 | GEO

Metabolic reprogramming with the induction of toxin production of Clostridioides difficile during the stationary phase

Project description:Systems biology approach of Clostridioides difficile to analyze the temporal changes in the intracellular and extracellular metabolme, transcriptome and proteome along the growth curve in casamino acids medium and the connection to toxin production.

2018-10-01 | GSE115054 | GEO

Influence of L-lactate and low glucose concentrations on the metabolism and the toxin formation of Clostridioides difficile

2020-12-23 | GSE149911 | GEO

Toxin-mediated downregulation of absorptive ion transporters NHE3, DRA, and SGLT1 in the colon contributes to diarrhea associated with Clostridioides difficile infection.

Project description:We defined global differences in transcriptome profiles between mice inoculated with toxin mutant strains of Clostridioides difficile. These data were mined to study differences in expression of ion transporters that may be implicated in diarrhea during disease.

2022-11-12 | GSE216919 | GEO

Beyond difficile: three novel toxin B-producing Clostridioides species from human patients with diarrhea (exoproteome)

Project description:Clostridioides difficile infection (CDI), caused by strains producing toxin B (TcdB), poses a significant global health threat. While C. difficile exhibits substantial diversity, functional studies have focused on a limited number of isolates, overlooking other genomospecies within the genus. We describe five isolates from patients suspected of having CDI who tested negative for the PaLoc marker gene tcdC. Through genomic, proteomic, and phenotypic analyses, we demonstrate that they correspond to three novel toxin-producing species, designated as Clostridioides cryptodifficilis sp. nov., Clostridioides divergens sp. nov., and Clostridioides subdifficilis sp. nov. These species are distinguished by unique MALDI-ToF signatures, metabolic capabilities, and genomic and proteomic architectures, underscoring their clear taxonomic and functional divergence from C. difficile. They secrete functionally active TcdB7 or TcdB11, as demonstrated by cytotoxicity assays in cultured cells and in vivo using the mouse ileal loop model, implicating them in disease pathology, albeit with lower virulence than C. difficile. Our findings expand the known diversity of TcdB-producing Clostridioides and have direct implications for diagnostics, surveillance, and clinical management of diarrheal diseases.

2026-05-06 | PXD067952 | Pride

Beyond difficile: three novel toxin B-producing Clostridioides species from human patients with diarrhea (spore proteome)

2026-05-06 | PXD066931 | Pride