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Items: 1 to 20 of 1092

1.

A conserved structured non-coding RNA coordinates growth and virulence in Clostridioides difficile. [dRNA-Seq ModT]

(Submitter supplied) Bacterial non-coding RNAs fulfill a variety of cellular functions, for example as catalysts, as structural components in multiprotein complexes or as regulators of gene expression at the transcriptional and post-transcriptional level. Some RNAs display exceptionally broad conservation across bacterial phyla and are involved in fundamental and unique cellular functions. Hence, the characterization of new RNA families with deep sequence and/or structure conservation has the potential to reveal new molecular and biological RNA functions. more...
Organism:
Clostridioides difficile
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25258
12 Samples
Download data: WIG
Series
Accession:
GSE273119
ID:
200273119
2.

A conserved structured non-coding RNA coordinates growth and virulence in Clostridioides difficile. [DMS-MaP]

(Submitter supplied) Bacterial non-coding RNAs fulfill a variety of cellular functions, for example as catalysts of chemical reactions, as structural components in multiprotein complexes or as regulators of gene expression at the transcriptional and post-transcriptional level. Some RNAs, such as ribosomal RNAs, display exceptionally broad conservation across bacterial phyla and are involved in fundamental and unique cellular functions. more...
Organism:
Clostridioides difficile
Type:
Other
Platform:
GPL30071
28 Samples
Download data: RC, XML
Series
Accession:
GSE273118
ID:
200273118
3.

Identification of a new family of peptidoglycan transpeptidases reveals unusualcrosslinking is essential for viability inC. difficile

(Submitter supplied) Most bacteria are surrounded by a peptidoglycan cell wall composed of glycan strands held together by short peptide crosslinks. There are two major types of crosslinks, termed 4-3 and 3-3 based on the amino acids involved. 4-3 crosslinks are created by penicillin-binding proteins (PBPs), while 3-3 crosslinks created byL,D-transpeptidases (LDTs). In well studied bacteria 3-3 crosslinks comprise only about 10% of the total and are not essential. more...
Organism:
Clostridioides difficile
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32868
6 Samples
Download data: XLSX
Series
Accession:
GSE270128
ID:
200270128
4.

Clostridioides difficile-mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation.

(Submitter supplied) In a healthy colon, the stratified mucus layer serves as a crucial innate immune barrier to protect the epithelium from microbes. Mucins are complex glycoproteins that serve as a nutrient source for resident microflora but can be exploited by pathogens. We aimed to understand how the intestinal pathogen, Clostridioides diffiicile, independently uses or manipulates mucus to its benefit. Using a 2-D primary human intestinal epithelial cell model to generate physiologic mucus, we assessed C. more...
Organism:
Clostridioides difficile R20291
Type:
Expression profiling by high throughput sequencing
Platform:
GPL34151
9 Samples
Download data: TXT
Series
Accession:
GSE254621
ID:
200254621
5.

Effects of vancomycin and ramoplanin on gene expression in Clostridioides difficile

(Submitter supplied) We compared transcriptomes of wild-type and ∆vanS strains of Clostridioides difficile 630 growing in the presence or absence of peptidoglycan-targeting antibiotics, vancomycin or ramoplanin. VanS is a histidine kinase of a two-component system that regulates expression of the vancomycin-induced vanG operon.
Organism:
Clostridioides difficile 630
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28932
14 Samples
Download data: TXT
Series
Accession:
GSE262388
ID:
200262388
6.

Exogenous butyrate inhibits butyrogenic metabolism and alters virulence phenotypes in Clostridioides difficile

(Submitter supplied) The gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance against C. difficile is short chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of C. more...
Organism:
Clostridioides difficile
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32868
24 Samples
Download data: TSV
Series
Accession:
GSE249810
ID:
200249810
7.

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

(Submitter supplied) 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.
Organism:
Clostridioides difficile R20291; Clostridioides difficile
Type:
Expression profiling by array
Platform:
GPL32901
6 Samples
Download data: TXT, XLSX
Series
Accession:
GSE219066
ID:
200219066
8.

Identification of DraRS in C. difficile, a two-component regulatory system that responds to lipid II interacting antibiotics

(Submitter supplied) Clostridioides difficile is a Gram-positive opportunistic pathogen that results in 220,000 infections, 12,000 deaths, and upwards of $1 billion in medical costs in the US each year. C. difficile is highly resistant to a variety of antibiotics, but we have a poor understanding of how C. difficile senses and responds to antibiotic stress, and how such sensory systems affect clinical outcomes. There has been recent interest in using a daptomycin analog, Surotomycin, to treat C. more...
Organism:
Clostridioides difficile
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33492
18 Samples
Download data: XLSX
Series
Accession:
GSE234961
ID:
200234961
9.

An intact S-layer is advantageous to Clostridioides difficile within the host.

(Submitter supplied) The S-layer of C. difficile is a paracrystalline array that covers the bacterial cell but its contribution to overall disease remains unclear. A previously described spontaneous slpA-null mutant, FM2.5, with a point mutation in slpA offers the opportunity to study the role of the S-layer in vivo. Here, we confirm our previous observation that this strain is less virulent in vivo despite effectively colonising the host and producing toxin. more...
Organism:
Clostridioides difficile
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25258
28 Samples
Download data: CSV, VCF
Series
Accession:
GSE205747
ID:
200205747
10.

Transcriptomic RNA-sequencing analysis of the hypervirulent Clostridioides difficile R20291 strain in response to trehalose

(Submitter supplied) Clostridioides difficile, the leading cause of antibiotic-associated diarrhoea worldwide, is a genetically diverse species which can metabolise a number of nutrient sources upon colonising a dysbiotic gut environment. Trehalose, a disaccharide sugar consisting of two glucose molecules bonded by an α 1,1-glycosidic bond, has been hypothesised to be involved in the emergence of C. difficile hypervirulence due to its increased utilisation by the RT027 and RT078 strains. more...
Organism:
Clostridioides difficile R20291
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33395
6 Samples
Download data: XLSX
Series
Accession:
GSE232033
ID:
200232033
11.

Extracellular succinate induces spatially organized biofilm formation in Clostridioides difficile

(Submitter supplied) we report that succinate, a metabolite abundantly produced by the dysbiotic gut microbiota, induces in vitro biofilm formation of C. difficile strains. We characterized the morphology and spatial composition of succinate- induced biofilms, and compared to non-induced or deoxycholate-induced biofilms, biofilms induced by succinate are significantly thicker, structurally more complex, and poorer in proteins and exopolysaccharides (EPS).
Organism:
Clostridioides difficile
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32868
16 Samples
Download data: CSV
Series
Accession:
GSE223108
ID:
200223108
12.

The cell wall lipoprotein CD1687 acts as a DNA binding protein during deoxycholate-induced biofilm formation in Clostridioides difficile

(Submitter supplied) The ability of bacterial pathogens to establish recurrent and persistent infections is frequently associated with their ability to form biofilms. Clostridioides difficile infections have a high rate of recurrence and relapses and it is hypothesised that biofilms are involved in its pathogenicity and persistence. Biofilm formation by C. difficile is still poorly understood. It has been shown that specific molecules such as deoxycholate (DCA) or metronidazole induce biofilm formation, but the mechanisms involved remain elusive. more...
Organism:
Clostridioides difficile
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32868
16 Samples
Download data: CSV
Series
Accession:
GSE218475
ID:
200218475
13.

A network of small RNAs regulates sporulation initiation in C. difficile

(Submitter supplied) The obligate anaerobic, enteric pathogen Clostridioides difficile persists in the intestinal tract by forming antibiotic resistant endospores that contribute to relapsing and recurrent infections. Despite the importance of sporulation for C. difficile pathogenesis, environmental cues, and molecular mechanisms regulating sporulation initiation remain ill defined. Here, using RIL-seq to capture the Hfq-dependent RNA-RNA interactome, we discovered a network of small RNAs that bind to mRNAs encoding sporulation-related genes. more...
Organism:
Clostridioides difficile
Type:
Other
Platform:
GPL30071
8 Samples
Download data: TXT
Series
Accession:
GSE213005
ID:
200213005
14.

HexSDF are Required for Synthesis of a Novel Glycolipid that Mediates Daptomycin and Bacitracin Resistance in C. difficile

(Submitter supplied) Clostridioides difficile is a Gram-positive opportunistic pathogen that results in 250,000 infections, 12,000 deaths, and $1 billion in medical costs in the US each year. There has been recent interest in using a daptomycin analog, Surotomycin, to treat C. difficile infections. Daptomycin interacts with both phosphatidylglycerol and Lipid II to disrupt the membrane and halt peptidoglycan synthesis. C. difficile has an unusual lipid membrane composition as it has no phosphatidylserine or phosphatidylethanolamine, and ~50% of its membrane is composed of glycolipids, including the unique C. difficile lipid aminohexosyl-hexosyldiradylglycerol (HNHDRG). We identified a two-component system (TCS) HexRK that is required for C. difficile resistance to daptomycin. Using RNAseq we found that HexRK regulates a three gene operon of unknown function hexSDF. Based on bioinformatic predictions, hexS encodes a monogalactosyldiacylglycerol synthase, hexD encodes a polysaccharide deacetylase, and hexF encodes an MprF-like flippase. We find that deletion of hexRK leads to a 4-fold decrease in daptomycin MIC, and that deletion of hexSDF leads to an 8-16-fold decrease in daptomycin MIC. The ∆hexSDF mutant is also 4-fold less resistant to bacitracin but no other cell wall active antibiotics. Our data indicate that in the absence of HexSDF the phospholipid membrane composition is altered. In WT C. difficile the unique glycolipid, HNHDRG makes up ~17% of the lipids in the membrane. However, in a ∆hexSDF mutant, HNHDRG is completely absent. While it is unclear how HNHDRG contributes daptomycin resistance, the requirement for bacitracin resistance suggests it has a general role in cell membrane biogenesis.
Organism:
Clostridioides difficile
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32868
6 Samples
Download data: TXT
Series
Accession:
GSE220119
ID:
200220119
15.

Enterococci enhance Clostridioides difficile pathogenesis

(Submitter supplied) Clostridioides difficile is one of the most common nosocomial pathogens and a global public health threat. Upon colonization of the gastrointestinal tract, C. difficile is exposed to a rapidly changing polymicrobial environment and a dynamic metabolic milieu. Despite the link between the gut microbiota and susceptibility to C. difficile, the impact of synergistic interactions between the microbiota and pathogens on the outcome of infection is largely unknown. more...
Organism:
Enterococcus faecalis; Clostridioides difficile
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL29669 GPL22510 GPL23172
9 Samples
Download data: BW, TSV
Series
Accession:
GSE165751
ID:
200165751
16.

Determination of the VanS regulon in Clostridioides difficile

(Submitter supplied) We isolated suppressors of a ∆ddl mutant strain with constitutively active allelles of the vanS gene. VanS is a histidine kinase of a two-component system that regulates expression of the vanG operon. Transcriptomes of wild-type and ∆ddl vanS (R334L) strains were compared.
Organism:
Clostridioides difficile 630
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28932
6 Samples
Download data: TXT
Series
Accession:
GSE212197
ID:
200212197
17.

Identification of a bile acid-binding transcription factor in Clostridioides difficile using chemical proteomics

(Submitter supplied) Clostridioides difficile is a Gram-positive anaerobic bacterium that is the leading cause of hospital-acquired gastroenteritis in the US. In the gut milieu, C. difficile encounters microbiota-derived bile acids capable of inhibiting its growth, which are thought to be a mechanism of colonization resistance. While the levels of certain bile acids in the gut correlate with susceptibility to C. difficile infection, their molecular targets in C. more...
Organism:
Clostridioides difficile
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32143
12 Samples
Download data: CSV
Series
Accession:
GSE205226
ID:
200205226
18.

Clostridioides difficile WalRK

(Submitter supplied) Effect on gene transcript levels upon up- or down-regulation of two component system WalRK (Wal-ON and Wal-OFF)
Organism:
Clostridioides difficile
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32143
21 Samples
Download data: CSV
Series
Accession:
GSE200346
ID:
200200346
19.

The licorice metabolite enoxolone attenuates Clostridioides difficile pathophysiology by corrupting its metabolic and toxin production networks

(Submitter supplied) Toxins TcdA and TcdB are the main virulence factors of Clostridioides difficile, a leading cause of hospital-acquired diarrhea. We investigated the therapeutic potential of inhibiting the biosynthesis of TcdA and TcdB. Accordingly, screening of structurally diverse phytochemicals with medicinal properties identified 18b-glycyrrhetinic acid (enoxolone) as an inhibitor of TcdA and TcdB biosynthesis. Enoxolone also inhibited sporulation. more...
Organism:
Clostridioides difficile
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30071
6 Samples
Download data: TXT
Series
Accession:
GSE199109
ID:
200199109
20.

c-di-AMP signaling is required for bile salts resistance and long-term colonization by Clostridioides difficile

(Submitter supplied) In this study, we showed for the first time that c-di-AMP is produced by C. difficile and controls the uptake of potassium, making it essential for growth. We found that c-di-AMP is involved in biofilm formation, cell wall homeostasis, osmotolerance as well as detergent and bile salt resistance in C. difficile. We identified BusR as a new regulator that binds c-di-AMP and represses the expression of the compatible solute transporter BusAA-AB. more...
Organism:
Clostridioides difficile 630
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28932
8 Samples
Download data: TXT
Series
Accession:
GSE192529
ID:
200192529
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