GEO DataSets

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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

(Submitter supplied) To understand the molecular mechanisms induced by deoxycholate (DCA) during biofilm formation and to identify factors implicated in the strong density of biofilms in this condition, we performed a transcriptomic analysis using microarrays. The microarrays were used to compare C. difficile transcription profiles of a 48 h biofilm (in BHISG medium) treated with DCA with an untreated biofilm.

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL18319

4 Samples

Download data: GPR, TXT, XLS

(Submitter supplied) Clostridioides difficile (formerly Clostridium difficile) colonizes the gastrointestinal tract following disruption of the microbiota and can initiate a spectrum of clinical manifestations ranging from asymptomatic to life-threatening colitis. Following antibiotic treatment, luminal oxygen concentrations increase, exposing gut microbes to potentially toxic reactive oxygen species (ROS). Though typically regarded as a strict anaerobe, C. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30071

12 Samples

Download data: XLSX

(Submitter supplied) We applied time-course transcriptomics and genetics to identify sigma factors, metabolic processes and adhesins that drive biofilm formation. These analyses revealed that extracellular pyruvate induces biofilm formation in the presence of DOC. In the absence of DOC, pyruvate supplementation was sufficient to induce biofilm formation in a process that was dependent on pyruvate transport by the membrane protein CstA.

Organism:

Clostridioides difficile

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22510

36 Samples

Download data: XLS

(Submitter supplied) Much of our current knowledge about cellular RNA–protein complexes in bacteria is derived from analyses in gram-negative model organisms, with the discovery of RNA-binding proteins (RBPs) generally lagging behind in Gram-positive species. Here, we have applied Grad-seq analysis of native RNA–protein complexes to a major Gram-positive human pathogen, Clostridioides difficile, whose RNA biology remains largely unexplored. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL25258

40 Samples

Download data: WIG

(Submitter supplied) Transcriptional profiling of C. difficile 630E strain vs. a sig54 mutant after 6h of growth in TY.

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL10556

4 Samples

Download data: GPR, TXT, XLS