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) Herbivorax saccincola A7 is an alkali-thermophilic lignocellulolytic bacterium that was known to possess a strong xylan degradation ability. They can utilize a wide range of carbon sources, however the response and regulation mechanisms to different carbon sources, in terms of genes expression, are still not identified. In this study, H. saccincola A7 was cultured with cellobiose, cellulose, xylan, cellulose-xylan mixture, and empty fruit bunch (EFB) as the sole carbon source. more...

Organism:

Acetivibrio saccincola

Type:

Expression profiling by RT-PCR

Platform:

GPL29661

5 Samples

Download data: TXT

(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) Purpose: The purpose of this study is to clarify the response of Clostridium perfringens ATCC 13124 to host polysaccharide. Methods: Clostridium perfringens ATCC 13124 cells were cultured anaerobically in a medium containing Minimal medium-like condition Poor + medium, medium in which hyaluronic acid or mucin was added to Poor + medium. Total RNA was extracted from bacterial cells by the Hot-Phenol method. more...

Organism:

Clostridium perfringens ATCC 13124

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33655

3 Samples

Download data: XLSX

(Submitter supplied) Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques—a known mucin-degrader that remains poorly studied despite its implication in inflammatory bowel diseases (IBDs)— degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. more...

Organism:

[Ruminococcus] torques VIII-239

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34352

6 Samples

Download data: GFF, XLSX

(Submitter supplied) Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. more...

Organism:

Clostridium autoethanogenum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24458

15 Samples

Download data: TXT

(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

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli; Clostridium senegalense

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL34292 GPL21222

8 Samples

Download data: BW

(Submitter supplied) TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life. IS605-family TnpB homologs function in bacteria as programmable RNA-guided homing endonucleases driving transposon maintenance through DSB-stimulated homologous recombination. Here we uncover molecular mechanisms of transposition lifecycle of IS607-family elements that, remarkably, also encode group I introns. more...

Organism:

Escherichia coli; Clostridium senegalense

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21222 GPL34292

4 Samples

Download data: BW

(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

(Submitter supplied) We investigate the underlying mechanism of the CP inhibition on F. prausnitzii by analysing its effects at the transcriptomic and lipidomic levels.

Organism:

Faecalibacterium prausnitzii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33148

12 Samples

Download data: TXT

(Submitter supplied) We performed a transcriptome analysis of Ruminococcus gnavus with and without 0.1% (w/w) agarooligosaccharide exposure to validate the mechanism of growth inhibition.

Organism:

Mediterraneibacter gnavus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33784

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) The aim of this RNA-sequencing study is to measure differential gene expression in 4 intestinal bacteria (Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Subdoligranulum variabile and Roseburia intestinalis). The data highlight the coordinated action of genes within the same locus involved in the degradation of complex carbohydrates. These loci are well characterized in Bacteroidetes species and referred to as polysaccharide utilization loci. more...

Organism:

Subdoligranulum variabile; Bacteroides thetaiotaomicron; Roseburia intestinalis; Bacteroides xylanisolvens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

36 Samples

Download data: CSV

(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; Clostridioides difficile R20291

Type:

Expression profiling by array

Platform:

GPL32901

6 Samples

Download data: TXT, XLSX

(Submitter supplied) Oal anaerobic bacteria have to face constant oxidative stress in order to survive in the inflammatory environment of the periodontal pocket. In this study, we analyzed the transcriptome profiles of P. gingivalis and Filifactor in monoculture as compared to P. gingivalis+F.alocis coculture under H2O2 stress condtions, to analyze the genes responsible for enhanced survival of P. gingivalis in presence of F. more...

Organism:

Filifactor alocis ATCC 35896; Porphyromonas gingivalis W83

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24003 GPL33711 GPL33710

9 Samples

Download data: CSV

(Submitter supplied) Transcriptome of 'Candidatus Epulopiscium viviparus' type B cells found in Naso tonganus guts. The purpose is to see how the transcriptome of type B changes throughout the day as its host feeding pattern changes.

Organism:

Candidatus Epulonipiscium viviparus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33177

7 Samples

Download data: XLSX

(Submitter supplied) The expression profile of C. autoethanogenum DSM 10061 grown autotrophically with H2:CO:CO2 under visible light at an intensity of 4200 lux versus the expression profile of C. autoethanogenum DSM 10061 grown autotrophically in the dark

Organism:

Clostridium autoethanogenum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32417

6 Samples

Download data: TXT

(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