GEO DataSets

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

Organism:

Clostridium senegalense; Escherichia coli

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:

Clostridium senegalense; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21222 GPL34292

4 Samples

Download data: BW

(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) Approximately 15% of US adults have circulating levels of uric acid above its solubility limit, which is causally linked to the inflammatory disease gout. In most mammals, uric acid elimination is facilitated by the enzyme uricase. However, human uricase is a pseudogene, having been inactivated early in hominid evolution. Though it has long been known that a substantial amount of uric acid is eliminated in the gut, the role of the gut microbiota in hyperuricemia has not been studied. more...

Organism:

[Clostridium] saccharolyticum WM1; Clostridium sporogenes ATCC 15579; Collinsella aerofaciens ATCC 25986

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32367 GPL32368 GPL32369

18 Samples

Download data: TXT

(Submitter supplied) Clonal bacterial populations rely on transcriptional variation across individual cells to commit to specialized states that increase the population’s fitness. Such heterogeneous gene expression is implicated in fundamental microbial processes including sporulation, cell communication, detoxification, substrate utilization, competence, biofilm formation, and motility1. To identify specialized cell states and determine the processes by which they develop, isogenic bacterial populations need to be studied at the single cell level2,3. more...

Organism:

Escherichia coli; Clostridium perfringens; Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

4 related Platforms

8 Samples

Download data: H5

(Submitter supplied) Transcriptome analysis via RNA sequencing (RNA-seq) has become a standard technique employed across a variety of biological fields of study. This rapid adoption of the RNA-seq approach has been mediated, in part, by the development of various commercial RNA-seq library preparation kits compatible with common next-generation sequencing (NGS) platforms. Generally, the essential steps of library preparation such as rRNA depletion and first-strand cDNA synthesis are tailored to a certain group of organisms (e.g. more...

Organism:

Clostridium autoethanogenum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32172

12 Samples

Download data: TXT

(Submitter supplied) Acetate is a simple carboxylic acid that is synthesized in various microorganisms. Although acetate toxicity and tolerance have been studied in many microorganisms, little is known about the effects of exogenous acetate on the cell growth of acetogenic bacteria. In this study, we report the phenotypic changes that occurred in the acetogenic bacterium Clostridium sp. AWRP as a result of an adaptive laboratory evolution under acetate challenge. more...

Organism:

Clostridium sp. AWRP

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32381

8 Samples

Download data: XLSX

(Submitter supplied) We developed Methyl-SNP-seq, a technology that takes advantage of the redundancy of the double helix, to extract the methylation and sequence information from a single original DNA molecule We demonstrate the usefulness of this technology on a broad spectrum of applications ranging from allele specific methylation analysis in humans to methylation identification in complex bacterial communities.

Organism:

Escherichia coli; Clostridium acetobutylicum; Homo sapiens

Type:

Other

4 related Platforms

9 Samples

Download data: COV, VCF

(Submitter supplied) Gas fermentation offers both fossil carbon-free sustainable production of fuels and chemicals and recycling of gaseous and solid waste using gas-fermenting microbes. Bioprocess development, systems-level analysis of biocatalyst metabolism, and engineering of cell factories are advancing the widespread deployment of the commercialised technology. Acetogens are particularly attractive biocatalysts but effects of the key physiological parameter – specific growth rate (μ) – on acetogen metabolism and the gas fermentation bioprocess have not been established yet. more...

Organism:

Clostridium autoethanogenum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24458

20 Samples

Download data: TXT

(Submitter supplied) We used RNA-seq to determine Clostridium tetani gene expression changes in response to culture conditions and time. Changes in response to time were more pronounced than those in response to culture conditions. The tetanus toxin gene is always highly expressed but does show expression changes between culture conditions. These results may become part of an approach to reduce animal testing during vaccine manufacturing.

Organism:

Clostridium tetani

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30527 GPL28078

39 Samples

Download data: XLSX

(Submitter supplied) The possibility of establishing a Clostridium-based biorefinery is an attractive and viable alternative, due to the wide metabolic versatility of these microorganisms. The Bioprocesses and Bioprospecting group of the Universidad Nacional de Colombia has obtained the genome of Clostridium sp. IBUN13A, which has shown the ability to produce solvents from various substrates and postulated the need to expand the knowledge of the physiology of the bacteria, so, this study establishes the differences in the transcriptomic profile of the strain when it is cultivated in glycerol respect to glucose after 24 hours of fermentation. more...

Organism:

Clostridium sp. IBUN13A

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30317

6 Samples

Download data: TXT

(Submitter supplied) Acetogenic bacteria utilize cellular redox energy to convert CO2 to acetate using the Wood-Ljungdahl (WL) pathway. Such redox energy can be derived from electrons generated from H2 as well as inorganic materials such as photo-responsive semiconductors. To reveal how acetogenic bacteria utilize electrons generated from external energy sources to reduce CO2, we developed a nanoparticle-microbe hybrid system and generated RNA-seq results.

Organism:

Clostridium autoethanogenum DSM 10061

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29115

9 Samples

Download data: TXT

(Submitter supplied) Clostridium tetani produces the tetanus-causing tetanus toxin (TeNT), one of the most powerful bacterial toxins known to humankind. The regulation of toxin expression is complex and involves the alternative sigma factor TetR as well as other regulators. Here, we identified a novel regulatory molecule, a non-coding small regulatory RNA (sRNA), located in the 3’ untranslated region of the tent gene. We show with an antisense RNA approach and recombinant expression of the tent locus with and without the sRNA in C. more...

Organism:

Clostridium tetani

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28508

4 Samples

Download data: WIG

(Submitter supplied) Bio-augmentation could be a promising strategy to improve processes for treatment and resource recovery from wastewater. In this study, the Gram-positive bacterium Bacillus subtilis was co-cultured with the microbial communities present in wastewater samples with high concentrations of nitrate or ammonium. Glucose supplementation (1%) was used to boost biomass growth in all wastewater samples. In anaerobic conditions, the indigenous microbial community bio-augmented with B. more...

Organism:

Clostridium beijerinckii; Clostridium butyricum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23579 GPL28541

32 Samples

Download data: CSV

(Submitter supplied) To develop a method for improved assessment of the genetic stability of bacterial vaccine strains, we applied next-generation sequencing to a Clostridium tetani model strain (including inter- and intra-lab replicates) and other strains. Data were processed to determine (gain or loss of) gene copy numbers. Strains could easily be distiguished based on gain/loss of prophage-like and CRISPR/Cas genes. We found that the model strain has multiple copies of the plasmid carrying the gene coding for tetanus toxin as well as several other genes. Data were reproducible within and between laboratories. The limit of detection of our method is an order of magnitude better than that of the pulsed-field gel electrophoresis (PFGE) currently used during manufacturing. This approach may part of an approach to reduce animal testing during vaccine manufacturing.

Organism:

Clostridium tetani

Type:

Other

Platforms:

GPL28077 GPL28078

14 Samples

Download data: XLSX

(Submitter supplied) Arthrobacter sp. CGMCC 3584 are able to produce high yields of extracellular cyclic adenosine monophosphate (cAMP), which plays a vital role in the field of treatment of disease and animal food, during aerobic fermentation. Comparative transcriptomic analysis revealed that arpde inactivation had two major effects on metabolism: inhibition of glycolysis, PP pathway, and amino acid metabolism; promotion of the purine metabolism and carbon flux from the precursor PRPP, which benefited cAMP production.

Organism:

Arthrobacter sp. CGMCC 3584; Clostridium acetobutylicum; Arthrobacter sp.

Type:

Expression profiling by array

Platform:

GPL19013

8 Samples

Download data: TXT

(Submitter supplied) Acetogens can fix carbon (CO or CO2) into acetyl-CoA via the Wood–Ljungdahl pathway (WLP) that also makes them attractive cell factories for the production of fuels and chemicals from waste feedstocks. Although most biochemical details of the WLP are well understood and systems-level characterization of acetogen metabolism has recently improved, key transcriptional features such as promoter motifs and transcriptional regulators are still unknown in acetogens. more...

Organism:

Clostridium autoethanogenum

Type:

Other

Platform:

GPL24458

4 Samples

Download data: TXT

(Submitter supplied) To identify the putative genes under the regulation of two component system BtrK/BtrR, we performed a comparative transcriptomic analysis of the BtrK/BtrR overexpressing strain and the contron strain. Finally, we found that BtrK/BtrR was a global regulator and exerted pleiotropic regulatory role in C. acetobutylicum

Organism:

Clostridium acetobutylicum

Type:

Expression profiling by array

Platform:

GPL27577

8 Samples

Download data: TXT