GEO DataSets

(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:

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:

GPL34292 GPL21222

4 Samples

Download data: BW

(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) 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:

Bacteroides xylanisolvens; Subdoligranulum variabile; Bacteroides thetaiotaomicron; Roseburia intestinalis

Type:

Expression profiling by high throughput sequencing

4 related Platforms

36 Samples

Download data: CSV

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

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32367 GPL32369 GPL32368

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) Little is known about the bacteria that reside in human gallbladder and the mechanisms that allow them to survive within this harsh environmental niche. Furthermore, certain bacterial species are considered to exhibit antagonistic activities whilst others may form mutualistic interactions through, for example, cross-feeding. We isolated two new strains from healthy human bile samples, one belonging to Ruminococcus gauvreauii, of Lachnospiraceae family, and other constituting a new specie in Ruminococcaceae family, named Ruminocoides biliarensis. more...

Organism:

Ruminococcus gauvreauii; Ruminococcoides bili

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27796 GPL27795 GPL27782

12 Samples

Download data: CSV, 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:

Homo sapiens; Clostridium acetobutylicum; Escherichia coli

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) Faecalibacterium prausnitzii is a dominant member of healthy human colon microbiota, regarded as a beneficial gut bacterium due to its ability to produce anti-inflammatory substances. However, little is known about how F. prausnitzii utilizes the nutrients present in the human gut, influencing its prevalence in the host intestinal environment. The phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) is a widely distributed and highly efficient carbohydrate transport system found in most bacterial species that catalyses the simultaneous phosphorylation and import of cognate carbohydrates; its components play physiological roles through interaction with other regulatory proteins. more...

Organism:

Faecalibacterium prausnitzii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29816

8 Samples

Download data: XLSX

(Submitter supplied) Investigation of sulfur metabolism in Clostridium thermocellum DSM 1313 ∆hpt, to determine growth and gene expression when the organism is incubated with either the oxidized (i.e., sulfate) or the reduced and assimilated (i.e., cysteine) forms of sulfur. A sulfite reductase (∆hpt ∆SO3R) knockout mutant to limit sulfur assimilation was created to compare the resulting gene expression patterns by RNAseq transciptomics against the parental strain (∆hpt) when both are grown in the presence of sulfate. more...

Organism:

Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20122

12 Samples

Download data: TXT, XLSX

(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 butyricum; Clostridium beijerinckii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23579 GPL28541

32 Samples

Download data: CSV