GEO DataSets

(Submitter supplied) Purpose:C. beijerinckii DSM 6423 is the most cited natural IpOH producer. Improving the natural production of this strain through a targeted approach required a full sequencing and characterization of its genome, together with transcriptomic analyses of its own regulations.The goals of this study are then to evaluate the transcriptional profile (RNA-Seq) of C. beijerinckii DSM6423, a natural isopropanol producer, during a fermentation of glucose in controlled bioreactors. more...

Organism:

Clostridium beijerinckii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23579

15 Samples

Download data: CSV

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

Organism:

Clostridium beijerinckii; Clostridium beijerinckii NCIMB 8052

Type:

Expression profiling by array

Platform:

GPL6990

21 Samples

Download data: GPR

(Submitter supplied) The fermentation culture of Clostridium beijerinckii mutant BA101 was monitored from exponential growth to stationary phase. During this period the culture underwent a shift from acidogenesis to solventogenesis. Acetone and butanol production was initiated with the onset of the solventogenic phase. Using DNA microarray changes in gene expression were examined during the transitional period.

Organism:

Clostridium beijerinckii NCIMB 8052; Clostridium beijerinckii

Type:

Expression profiling by array

Platform:

GPL6990

11 Samples

Download data: GPR

(Submitter supplied) The Clostridium beijerinckii NCIMB 8052 wild-type culture was monitored from exponential growth to stationary phase. During this period the culture underwent a shift from acidogenesis to solventogenesis. Acetone and butanol production was initiated with the onset of the solventogenic phase. Using DNA microarray changes in gene expression were examined during the transitional period.

Organism:

Clostridium beijerinckii NCIMB 8052

Type:

Expression profiling by array

Platform:

GPL6990

10 Samples

Download data: GPR

(Submitter supplied) Clostridium phytofermentans ferments all major component of the plant cell wall to alcohols and is an emerging model organism for understanding the direct conversion of plant biomass into biofuels. Encoded in the genome of C. phytofermentans are three large genetic loci for the production of polyhedral microcompartments (PMCs) that may function as metabolic centers for the dissimilation of plant cell wall components into primary alcohols. more...

Organism:

Lachnoclostridium phytofermentans

Type:

Expression profiling by array

Platform:

GPL7481

6 Samples

Download data: CEL

(Submitter supplied) Furfural is the prevalent microbial inhibitor generated during pretreatment and hydrolysis of lignocellulosic biomass to monomeric sugars, but the molecular response of Clostridium beijerinckii NCIMB 8052 to this compound is unknown. To discern the effect of furfural on C. beijerinckii and to gain insights into the molecular mechanisms of action and detoxification, we studied the physiological changes of furfural-stressed cultures during acetone-butanol-ethanol (ABE) fermentation, and profiled differentially expressed genes by genome-wide transcriptional analysis. more...

Organism:

Clostridium beijerinckii NCIMB 8052

Type:

Expression profiling by array

Platform:

GPL16336

4 Samples

Download data: GPR

(Submitter supplied) Solventogenic Clostridium species ferment carbohydrates to acetone, butanol and ethanol which are well-known next-generation biofuels. However, repeated subculture of or continuous fermentation by Clostridium often decreases and eventually terminates the solvent production and spore formation, which is a process called strain degeneration. Supplementation of CaCO3 to fermentation medium could partially recover metabolism of degenerated strain by more than 50% increase of cell growth and solvent production. more...

Organism:

Clostridium beijerinckii NCIMB 8052

Type:

Expression profiling by array

Platform:

GPL19469

6 Samples

Download data: TXT

(Submitter supplied) The transcriptome analysis by microarray was applied on wild-type and degenerated strains of C. beijerinckii NCIMB8052 (WT-8052 and DG-8052, respectively) to elucidate its mechanism of degeneration during solvent fermentation. The comparison of gene expression pattern in relation to ABE production is expected to provide insights toward metabolically engineering of C. beijerinckii NCIMB8052 with prevention of degeneration and eventually enhancement of ABE production.

Organism:

Clostridium beijerinckii NCIMB 8052

Type:

Expression profiling by array

Platform:

GPL19469

6 Samples

Download data: TXT

(Submitter supplied) Background: Bacterial fermentation of carbohydrates from sustainable lignocellulosic biomass into biofuels by the anaerobic bacterium Clostridium acetobutylicum is a promising alternative energy source to fossil fuels. Understanding the complex metabolic pathways it employs and how they are regulated will contribute to improved biofuel production. Recently, it has been demonstrated that xylose is not appreciably fermented in the presence of arabinose, suggesting a hierarchy of pentose utilization in this organism. more...

Organism:

Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24347

48 Samples

Download data: CSV

(Submitter supplied) Biorefining of renewable feedstocks is one of the most promising routes to replace fossil-based products. Since many common fermentation hosts, such as Saccharomyces cerevisiae, are naturally unable to convert many component plant cell wall polysaccharides, the identification of organisms with broad catabolism capabilities represents an opportunity to expand the range of substrates used in fermentation biorefinery approaches. more...

Organism:

Rhodotorula toruloides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26239

9 Samples

Download data: TAB

(Submitter supplied) The presence of anti-microbial phenolic compounds, such as the model compound ferulic acid, in biomass hydrolysates poses significant challenges to the widespread use of biomass in conjunction with whole cell biocatalysis or fermentation. Biofuel toxicity must also be overcome to allow for efficient production of next generation biofuels such as butanol, isopropanol, and others for widespread usage. more...

Organism:

Levilactobacillus brevis

Type:

Expression profiling by array

Platform:

GPL10674

21 Samples

Download data: GPR

(Submitter supplied) Background Lignocellulosic biomass is a promising renewable feedstock for biofuel production. Acetate is one of the major inhibitors liberated from hemicelluloses during hydrolysis. An understanding of the toxic effects of acetate on the fermentation microorganism and the efficient utilization of mixed sugars of glucose and xylose in the presence of hydrolysate inhibitors is crucial for economic biofuel production. more...

Organism:

Zymomonas mobilis

Type:

Expression profiling by genome tiling array

Platform:

GPL18675

30 Samples

Download data: TXT

(Submitter supplied) The impacts of ferulic acid, a phenolic compound commonly found in lignin hydrolysates, on the growth, solvent production and transcriptional responses of C. beijerinckii NCIMB 8052 were determined. Addition of ferulic acid to growing cultures resulted in a decrease in the growth and solvent production by 30 and 25%, respectively, when compared to the control cultures. To better understand the toxicity of this compound, microarray analyses were performed using samples taken from these cultures at three different growth states. more...

Organism:

Clostridium beijerinckii; Clostridium beijerinckii NCIMB 8052

Type:

Expression profiling by array

Platform:

GPL19923

16 Samples

Download data: TXT

(Submitter supplied) The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. To gain insights into the C. thermocellum genes, using an updated version of the C. thermocellum ATCC 27405 genome annotation, that are required for specific growth on the cellulosic feedstocks of either pretreated switchgrass or Populus, duplicate fermentations were conducted with a 5 g/L solid substrate loading. more...

Organism:

Acetivibrio thermocellus 27405; Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL17171

8 Samples

Download data: CALLS, PAIR

(Submitter supplied) This study determined the patterns of gene expression of Clostridium novyi-NT in different growth phases in vitro as well as gene expression patterns from infection of tumors in vivo. Keywords: Growth phase analysis; tumor infection

Organism:

Homo sapiens; Mus musculus; Clostridium novyi NT

Type:

Expression profiling by array

Platform:

GPL4463

30 Samples

Download data: GPR

(Submitter supplied) Propionic acid (PA) is a three-carbon molecule commonly used as a food preservative and increasingly, as a precursor for the synthesis of monomers. Propionibacterium spp. are the best biological producers of PA. In fact, a recent report showed that if a yield of 0.6 g/g is achieved, biological production of PA would be economically competitive with petrochemical production. To achieve that yield, a library of Propionibacterium strains was used to generate a new strain that can achieve the commercially desirable yield from sucrose. more...

Organism:

Acidipropionibacterium acidipropionici

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22433

4 Samples

Download data: XLSX