Clostridium
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA504543 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Caldicellulosiruptor bescii is an anaerobic hyper thermophile that can utilize a wide range of substrates. However, inhibitors released from biomass can result in unfavorable growth conditions and limit bioconversion to products. Medium as well as intracellular pH are conditions critical for growth and prone to change in effect of fermentation end or by products such as, CO2, organic acids etc. Growth pH for C. bescii as currently reported is a narrow range of 6.8-7.3. In this study, we examined the physiological and systems level responses of C. bescii to growth at acidic pH. Samples collected from bottles, controlled batch, fed-batch and chemostat systems were subjected to growth, product and integrated omics profiling. It was discovered that in batch reactors, lowering pH from 7.2 to 6.0 at the mid-log phase, led to a significant increase in growth and product yields. Time course transcriptomics data collected from these batch reactors was analyzed to try and get a better understanding of the underlying mechanisms for improved growth.
2020-06-19 | GSE109442 | GEO
Project description:Population dynamics of methanogenic genera was investigated in pilot anaerobic digesters. Cattle manure and two-phase olive mill wastes were codigested at a 3:1 ratio in two reactors operated at 37 ï¾°C and 55 ï¾°C. Other two reactors were run with either residue at 37 ï¾°C. Sludge DNA extracted from samples taken from all four reactors on days 4, 14 and 28 of digestion was used for hybridisation with the AnaeroChip, an oligonucleotide microarray targeting those groups of methanogenic archaea that are commonly found under mesophilic and thermophilic conditions (Franke-Whittle et al. 2009, in press, doi:10.1016/j.mimet.2009.09.017).
2010-11-10 | E-MEXP-2453 | biostudies-arrayexpress
Project description:The anaerobic and spore-forming bacterium Clostridium difficile has turned into an intensively studied species which can be attributed to increasing numbers of infections and rising costs for the health care system. This dataset represents a benchmark proteome of reference strain C. difficile 630erm and provides mass spectrometry based details on identified proteins which was generally missing from hitherto published datasets. An elaborate annotation and visualization of the 3764 open reading frames will serve as a valuable base for researchers trying to evaluate results of global expression studies. Furthermore, protein expression of late exponentially growing cells in the complex medium BHI and in C. difficile minimal medium was compared. Whereas abundance of proteins of DNA metabolism, protein synthesis and cell envelope showed no variation, enzymes for the biosynthesis of some vitamins and purine as well as proteins involved in butanoate fermentation differed significantly depending on the growth medium.
2016-08-12 | PXD003659 | Pride
Project description:Clostridium beijerinckii is an anaerobic strain and well known for acetone-ethanol-butanol (ABE) fermentation using carbohydrates derived from cellulose or starch. During ABE fermentation, various byproducts are formed, mainly including acids (acetate, butyrate and lactate) and gas (hydrogen and carbon dioxide). recently, we found that Clostridium beijerinckii is able to produce a new product that had never been reported before and tightly regulated by pH and nitrogen source.
2021-12-02 | E-MTAB-11154 | biostudies-arrayexpress
Project description: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. Our goal is to uncover if transcriptional regulation contributes to this hierarchy. Results: Growth and sugar consumption rates showed that arabinose, like glucose, actively represses xylose utilization in cultures fermenting xylose. RNA-Seq revealed there was a large overlap in differentially regulated genes after addition of arabinose or glucose, suggesting a common mechanism of regulation. A putative ORF was identified that may be important for transcriptional regulation in response to the nutritional state of the cells. Conclusions: Decreased xylose consumption, increased acetate production, and transcription of the phosphoketolase gene (CA_C1343) revealed a transition of pentose catabolism from the pentose phosphate pathway to the phosphoketolase pathway after addition of arabinose. Together, these results substantiate the claim that arabinose is utilized preferentially over xylose in C. acetobutylicum. Furthermore, they demonstrate that this phenomenon is modulated in part at the transcriptional level, and they provide valuable insight into potential mechanisms for altering pentose utilization to modulate fermentation products for biofuel production.
2017-12-20 | GSE107804 | GEO
Project description: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. The transcriptome profile of Clostridium beijerinckii NCIMB 8052 (DG-8052) and its response to CaCO3 treatment were analysed by microarray. Since fermentation by C. beijerinckii NCIMB 8052 is a biphasic process, gene expressions of two fermentations were compared at each stage, i.e. 12h and 24h fermentation time representing acidogenic phase and solventogenic phase, respectively. This study examined expression of 5168 genes capturing 98.6% of the C. beijerinckii NCIMB 8052 genome. With the addition of CaCO3, DG-8052 had 565 and 916 genes significantly up-regulated at acidogenic phase and solventogenic phase, respectively. According to the enrichment analysis of pathway and Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, these genes were significantly overrepresented in cellular functions such as Amino acid transport and metabolism, organic acid biosynthetic process, bacteria chemotaxis and defense mechanisms. On the other hand, there were 704 and 1044 genes significantly down-regulated at acidogenic phase and solventogenic phase, respectively. These repressed genes were mainly enriched in functions such as ion transmembrane transport, ATP synthesis, oxidative phosphorylation.
2017-01-02 | GSE81808 | GEO
Project description:Artificial electron carriers have been widely used to shift the solvent ratio towards butanol in acetone-butanol-ethanol (ABE) fermentation of solventogenic clostridia according to decreased hydrogen production. In this study, first insights on the molecular level were gained to explore the effect of methyl viologen addition to cultures of Clostridium acetobutylicum. Employing batch fermentation in mineral salts medium, the butanol:acetone ratio was successively increased from 2.3 to 12.4 on a 100 ml scale in serum bottles and from 1.4 to 16.5 on a 1,300 ml scale in bioreactors, respectively. The latter cultures were used for DNA microarray analyses to provide new information on the transcriptional changes referring to methyl viologen exposure and thus, exhibing gene expression patterns according to the manipulation of the cellular redox balance.
2012-03-31 | E-MEXP-3417 | biostudies-arrayexpress
Project description:Previously, we performed DNA array-based transcriptomic analysis of Clostridium acetobutylicum biofilm adsorbed onto fibrous matrix in batch fermentation. Here, to further shed light on the transcriptomic modulation of maturing Clostridium acetobutylicum biofilm, we performed the DNA array-based transcriptomic analysis in repeated-batch fermentation. Significant time course changes in expression levels were observed for the genes involved in amino acid metabolism, oligopeptide ABC transporter, nitrogen fixation, and various other processes. Repeated-batch fermentation was carried out in 2-L stainless steel columns packed with 40 g of cotton towel ?cut into pieces?approximately 3 cm × 5 cm) containing 1.5 L of P2 medium. Medium circulation rate was maintained at 35 mL/min via a peristaltic pump and the temperature was controlled at 37°C. Fermentation broth was replaced with fresh P2 medium every 12 h. Samples were withdrawn at 6 h after the medium replacement at predetermined interval, except for the last 3 samples. The last 3 samples were withdrawn at 12 h, 15 h, and 17 h after the medium replacement, respectively, to study the transcriptomic response to the adverse condition at the end of fermentation. A total of 8 samples were withdrawn over a period of 7 days, and time course gene expression profiles were studied.
2015-09-09 | E-GEOD-72765 | biostudies-arrayexpress
Project description:Biofuel production from lignocellulosic waste and residues is a promising option to mitigate the environmental costs associated to energy production. However, the difficulty to cost-effectively overcome lignocellulose recalcitrance hampers a widespread application of such bioprocesses. Through an integrated approach, we focused on the factors affecting cellulose reactivity and their impact on downstream fermentation. Three cellulosic manufactured materials were characterized in details: facial tissue, Whatman paper, cotton pads. The model mesophilic cellulolytic bacterium Clostridium cellulolyticum was used to study colonization and metabolic patterns during fermentation of these materials. Facial tissue was extensively colonized and exhibited the fastest degradation and the highest ethanol-to-acetate ratio. Comparing facial tissue fermentation to Whatman paper fermentation by label-free quantitative shotgun proteomics and statistical analyses, 187 proteins showed a different behavior; higher concentration levels were detected for many enzymes from the carbohydrate central metabolic pathway; distinct patterns of expression levels were observed for carbohydratases degrading cellulose and hemicellulose. Overall, lower degrees of polymerization, lower crystallinity index, and the presence of hemicelluloses could explain the higher biological reactivity and bioethanol production yields.
2017-01-30 | PXD001051 | Pride