Clostridium jeddahense strain JCD(T) (= CSUR P693 = DSM 27834) is the type strain of C. jeddahense sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of an obese 24 year-old Saudian male (BMI=52 kg/m(2)). Clostridium jeddahense strain JCD(T) is an obligate Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,613,503 bp long genome (1 chromosome, no plasmid) exhibits a G+C cont ...[more]
Project description:This SuperSeries is composed of the following subset Series: GSE12358: Clostridium beijerinckii NCIMB 8052 wild-type fermentation time course GSE12359: Clostridium beijerinckii BA101 mutant fermentation time course Refer to individual Series
Project description:Transcriptional analysis of Clostridium difficile R20291 in biofilm formation, planktonic state and grown on blood agar RNA sequencing was performed on Clostridium difficile R20291 in three different conditions: Biofilm formation, plantonic state and grown on blood agar plates. Each condtion has 3 replicates.
Project description: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 Overall design: For gene expression of Clostridium novyi-NT in different growth phases in vitro, we had 4 replicates for early log phase, 3 replicates for mid log phase, 4 replicates for late log phase and 5 replicates for mature spore. For gene expression of Clostridium novyi-NT from infection of tumors in vivo, we had 5 replicates for infected CT26 tumors and 5 replicates for infected HCT116 tumors. To control for cross hybridization with mammalian mRNAs, we also included 2 replicates for uninfected CT26 tumors and 2 replicates for uninfected HCT116 tumors for hybridization to parallel arrays.
Project description: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. Overall design: RNA samples were taken from Clostridium beijerinckii mutant BA101 fermentation culture at individual time points during the acidogenic phase and the solventogenic phase. The samples were used for microarray hybridization.
Project description:Analysis of Clostridium difficile (Cd) from the cecal contents of germ-free mice or Bacteroides thetaiotaomicron (Bt)-monocolonized mice on a standard, polysaccharide rich diet or polysaccharide deficient diet 5 days after infection. Results identify genes that are involved in the Cd response to diet, in vivo colonization and in interactions with Bt. In vitro transcriptional profiles of Clostridium difficile obtained from cecal contents of germ-free or Bt-monocolonized mice on a standard, polysaccharide rich or polysaccharide deficient diet. 4 samples/group. 2 control genomic DNA samples for Clostridium difficile and 2 reference genomic DNA samples for Bacteroides thetaiotaomicron Please note that 4 control samples (genomic DNA) were used to determine whether the genomic DNA correctly bound to the probes and thus, were not included in data processing (i.e no processed/normalized data).
Project description: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. Overall design: RNA samples were taken from Clostridium beijerinckii NCIMB 8052 wild-type fermentation culture at individual time points during the acidogenic phase and the solventogenic phase. The samples were used for microarray hybridization.
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. Overall design: Clostridium beijerinckii NCIMB8052 degenerated strain cells in P2 medium vs. Clostridium beijerinckii NCIMB8052 degenerated strain cells in P2 medium with 4g/L CaCO3 Two-fermentation time points (12h and 24h) experiments (degenerated strain cells in P2 vs.degenerated strain cells in P2 with CaCO3);Biological replicates: 3 replicates of degenerated strain cells in P2 at 12h; 3 replicates of degenerated strain cells in P2 at 24h;3 replicates of degenerated cells in P2 with CaCO3 at 12h;3 replicates of degenerated cells with CaCO3 at 24h.
Project description:Transcriptome profiles for Clostridium thermocellum ATCC 27405 wild type strain and two ethanol-adapted strains, E50A and E50C were generated to gain insights into ethanol tolerance. Details of the strains have been described, Shao X., et al. Appl Microbiol Biotechnol (2011) 92:641–652. Overall design: Duplicate fermentations using MTC medium were conducted for Clostridium thermocellum strains, ATCC 27405 wild-type; ethanol adapted strain E50A (adapted to grow in presence of up to 50 g/L ethanol on Avicel); and ethanol adapted strain E50C (adapted to grow in presence of up to 50 g/L ethanol on cellobiose). These strains have been described previously by Shao X., et al Appl Microbiol Biotechnol (2011) 92:641–652. A fifty two array study using total RNA processed from fermenation cultures of Clostridium thermocellum ATCC 27405 and ethanol adapted strains E50C and E50A, which were shocked with either 10 or 40 g/L ethanol. Cells were harvested immediately after, 15 minutes, 1 hour, 2 hours, and 4 hours after ethanol shock.