Complete Genome Sequence of Solvent-Tolerant Clostridium beijerinckii Strain SA-1

Noar, Jesse D.; Makwana, S. T.; Bruno-Bárcena, José M.

doi:10.1128/genomea.01310-14

Cited by 6 publications

(3 citation statements)

References 8 publications

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“…To this end, we established a Pathway Tools Database (Karp et al ., 2002, ) using the core genes present in one of the species (note: the genome of a single species by definition contains all of the core genes of the genus, as defined in this study). The core genome that we chose for this analysis was C. beijerinckii NCBIM 8052 because it is well annotated (Wilkinson and Young, ; Noar et al ., ; Schwarz and Kengen, ; Sandoval‐Espinola et al ., ) and because the number of core genes present are highest due to the existence of paralogous genes. In all, 598 annotated proteins were mapped, which catalyzed 446 enzymatic reactions giving rise to 49 complete and incomplete pathways.…”

Section: Resultsmentioning

confidence: 99%

The pangenome of the genus Clostridium

Udaondo

Duque

Ramos

2017

Environmental Microbiology

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The pangenome for the genus Clostridium sensu stricto, which was obtained using highly curated and annotated genomes from 16 species is presented; some of these cause disease, while others are used for the production of added-value chemicals. Multilocus sequencing analysis revealed that species of this genus group into at least two clades that include non-pathogenic and pathogenic strains, suggesting that pathogenicity is dispersed across the phylogenetic tree. The core genome of the genus includes 546 protein families, which mainly comprise those involved in protein translation and DNA repair. The GS-GOGAT may represent the central pathway for generating organic nitrogen from inorganic nitrogen sources. Glycerol and glucose metabolism genes are well represented in the core genome together with a set of energy conservation systems. A metabolic network comprising proteins/enzymes, RNAs and metabolites, whose topological structure is a non-random and scale-free network with hierarchically structured modules was built. These modules shed light on the interactions between RNAs, proteins and metabolites, revealing biological features of transcription and translation, cell wall biosynthesis, C1 metabolism and N metabolism. Network analysis identified four nodes that function as hubs and bottlenecks, namely, coenzyme A, HPr kinases, S-adenosylmethionine and the ribonuclease P-protein, suggesting pivotal roles for them in Clostridium.

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Section: Resultsmentioning

confidence: 99%

The pangenome of the genus Clostridium

Udaondo

Duque

Ramos

2017

Environmental Microbiology

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“…The former enzyme catalyzes the activation of pyruvate to acetyl-CoA with the concomitant production of formate and CO2, while the later catalyzes the synthesis of formate from NADH2 + and CO2. The pfl is broadly found in facultative anaerobes, but it has been also found in the genome of different Clostridium species such as C. butyricum , C. acetobutylicum, C. beijirinkii, C. pasteurianum, and C. tyrobutyricum (Nölling et al 2001;Pyne et al 2014;Noar et al 2014;Kwok et al 2014;Lee et al 2016) In addition, the gene of fdh enzyme has been reported to be part of the genome of different Clostridium species, such as C. carboxidivorans (Bruant et al 2010), C.…”

Section: Lactate and Formate Favored At High Olrmentioning

confidence: 99%

Hydrogen metabolic patterns driven by Clostridium-Streptococcus community shifts in a continuous stirred tank reactor

Palomo-Briones

Trably

López-Lozano

et al. 2018

Appl Microbiol Biotechnol

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The hydrogen (H) production efficiency in dark fermentation systems is strongly dependent on the occurrence of metabolic pathways derived from the selection of microbial species that either consume molecular H or outcompete hydrogenogenic bacteria for the organic substrate. In this study, the effect of organic loading rate (OLR) on the H production performance, the metabolic pathways, and the microbial community composition in a continuous system was evaluated. Two bacterial genera, Clostridium and Streptococcus, were dominant in the microbial community depending on the OLR applied. At low OLR (14.7-44.1 g/L-d), Clostridium sp. was dominant and directed the system towards the acetate-butyrate fermentation pathway, with a maximum H yield of 2.14 mol/mol obtained at 29.4 g/L-d. Under such conditions, the volumetric hydrogen production rate (VHPR) was between 3.2 and 11.6 L/L-d. In contrast, relatively high OLR (58.8 and 88.2 g/L-d) favored the dominance of Streptococcus sp. as co-dominant microorganism leading to lactate production. Under these conditions, the formate production was also stimulated serving as a strategy to dispose the surplus of reduced molecules (e.g., NADH), which theoretically consumed up to 5.72 L/L-d. In such scenario, the VHPR was enhanced (13.7-14.5 L/L-d) but the H yield dropped to a minimum of 0.74 mol/mol at OLR = 58.8 g/L-d. Overall, this research brings clear evidence of the intrinsic occurrence of metabolic pathways detrimental for biohydrogen production, i.e., lactic acid fermentation and formate production, suggesting the use of low OLR as a strategy to control them.

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“…Ne1 was the second most abundant clostridia in the 1 TC consortia, accounting for 27% of the reads in the 1 TC metagenome. In total, the draft Ne1 genome includes 290 large (>200 bp) contigs which total ~5.6 Mbp in length, a size similar to previously published C. beijerinckii genomes ( 8 – 10 ). The longest contig was ~110 kbp, and the size distribution of the other contigs had mean, median, and N 50 lengths of 19,163 bp, 12,981 bp, and 25,991 bp, respectively.…”

Section: Genome Announcementmentioning

confidence: 62%