2017
DOI: 10.1099/jmm.0.000427
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Manual curation and reannotation of the genomes of Clostridium difficile 630Δerm and C. difficile 630

Abstract: Based on the genomic analysis, several new metabolic features of C. difficile are proposed and could be supported by literature and subsequent experiments.

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Cited by 49 publications
(66 citation statements)
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“…However, both cultures were apparently stressed by the increased agitation due to the gas flow. The influence of agitation on C. difficile has been observed before and may be attributed to a disruption of the fragile exopolysaccharide matrix [39]. Oxygen stressed cultures turned darker compared to reference cultures which may be attributed to increased iron sulfide precipitation.…”
Section: General Observationsmentioning
confidence: 68%
See 1 more Smart Citation
“…However, both cultures were apparently stressed by the increased agitation due to the gas flow. The influence of agitation on C. difficile has been observed before and may be attributed to a disruption of the fragile exopolysaccharide matrix [39]. Oxygen stressed cultures turned darker compared to reference cultures which may be attributed to increased iron sulfide precipitation.…”
Section: General Observationsmentioning
confidence: 68%
“…For analysis of the metabolome, cell lysis and metabolite extraction were performed for five independent experiments as described previously [39]. Extracellular samples were prepared and volatile and non-volatile compounds in the culture supernatants and cell extracts were analyzed as described by Neumann-Schaal et al [24].…”
Section: Metabolomics Analysismentioning
confidence: 99%
“…Despite the considerable effect of CD2068 on drug resistance and transport in E. coli , the susceptibility profiles of the cd2068 mutant and the complemented strains revealed that CD2068 could significantly confer the resistance to certain antibiotics with a relatively low level in C. difficile . It might be explained by the facts that (i) CD2068 may be poorly expressed in its native host, C. difficile , under our experimental settings, however, it can still effectively pump drugs when overexpressed from a plasmid in E. coli ; (ii) there are a total of 243 genes annotated to encode for putative ABC transporters present in the genome of C. difficile 630 34 and they may exhibit an overlapping activity to compensate the loss of CD2086 in the mutant strain; and (iii) the resistance to certain antibiotics may also be mediated by other mechanisms in C. difficile .…”
Section: Discussionmentioning
confidence: 99%
“…Briefly, ∗ .raw files were searched with Sorcerer SEQUEST v. 27, rev. 11 (Thermo Fisher Scientific, United States) against a C. difficile 630Δ erm database ( Dannheim et al, 2017 ) containing 7646 protein entries (common laboratory contaminations and all reversed sequences added). The search was performed in two iterations using full digest with trypsin (after KR/); 10 ppm peptide mass tolerance; variable modification methionine oxidation (15.99 amu); and for the second iteration, mass shift of all amino acids completely labeled with 15 N-nitrogen.…”
Section: Methodsmentioning
confidence: 99%