Project description:The taxonomic classification of 182 phenotypically similar isolates was evaluated using DNA-DNA hybridization and 16S rRNA gene sequence analysis. These bacterial isolates were mainly derived from clinical sources; all were Gram-negative non-fermenters and most were indole-producing. Phenotypically, they resembled species from the genera Chryseobacterium, Elizabethkingia or Empedobacter or belonged to CDC groups IIc, IIe, IIh and IIi. Based on these analyses, four novel species are described: Chryseobacterium bernardetii sp. nov. (type strain NCTC 13530(T)?=?CCUG 60564(T)?=?CDC G229(T)), Chryseobacterium carnis sp. nov. (type strain NCTC 13525(T)?=?CCUG 60559(T)?=?CDC G81(T)), Chryseobacterium lactis sp. nov. (type strain NCTC 11390(T)?=?CCUG 60566(T)?=?CDC KC1864(T)) and Chryseobacterium nakagawai sp. nov. (type strain NCTC 13529(T)?=?CCUG 60563(T)?=?CDC G41(T)). The new combination Chryseobacterium taklimakanense comb. nov. (type strain NCTC 13490(T)?=?X-65(T)?=?CCTCC AB 208154(T)?=?NRRL B-51322(T)) is also proposed to accommodate the reclassified Planobacterium taklimakanense.
Project description:A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming, aerobic, yellow-pigmented bacterium was isolated from chicken feather waste collected from an abattoir in Bloemfontein, South Africa. A polyphasic taxonomy study was used to describe and name the bacterial isolate, strain 1_F178<sup>T</sup>. The 16S rRNA gene sequence analysis and sequence comparison data indicated that strain 1_F178<sup>T</sup> was a member of the genus <i>Chryseobacterium</i> and was closely related to <i>Chryseobacterium jejuense</i> (99.1%) and <i>Chryseobacterium nakagawai</i> (98.7%). Overall genome similarity metrics (average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity) revealed greatest similarity to the <i>C. jejuense</i> and <i>C. nakagawai</i> type strains but were below the threshold for species delineation. Genome sequencing revealed a genome size of 6.18 Mbp and a G+C content of 35.6 mol%. The major respiratory quinone and most abundant polar lipid of strain 1_F178<sup>T</sup> were menaquinone-6 and phosphatidylethanolamine, respectively. Strain 1_F178<sup>T</sup> had a typical fatty acid composition for <i>Chryseobacterium</i> species. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic data, strain 1_F178<sup>T</sup> constitutes a novel species of <i>Chryseobacterium</i>, for which the name <i>Chryseobacterium pennae</i> sp. nov. is proposed. The type strain is 1_F178<sup>T</sup> (=LMG 30779<sup>T</sup>=KCTC 62759<sup>T</sup>).
Project description:Yellow-pigmented, circular bacteria (strain SNU WT7) were isolated from the liver of moribund eastern catfish (Silurus asotus). Our study focused on the taxonomic description of SNU WT7 using phylogenetic, phenotypic, and chemotaxonomic analyses. The 16S rRNA gene sequence of the SNU WT7 strain was highly similar to that of Chryseobacterium haifense H38T (97.29% similarity), followed by Chryseobacterium hominis P2K6T (97.22% similarity), while other species exhibited similarity values of less than 97.0%. The genome of strain SNU WT7 displayed average nucleotide identity and genome-to-genome distance values of 72.35% and 22.0%, respectively, which clearly indicated that the novel species was distant from the other Chryseobacterium species, with its closest relative being C. haifense H38T. Furthermore, the phenotypic characteristics, including acid production from glucose, D-fructose, lactose, and maltose, of strain SNU WT 7 differed from those of C. haifense H38T. The major polar lipid of the strain was phosphatidylethanolamine, and several unidentified aminolipids and lipids were also present. Similar to other Chryseobacterium species, the quinone system was composed mainly of MK-6. The genome of SNU WT7 is 2,690,367 bp with a G + C content of 43.6%. Taken together, our data indicate that the isolate SNU WT7 represents a novel species of the genus Chryseobacterium. Thus, we present the name Chryseobacterium siluri sp. nov. for the novel type strain SNU WT7T (KCTC 72626, JCM 33707).
Project description:A novel protein-deamidating enzyme, which has potential for industrial applications, was purified from the culture supernatant of Chryseobacterium proteolyticum strain 9670(T) isolated from rice field soil in Tsukuba, Japan. The deamidating activities on carboxybenzoxy (Cbz)-Gln-Gly and caseins and protease activity were produced synchronously by the isolate. Both deamidating activities were eluted as identical peaks separated from several proteases by phenyl-Sepharose chromatography of the culture supernatant. The enzyme catalyzed the deamidation of native caseins with no protease and transglutaminase activities. Phenotypic characterization and DNA analyses of the isolate were performed to determine its taxonomy. Physiological and biochemical characteristics, 16S rRNA gene sequence analysis, and DNA-DNA relatedness data indicated that the isolate should be placed as a new species belonging to the genus Chryseobacterium. The isolate showed no growth on MacConkey agar and produced acid from sucrose. The levels of DNA-DNA relatedness between the isolate and other related strains were less than 17%. The name Chryseobacterium proteolyticum is proposed for the new species; strain 9670 is the type strain (=FERM P-17664).
Project description:<h4>Background</h4>Industrial biofuels and other value-added products can be produced from metabolically engineered microorganisms. Methylomonas sp. DH-1 is a candidate platform for bioconversion that uses methane as a carbon source. Although several genetic engineering techniques have been developed to work with Methylomonas sp. DH-1, the genetic manipulation of plasmids remains difficult because of the restriction-modification (RM) system present in the bacteria. Therefore, the RM system in Methylomonas sp. DH-1 must be identified to improve the genetic engineering prospects of this microorganism.<h4>Results</h4>We identified a DNA methylation site, TGGCCA, and its corresponding cytosine methyltransferase for the first time in Methylomonas sp. DH-1 through whole-genome bisulfite sequencing. The methyltransferase was confirmed to methylate the fourth nucleotide of TGGCCA. In general, methylated plasmids exhibited better transformation efficiency under the protection of the RM system than non-methylated plasmids did. As expected, when we transformed Methylomonas sp. DH-1 with plasmid DNA harboring the psy gene, the metabolic flux towards carotenoid increased. The methyltransferase-treated plasmid exhibited an increase in transformation efficiency of 2.5?×?10<sup>3</sup> CFU/?g (124%). The introduced gene increased the production of carotenoid by 26%. In addition, the methyltransferase-treated plasmid harboring anti-psy sRNA gene exhibited an increase in transformation efficiency by 70% as well. The production of carotenoid was decreased by 40% when the psy gene was translationally repressed by anti-psy sRNA.<h4>Conclusions</h4>Plasmid DNA methylated by the discovered cytosine methyltransferase from Methylomonas sp. DH-1 had a higher transformation efficiency than non-treated plasmid DNA. The RM system identified in this study may facilitate the plasmid-based genetic manipulation of methanotrophs.
Project description:We report the draft genome sequence of Chryseobacterium sp. JV274. This strain was isolated from the rhizosphere of maize during a greenhouse experiment. JV274 harbors genes involved in flexirubin production (darA and darB genes), bacterial competition (type VI secretion system), and gliding (bacterial motility; type IX secretion system).
Project description:In the present study, carbendazim (MBC) degrading bacterial strains were isolated and identified as <i>Chryseobacterium</i> sp. JAS14 and <i>Aeromonas caviae</i> JAS15. Both the strains completely degraded 200 mg l<sup>-1</sup> of MBC in the aqueous medium and soil within 4-9 days of incubation. In an aqueous medium, the degradation process was characterized by a rate constant of 53.16 day<sup>-1</sup> and 42.60 day<sup>-1</sup>, following zero order model and DT<sub>50</sub> was 1.8 days and 2.34 days for <i>Chryseobacterium</i> sp. JAS14 and <i>A. caviae</i> JAS15, respectively. A <i>Chryseobacterium</i> sp. JAS14 and <i>A. caviae</i> JAS15 inoculated into the soil without the addition of nutrients showed the degradation rate constant of 27.30 day<sup>-1</sup> and 23.87 day<sup>-1</sup>, and DT<sub>50</sub> was 3.66 days and 4.18 days, respectively. The metabolites during MBC biodegradation by <i>Chryseobacterium</i> sp. JAS14 and <i>A. caviae</i> JAS15 were identified as 2-aminobenzimidazole, 2-hydroxybenzimidazole, 1, 2 diaminobenzene and catechol. To our knowledge, this is the first study of the detailed biodegradation pathway of MBC by <i>Chryseobacterium</i> sp. JAS14 was proposed. Phytotoxicity and cytogenotoxicity assays showed that the toxicity of the MBC reduced after biodegradation by <i>Chryseobacterium</i> sp. JAS14 and <i>A. caviae</i> JAS15. In addition, <i>A. caviae</i> JAS15 possess important plant growth promoting traits under normal and MBC stress condition. These results suggest the <i>Chryseobacterium</i> sp. JAS14 and <i>A. caviae</i> JAS15 could be used as a bioresource for the reclamation of MBC contaminated soil.
Project description:Marseille-P9602<sup>T</sup> is a Chryseobacterium-like strain that we isolated from planarian Schmidtea mediterranea and characterized by taxono-genomic approach. We found that Marseille-P9602<sup>T</sup> strain exhibits a 16S rRNA gene sequence similarity of 98.76% with Chryseobacterium scophthalmum LMG 13028<sup>T</sup> strain, the closest phylogenetic neighbor. Marseille-P9602<sup>T</sup> strain was observed to be a yellowish-pigmented, Gram-negative, rod-shaped bacterium, growing in aerobic conditions and belonging to the Flavobacteriaceae family. The major fatty acids detected are 13-methyl-tetradecanoic acid (57%), 15-methylhexadecenoic acid (18%) and 12-methyl-tetradecanoic acid (8%). Marseille-P9602 strain size was found from genome assembly to be of 4,271,905 bp, with a 35.5% G + C content. The highest values obtained for Ortho-ANI and dDDH were 91.67% and 44.60%, respectively. Thus, hereby we unravel that Marseille-P9602 strain is sufficiently different from other closed related species and can be classified as a novel bacterial species, for which we propose the name of Chryseobacterium schmidteae sp. nov. Type strain is Marseille-P9602<sup>T</sup> (= CSUR P9602<sup>T</sup> = CECT 30295<sup>T</sup>).
Project description:CPS-1 is a subclass B3 metallo-?-lactamase from a Chryseobacterium piscium isolate collected from soil, showing 68% amino acid identity to the GOB-1 enzyme. CPS-1 was overproduced in Escherichia coli Rosetta (DE3), purified by chromatography, and biochemically characterized. This enzyme exhibits a broad-spectrum substrate profile, including penicillins, cephalosporins, and carbapenems, which overall resembles those of L1, GOB-1, and acquired subclass B3 enzymes AIM-1 and SMB-1.
Project description:A new natural IND-type metallo-beta-lactamase variant, IND-5, was identified in a clinical isolate of Chryseobacterium indologenes. IND-5 shared 92.8% and 92.4% amino acid homology with IND-1 and IND-3, respectively. Purified enzyme (pI = 8.8, M(r) = 25,000) was able to hydrolyze penicillins, some narrow- and expanded-spectrum cephalosporins, and carbapenems but not monobactams.