Chryseobacterium metallicongregator, sp. nov., a bacterium possessing metallophore activity towards rare earth elements

A polyphasic taxonomic study was carried out on strain ES2T, isolated from sediment of a wetland created to remediate acid drainage from a coal mine. The rod-shaped bacterium formed yellow/orange pigmented colonies and produced the pigment flexirubin. The 16S rRNA gene sequence results assigned the strain to Chryseobacterium, with 98.9 and 98.3 % similarity to Chryseobacterium vietnamense and Chryseobacterium cucumeris, respectively. Computation of the average nucleotide identity and digital DNA-DNA hybridization values with the closest phylogenetic neighbours of ES2T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The dominant fatty acids of strain ES2T were iso-C15 : 0, iso-C17 : 1 ω9c, iso C17 : 0 3-OH, and iso-C15 : 0 2-OH. The DNA G+C content was 35.5 mol%. The major polar lipid was phosphatidylethanolamine while menaquinone-6 was the only menaquinone found. This bacterium has been previously shown to possess metallophore activity towards rare earth elements, and based on genome sequencing, possesses all required genes for siderophore production/activity, possibly identifying the source of this unique ability. On the basis of the results obtained here, this bacterium is assigned to the genus Chryseobacterium as representing a new species with the name Chryseobacterium metallicongregator sp. nov., type strain ES2T (=NRRL B-65679T=KCTC 102120T).

Polar lipid characterization and description of Chryseobacterium capnotolerans sp. nov., isolated from high CO2-containing atmosphere and emended descriptions of the genus Chryseobacterium, and the species C. balustinum, C. daecheongense, C. formosense, C. gleum, C. indologenes, C. joostei, C. scophthalmum and C. ureilyticum

Modified atmosphere (MA) packaging plays an important role in improving food quality and safety. By using different gas mixtures and packaging materials the shelf life of fresh produce can significantly be increased. A Gram-negative-staining, rod-shaped, orange-pigmented strain DH-B6T, has been isolated from MA packed raw pork sausage (20% CO2, 80% O2). The strain produced biofilms and showed growth at high CO2 levels of up to 40%. Complete 16S rRNA gene and whole-genome sequences revealed that strain DH-B6T belongs to the genus Chryseobacterium , being closely related to strain Chryseobacterium indologenes DSM 16777T (98.4%), followed by Chryseobacterium gleum NCTC11432T (98.3%) and Chryseobacterium lactis KC1864T (98.2%). Average nucleotide identity value between DH-B6T and C. indologenes DSM 16777T was 81.1% and digital DNA–DNA hybridisation was 24.9%, respectively. The DNA G+C content was 35.51 mol%. Chemotaxonomical analysis revealed the presence of the rare glycine lipid cytolipin, the serine-glycine lipid flavolipin and the sulfonolipid sulfobacin A, as well as phosphatidylethanolamine, monohexosyldiacylglycerol and ornithine lipid, including the hydroxylated forms. Major fatty acids were iC15 : 0 (50.7%) and iC17 : 1 cis 9 (28.7%), followed by iC15 : 0 2-OH (7.0%) and iC17 : 0 3-OH (6.2%). The isolated strain contained MK-6 as the only respiratory quinone and flexirubin-like pigments were detected as the major pigments. Based on the phenotypic, chemotaxonomic and phylogenetic characteristics, the strain DH-B6T (=DSM 110542T=LMG 31915T) represents a novel species of the genus Chryseobacterium , for which the name Chryseobacterium capnotolerans sp. nov. is proposed. Emended descriptions of the genus Chryseobacterium and eight species of this genus based on polar lipid characterisation are also proposed.

Pathogenic Potential and Control of Chryseobacterium Species from Clinical, Fish, Food and Environmental Sources

Chryseobacterium species are isolated and taxonomically evaluated from a wide range of sources. While C. gleum and C. indologenes have been implicated in human disease, the potential pathogenicity of numerous other species have not been investigated. The aims were therefore to evaluate 37 Chryseobacterium species and Elizabethkingia meningoseptica from environmental, food, fish, water and clinical sources for production of haemolysis, growth at 37 °C, and production of virulence enzymes. The control of these strains were investigated by determination of antimicrobial and disinfectant resistance. All the species produced α- or β-haemolysis. In terms of growth at 37 °C and production of virulence enzymes, C. soldanellicola (environmental), C. oranimense (food) and C. koreense (natural mineral water) could be potential human pathogens. Chryseobacterium piscium might be pathogenic to fish. Trimethoprim could be the most effective antimicrobial for the treatment of a Chryseobacterium species infection, while the disinfectants that contain poly-dimethyl ammonium chloride or benzalkonium chloride could be regarded as the most effective for decontamination of surfaces contaminated with Chryseobacterium species.

Septic Arthritis and Osteomyelitis Caused by Chryseobacterium indologenes in a Mute Swan (Cygnus olor) and a Ring-Billed Gull (Larus delawarensis)

A 20-year-old female mute swan (Cygnus olor) originally in a flock of free-living swans on a Long Island, New York, lake, was presented for facial swelling and decreased appetite. An adult male ring-billed gull (Larus delawarensis) was also presented to the same wildlife rescue center for bilateral lameness of 1-week duration. Once referred for veterinary evaluation and care, both species were diagnosed with septic arthritis and osteomyelitis caused by Chryseobacterium indologenes and treated with orbifloxacin until complete recovery. Chryseobacterium indologenes is infrequently diagnosed as an opportunistic pathogen in human medicine, and less so in veterinary medicine. In human patients, this bacterium is the cause of various infections, including meningitis, pneumonia, and implant failure. However, in veterinary medicine its pathogenicity has only been reported in fish, and sporadically mentioned as a culture result in tree frogs and turtles, where it was generally considered insignificant. In this report a clinical presentation, diagnosis, treatment, and outcome of osteomyelitis and septic arthritis caused by C indologenes is described in 1 anseriforme and in 1 charadriiforme species.

Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere

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).

Chryseobacterium zhengzhouense sp. nov., isolated from groundwater of the well in a vegetable field, and emended description of the genus Chryseobacterium

A Gram-negative, strictly aerobic, non-motile, asporogenous rod-shaped bacterium, designated M05W1-39A1(T), was isolated from a Chinese cabbage farmland located in Zhengzhou. China, and subjected to a taxonomic study. Strain M05W1-39A1(T) was found to grow optimally at 25-30 °C, at pH 6.0-7.0 and in the presence of 0.5-2.0 % (w/v) NaCl. According to phylogenetic analysis using 16S rRNA gene sequences, strain M05W1-39A1(T) belongs to the genus Chryseobacterium and is closely related to Chryseobacterium arachidis LMG 27813(T) (98.8 %) and Chryseobacterium geocarposphaera LMG 27811(T) (98.1 %). The DNA G + C content was determined to be 35.3 mol%. The respiratory quinone was identified as MK-6 and the predominant cellular fatty acids as iso-C15:0, Summed feature 3 (C16:1 ω7c/C16:1 ω6c), iso-C17:0 3-OH and Summed feature 9 (iso-C17:1 ω9c). Based on the genotypic, chemotaxonomic and phenotypic data, strain M05W1-39A1(T) is concluded to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium zhengzhouense sp. nov. is proposed. The type strain is M05W1-39A1(T) (=HNMC11208(T) = CGMCC 1.15067(T) = JCM 30863(T)).

Emerging flavobacterial infections in fish: A review

Flavobacterial diseases in fish are caused by multiple bacterial species within the family Flavobacteriaceae and are responsible for devastating losses in wild and farmed fish stocks around the world. In addition to directly imposing negative economic and ecological effects, flavobacterial disease outbreaks are also notoriously difficult to prevent and control despite nearly 100 years of scientific research. The emergence of recent reports linking previously uncharacterized flavobacteria to systemic infections and mortality events in fish stocks of Europe, South America, Asia, Africa, and North America is also of major concern and has highlighted some of the difficulties surrounding the diagnosis and chemotherapeutic treatment of flavobacterial fish diseases. Herein, we provide a review of the literature that focuses on Flavobacterium and Chryseobacterium spp. and emphasizes those associated with fish.

Inhibition of Batrachochytrium dendrobatidis Caused by Bacteria Isolated from the Skin of Boreal Toads, Anaxyrus (Bufo) boreas boreas, from Grand Teton National Park, Wyoming, USA

The chytrid fungus Batrachochytrium dendrobatidis is a significant cause of the worldwide decline in amphibian populations; however, various amphibian species are capable of coexisting with B. dendrobatidis. Among them are boreal toads (Anaxyrus (Bufo) boreas boreas) located in Grand Teton National Park (GTNP) in Wyoming, USA. The purpose of this study was to identify cultivable bacterial isolates from the skin microbiota of boreal toads from GTNP and determine if they were capable of inhibiting B. dendrobatidis in vitro, and therefore might be a factor in the toad's coexistence with this pathogen. Isolates from 6 of 21 genera tested were found to inhibit the growth of B. dendrobatidis. These bacteria represent diverse lineages such as the Gammaproteobacteria, the Betaproteobacteria, and the Bacteroidetes/Chlorobium groups. We propose that these bacteria compete via microbial antagonism with B. dendrobatidis.

Chryseobacterium angstadtii sp. nov., isolated from a newt tank

As part of an undergraduate microbiology course, a yellow-orange-pigmented, Gram-staining negative, rod-shaped, non-motile bacterial strain was isolated from a glass tank housing several red-spotted newts (Notophthalmus viridescens). The sequence of the 16S rRNA gene of this strain, designated KM(T), was 97.4-98.0 % similar to those of the type strains of Chryseobacterium luteum, C. shigense and C. vrystaatense, while the similarity levels for protein-coding genes were less than 94.7 % for rpoB, less than 92.1 % for groEL and less than 87.1 % for gyrB. These values are lower than for many other established distinct species. Polyphasic characterization and comparison to these relatives revealed that strain KM(T) was similar to other Chryseobacterium strains in that it contained MK-6 as its major respiratory quinone and phosphatidylethanolamine as the most abundant polar lipid, produced flexirubin-type pigments, oxidase and catalase and primarily contained the fatty acids iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). Based on the results of this study, strain KM(T) represents a novel species, for which the name Chryseobacterium angstadtii sp. nov. is proposed. The type strain is KM(T) ( = ATCC BAA-2160(T) = NRRL B-59516(T) = KCTC 23297(T)).

Identification and virulence of Chryseobacterium indologenes isolated from diseased yellow perch (Perca flavescens)

AIM

To identify pathogen of diseased yellow perch and determine their virulence.

METHODS AND RESULTS

Fifteen Gram-negative bacterial isolates were recovered from the skin lesions of diseased yellow perch (Perca flavescens). Based on API 20NE test, ten isolates were found to share 67.2-99.9% homologies with Chryseobactertium indologenes. Based on fatty acid methyl ester analysis, 13 isolates were found to share similarities with C. indologenes and other species of Chryseobacterium. Based on sequencing results of partial 16S rRNA gene, 13 isolates shared 99% identities (e value = 2e-50) with the 16S rRNA sequence of C. indologenes (GenBank HQ259684). Based on the 16S-23S rRNA intergenic spacer region (ISR) sequence, the 13 isolates shared 88% identity (e value = 1e-165) with the 16S-23S ISR sequence of C. indologenes (GenBank EU014570). T-coffee multiple sequence alignment revealed that the partial 16S rRNA or the 16S-23S ISR sequence of the 13 isolates shared 100% identity with each other. When healthy yellow perch were exposed to the 15 isolates by bath immersion (c. 6 × 10(7) CFU ml(-1) for 1 h), only C. indologenes isolates killed 10-20% of fish, whereas other isolates were avirulent. When yellow perch were exposed to C. indologenes by intraperitoneal injection, mortality was dose dependent, with LD(50) and LD(95) values of 1.5 × 10(8) and 3.2 × 10(8) CFU per fish, respectively.

CONCLUSIONS

Chryseobactertium indologenes could be pathogenic to yellow perch.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report on the isolation of C. indologenes from diseased yellow perch. Virulence studies suggested that C. indologenes could become pathogenic to yellow perch.

Chryseobacterium viscerum sp. nov., isolated from diseased fish

A taxonomic study was carried out on five Gram-staining-negative, catalase- and oxidase-positive, rod-shaped bacteria isolated from the gills and livers of five diseased rainbow trout. The five novel isolates were designated strains 687B-08T, 445-08, 452-08, 453B-08 and 967B-08. In phylogenetic analyses based on 16S rRNA gene sequences, the five novel strains appeared almost identical (99.0–100 % sequence similarity) and to belong to the genus Chryseobacterium . Strain 687B-08T (the strain selected to represent the five novel isolates) was found to be most closely related to Chryseobacterium oncorhynchi 701B-08T (98.9 % sequence similarity), Chryseobacterium ureilyticum F-Fue-04IIIaaaaT (98.6 %), Chryseobacterium indologenes ATCC 29897T (98.3 %), Chryseobacterium jejuense JS17-8T (98.1 %) and Chryseobacterium gleum ATCC 35910T (98.1 %). In DNA–DNA hybridizations, DNA–DNA relatedness values of 99–100 % were recorded between the five novel strains. Lower DNA–DNA relatedness values (21–57 %) were recorded between strain 687B-08T and C. oncorhynchi 701B-08T, C. ureilyticum F-Fue-04IIIaaaaT and the type strains of other closely related, established species of the genus Chryseobacterium . The predominant respiratory quinone of strain 687B-08T was MK-6 and the major cellular fatty acids were iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and C16 : 1ω6c. The G+C content of the genomic DNA of strain 687B-08T was 38.6 mol%. Based on the phenotypic and genotypic evidence, the five novel strains isolated from rainbow trout represent a single, novel species of the genus Chryseobacterium , for which the name Chryseobacterium viscerum sp. nov. is proposed. The type strain is 687B-08T ( = CECT 7793T  = CCUG 60103T).

Chryseobacterium rigui sp. nov., isolated from an estuarine wetland

A bacterium, designated strain CJ16(T), was isolated from the estuarine wetland of the Han River. Cells of the isolate were yellow-pigmented, Gram-stain-negative, non-motile and rod-shaped. Growth of strain CJ16(T) was observed in TSB at 5-37 °C (optimum 30 °C), at pH 5.0-9.0 (optimum pH 6.0) and with 0-3 % (w/v) NaCl (optimum 0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CJ16(T) was most closely related to Chryseobacterium hagamense KCTC 22545(T) (97.2 % 16S rRNA gene sequence similarity). Genomic relatedness based on DNA-DNA hybridization between strain CJ16(T) and C. hagamense KCTC 22545(T) was 23 % (strain CJ16(T) as probe) and 19 % (strain KCTC 22545(T) as probe). Chemotaxonomic analysis revealed that strain CJ16(T) possessed MK-6 as the major isoprenoid quinone and sym-homospermidine as the predominant polyamine. The predominant fatty acids were iso-C15 : 0 (26.9 %), iso-C17 : 0 3-OH (16.8 %) and summed feature 9 (comprising C16 : 0 10-methyl and/or iso-C17 : 1ω9c; 10.5 %). The DNA G+C content of strain CJ16(T) was 37.9 mol%. Based on phenotypic, genotypic and phylogenetic studies, strain CJ16(T) represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium rigui sp. nov. is proposed. The type strain is CJ16(T) ( = KACC 16560(T)  = JCM 18078(T)).

Chryseobacterium vietnamense sp. nov., isolated from forest soil

A Gram-reaction-negative bacterial strain, designated GIMN1.005T, was isolated from a forest soil sample in Vietnam. The isolate was yellow-pigmented, strictly aerobic, and unable to grow below 5 °C or above 37 °C and in the presence of more than 2.0 % NaCl. Cells were non-motile, non-gliding and non-spore-forming. The yellow pigment was of the flexirubin type, non-diffusible and non-fluorescent. Analysis of 16S rRNA gene sequences showed that strain GIMN1.005T occupied a distinct lineage within the genus Chryseobacterium , with sequence similarity values of 98.6, 98.5 and 98.3 % to Chryseobacterium aquifrigidense KCTC 12894T, Chryseobacterium jejuense KACC 12501T and Chryseobacterium indologenes GIFU 1347T, respectively. The level of DNA–DNA relatedness between strain GIMN1.005T and C. jejuense KACC 12501T was <30 %. The DNA G+C content of strain GIMN1.005T was 42.1 mol%. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c); menaquinone 6 (MK-6) was the sole respiratory quinone. On the basis of phenotypic properties and phylogenetic distinctiveness, strain GIMN1.005T is considered to represent a novel species of the genus Chryseobacterium , for which the name Chryseobacterium vietnamense sp. nov. is proposed. The type strain is GIMN1.005T ( = CCTCC M 209230T = NRRL B-59550T).

Chryseobacterium piperi sp. nov., isolated from a freshwater creek

As part of an undergraduate microbiology course, a yellow–orange pigmented, Gram-staining negative, rod-shaped, non-motile bacterial strain, designated CTMT, was isolated from a creek in North-central Pennsylvania during the winter of 2006. The 16S rRNA gene sequence of the strain showed ~97 % similarity to that of Chryseobacterium soldanellicola PSD1-4T and Chryseobacterium soli JS6-6T, while the protein-coding gyrB gene sequence of strain CTMT showed <87 % similarity to those of its two closest relatives. Using a polyphasic approach, strain CTMT was characterized and compared to these and other closely related species of the genus Chryseobacterium. Strain CTMT was similar to other strains of the genus Chryseobacterium in that it contained MK-6 as its major respiratory quinone, produced flexirubin-type pigments, oxidase and catalase, hydrolysed DNA, gelatin and aesculin and contained the fatty acids iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω6c, C16 : 1ω7c and/or iso-C15 : 0 2-OH). Based on the results of this study, strain CTMT represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium piperi sp. nov. is proposed. The type strain is CTMT ( = ATCC BAA-1782T  = CCUG 57707T  = JCM 15960T  = DSM 22249T  = KCTC 23267T).

Chryseobacterium treverense sp. nov., isolated from a human clinical source

A yellow-pigmented, Gram-reaction-negative bacterium isolated from a human clinical source was investigated using a polyphasic approach in order to clarify its taxonomic status. Comparative 16S rRNA gene sequence analysis showed that the new isolate constituted a distinct phyletic line within the genus Chryseobacterium, displaying >2.8 % sequence divergence with recognized species of this genus. The generic assignment was confirmed by chemotaxonomic data which revealed a fatty acid profile consisting of straight-chain saturated, monounsaturated and branched-chain fatty acids of iso-/anteiso-types as well as 3-hydroxylated fatty acids; a menaquinone with six isoprene units (MK-6) as the predominant respiratory quinone and sym-homospermidine as the predominant polyamine. The novel isolate could be distinguished from other members of the genus Chryseobacterium by a set of distinct biochemical properties. On the basis of phenotypic and phylogenetic evidence, it is proposed that the new isolate represents a novel species of the genus Chryseobacterium for which the name Chryseobacterium treverense sp. nov. is proposed. The type strain is IMMIB L-1519(T) (=DSM 22251(T)=CCUG 57657(T)).