Chryseobacterium panacisoli sp. nov., isolated from ginseng-cultivation soil with ginsenoside-converting activity.

A Gram-stain-negative, non-motile, non-spore-forming, aerobic, rod-shaped and yellow-pigmented bacterium, designated strain Gsoil 183T, was isolated from ginseng-cultivation soil sampled in Pocheon Province, Republic of Korea. This bacterium was characterized to determine its taxonomic position by using a polyphasic approach. Strain Gsoil 183T grew at 10-37 °C and at pH 5.0-9.0 on tryptic soy agar. Strain Gsoil 183T had ß-glucosidase activity, which was responsible for its ability to convert ginsenoside Rb1 (one of the dominant active components of ginseng) to F2. Based on 16S rRNA gene sequencing, strain Gsoil 183T clustered with species of the genus Chryseobacterium and appeared to be closely related to Chryseobacterium sediminis LMG 28695T (99.1 % sequence similarity), Chryseobacterium lactis NCTC 11390T (98.6%), Chryseobacterium rhizoplanae LMG 28481T (98.6%), Chryseobacterium oncorhynchi CCUG 60105T (98.5%), Chryseobacterium viscerum CCUG 60103T (98.4%) and Chryseobacterium joostei DSM 16927T (98.3%). Menaquinone MK-6 was the predominant respiratory quinone and the major fatty acids were iso-C15 : 0, iso-C17 : 0-3OH and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The polar lipids were phosphatidylethanolamine, six unidentified glycolipids, five unidentified aminolipids and three unidentified lipids. The G+C content of the genomic DNA was 36.6 mol%. Digital DNA-DNA hybridization between strain Gsoil 183T and the type strains of C. sediminis, C. lactis, C. rhizoplanae, C. oncorhynchi, C. viscerum and C. joostei resulted in values below 70 %. Strain Gsoil 183T could be differentiated genotypically and phenotypically from the recognized species of the genus Chryseobacterium. The isolate therefore represents a novel species, for which the name Chryseobacterium panacisoli sp. nov. is proposed, with the type strain Gsoil 183T (=KACC 15033T=LMG 23397T).

Chryseobacterium mulctrae sp. nov., isolated from raw cow's milk.

A Gram-stain-negative bacterial strain, designated CA10T, was isolated from bovine raw milk sampled in Anseong, Republic of Korea. Cells were yellow-pigmented, aerobic, non-motile bacilli and grew optimally at 30 °C and pH 7.0 on tryptic soy agar without supplementation of NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain CA10T belonged to the genus Chryseobacterium, family Flavobacteriaceae, and was most closely related to Chryseobacterium indoltheticum ATCC 27950T (98.75 % similarity). The average nucleotide identity and digital DNA-DNA hybridization values of strain CA10T were 94.4 and 56.9 %, respectively, relative to Chryseobacterium scophthalmum DSM 16779T, being lower than the cut-off values of 95-96 and 70 %, respectively. The predominant respiratory quinone was menaquinone-6; major polar lipid, phosphatidylethanolamine; major fatty acids, iso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The results of physiological, chemotaxonomic and biochemical analyses suggested that strain CA10T is a novel species of genus Chryseobacterium, for which the name Chryseobacterium mulctrae sp. nov. is proposed. The type strain is CA10T (=KACC 21234T=JCM 33443T).

Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil.

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

Comparison of the therapeutic efficacy of fluoroquinolone and non-fluoroquinolone treatment in patients with Elizabethkingia meningoseptica bacteraemia.

Elizabethkingia meningoseptica is a non-fermentative Gram-negative bacillus that has emerged as an important pathogen in nosocomial infections and is usually associated with high mortality. E. meningoseptica is inherently resistant to many broad-spectrum antibiotics, and appropriate antibiotic selection is crucial for survival. Data about the therapeutic efficacy of fluoroquinolone in E. meningoseptica bacteraemia are limited. We retrospectively enrolled patients with E. meningoseptica bacteraemia who were treated with a single antimicrobial agent with in vitro activity against E. meningoseptica for at least 48 hours in a Taiwanese medical centre between January 2011 and June 2016. We compared the therapeutic efficacy of fluoroquinolone and non-fluoroquinolone treatment. A logistic regression and a propensity score-adjusted model were used to evaluate the risk factors for 14-day mortality. A total of 66 patients were identified, 24 who received fluoroquinolone treatment (ciprofloxacin, n = 9; levofloxacin, n = 15) and 42 who received non-fluoroquinolone treatment (piperacillin/tazobactam, n = 26; trimethoprim/sulfamethoxazole, n = 15; minocycline, n = 1). The fluoroquinolone group had significantly lower 14-day mortality than the non-fluoroquinolone group (8.3% vs. 33.3%, P = 0.023). The APACHE II score was significantly higher in the non-fluoroquinolone group than in the fluoroquinolone group. In a propensity-adjusted analysis, fluoroquinolone use was an independent factor associated with 14-day survival. After stratification using the APACHE II score, treatment with fluoroquinolone was associated with 14-day survival, but did not reach statistical significance in both groups with greater and lesser severity. Therefore, fluoroquinolone is a suitable antimicrobial agent for treating E. meningoseptica bacteraemia.

Chryseobacterium ginsengiterrae sp. nov., with Beta-Glucosidase Activity Isolated from Soil of a Ginseng Field.

The isolated Chryseobacterium ginsengiterrae sp. nov DCY68T was found to be Gram-negative, aerobic, non-motile, non-flagellate and rod-shaped. Their size was approximately 0.40-0.46 × 1.0-1.27 µm. The colonies were yellow-pigmented, convex, circular and 0.5-1.3 mm in diameter when grown on R2A agar for 2 days. DNA, esculin, skim milk, gelatine, starch, Tween 20, and Tween 80 were hydrolyzed, but not cellulose. The cells grew on R2A, TSA, and NA but not on MacConkey agars. Growth occured at 4-33 °C (optimum, 30 °C), at pH 5.0-8.0 (optimum, pH 6.5), and 0-2.5% NaCl. Nitrate was not reduced to nitrite. Oxidase and catalase activity were positive. Strain DCY68T contained ß-glucosidase activity in which ginsenoside Rb1 was enzymatically converted to ginsenoside F2. Analysis of the16S rRNA gene sequence revealed that strain C. ginsengiterrae sp. nov DCY68T belonged to the family Flavobacteriaceae and was most closely related to C. limigenitum SUR2T (97.4%). The genomic DNA G+C content was 42.0 mol%. The predominant quinones were MK-6 (74.5%) and MK-7 (25.5%). The major fatty acids were iso-C15:0, summed feature 3 (containing C16:1 ω7c and/or C16:1 ω6c) and iso-C17:0 3-OH. On the basis of these phenotypic, genotypic and chemotaxonomic studies, strain DCY68T represents a novel species of the genus Chryseobacterium, for which name C. ginsengiterrae sp. nov. is proposed. The type strain is DCY68T (=KCTC 32089T = JCM 18517T).

Chryseobacterium panacis sp. nov., isolated from ginseng soil.

A novel strain, DCY107(T), was isolated from soil collected from a ginseng field in Gochang, Republic of Korea. Strain DCY107(T) is Gram-negative, yellow pigmented, non-motile, non-flagellate, rod-shaped and aerobic. The strain was found to grow optimally at 25-30 °C and pH 6.5-7. Phylogenetically, strain DCY107(T) is closely related to Chryseobacterium polytrichastri DSM 26899(T) (98.49 % 16S rRNA gene sequence similarity), Chryseobacterium yeoncheonense JCM 18516(T) (97.78 %), Chryseobacterium aahli LMG 27338(T) (97.74 %), Chryseobacterium limigenitum LMG28734(T) (97.74 %), Chryseobacterium ginsenosidimutans JCM 16719(T) (97.47 %) and Chryseobacterium gregarium LMG 24052(T) (97.31 %). The DNA-DNA relatedness values between strain DCY107(T) and reference strains were found to be clearly below 70 %. The DNA G+C content of strain DCY107(T) was determined to be 34.2 mol%. The predominant quinone was identified menaquinone 6 (MK-6). The major polar lipids were identified as phosphatidylethanolamine and unidentified lipids: aminolipids AL1, AL2 and lipid L2. C16:00, iso-C15:00, iso-C15:02OH, iso-C17:03OH and summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl) were identified as the major fatty acids present in strain DCY107(T). The results of physiological and biochemical tests allowed strain DCY107(T) to be differentiated phenotypically from other recognised species belonging to the genus Chryseobacterium. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Chryseobacterium panacis sp. nov. is proposed, with the type strain designated as DCY107(T) (=CCTCC AB 2015195(T) = KCTC 42750(T)).

Chryseobacterium camelliae sp. nov., isolated from green tea.

A Gram-staining-negative, strictly aerobic, non-motile, rod-shaped and flexirubin-type-pigmented strain, THG C4-1(T), was isolated from green tea leaves in Jangheung-gun, Republic of Korea. Strain THG C4-1(T) grew well at 20-30 °C, at pH 7.0-7.5 and in the absence of NaCl on nutrient agar. Based on 16S rRNA gene sequence comparisons, strain THG C4-1(T) was most closely related to Chryseobacterium taiwanense Soil-3-27(T) (97.7 %), C. hagamense RHA2-9(T) (97.2 %), C. gregarium P 461/12(T) (97.2 %), C. ginsenosidimutans THG 15(T) (97.1 %), C. taeanense PHA3-4(T) (97.0 %) and C. daeguense K105(T) (97.0 %), but DNA-DNA relatedness between strain THG C4-1(T) and its closest phylogenetic neighbours was below 21 %. The DNA G+C content was 41.7 mol%. The only isoprenoid quinone detected in strain THG C4-1(T) was menaquinone 6 (MK-6). The major component of the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylethanolamine and unidentified aminolipids. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. These data supported the affiliation of strain THG C4-1(T) to the genus Chryseobacterium. The results of physiological and biochemical tests enabled strain THG C4-1(T) to be differentiated genotypically and phenotypically from recognized species of the genus Chryseobacterium. Therefore, the novel isolate represents a novel species, for which the name Chryseobacterium camelliae sp. nov. is proposed, with THG C4-1(T) ( = KACC 16985(T) = JCM 18745(T)) as the type strain.

Chryseobacterium yeoncheonense sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field.

A Gram-staining negative, aerobic, non-motile, non-flagellate, yellow-pigmented, rod-shaped bacterial strain, designated strain DCY67(T), was isolated from ginseng field in Republic of Korea. Strain DCY67(T) contained ß-glucosidase activity which converts ginsenoside Rb1 to compound K. Optimum growth of DCY67(T) occurred at 30 °C and pH 6.0-6.5. Analysis of the 16S rRNA gene sequences revealed that strain DCY67(T) belonged to the family Flavobacteriaceae and was most closely related to Chryseobacterium ginsenosidimutans THG 15(T) (97.5 %). The genomic DNA G+C content was 36.1 mol%. The predominant quinones were MK-6 (90.9 %) and MK-7 (9.15 %). The major fatty acids were iso-C15:0, summed feature 3 (containing C16:1 ω7c and/or C16:1 ω6c) and iso-C17:0 3-OH. On the basis of these phenotypic, genotypic and chemotaxonomic studies, strain DCY67(T) represents a novel species of the genus Chryseobacterium, for which, name Chryseobacterium yeoncheonense sp. nov. proposed the type strain is DCY67(T) (=KCTC 32090(T) = JCM 18516(T)).

Chryseobacterium ginsengisoli sp. nov., isolated from the rhizosphere of ginseng and emended description of Chryseobacterium gleum.

Strain DCY 63(T), isolated from the rhizosphere of ginseng, was a Gram-reaction-negative, strictly aerobic, non-motile, catalase- and oxidase-positive rod. 16S rRNA gene sequence analysis revealed that strain DCY 63(T) belonged to the genus Chryseobacterium and was closely related to Chryseobacterium indoltheticum LMG 4025(T) (98.1 %), Chryseobacterium ginsenosidimutans THG 15(T) (98.0 %) and Chryseobacterium scophthalmum LMG 13028(T) (97.1 %). The major polar lipids of strain DCY 63(T) were phosphatidylethanolamine (PE), four unidentified aminolipids and three unidentified polar lipids, and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl). The predominant isoprenoid quinone of strain DCY 63(T) was MK-6 and the G+C content of the genomic DNA was 31.6 mol%. The DNA-DNA relatedness values between strain DCY 63(T) and C. indoltheticum LMG 4025(T), C. ginsenosidimutans THG 15(T) and C. scophthalmum LMG 13028(T) were less than 30 %. On the basis of these data, strain DCY 63(T) is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium ginsengisoli sp. nov. is proposed. The type strain is DCY 63(T) (= KCTC 23760(T) = JCM 18019(T)). An emended description of Chryseobacterium gleum is also proposed.