Chryseobacterium viscerum sp. nov., isolated from diseased fish

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2934-2940 ◽  
Author(s):  
L. Zamora ◽  
A. I. Vela ◽  
M. A. Palacios ◽  
C. Sánchez-Porro ◽  
L. A. Svensson-Stadler ◽  
...  

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).

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1557-1561 ◽  
Author(s):  
Ying Liu ◽  
Jing-Hua Jin ◽  
Hong-Can Liu ◽  
Zhi-Pei Liu

A Gram-staining-negative, non-endospore-forming, non-flagellated, non-motile and rod-shaped bacterium, designated strain LM2-5T, was isolated from activated sludge in a sequencing batch reactor used for the treatment of triphenylmethane dye effluent. The taxonomy of strain LM2-5T was studied by phenotypic, chemotaxonomic and phylogenetic methods. Strain LM2-5T was aerobic, heterotrophic and positive for oxidase but negative for catalase activity. It grew at 16–37 °C (optimum 25 °C) and at pH 5.0–8.5 (optimum between pH 6.5 and pH 7.0). NaCl was not obligatory for growth but was tolerated at concentrations up to 2.0 % (w/v) NaCl. The novel strain formed yellow colonies on trypticase soy agar. Cells of strain LM2-5T were rods that measured 0.3–0.5 µm in width and 3.0–5.0 µm in length. The predominant respiratory quinone was Q-8. The major fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c. The genomic DNA G+C content was 66.7 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, strain LM2-5T clustered with members of the genus Dokdonella and appeared most closely related to Dokdonella koreensis DS-123T (96.4 % sequence similarity), Dokdonella fugitiva A3T (96.1 %), Dokdonella soli KIS28-6T (95.7 %) and Dokdonella ginsengisoli Gsoil 191T (95.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain LM2-5T was considered to represent a novel species of the genus Dokdonella , for which the name Dokdonella immobilis is proposed. The type strain is LM2-5T ( = CGMCC 1.7659T  = JCM 15763T).


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2844-2850 ◽  
Author(s):  
Sathiyaraj Srinivasan ◽  
Jae-Jin Lee ◽  
Sangyong Lim ◽  
Minho Joe ◽  
Myung Kyum Kim

A Gram-staining-positive, strictly aerobic, spherical, non-motile, red-pigmented bacterium, designated strain MK03T, was isolated from a soil sample collected in South Korea. The taxonomic position of the novel strain was investigated using a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain MK03T was placed in a clade formed by members of the genus Deinococcus in the family Deinococcaceae and appeared to be most closely related to Deinococcus aerolatus 5516T-9T (97.4 % sequence similarity), Deinococcus marmoris AA-63T (97.2 %), Deinococcus radiopugnans ATCC 19172T (97.2 %) and Deinococcus saxicola AA-1444T (96.9 %). The genomic DNA G+C content of the novel strain was 64.5 mol%. The chemotaxonomic characteristics of strain MK03T were typical of members of the genus Deinococcus : MK-8 was identified as the predominant respiratory quinine, the major fatty acids were C16 : 1ω7c, C15 : 1ω6c, C16 : 0 and C15 : 0, ornithine was found to be the diamino acid in the cell-wall peptidoglycan and the novel strain showed resistance to gamma radiation, with a D10 value (i.e. the dose required to reduce the bacterial population by 10-fold) in excess of 9 kGy. In hybridization experiments, only low DNA–DNA relatedness values (11.6–34.5 %) were recorded between the novel strain and its closest relatives in the genus Deinococcus . Based on the phylogenetic, chemotaxonomic, phenotypic and DNA–DNA relatedness data, strain MK03T represents a novel species of the genus Deinococcus , for which the name Deinococcus humi sp. nov. is proposed. The type strain is MK03T ( = KCTC 13619T  = JCM 17915T).


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1421-1426 ◽  
Author(s):  
Byoung-Jun Yoon ◽  
Dong-Heon Lee ◽  
Duck-Chul Oh

A Gram-staining-negative, yellow-pigmented, non-motile, strictly aerobic, rod-shaped bacterium, designated strain CNU001T, was isolated from seawater collected on the coast of Jeju Island, South Korea, and subjected to a polyphasic taxonomic study. The temperature, pH and NaCl ranges for growth were 10–30 °C, pH 6.0–10.0 and 2.0–5.0 %, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CNU001T belonged to the genus Erythrobacter in the family Erythrobacteraceae , with Erythrobacter longus DSM 6997T (96.6 % sequence similarity), Erythrobacter gaetbuli SW-161T (96.3 %), Erythrobacter vulgaris 022 2-10T (96.2 %), Erythrobacter nanhaisediminis T30T (96.1 %) and other members of the genus Erythrobacter (<96.0 %) identified as the novel strain’s closest relatives. The major cellular fatty acids were C18 : 1ω7c and C17 : 1ω6c. The polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one sphingoglycolipid, one unidentified aminolipid and six other unidentified lipids. The major respiratory quinone was ubiquinone-10 (UQ-10) and the genomic DNA G+C content of the novel strain was 58.9 mol%. On the basis of phenotypic, phylogenetic and genotypic data, strain CNU001T represents a novel species within the genus Erythrobacter , for which the name Erythrobacter jejuensis sp. nov. is proposed. The type strain is CNU001T ( = KCTC 23090T  = JCM 16677T).


2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1636-1643 ◽  
Author(s):  
Hye-Ri Sung ◽  
Jung-Hoon Yoon ◽  
Sa-Youl Ghim

A novel bacterial strain, designated UDC329T, was isolated from a sample of seawater collected at Dong-do, on the coast of Dokdo Island, in the East Sea of the Republic of Korea. The Gram-staining-negative, motile, facultatively anaerobic, non-spore-forming rods of the strain developed into dark orange–yellow colonies. The strain grew optimally between 25 and 30 °C, with 1 % (w/v) NaCl and at pH 7. It grew in the absence of NaCl, but not with NaCl at >7 % (w/v). The predominant menaquinone was MK-7, the predominant ubiquinones were Q-7 and Q-8, and the major fatty acids were iso-C15 : 0 (33.52 %) and C17 : 1ω8c (11.73 %). The genomic DNA G+C content of strain UDC329T was 50.2 mol%. In phylogenetic analyses based on 16S rRNA and gyrB gene sequences, strain UDC329T was grouped with members of the genus Shewanella and appeared most closely related to Shewanella fodinae JC15T (97.9 % 16S rRNA gene sequence similarity), Shewanella indica KJW27T (95.0 %), Shewanella algae ATCC 51192T (94.8 %), Shewanella haliotis DW01T (94.5 %) and Shewanella chilikensis JC5T (93.9 %). The level of DNA–DNA relatedness between strain UDC329T and S. fodinae JC15T was, however, only 27.4 %. On the basis of phenotypic, genotypic and DNA–DNA relatedness data, strain UDC329T represents a novel species in the genus Shewanella , for which the name Shewanella dokdonensis sp. nov. is proposed. The type strain is UDC329T ( = KCTC 22898T = DSM 23626T).


2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1622-1627 ◽  
Author(s):  
Zhi-Ping Zhong ◽  
Ying Liu ◽  
Ting-Ting Hou ◽  
Yu-Guang Zhou ◽  
Hong-Can Liu ◽  
...  

A Gram-staining-negative bacterium, strain TS-T86T, was isolated from Lake Tuosu, a saline lake (salinity 5.4 %, w/w) in Qaidam basin, China. Its taxonomic position was determined by using a polyphasic approach. Strain TS-T86T was strictly heterotrophic, aerobic and catalase- and oxidase-positive. Cells were non-spore-forming, non-motile rods, 0.4–0.6 µm wide and 1.2–2.3 µm long. Growth was observed in the presence of 0–9.0 % (w/v) NaCl (optimum, 2.0 %), at 4–35 °C (optimum, 25 °C) and at pH 7.0–10.5 (optimum, pH 8.5–9.0). Strain TS-T86T contained MK-7 as the predominant respiratory quinone. The major fatty acids (>10 %) were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, an unknown phospholipid, six unidentified aminolipids and two uncharacterized lipids. The DNA G+C content was 35 mol% (T m). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T86T was associated with the genus Belliella , and showed the highest sequence similarity to Belliella baltica BA134T (98.5 %) and then to Belliella kenyensis No.164T (95.7 %) and Belliella pelovolcani CC-SAL-25T (95.3 %). DNA–DNA relatedness of strain TS-T86T to Belliella baltica DSM 15883T was 32±3 %. It is concluded that strain TS-T86T represents a novel species of the genus Belliella , for which the name Belliella aquatica sp. nov. is proposed. The type strain is TS-T86T ( = CGMCC 1.12479T = JCM 19468T).


2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1207-1212 ◽  
Author(s):  
Hong-Fei Wang ◽  
Yong-Guang Zhang ◽  
Ji-Yue Chen ◽  
Jian-Wei Guo ◽  
Li Li ◽  
...  

A novel endophytic actinobacterium, designated EGI 6500707T, was isolated from the surface-sterilized root of a halophyte Anabasis elatior (C. A. Mey.) Schischk collected from Urumqi, Xinjiang province, north-west China, and characterized using a polyphasic approach. Cells were Gram-stain-positive, non-motile, short rods and produced white colonies. Growth occurred at 10–45 °C (optimum 25–30 °C), at pH 5–10 (optimum pH 8) and in presence of 0–4 % (w/v) NaCl (optimum 0–3 %). The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content of strain EGI 6500707T was 69.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain EGI 6500707T should be placed in the genus Frigoribacterium (family Microbacteriaceae , phylum Actinobacteria ), and that the novel strain exhibited the highest 16S rRNA gene sequence similarity to Frigoribacterium faeni JCM 11265T (99.1 %) and Frigoribacterium mesophilum MSL-08T (96.5 %). DNA–DNA relatedness between strain EGI 6500707T and F. faeni JCM 11265T was 47.2 %. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain EGI 6500707T represents a novel species of the genus Frigoribacterium , for which the name Frigoribacterium endophyticum sp. nov. is proposed. The type strain is EGI 6500707T ( = JCM 30093T = KCTC 29493T).


2020 ◽  
Vol 70 (11) ◽  
pp. 5943-5949 ◽  
Author(s):  
Yun-zhen Yang ◽  
Ji-feng Chen ◽  
Wan-ru Huang ◽  
Ran-ran Zhang ◽  
Shuangjiang Liu ◽  
...  

A novel Gram-stain-negative, strictly aerobic, rod-shaped, brick red-pigmented bacterium, designated R-22-1 c-1T, was isolated from water from Baiyang Lake, Hebei Province, PR China. The strain was able to grow at 20–30 °C (optimum, 30 °C) and pH 6–7 (optimum, pH 6) in Reasoner’s 2A medium. 16S rRNA gene sequence and phylogenetic analyses of R-22-1 c-1T revealed closest relationships to Rufibacter immobilis MCC P1T (97.8 %), Rufibacter sediminis H-1T (97.9 %) and Rufibacter glacialis MDT1-10-3T (97.0 %), with other species of the genus Rufibacter showing less than 97.0 % sequence similarity. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids and three unidentified lipids. The major cellular fatty acids were iso-C15 : 0, C15 : 1  ω6c, C17 : 1  ω6c, anteiso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B). The respiratory quinone was MK-7. The draft genome of R-22-1 c-1T was 5.6 Mbp in size, with a G+C content of 50.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain R-22-1 c-1T and related type strains were R. immobilis MCC P1T (77.2 and 21.8 %), R. sediminis H-1T (81.6 and 21.4 %) and R. tibetensis 1351T (78.5 and 22.9 %). Based on these phylogenetic, chemotaxonomic and genotypic results, strain R-22-1 c-1T represents a novel species in the genus Rufibacter , for which the name Rufibacter latericius sp. nov. is proposed. The type strain is R-22-1 c-1T (=CGMCC 1.13570T=KCTC 62781T).


2020 ◽  
Vol 70 (3) ◽  
pp. 2132-2136 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Kyung-Sook Whang

A Gram-stain-negative bacterium, designated strain PF-30T, was isolated from floodwater of a paddy field in South Korea. Strain PF-30T was found to be a strictly aerobic, motile and pink-pigmented rods which can grow at 25–40 °C (optimum, 28 °C), at pH 5.0–9.0 (optimum pH 7.0) and at salinities of 0.5–3.0 % NaCl (optimum 0.5 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PF-30T belongs to the genus Elioraea , showing highest sequence similarity to Elioraea tepidiphila TU-7T (97.1%) and less than 91.3 % similarity with other members of the family Acetobacteraceae . The average nucleotide identity (ANI) and DNA–DNA relatedness between the strain PF-30T and E. tepidiphila TU-7T yielded an ANI value of 75.1 % and DNA–DNA relatedness of 11.7±0.7 %, respectively. The major fatty acids were identified as C18 : 0 and C18 : 1 ω7c. The predominant respiratory quinone was identified as Q-10. The DNA G+C content was determined to be 69.9 mol%. The strain PF-30T was observed to produce plant-growth-promoting materials such as indole-3-acetic acid (IAA), siderophore and phytase. On the basis of the results from phylogenetic, chemotaxonomic and phenotypic data, we concluded that strain PF-30T represents a novel species of the genus Elioraea , for which the name Elioraea rosea sp. nov. is proposed. The type strain is PF-30T (=KACC 19985T=NBRC 113984T).


Author(s):  
Renju Liu ◽  
Qiliang Lai ◽  
Li Gu ◽  
Peisheng Yan ◽  
Zongze Shao

A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9T, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1–8 %, at pH 6.5–8 and at temperatures of 10–40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae , and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T, followed by similarities of 90.4, 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T, Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA–DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %), iso-C16 : 0 3-OH (12.4 %), and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c, 11.6 %). Combining the genotypic and phenotypic data, A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus, for which the name Croceimicrobium hydrocarbonivorans gen. nov., sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).


Author(s):  
Xiao-Xian Huang ◽  
Jia Shang ◽  
Lian Xu ◽  
Rui Yang ◽  
Ji-Quan Sun

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, named SJ-16T, was isolated from desert soil collected in Inner Mongolia, northern PR China. Strain SJ-16T grew at pH 6.0–11.0 (optimum, pH 8.0–9.0), 4–40 °C (optimum, 30–35 °C) and in the presence of 0–8 % (w/v) NaCl (optimum, 0–2 %). The strain was negative for catalase and positive for oxidase. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SJ-16T clustered with Luteimonas chenhongjianii 100111T and Luteimonas terrae THG-MD21T, and had 98.8, 98.6, 98.3 and <97.9 % of 16S rRNA gene sequence similarity to strains L. chenhongjianii 100111T, L. terrae THG-MD21T, L. aestuarii B9T and all other type strains of the genus Luteimonas , respectively. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1  ω9c). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids, and ubiquinone-8 was the only respiratory quinone. The genomic DNA G+C content was 69.3 mol%. The digital DNA–DNA hybridization and average nucleotide identity values of strain SJ-16T to L. chenhongjianii 100111T, L. terrae THG-MD21T, L. rhizosphaerae 4-12T and L. aestuarii B9T were 36.9, 37.5, 24.0 and 21.1 %, and 80.9, 80.6, 80.7 and 76.3 %, respectively. Based on phenotypic, physiological and phylogenetic results, strain SJ-16T represents a novel species of the genus Luteimonas , for which the name Luteimonas deserti is proposed. The type strain is SJ-16T (=CGMCC 1.17694T=KCTC 82207T).


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