scholarly journals Cloacibacterium rupense sp. nov., isolated from freshwater lake sediment

2010 ◽  
Vol 60 (9) ◽  
pp. 2023-2026 ◽  
Author(s):  
Shu-Juan Cao ◽  
Chun-Ping Deng ◽  
Bao-Zhen Li ◽  
Xiu-Qin Dong ◽  
Hong-Li Yuan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
The Family ◽  
Taxonomic Approach

A Gram-negative, yellow-pigmented bacterium, designated strain R2A-16T, was isolated from sediment of Rupa Lake in Nepal and analysed using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain R2A-16T is affiliated to the genus Cloacibacterium of the family Flavobacteriaceae; 16S rRNA gene sequence similarity between strain R2A-16T and Cloacibacterium normanense CCUG 46293T was 98.07 %. The isolate contained iso-C15 : 0 (35.6 %) as the major fatty acid and menaquinone MK-6 as the predominant respiratory quinone. The G+C content of the genomic DNA was 33.3 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain R2A-16T represents a novel species of the genus Cloacibacterium, for which the name Cloacibacterium rupense sp. nov. is proposed; the type strain is R2A-16T (=CGMCC 1.7656T =NBRC 104931T).

scholarly journals Chryseobacterium caeni sp. nov., isolated from bioreactor sludge

2007 ◽  
Vol 57 (1) ◽  
pp. 141-145 ◽  
Author(s):  
Zhe-Xue Quan ◽  
Kwang Kyu Kim ◽  
Myung-Kyum Kim ◽  
Long Jin ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
The Family ◽  
Bacterium Strain

A Gram-negative, non-spore-forming, yellow-pigmented bacterium, strain N4T, was isolated from a nickel-complexed cyanide-degrading bioreactor and subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain N4T is affiliated to the genus Chryseobacterium of the family Flavobacteriaceae. The levels of 16S rRNA gene sequence similarity between strain N4T and the type strains of all known Chryseobacterium species were 93.2–95.8 %, suggesting that strain N4T represents a novel species within the genus Chryseobacterium. The strain contained iso-C15 : 0 and summed feature 4 as the major fatty acids and menaquinone MK-6 as the predominant respiratory quinone. The G+C content of the genomic DNA was 38.2 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain N4T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium caeni sp. nov. is proposed. The type strain is N4T (=KCTC 12506T=CCBAU 10201T=DSM 17710T).

scholarly journals Erythrobacter luteolus sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2005 ◽  
Vol 55 (3) ◽  
pp. 1167-1170 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Kook Hee Kang ◽  
Soo-Hwan Yeo ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties

A Gram-negative, non-spore-forming, yellow-pigmented, slightly halophilic bacterial strain, SW-109T, was isolated from a tidal flat of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. This isolate did not produce bacteriochlorophyll a and contained ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c as the major fatty acid. The DNA G+C content was 60·3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SW-109T is phylogenetically affiliated to the genus Erythrobacter of the family Sphingomonadaceae. Strain SW-109T exhibited levels of 16S rRNA gene sequence similarity to the type strains of Erythrobacter species of 94·0–96·3 %, making it possible to categorize strain SW-109T as a species that is separate from previously recognized Erythrobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, SW-109T (=KCTC 12311T=JCM 12599T) was classified as the type strain of a novel Erythrobacter species, for which the name Erythrobacter luteolus sp. nov. is proposed.

scholarly journals Ruegeria faecimaris sp. nov., isolated from a tidal flat sediment

2011 ◽  
Vol 61 (5) ◽  
pp. 1182-1188 ◽  
Author(s):  
Ki-Hoon Oh ◽  
Yong-Taek Jung ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Phenotypic Properties

A Gram-negative-staining, non-motile and rod-shaped bacterial strain, HD-28T, was isolated from a tidal flat of the Yellow Sea, Korea. Strain HD-28T grew optimally at pH 7.0–8.0 and 30 °C in the presence of 2–3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HD-28T was most closely related to species of the genus Ruegeria and exhibited 95.5–96.9 % 16S rRNA gene sequence similarity to the type strains of Ruegeria species. A neighbour-joining phylogenetic tree based on gyrB gene sequences also showed that strain HD-28T fell within the cluster comprising recognized species of the genus Ruegeria, showing 77.5–83.9 % sequence similarity. Strain HD-28T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain HD-28T were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. The DNA G+C content was 57.9 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain HD-28T could be distinguished from recognized species of the genus Ruegeria. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain HD-28T is considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria faecimaris sp. nov. is proposed. The type strain is HD-28T ( = KCTC 23044T = CCUG 58878T).

scholarly journals Mariniflexile aquimaris sp. nov., isolated from seawater, and emended description of the genus Mariniflexile Nedashkovskaya et al. 2006

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 539-544 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Polar Lipid Profile ◽  
The Family ◽  
Emended Description

A Gram-staining-negative, non-flagellated, non-gliding and rod-shaped bacterial strain, designated HWR-17T, was isolated from seawater of the Yellow Sea in Korea. Strain HWR-17T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HWR-17T clustered with the two Mariniflexile species in the family Flavobacteriaceae, exhibiting 16S rRNA gene sequence similarity of 97.1–97.2 % to their type strains and less than 95.7 % sequence similarity to other members of the family Flavobacteriaceae. Strain HWR-17T contained MK-6 as the predominant menaquinone and iso-C15 : 0 as the major fatty acid. The polar lipid profile of strain HWR-17T contained phosphatidylethanolamine, an unidentified aminolipid and four unidentified lipids. The DNA G+C content of strain HWR-17T was 35.7 mol% and it exhibited 11 and 10 % DNA–DNA relatedness, respectively, with Mariniflexile gromovii KCTC 12570T and Mariniflexile fucanivorans DSM 18792T. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain HWR-17T is distinguishable from the two recognized Mariniflexile species. On the basis of the data presented, strain HWR-17T is considered to represent a novel species of the genus Mariniflexile, for which the name Mariniflexile aquimaris sp. nov. is proposed. The type strain is HWR-17T ( = KCTC 23346T  = CCUG 60529T). An emended description of the genus Mariniflexile is also proposed.

Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2224-2228 ◽  
Author(s):  
Hiromi Uchida ◽  
Koei Hamana ◽  
Masayuki Miyazaki ◽  
Takao Yoshida ◽  
Yuichi Nogi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-stain-negative, aerobic, motile, orange-pigmented, slightly halophilic, rod-shaped bacterium, designated strain JAMH 0132T, was isolated from the trophosome of a tubeworm in Kagoshima Bay, Japan, and its taxonomic position was investigated using a polyphasic approach. The novel strain grew optimally at 28–30 °C and with about 2.0 % (w/v) NaCl. Chemotaxonomic analysis showed that Q-10 was the predominant respiratory quinone and that C18 : 1ω7c, C16 : 0 2-OH and C16 : 0 were the major fatty acids. Sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. The genomic DNA G+C content was 60.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JAMH 0132T belonged to the family Sphingomonadaceae , within the class Alphaproteobacteria . The novel strain appeared most closely related to Sphingopyxis baekryungensis SW-150T (95.1 % 16S rRNA gene sequence similarity) and showed less sequence similarity with representatives of the genera Blastomonas , Sphingomonas , Sphingosinicella and Novosphingobium (<94.8 %). In having no detectable polyamine, strain JAMH 0132T differed from members of all genera currently in the family Sphingomonadaceae . On the basis of its phenotypic properties and phylogenetic distinctiveness, strain JAMH 0132T represents a novel species of a new genus in the family Sphingomonadaceae for which the name Parasphingopyxis lamellibrachiae gen. nov., sp. nov. is proposed. The type strain of Parasphingopyxis lamellibrachiae gen. nov., sp. nov. is JAMH 0132T ( = JCM 15549T  = NCIMB 14486T).

scholarly journals Lutibacter maritimus sp. nov., isolated from a tidal flat sediment

2010 ◽  
Vol 60 (3) ◽  
pp. 610-614 ◽  
Author(s):  
Sooyeon Park ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Tidal Flat Sediment ◽  
Gram Staining ◽  
Taxonomic Approach

A Gram-staining-negative, aerobic, non-motile, non-gliding, yellow-pigmented and rod-shaped bacterial strain, designated S7-2T, was isolated from a tidal flat sediment at Saemankum on the west coast of Korea and investigated using a polyphasic taxonomic approach. Strain S7-2T grew optimally at pH 7.0–8.0, at 25–30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain S7-2T clustered with Lutibacter litoralis CF-TF09T, a member of the family Flavobacteriaceae, with which it showed 95.8 % 16S rRNA gene sequence similarity. It contained MK-6 as the predominant menaquinone and iso-C15 : 0 and C15 : 1 ω6c as the major fatty acids. The major polar lipids of strain S7-2T and L. litoralis JCM 13034T were phosphatidylethanolamine and three unidentified lipids. The DNA G+C content was 34.6 mol%. Differential phenotypic properties and phylogenetic distinctiveness suggested that strain S7-2T represents a novel species of the genus Lutibacter, for which the name Lutibacter maritimus sp. nov. is proposed. The type strain is S7-2T (=KCTC 22635T=CCUG 57524T).

Pseudoruegeria lutimaris sp. nov., isolated from a tidal flat sediment, and emended description of the genus Pseudoruegeria

2010 ◽  
Vol 60 (5) ◽  
pp. 1177-1181 ◽  
Author(s):  
Yong-Taek Jung ◽  
Bong-Hee Kim ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Tidal Flat Sediment ◽  
The Mean

A Gram-negative-staining, non-motile and rod-shaped bacterial strain, HD-43T, was isolated from a tidal flat sediment collected from Hwang-do, an island of Korea. Strain HD-43T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HD-43T clustered with Pseudoruegeria aquimaris SW-255T. It exhibited 96.6 % 16S rRNA gene sequence similarity and 79.4 % gyrB sequence similarity with P. aquimaris SW-255T. Strain HD-43T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. The DNA G+C content was 73.5 mol%. The mean DNA–DNA relatedness between strain HD-43T and P. aquimaris SW-255T was 5 %. Differential phenotypic properties demonstrated that strain HD-43T is clearly distinguishable from P. aquimaris. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain HD-43T is considered to represent a novel species of the genus Pseudoruegeria, for which the name Pseudoruegeria lutimaris sp. nov. is proposed. The type strain is HD-43T (=KCTC 22690T =CCUG 57754T).

scholarly journals Pedobacter terrae sp. nov., isolated from soil

2007 ◽  
Vol 57 (11) ◽  
pp. 2462-2466 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Dna Relatedness ◽  
The Family ◽  
Type Strains

A Gram-negative, non-motile, rod-shaped bacterial strain, DS-57T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated using a polyphasic approach. It grew optimally at 25 °C and in trypticase soy broth without NaCl and trypticase soy broth with 0.5 % NaCl. Strain DS-57T contained MK-7 as the predominant menaquinone and iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 39.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-57T was most closely related to the genus Pedobacter of the family Sphingobacteriaceae, clustering coherently with Pedobacter suwonensis, Pedobacter roseus and Pedobacter sandarakinus. Strain DS-57T exhibited 16S rRNA gene sequence similarity values of 99.2, 97.9 and 97.2 % with respect to the type strains of P. suwonensis, P. roseus and P. sandarakinus, respectively, and values less than 95.6 % with respect to the type strains of other Pedobacter species. Strain DS-57T exhibited levels of DNA–DNA relatedness of 45, 17 and 15 % with respect to the type strains of P. suwonensis, P. roseus and P. sandarakinus, respectively. Differential phenotypic properties, together with the phylogenetic distinctiveness and the DNA–DNA relatedness data, were sufficient to allow the classification of strain DS-57T as a species that is separate from recognized Pedobacter species. On the basis of phenotypic properties and phylogenetic distinctiveness, therefore, strain DS-57T represents a novel species of the genus Pedobacter, for which the name Pedobacter terrae sp. nov. is proposed. The type strain is DS-57T (=KCTC 12762T=DSM 17933T).

Tropicimonas aquimaris sp. nov., isolated from seawater, and emended description of the genus Tropicimonas Harwati et al. 2009

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 688-692 ◽  
Author(s):  
Ki-Hoon Oh ◽  
Won-Chan Choi ◽  
Yong-Taek Jung ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Properties ◽  
Polar Lipid Profile ◽  
Gram Staining ◽  
Taxonomic Approach

A Gram-staining-negative, aerobic, non-motile and rod-shaped bacterial strain, designated DPG-21T, was isolated from seawater from the South Sea in Korea, and investigated using a polyphasic taxonomic approach. Strain DPG-21T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. In a neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain DPG-21T clustered with Tropicimonas isoalkanivorans B51T (with a sequence similarity of 97.1 %); the novel strain showed lower 16S rRNA gene sequence similarities (<95.4 %) with the other species included in the tree. The mean DNA–DNA relatedness value between strain DPG-21T and T. isoalkanivorans DSM 19548T was 12 %. The predominant ubiquinones of strain DPG-21T were Q-10 and Q-9 while C18 : 1ω7c was the strain’s major fatty acid. The polar lipid profile of strain DPG-21T was similar to that of T. isoalkanivorans DSM 19548T. The genomic DNA G+C content of the novel strain was 69.6 mol%. Some phenotypic properties and the phylogenetic and genetic data indicated that strain DPG-21T was distinct from T. isoalkanivorans and represents a novel species of the genus Tropicimonas, for which the name Tropicimonas aquimaris sp. nov. is proposed. The type strain is DPG-21T ( = KCTC 23424T = CCUG 60524T).

scholarly journals Description of Olleya aquimaris sp. nov., isolated from seawater, and emended description of the genus Olleya Mancuso Nichols et al. 2005

2010 ◽  
Vol 60 (4) ◽  
pp. 887-891 ◽  
Author(s):  
Soo-Young Lee ◽  
Sooyeon Park ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
The Family ◽  
Emended Description

A Gram-stain-negative, non-flagellated, motile (by gliding), yellow-pigmented, rod-shaped bacterial strain, designated L-4T, was isolated from seawater of Baekdo harbour in the East Sea, Korea. Strain L-4T grew optimally at 37 °C, at pH 6.5–7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain L-4T clustered with Olleya marilimosa CAM030T, a member of the family Flavobacteriaceae. Strain L-4T exhibited 16S rRNA gene sequence similarity values of 97.2 % to O. marilimosa CAM030T and less than 95.8 % to other members of the family Flavobacteriaceae. Strain L-4T and O. marilimosa CIP 108537T contained MK-6 as the predominant menaquinone. The fatty acid and polar lipid profiles of strain L-4T were similar to those of O. marilimosa CIP 108537T. The DNA G+C content of strain L-4T was 35 mol% and DNA–DNA relatedness between strain L-4T and O. marilimosa CIP 108537T was 7 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, enable strain L-4T to be distinguished from O. marilimosa. On the basis of these data, strain L-4T is considered to represent a novel species of the genus Olleya for which the name Olleya aquimaris sp. nov. is proposed; the type strain is L-4T (=KCTC 22661T =CCUG 58074T). An emended description of the genus Olleya is also provided.

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