Pedobacter ginsengiterrae sp. nov., isolated from soil of a ginseng field

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1273-1279 ◽  
Author(s):  
Van-An Hoang ◽  
Yeon-Ju Kim ◽  
Ngoc-Lan Nguyen ◽  
Jin-Woo Min ◽  
Deok-Chun Yang
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Pink Pigment ◽  
Motile By Gliding

A Gram-stain-negative, oxidase- and catalase-positive bacterial strain that was motile by gliding and produced a pink pigment, designated DCY49T, was isolated from soil of a ginseng field in a mountainous region of Chungbuk province, South Korea. 16S rRNA gene sequence analysis revealed that strain DCY49T belonged to the genus Pedobacter (93.0–96.3 % similarity). Strain DCY49T contained MK-7 as the predominant menaquinone. The major fatty acids were summed feature 3 (containing C16 : 1ω7c, C16 : 1ω6c and/or iso-C15 : 0 2-OH), iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0, and the main polar lipid was phosphatidylethanolamine. The G+C content of the genomic DNA of strain DCY49T was 40.5 mol%. Strain DCY49T differed from related Pedobacter species by a number of phenotypic characteristics. On the basis of data from the present polyphasic study, strain DCY49T is described as representing a novel species of the genus Pedobacter , for which the name Pedobacter ginsengiterrae sp. nov. is proposed. The type strain is DCY49T ( = KCTC 23317T = JCM 17338T).

scholarly journals Sphingobacterium hungaricum sp. nov. a novel species on the borderline of the genus Sphingobacterium

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Ákos Tóth ◽  
Rózsa Máté ◽  
József Kutasi ◽  
Erika Tóth ◽  
Károly Bóka ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-reaction-negative bacterial strain, designated Kb22T, was isolated from agricultural soil and characterized using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain shows highest similarity (94.39 %) to Sphingobacterium nematocida M-SX103T. The highest average nucleotide identity value (71.83 %) was found with Sphingobacterium composti T5-12T, and the highest amino acid identity value (66.65 %) was found with Sphingobacterium olei HAL-9T. Cells are aerobic, non-motile rods. The isolate was found to be positive for catalase and oxidase tests. The assembled genome of strain Kb22T has a total length of 4,06 Mb, the DNA G+C content is 38.1 mol%. The only isoprenoid quinone is menaquinone 7 (MK-7). The major fatty acids are iso-C15:0 (28.4%), summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) (25.7 %) and iso-C17:0 3-OH (19.7 %). Based on phenotypic characteristics and phylogenetic results, it is concluded that strain Kb22T is a member of the genus Sphingobacterium and represents a novel species for which the name Sphingobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb22T (=LMG 31574T=NCAIM B.02638T).

Sphingomonas kyungheensis sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3848-3853 ◽  
Author(s):  
Heung-Min Son ◽  
Jung-Eun Yang ◽  
YongJin Park ◽  
Chang-Kyun Han ◽  
Song-Gun Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Family

A bacterial strain THG-B283T, which has β-glucosidase activity, was isolated from soil of a ginseng field. Cells were Gram-reaction-negative, oxidase- and catalase-positive, aerobic, motile with one polar flagellum and rod-shaped. The strain was subjected to a polyphasic taxonomic study. Strain THG-B283T grew optimally at around pH 7.0, at 25–28 °C and in the absence of NaCl on R2A agar. 16S rRNA gene sequence analysis revealed that strain THG-B283T belongs to the family Sphingomonadaceae and is closely related to Sphingomonas melonis DAPP-PG 224T (98.2 %), S. aquatilis JSS7T (98.1 %), S. insulae DS-28T (97.6 %), S. mali IFO 15500T (97.1 %) and S. pruni IFO 15498T (97.0 %). Strain THG-B283T contained Q-10 as the predominant ubiquinone. The major fatty acids included summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c, C14 : 0 2-OH and C16 : 0. The DNA G+C content was 72.2 mol%. The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipid, diphosphatidylglycerol, an unidentified glycolipid, unidentified aminolipids, an unidentified phospholipid and unidentified lipids. Genomic and chemotaxonomic data supported the affiliation of strain THG-B283T to the genus Sphingomonas . DNA–DNA relatedness between strain THG-B283T and its closest phylogenetic neighbours was below 23 %. On the basis of phenotypic, phylogenetic and genetic data, strain THG-B283T represents a novel species of genus Sphingomonas , for which the name Sphingomonas kyungheensis sp. nov. is proposed. The type strain is THG-B283T ( = KACC 16224T = LMG 26582T).

Duganella sacchari sp. nov. and Duganella radicis sp. nov., two novel species isolated from rhizosphere of field-grown sugar cane

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1126-1131 ◽  
Author(s):  
M. Madhaiyan ◽  
S. Poonguzhali ◽  
V. S. Saravanan ◽  
K. Hari ◽  
K.-C. Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

Two strains, designated Sac-22T and Sac-41T, were isolated from rhizosphere soil and rhizoplane of field-grown sugar cane clone Co86032. Comparative 16S rRNA gene sequence analysis showed a clear affiliation of these two bacteria with the class Betaproteobacteria , their closest relatives being Pseudoduganella violaceinigra and Duganella zoogloeoides with 16S rRNA gene sequence pairwise similarities of 96.4–97.2 % to the two novel strains. Strains Sac-22T and Sac-41T shared a 16S rRNA gene sequence similarity value of 97.6 %. Cells of the two strains were Gram-reaction-negative, aerobic, motile and rod-shaped. Ubiquinone (Q-8) was the respiratory quinone and the predominant polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The main cellular fatty acids were C16 : 0, C16 : 1ω7c/iso-C15 : 0 2-OH, C17 : 0 cyclo, C10 : 0 3-OH and C12 : 0. The DNA G+C content of the genomic DNA was 56.4 mol% for strain Sac-22T and 54.9 mol% for strain Sac-41T. Based on the results of 16S rRNA gene sequence analysis and physiological and biochemical characterization, that differentiated strains Sac-22T and Sac-41T from all recognized species of the genus Duganella , it was concluded that strains represent two novel species in the genus Duganella for which the names Duganella sacchari sp. nov. (type strain Sac-22T = KCTC 22381T = NCIMB 14475T) and Duganella radicis sp. nov. (type strain Sac-41T = KCTC 22382T = NCIMB 14476T) are proposed.

scholarly journals Actinoplanes lutulentus sp. nov., isolated from mucky soil in China

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1782-1788 ◽  
Author(s):  
Ruixia Gao ◽  
Chongxi Liu ◽  
Junwei Zhao ◽  
Feiyu Jia ◽  
Chuang Li ◽  
...  
Keyword(s):  
Type Species ◽  
North China ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type

A novel actinomycete, designated strain NEAU-GRX6T, was isolated from mucky soil collected from a stream of Jinlong Mountain in Harbin, Heilongjiang Province, north China, and characterized using a polyphasic approach. The isolate formed irregular sporangia containing motile sporangiospores on the substrate mycelium. The whole-cell sugars were xylose, glucose and galactose. The predominant menaquinones were MK-9(H6), MK-10(H4) and MK-9(H4). The major fatty acids were C16 : 0, C15 : 0, C18 : 1ω9c, C17 : 1ω7c and C18 : 0. The phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The DNA G+C content was 67 mol%. 16S rRNA gene sequence similarity studies showed that strain NEAU-GRX6T belonged to the genus Actinoplanes , being most closely related to Actinoplanes palleronii IFO 14916T (97.80 % similarity) and Actinoplanes missouriensis NBRC 102363T (97.76 %). However, the low observed levels of DNA–DNA relatedness allowed the isolate to be differentiated from the above-mentioned species of the genus Actinoplanes . Moreover, strain NEAU-GRX6T could also be distinguished from A. palleronii IFO 14916T and A. missouriensis NBRC 102363T by phenotypic characteristics. Therefore, it is proposed that strain NEAU-GRX6T represents a novel species of the genus Actinoplanes , for which the name Actinoplanes lutulentus sp. nov. is proposed. The type strain is strain NEAU-GRX6T ( = CGMCC 4.7090T = DSM 45883T).

Weissella diestrammenae sp. nov., isolated from the gut of a camel cricket (Diestrammena coreana)

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2951-2956 ◽  
Author(s):  
Sei Joon Oh ◽  
Na-Ri Shin ◽  
Dong-Wook Hyun ◽  
Pil Soo Kim ◽  
Joon Yong Kim ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod- or coccoid-shaped bacterium, designated strain ORY33T, was isolated from the gut of a camel cricket (Diestrammena coreana). The 16S rRNA gene sequence analysis showed that strain ORY33T belonged to the genus Weissella , with highest sequence similarity to Weissella koreensis S-5623T (97.7 %). The strain grew optimally at 30 °C and pH 7 in the presence of 0 % (w/v) NaCl. Catalase and oxidase activities were negative. The genomic DNA G+C content of strain ORY33T was 45.1 mol%. DNA–DNA hybridization values between strain ORY33T and closely related members of the genus Weissella were less than 27 %. The major fatty acids of strain ORY33T were C18 : 1ω9c, C16 : 0 and C14 : 0. Based on these phenotypic, phylogenetic and genotypic analyses, strain ORY33T represents a novel species belonging to the genus Weissella , for which the name Weissella diestrammenae sp. nov. is proposed. The type strain is ORY33T ( = KACC 16890T = JCM 18559T).

Anaerostipes rhamnosivorans sp. nov., a human intestinal, butyrate-forming bacterium

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 787-793 ◽  
Author(s):  
Thi Phuong Nam Bui ◽  
Willem M. de Vos ◽  
Caroline M. Plugge
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Physiological And Biochemical

A novel butyrate-producing bacterium, strain 1y-2T, was isolated from a stool sample of a 1-year-old, healthy Dutch infant. The isolate was obtained by using lactate and acetate as sources of carbon and energy. The strain was Gram-variable, strictly anaerobic and spore-forming and formed curly rod-shaped cells that fermented glucose into butyrate, lactate, formate and acetate as main products. The DNA G+C content of the strain was 44.5 mol% and its major cellular fatty acids were C12 : 0, iso-C19 : 1 I and C16 : 0. Strain 1y-2T was related to Anaerostipes caccae DSM 14662T based on 16S rRNA gene sequence analysis, with 3 % divergence, but hybridization studies of their genomic DNA revealed only 33 % relatedness. Moreover, strain 1y-2T showed marked physiological and biochemical differences from known species of the genus Anaerostipes . Based on phylogenetic, chemotypic and phenotypic criteria, we propose that strain 1y-2T should be classified in the genus Anaerostipes within a novel species, Anaerostipes rhamnosivorans sp. nov. The type strain is 1y-2T ( = DSM 26241T = KCTC 15316T).

scholarly journals Lysobacter panacisoli sp. nov., isolated from ginseng soil

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2193-2197 ◽  
Author(s):  
Jung-Hye Choi ◽  
Ji-Hye Seok ◽  
Ju-Hee Cha ◽  
Chang-Jun Cha
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Ginseng Soil

A novel bacterial strain, designated CJ29T, was isolated from ginseng soil of Anseong in South Korea. Cells of strain CJ29T were Gram-stain-negative, facultatively anaerobic, rod-shaped and non-motile. Strain CJ29T grew optimally at 28–30 °C and pH 7.0. Based on 16S rRNA gene sequence analysis, strain CJ29T was shown to belong to the genus Lysobacter within the class Gammaproteobacteria and was related most closely to Lysobacter soli DCY21T (98.5 % similarity) and Lysobacter niastensis GH41-7T (98.2 %). DNA–DNA relatedness between strain CJ29T and its closest relatives was below 55.6 %. The predominant cellular fatty acids of strain CJ29T were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major isoprenoid quinone was ubiquinone 8 (Q-8). The G+C content of the genomic DNA was 65.6 mol%. Phenotypic, genotypic and phylogenetic characteristics strongly supported the differentiation of strain CJ29T from related species of the genus Lysobacter . On the basis of data from this polyphasic taxonomic study, strain CJ29T is considered to represent a novel species of the genus Lysobacter , for which the name Lysobacter panacisoli sp. nov. is proposed. The type strain is CJ29T ( = KACC 17502T = JCM 19212T).

scholarly journals Pontibacter saemangeumensis sp. nov., isolated from seawater

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 565-569 ◽  
Author(s):  
Ji Young Kang ◽  
Yochan Joung ◽  
Jeesun Chun ◽  
Haneul Kim ◽  
Kiseong Joh ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Type Strains

A Gram-negative, rod-shaped, non-motile and pink bacterial strain, designated strain GCM0142T, was isolated from the confined seawater in the Saemangeum Tide Embankment of South Korea, and characterized using a polyphasic approach. 16S rRNA gene sequence analysis of strain GCM0142T indicated that the isolate belonged to the phylum Bacteroidetes and exhibited similarity levels of 94.0–96.4 % to the type strains of recognized Pontibacter species. Strain GCM0142T was oxidase- and catalase-positive. The major cellular fatty acids of the novel strain were summed feature 4 (comprising iso-C17 : 1I and/or anteiso-C17 : 1B, 36.8 %), iso-C15 : 0 (22.3 %) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 6.2 %). The DNA G+C content of strain GCM0142T was 48.9 mol% and the major quinone was MK-7. The polar lipid profile consisted of phosphatidylethanolamine, two unknown aminolipids (AL1–2), an unknown aminophospholipid, five unknown lipids (L1–5) and an unknown glycolipid. On the basis of the evidence presented, strain GCM0142T is considered to represent a novel species of the genus Pontibacter , for which the name Pontibacter saemangeumensis sp. nov. is proposed. The type strain is GCM0142T ( = KACC 16448T = JCM 17926T).

Microvirga vignae sp. nov., a root nodule symbiotic bacterium isolated from cowpea grown in semi-arid Brazil

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 725-730 ◽  
Author(s):  
Viviane Radl ◽  
Jean Luiz Simões-Araújo ◽  
Jakson Leite ◽  
Samuel Ribeiro Passos ◽  
Lindete Míria Vieira Martins ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Semi Arid

16S rRNA gene sequence analysis of eight strains (BR 3299T, BR 3296, BR 10192, BR 10193, BR 10194, BR 10195, BR 10196 and BR 10197) isolated from nodules of cowpea collected from a semi-arid region of Brazil showed 97 % similarity to sequences of recently described rhizobial species of the genus Microvirga . Phylogenetic analyses of four housekeeping genes (gyrB, recA, dnaK and rpoB), DNA–DNA relatedness and AFLP further indicated that these strains belong to a novel species within the genus Microvirga . Our data support the hypothesis that genes related to nitrogen fixation were obtained via horizontal gene transfer, as sequences of nifH genes were very similar to those found in members of the genera Rhizobium and Mesorhizobium , which are not immediate relatives of the genus Microvirga , as shown by 16S rRNA gene sequence analysis. Phenotypic traits, such as host range and carbon utilization, differentiate the novel strains from the most closely related species, Microvirga lotononidis , Microvirga zambiensis and Microvirga lupini . Therefore, these symbiotic nitrogen-fixing bacteria are proposed to be representatives of a novel species, for which the name Microvirga vignae sp. nov. is suggested. The type strain is BR3299T ( = HAMBI 3457T).

Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2588-2593 ◽  
Author(s):  
Bárbara Almeida ◽  
Ivone Vaz-Moreira ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
Gilda Carvalho ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11T, was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11T were Patulibacter ginsengiterrae CECT 7603T (96.8 % similarity), Patulibacter minatonensis DSM 18081T (96.6 %) and Patulibacter americanus DSM 16676T (96.6 %). Phenotypic characterization supports the inclusion of strain I11T within the genus Patulibacter (phylum Actinobacteria) . However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11T ( = DSM 25962T = CECT 8141T).

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