scholarly journals Massilia arvi sp. nov., isolated from fallow-land soil previously cultivated with Brassica oleracea, and emended description of the genus Massilia

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3690-3696 ◽  
Author(s):  
Hina Singh ◽  
Juan Du ◽  
KyungHwa Won ◽  
Jung-Eun Yang ◽  
ChangShik Yin ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Brassica Oleracea ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Fallow Land ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

A novel bacterial strain, designated THG-RS2OT, was isolated from fallow-land soil previously cultivated with Brassica oleracea in Yongin, South Korea. Cells were Gram-stain-negative, aerobic, non-motile rods, catalase- and oxidase-positive. Strain THG-RS2OT grew optimally at 25–37 °C, at pH 7.0 and in the absence of NaCl. 16S rRNA gene sequence analysis demonstrated that strain THG-RS2OT shows highest sequence similarity with Massilia kyonggiensis KACC 17471T followed by Massilia aerilata KACC 12505T, Massilia niastensis KACC 12599T, Massilia tieshanensis KACC 14940T and Massilia haematophila KCTC 32001T. Levels of DNA–DNA relatedness between strain THG-RS2OT and the closest phylogenetic neighbours were below 55.0 % and the DNA G+C content of strain THG-RS2OT was 63.2 mol%. Major fatty acids were C16 : 0, cyclo-C17 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The major respiratory quinone was identified as ubiquonone-8 and predominant polar lipids were determined to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Characterization by 16S rRNA gene sequence analysis, DNA–DNA hybridization, ubiquinone, polar lipid, fatty acid composition, and physiological and biochemical parameters revealed that strain THG-RS2OT represents a novel species of the genus Massilia. Hence, the present study describes a novel species for which the name Massilia arvi sp. nov. is proposed. The type strain is THG-RS2OT ( = KCTC 42609T = CCTCC AB 2015115T).

scholarly journals Planococcus stackebrandtii sp. nov., isolated from a cold desert of the Himalayas, India

2005 ◽  
Vol 55 (1) ◽  
pp. 91-94 ◽  
Author(s):  
S. Mayilraj ◽  
G. S. Prasad ◽  
K. Suresh ◽  
H. S. Saini ◽  
S. Shivaji ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cold Desert ◽  
Gene Sequence Analysis

The taxonomic position of a bacterium isolated from a cold desert of the Himalayas, India, was analysed by using a polyphasic approach. The isolated strain, designated K22-03T, had phenotypic characteristics that matched those of the genus Planococcus and it represents a novel species. The almost-complete 16S rRNA gene sequence (1464 bases) of the novel strain was compared with those of previously studied Planococcus type strains and confirmed that the strain belongs to the genus Planococcus. 16S rRNA gene sequence analysis indicated that strain K22-03T differs from all other species of Planococcus by at least 2·5 %. DNA–DNA hybridization showed that it had low genomic relatedness with Planomicrobium mcmeekinii (MTCC 3704T, 23 %), Planococcus psychrophilus (MTCC 3812T, 61 %), Planococcus antarcticus (MTCC 3854T, 45 %) and Planomicrobium okeanokoites (MTCC 3703T, 51 %), the four species with which it was most closely related based on 16S rRNA gene sequence analysis (97–97·5 % similarity). Therefore, strain K22-03T should be recognized as a novel species, for which the name Planococcus stackebrandtii sp. nov. is proposed. The type strain is K22-03T (=MTCC 6226T=DSM 16419T=JCM 12481T).

scholarly journals Echinicola vietnamensis sp. nov., a member of the phylum Bacteroidetes isolated from seawater

2007 ◽  
Vol 57 (4) ◽  
pp. 761-763 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Seung Bum Kim ◽  
Bart Hoste ◽  
Dong Sung Shin ◽  
Irina A. Beleneva ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Taxonomic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

The taxonomic position of a novel marine, heterotrophic, gliding, halotolerant and light-pink-pigmented bacterium, designated strain KMM 6221T, was examined by using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain KMM 6221T is affiliated with the genus Echinicola, a member of the phylum Bacteroidetes, with levels of similarity of 94.7–95.0 % to strains of Echinicola pacifica. Growth of strain KMM 6221T was observed with 0–15 % NaCl and at 6–44 °C. The DNA G+C content of strain KMM 6221T was 45.9 mol%. On the basis of molecular distinctiveness supported by phenotypic and chemotaxonomic data, strain KMM 6221T is considered to represent a novel species of the genus Echinicola, for which the name Echinicola vietnamensis sp. nov. is proposed. The type strain is KMM 6221T (=DSM 17526T=LMG 23754T).

scholarly journals Nocardia araoensis sp. nov. and Nocardia pneumoniae sp. nov., isolated from patients in Japan

2004 ◽  
Vol 54 (6) ◽  
pp. 2025-2029 ◽  
Author(s):  
Akiko Kageyama ◽  
Katsukiyo Yazawa ◽  
Akira Mukai ◽  
Tadahiro Kohara ◽  
Kazuko Nishimura ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Dna Relatedness ◽  
Gene Sequence Analysis

Two actinomycete strains isolated from two patients with lung nocardiosis between 1995 and 1997 in Japan were assigned to novel species of the genus Nocardia based on morphological and chemical criteria. Comparative 16S rRNA gene sequence analysis of the two strains revealed that they belong to the genus Nocardia and are most closely related to the species Nocardia beijingensis. Determination of DNA–DNA relatedness indicated that these strains could be assigned to two novel species. Based on their phenotypic and phylogenetic characters, two novel species of the genus Nocardia are proposed: Nocardia araoensis sp. nov. for IFM 0575T (=NBRC 100135T=JCM 12118T=DSM 44729T) and Nocardia pneumoniae sp. nov. for IFM 0784T (=NBRC 100136T=JCM 12119T=DSM 44730T).

scholarly journals Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

scholarly journals Parabacteroides johnsonii sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (2) ◽  
pp. 293-296 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Maki Kitahara ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Faeces ◽  
Gene Sequence Analysis

A bacterial strain isolated from human faeces, M-165T, was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile, menaquinone profile and phylogenetic position (based on 16S rRNA gene sequence analysis). A 16S rRNA gene sequence analysis showed that the isolate was a member of the genus Parabacteroides. Strain M-165T was closely related to Parabacteroides merdae strains, showing 98 % sequence similarity. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative, rod-shaped and was able to grow on media containing 20 % bile. Although the phenotypic characteristics of the strain M-165T were similar to those of P. merdae, the isolate could be differentiated from P. merdae by means of API 20A tests for l-arabinose and l-rhamnose fermentation. DNA–DNA hybridization experiments revealed the genomic distinctiveness of the novel strain with respect to P. merdae JCM 9497T (⩽60 % DNA–DNA relatedness). The DNA G+C content of the strain is 47.6 mol%. On the basis of these data, strain M-165T represents a novel species of the genus Parabacteroides, for which the name Parabacteroides johnsonii sp. nov. is proposed. The type strain is M-165T (=JCM 13406T=DSM 18315T).

scholarly journals Phoenix 2: A locally installable large-scale 16S rRNA gene sequence analysis pipeline with Web interface

2013 ◽  
Vol 167 (4) ◽  
pp. 393-403 ◽  
Author(s):  
Jung Soh ◽  
Xiaoli Dong ◽  
Sean M. Caffrey ◽  
Gerrit Voordouw ◽  
Christoph W. Sensen
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Large Scale ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Web Interface ◽  
Rrna Gene Sequence ◽  
Analysis Pipeline ◽  
Gene Sequence Analysis

scholarly journals Micrococcus lactis sp. nov., isolated from dairy industry waste

2011 ◽  
Vol 61 (12) ◽  
pp. 2832-2836 ◽  
Author(s):  
Chittpurna ◽  
Pradip K. Singh ◽  
Dipti Verma ◽  
Anil Kumar Pinnaka ◽  
Shanmugam Mayilraj ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Dairy Industry ◽  
Effluent Treatment ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

A Gram-positive, yellow-pigmented, actinobacterial strain, DW152T, was isolated from a dairy industry effluent treatment plant. 16S rRNA gene sequence analysis indicated that strain DW152T exhibited low similarity with many species with validly published names belonging to the genera Micrococcus and Arthrobacter. However, phenotypic properties including chemotaxonomic markers affiliated strain DW152T to the genus Micrococcus. Strain DW152T had ai-C15 : 0 and i-C15 : 0 as major cellular fatty acids, and MK-8(H2) as the major menaquinone. The cell-wall peptidoglycan of strain DW152T had l-lysine as the diagnostic amino acid and the type was A4α. The DNA G+C content of strain DW152T was 68.0 mol%. In 16S rRNA gene sequence analysis, strain DW152T exhibited significant similarity with Micrococcus terreus NBRC 104258T, but the mean value of DNA–DNA relatedness between these strains was only 42.3 %. Moreover, strain DW152T differed in biochemical and chemotaxonomic characteristics from M. terreus and other species of the genus Micrococcus. Based on the above differences, we conclude that strain DW152T should be treated as a novel species of the genus Micrococcus, for which the name Micrococcus lactis sp. nov. is proposed. The type strain of Micrococcus lactis sp. nov. is DW152T ( = MTCC10523T  = DSM 23694T).

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