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 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 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).

scholarly journals Marichromatium fluminis sp. nov., a slightly alkaliphilic, phototrophic gammaproteobacterium isolated from river sediment

2010 ◽  
Vol 60 (5) ◽  
pp. 1103-1107 ◽  
Author(s):  
K. Sucharita ◽  
E. Shiva Kumar ◽  
Ch. Sasikala ◽  
B. B. Panda ◽  
S. Takaichi ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Dna Base Composition ◽  
Dna Base ◽  
Gene Sequence Analysis

An anoxygenic, phototrophic gammaproteobacterium designated strain JA418T was isolated from a sediment sample collected from the Baitarani River, Orissa, India. The bacterium was a Gram-negative, motile rod with a single polar flagellum. Bacteriochlorophyll a and rhodopin were the major photosynthetic pigments. The organism grew best at slightly alkaline pH (8–8.5) and lacked chemotrophic growth. The major fatty acids were C16 : 0, C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω7c. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain JA418T clusters with species of the genus Marichromatium belonging to the class Gammaproteobacteria. The highest 16S rRNA gene sequence similarities of strain JA418T were found with the type strains of Marichromatium gracile (95.9 %), Marichromatium indicum (95.6 %), Marichromatium purpuratum (95.5 %) and Marichromatium bheemlicum (95.6 %). The DNA base composition of strain JA418T was 71.4 mol% G+C (by HPLC). Based on the 16S rRNA gene sequence analysis and physiological and chemotaxonomic characteristics, strain JA418T is sufficiently different from other Marichromatium species to merit the description of a novel species, Marichromatium fluminis sp. nov., to accommodate it. The type strain is JA418T (=KCTC 5717T =NBRC 105221T).

scholarly journals Nonomuraea wenchangensis sp. nov., isolated from mangrove rhizosphere soil

2011 ◽  
Vol 61 (6) ◽  
pp. 1304-1308 ◽  
Author(s):  
Fan Wang ◽  
Xiao-Xiong Xu ◽  
Zhi Qu ◽  
Cheng Wang ◽  
Hai-Peng Lin ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

Strain 210417T, which forms highly branched substrate and aerial mycelia, is a Gram-positive, aerobic and non-motile actinomycete isolated from mangrove rhizosphere soil. 16S rRNA gene sequence analysis showed that the strain should be classified in the genus Nonomuraea, being most closely related to the type strains of Nonomuraea coxensis (99.6 %) and Nonomuraea bangladeshensis (99.3 %). Chemotaxonomic properties [madurose as the major sugar in the cell wall; meso-diaminopimelic acid and N-acetylmuramic acid in the peptidoglycan; MK-9(H4) as the major menaquinone; iso-C16 : 0 (24.1 %) as major fatty acid; and phospholipid pattern type IV] are consistent with the assignment of strain 210417T to the genus Nonomuraea. Strain 210417T could be differentiated from the closely related species N. coxensis and N. bangladeshensis by morphological, physiological, biochemical and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA–DNA hybridization results. It is therefore proposed that strain 210417T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea wenchangensis sp. nov. is given; the type strain is 210417T ( = CGMCC 4.5598T  = DSM 45477T).

scholarly journals Pseudosphingobacterium domesticum gen. nov., sp. nov., isolated from home-made compost

2007 ◽  
Vol 57 (7) ◽  
pp. 1535-1538 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
M. Fernanda Nobre ◽  
Olga C. Nunes ◽  
Célia M. Manaia
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family

A bacterial strain, DC-186T, isolated from home-made compost, was characterized for its phenotypic and phylogenetic properties. The isolate was a Gram-negative rod that was able to grow at 15–36 °C and pH 5.5–8.0. Strain DC-186T was positive in tests for catalase, oxidase and β-galactosidase activities and aesculin hydrolysis. The predominant fatty acids were the summed feature C16 : 1/iso-C15 : 0 2-OH (42 %) and iso-C15 : 0 (26 %), the major respiratory quinone was menaquinone-7 and the genomic DNA G+C content was 42 mol%. 16S rRNA gene sequence analysis and phenetic characterization indicated that this organism belongs to the phylum Bacteroidetes and revealed its affiliation to the family Sphingobacteriaceae. Of recognized taxa, strain DC-186T was most closely related to Sphingobacterium daejeonense (90 % sequence similarity) based on 16S rRNA gene sequence analysis. The low 16S rRNA gene sequence similarity with other recognized taxa and the identification of distinctive phenetic features for this isolate support the definition of a new genus within the family Sphingobacteriaceae. The name Pseudosphingobacterium domesticum gen. nov., sp. nov. is proposed, with strain DC-186T (=CCUG 54353T=LMG 23837T) as the type strain.

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