scholarly journals Rheinheimera nanhaiensis sp. nov., isolated from marine sediments, and emended description of the genus Rheinheimera Brettar et al. 2002 emend. Merchant et al. 2007

2011 ◽  
Vol 61 (5) ◽  
pp. 1016-1022 ◽  
Author(s):  
Hui-Juan Li ◽  
Xi-Ying Zhang ◽  
Yan-Jiao Zhang ◽  
Ming-Yang Zhou ◽  
Zhao-Ming Gao ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Cellular Fatty Acids ◽  
Emended Description ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, facultatively aerobic, oxidase- and catalase-positive, rod-shaped bacterium, designated strain E407-8T, was isolated from a sediment sample from the South China Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain E407-8T was affiliated with the genus Rheinheimera, sharing the highest sequence similarity with Rheinheimera pacifica KMM 1406T (97.5 %) and Rheinheimera aquimaris SW-353T (97.4 %) and showing less than 97 % sequence similarity to the type strains of other recognized Rheinheimera species. Levels of DNA–DNA relatedness of strain E407-8T to R. pacifica DSM 17616T and R. aquimaris JCM 14331T were 25.2 % (25.3 % in the duplicate measurement) and 9.4 % (6.5 %), respectively. The bacterium could grow at 10–48 °C (optimum 37 °C) and in the presence of 0–8 % (w/v) NaCl (optimum 0.5–2.5 %). The major cellular fatty acids of strain E407-8T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C17 : 1ω8c, C16 : 0 and C18 : 1ω7c. The predominant respiratory quinone was ubiquinone Q-8. The DNA G+C content was 51.0 mol%. Based on the results of our polyphasic taxonomic study, strain E407-8T represents a novel species in the genus Rheinheimera, for which the name Rheinheimera nanhaiensis sp. nov. is proposed. The type strain is E407-8T ( = CCTCC AB 209089T  = KACC 14030T). An emended description of the genus Rheinheimera Brettar et al. 2002 emend. Merchant et al. 2007 is also proposed.

scholarly journals Tumebacillus ginsengisoli sp. nov., isolated from soil of a ginseng field

2011 ◽  
Vol 61 (7) ◽  
pp. 1715-1719 ◽  
Author(s):  
Sang-Hoon Baek ◽  
Yingshun Cui ◽  
Sun-Chang Kim ◽  
Chang-Hao Cui ◽  
Chengri Yin ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene

A Gram-reaction-positive, rod-shaped, spore-forming bacterium, designated Gsoil 1105T, was isolated from soil of a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the order Bacillales, showing the highest level of sequence similarity with respect to Tumebacillus permanentifrigoris Eur1 9.5T (94.6 %). The phylogenetic distances from other described species with validly published names within the order Bacillales were greater than 9.0 %. Strain Gsoil 1105T had a genomic DNA G+C content of 55.6 mol% and menaquinone 7 (MK-7) as the major respiratory quinone. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1105T represents a novel species of the genus Tumebacillus, for which the name Tumebacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 1105T ( = KCTC 13942T  = DSM 18389T).

scholarly journals Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.)

2010 ◽  
Vol 60 (1) ◽  
pp. 21-26 ◽  
Author(s):  
Rangasamy Anandham ◽  
Pandiyan Indiragandhi ◽  
Soon Wo Kwon ◽  
Tong Min Sa ◽  
Che Ok Jeon ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Sesamum Indicum ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Rhizosphere Soils ◽  
Cellular Fatty Acids ◽  
Gene Sequence Analysis

A facultatively chemolithoautotrophic, thiosulfate-oxidizing, Gram-negative, aerobic, motile, rod-shaped bacterial strain, designated ATSB16T, was isolated from rhizosphere soils of sesame (Sesamum indicum L.). 16S rRNA gene sequence analysis demonstrated that this strain was closely related to Pandoraea pnomenusa LMG 18087T (96.7 % similarity), P. pulmonicola LMG 18016T (96.5 %), P. apista LMG 16407T (96.2 %), P. norimbergensis LMG 18379T (96.1 %) and P. sputorum LMG 18819T (96.0 %). Strain ATSB16T shared 96.0–96.4 % sequence similarity with four unnamed genomospecies of Pandoraea. The major cellular fatty acids of the strain ATSB16T were C17 : 0 cyclo (33.0 %) and C16 : 0 (30.6 %). Q-8 was the predominant respiratory quinone. The major polar lipids were phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified aminophospholipids. Hydroxyputrescine and putrescine were the predominant polyamines. The genomic DNA G+C content of the strain was 64.0 mol%. On the basis of the results obtained from this study, strain ATSB16T represents a novel species of the genus Pandoraea, for which the name Pandoraea thiooxydans sp. nov. is proposed. The type strain is ATSB16T (=KACC 12757T =LMG 24779T).

scholarly journals Nocardia terpenica sp. nov., isolated from Japanese patients with nocardiosis

2007 ◽  
Vol 57 (7) ◽  
pp. 1456-1460 ◽  
Author(s):  
Yasutaka Hoshino ◽  
Kayo Watanabe ◽  
Soji Iida ◽  
Shin-ichi Suzuki ◽  
Takuji Kudo ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Japanese Patients ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Polyphasic Analysis ◽  
Type Strains ◽  
The 16S Rrna Gene

Two bacterial strains isolated from different hospitals in Japan were subjected to a polyphasic analysis. Strains IFM 0406 and IFM 0706T, producers of novel terpenoid antibiotics, were found to have morphological, biochemical, physiological and chemotaxonomic properties consistent with their classification in the genus Nocardia, except for the presence of MK-8(H4) as one of the predominant menaquinones in addition to the major menaquinone MK-8(H4ω-cyc). The 16S rRNA gene sequence similarity of strains IFM 0406 and IFM 0706T was 99.9 %, and the closest members of Nocardia to these strains were the type strains of Nocardia nova and Nocardia mexicana, showing similarity of 97.5 and 97.1 %, respectively. Based on their characteristic phenotypic and phylogenetic properties, a novel species of the genus Nocardia, Nocardia terpenica sp. nov. is proposed for the two strains. The type strain is IFM 0706T (=JCM 13033T=DSM 44935T=NBRC 100888T).

Rhodanobacter soli sp. nov., isolated from soil of a ginseng field

2010 ◽  
Vol 60 (12) ◽  
pp. 2935-2939 ◽  
Author(s):  
Thi Phuong Nam Bui ◽  
Yeon-Ju Kim ◽  
Hobin Kim ◽  
Deok-Chun Yang
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Respiratory Quinone ◽  
Yellow Pigments ◽  
Type Strains ◽  
The 16S Rrna Gene

Strain DCY45T was isolated from soil of a ginseng field in Pocheon Province, Korea. Strain DCY45T was Gram-negative, oxidase- and catalase-positive, motile and rod-shaped and produced yellow pigments on R2A agar. The organism grew optimally at 30 °C and at pH 7.0. The G+C content of the genomic DNA was 65.4 mol%. The predominant respiratory quinone was Q-8. The major fatty acids were iso-C17 : 1 ω9c, iso-C16 : 0 and iso-C15 : 0. Phylogenetic analysis based on the 16S rRNA gene sequence was used to determine the taxonomic position of strain DCY45T, which is most closely related to species of the genus Rhodanobacter, with similarity levels of 96.0–98.4 %; DNA–DNA relatedness with related strains was lower than 60 %. Strain DCY45T differed significantly from related type strains in phenotypic characteristics. On the basis of these phenotypic, genotypic and chemotaxonomic studies, strain DCY45T represents a novel species of the genus Rhodanobacter, for which the name Rhodanobacter soli sp. nov. is proposed. The type strain is DCY45T (=KCTC 22620T =JCM 16126T).

scholarly journals Planotetraspora silvatica sp. nov. and emended description of the genus Planotetraspora

2004 ◽  
Vol 54 (6) ◽  
pp. 2053-2056 ◽  
Author(s):  
Tomohiko Tamura ◽  
Takeshi Sakane
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Subtropical Forest ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Monophyletic Cluster ◽  
Aerial Hyphae ◽  
Emended Description ◽  
The 16S Rrna Gene

An actinomycete that developed sporangia containing four spores in a single row at the ends of short sporangiophores on branched aerial hyphae was isolated from subtropical forest soil. The isolate contained menaquinone MK-9(H4), glutamic acid, alanine and meso-diaminopimelic acid as cell-wall amino acids and madurose in the whole-cell hydrolysate. The 16S rRNA gene sequence indicated that the isolate formed a monophyletic cluster with Planotetraspora mira. On the basis of morphological and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species of the genus Planotetraspora is proposed, Planotetraspora silvatica sp. nov. (type strain, TT 00-51T=NBRC 100141T=DSM 44746T).

scholarly journals Paenibacillus algorifonticola sp. nov., isolated from a cold spring

2011 ◽  
Vol 61 (9) ◽  
pp. 2167-2172 ◽  
Author(s):  
Qi-Yong Tang ◽  
Na Yang ◽  
Jian Wang ◽  
Yu-Qing Xie ◽  
Biao Ren ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Cold Spring ◽  
Xinjiang Uyghur Autonomous Region ◽  
The 16S Rrna Gene

A Gram-stain-positive, endospore-forming, rod-shaped bacterium, designated XJ259T, was isolated from a cold spring sample from Xinjiang Uyghur Autonomous Region, China. The isolate grew optimally at 20–30 °C and pH 7.3–7.8. Comparative analysis of the 16S rRNA gene sequence showed that isolate XJ259T belonged phylogenetically to the genus Paenibacillus, and was most closely related to Paenibacillus xinjiangensis B538T (with 96.6 % sequence similarity), Paenibacillus glycanilyticus DS-1T (96.3 %) and Paenibacillus castaneae Ch-32T (96.1 %), sharing less than 96.0 % sequence similarity with all other members of the genus Paenibacillus. Chemotaxonomic analysis revealing menaquinone-7 (MK-7) as the major isoprenoid quinone, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phosphoglycolipids as the major cellular polar lipids, a DNA G+C content of 47.0 mol%, and anteiso-C15 : 0 and C16 : 0 as the major fatty acids supported affiliation of the new isolate to the genus Paenibacillus. Based on these data, isolate XJ259T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus algorifonticola sp. nov. is proposed. The type strain is XJ259T ( = CGMCC 1.10223T  = JCM 16598T).

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

2012 ◽  
Vol 62 (1) ◽  
pp. 13-17 ◽  
Author(s):  
Yong-Taek Jung ◽  
Soo-Young Lee ◽  
Won-Chan Choi ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, non-sporulating, non-flagellated rod, designated BR-9T, was isolated from soil collected on the Korean peninsula. Strain BR-9T grew optimally at pH 6.0–7.0, at 30 °C and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BR-9T belonged to the genus Pedobacter and clustered with Pedobacter insulae DS-139T and Pedobacter koreensis WPCB189T. Strain BR-9T exhibited 98.2 and 97.5 % 16S rRNA gene sequence similarity with P. insulae DS-139T and P. koreensis WPCB189T, respectively, and <96.7 % sequence similarity with the type strains of other species in the genus Pedobacter. Strain BR-9T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C content of strain BR-9T was 38.5 mol%. DNA–DNA relatedness between strain BR-9T and P. insulae DS-139T and P. koreensis KCTC 12536T was 3.4–4.2 %, which indicated that the isolate was genetically distinct from these type strains. Strain BR-9T was also distinguishable by differences in phenotypic properties. On the basis of the data presented, strain BR-9T is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter boryungensis sp. nov. is proposed. The type strain is BR-9T ( = KCTC 23344T  = CCUG 60024T).

scholarly journals Flavobacterium terrigena sp. nov., isolated from soil

2007 ◽  
Vol 57 (5) ◽  
pp. 947-950 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Jung-Sook Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Type Strains

A Gram-negative, rod-shaped, Flavobacterium-like bacterial strain, DS-20T, was isolated from soil from the island of Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-20T grew optimally at pH 6.5–7.0 and 25 °C. It contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1 ω9c as the major fatty acids. The DNA G+C content was 38.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-20T belonged to the genus Flavobacterium. Levels of 16S rRNA gene sequence similarity between strain DS-20T and the type strains of recognized Flavobacterium species were below 94.9 %. Strain DS-20T differed from phylogenetically related Flavobacterium species in several phenotypic characteristics. On the basis of its phenotypic and phylogenetic distinctiveness, strain DS-20T was classified in the genus Flavobacterium as representing a novel species, for which the name Flavobacterium terrigena sp. nov. is proposed. The type strain is DS-20T (=KCTC 12761T=DSM 17934T).

scholarly journals Kocuria koreensis sp. nov., isolated from fermented seafood

2010 ◽  
Vol 60 (1) ◽  
pp. 140-143 ◽  
Author(s):  
Eun-Jin Park ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Mi-Ja Jung ◽  
Kee-Sun Shin ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
The 16S Rrna Gene

A Gram-positive, aerobic, non-motile and coccoid actinobacterium, designated P31T, was isolated from a traditional, fermented seafood. The strain was catalase-positive and oxidase-negative. Cells grew in the presence of 0–15.0 % (w/v) NaCl, and at pH 5–10 and 15–37 °C. Major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. Strain P31T contained MK-7 as the predominant menaquinone. The DNA G+C content of the genomic DNA of strain P31T was 65.2 mol%. A phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain P31T was most closely related to Kocuria kristinae DSM 20032T, with 96.9 % similarity, and these two strains clustered together in constructed phylogenetic trees. The DNA–DNA hybridization value between strain P31T and K. kristinae DSM 20032T was 21.1 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it is suggested that strain P31T represents a novel species of the genus Kocuria, for which the name Kocuria koreensis sp. nov. is proposed. The type strain is P31T (=KCTC 19595T=JCM 15915T).

scholarly journals Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3′-dithiodipropionic acid

2006 ◽  
Vol 56 (6) ◽  
pp. 1305-1310 ◽  
Author(s):  
Jan Hendrik Wübbeler ◽  
Tina Lütke-Eversloh ◽  
Stefanie Van Trappen ◽  
Peter Vandamme ◽  
Alexander Steinbüchel
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Alcaligenes Faecalis ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Rrna Gene Sequence ◽  
Nearest Neighbours ◽  
The 16S Rrna Gene

In this study, a novel betaproteobacterium, strain DPN7T, was isolated under mesophilic conditions from compost because of its capacity to utilize the organic disulfide 3,3′-dithiodipropionic acid. Analysis of the 16S rRNA gene sequence of strain DPN7T revealed 98.5 % similarity to that of Tetrathiobacter kashmirensis LMG 22695T. Values for sequence similarity to members of the genera Alcaligenes, Castellaniella and Taylorella, the nearest neighbours of the genus Tetrathiobacter, were about 95 % or less. The DNA G+C content of strain DPN7T was 55.1 mol%. The level of DNA–DNA hybridization between strain DPN7T and T. kashmirensis LMG 22695T was 41 %, whereas it was much lower between strain DPN7T and Alcaligenes faecalis LMG 1229T (7 %) or Castellaniella defragrans LMG 18538T (5 %). This genotypic divergence was supported by differences in biochemical and chemotaxonomic characteristics. For this reason, and because of the differences in the protein and fatty acid profiles, strain DPN7T should be classified within a novel species of Tetrathiobacter, for which the name Tetrathiobacter mimigardefordensis sp. nov. is proposed. The type strain is strain DPN7T (=DSM 17166T=LMG 22922T).

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