scholarly journals Two novel species, Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils

2006 ◽  
Vol 56 (5) ◽  
pp. 947-951 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Youn-Kyung Baek ◽  
Seung-Hee Yoo ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Bacterial Strains ◽  
Lysobacter Enzymogenes ◽  
Greenhouse Soils ◽  
Taxonomic Studies ◽  
Type Strains

Two bacterial strains were isolated from greenhouse soils of Daejeon and Yangpyeong regions in Korea. The strains, designated GH1-9T and GH19-3T, were Gram-negative and aerobic, with rod-shaped cells. Their DNA G+C contents were 61.7 and 67.3 mol%, respectively. The major fatty acids of strain GH1-9T were iso-C16 : 0, iso-C15 : 0, iso-C14 : 0, iso-C17 : 1 ω9c and iso-C11 : 0 3-OH and the major components of strain GH19-3T were iso-C16 : 0, iso-C15 : 0, C16 : 1 ω7c alcohol, iso-C17 : 1 ω9c and iso-C11 : 0 3-OH. None of the species of the genus Lysobacter with validly published names showed 16S rRNA gene sequence similarity values of more than 97 % with respect to the novel isolates. The closest sequence similarity of strain GH1-9T was with Lysobacter concretionis DSM 16239T (96.4 %), whereas strain GH19-3T showed the highest sequence similarity with Lysobacter enzymogenes DSM 2043T (96.6 %). Polyphasic taxonomic studies indicated that the two strains should be classified as representing novel members of the genus Lysobacter. The names Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov. are proposed, with strains GH1-9T (=KACC 11406T=DSM 17634T) and GH19-3T (=KACC 11407T=DSM 17635T), respectively, as the type strains.

scholarly journals Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea

2007 ◽  
Vol 57 (3) ◽  
pp. 548-551 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Min-Kyeong Kim ◽  
Seung-Hee Yoo ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Bacterial Strains ◽  
Lysobacter Enzymogenes ◽  
Gene Sequence Analysis ◽  
Greenhouse Soils

Two bacterial strains, designated GH34-4T and GH41-7T, were isolated from greenhouse soil cultivated with cucumber. The bacteria were strictly aerobic, Gram-negative, rod-shaped and oxidase- and catalase-positive. 16S rRNA gene sequence analysis indicated that these strains belong to the genus Lysobacter within the Gammaproteobacteria. Strain GH34-4T showed highest sequence similarity to Lysobacter yangpyeongensis GH19-3T (97.5 %) and Lysobacter koreensis Dae16T (96.4 %), and strain GH41-7T showed highest sequence similarity to Lysobacter antibioticus DSM 2044T (97.5 %), Lysobacter enzymogenes DSM 2043T (97.5 %) and Lysobacter gummosus ATCC 29489T (97.4 %). Levels of DNA–DNA relatedness indicated that strains GH34-4T and GH41-7T represented species clearly different from L. yangpyeongensis, L. antibioticus, L. enzymogenes and L. gummosus. The major cellular fatty acids of strains GH34-4T and GH41-7T were iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c, and the major isoprenoid quinone was Q-8. The DNA G+C contents of GH34-4T and GH41-7T were 62.5 and 66.6 mol%, respectively. On the basis of the polyphasic taxonomic data presented, it is evident that each of these strains represents a novel species of the genus Lysobacter, for which the names Lysobacter niabensis sp. nov. (type strain GH34-4T=KACC 11587T=DSM 18244T) and Lysobacter niastensis sp. nov. (type strain GH41-7T=KACC 11588T=DSM 18481T) are proposed.

Lactobacillus odoratitofui sp. nov., isolated from stinky tofu brine

2010 ◽  
Vol 60 (12) ◽  
pp. 2903-2907 ◽  
Author(s):  
Shiou-Huei Chao ◽  
Masae Sasamoto ◽  
Yuko Kudo ◽  
Junji Fujimoto ◽  
Ying-Chieh Tsai ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Positive Staining ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Dna Reassociation ◽  
Type Strains

Three Gram-positive-staining strains isolated from fermented stinky tofu brine were rod-shaped, non-motile, asporogenous, facultatively anaerobic, heterofermentative and did not exhibit catalase activity. Comparative analyses of 16S rRNA, rpoA and pheS gene sequences demonstrated that the novel strains were members of the genus Lactobacillus. On the basis of 16S rRNA gene sequence similarity, the type strains of Lactobacillus collinoides (98.6 %), Lactobacillus paracollinoides (98.6 %) and Lactobacillus similis (99.6 %) were the closest neighbours. However, DNA–DNA reassociation values with these strains were less than 10 %. The phenotypic and genotypic features demonstrated that these isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillus odoratitofui sp. nov. is proposed. The type strain is YIT 11304T (=JCM 15043T =BCRC 17810T =DSM 19909T).

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).

scholarly journals Micromonospora fluostatini sp. nov., isolated from marine sediment

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4417-4423 ◽  
Author(s):  
Wongsakorn Phongsopitanun ◽  
Takuji Kudo ◽  
Mihoko Mori ◽  
Kazuro Shiomi ◽  
Pattama Pittayakhajonwut ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Actinomycete Strain ◽  
Sequence Similarity Analysis ◽  
Type Strains

The novel actinomycete strain PWB-003T, which produced fluostatins B and C antibiotics, was isolated from nearshore sediment collected from Panwa Cape, Phuket Province, Thailand. Data from the present polyphasic study indicated that strain PWB-003T represented a member of the genus Micromonospora. It produced single spores on substrate mycelia and contained meso-diaminopimelic acid in the cell-wall peptidoglycan. Whole-cell hydrolysate contained ribose, xylose, arabinose, mannose and glucose. The predominant menaquinone was MK-10 (H4). Cellular fatty acids comprised C18 : 1ω9c, iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C17 : 0. On the basis of 16S rRNA gene sequence similarity analysis, the novel strain was closely related to Micromonospora eburnea LK2-10T (99.38 %), Micromonospora chaiyaphumensis MC5-1T (99.16 %), Micromonospora yangpuensis FXJ6.011T (98.97 %), Micromonospora echinaurantiaca DSM 43904T (98.97 %), Micromonospora pallida DSM 43817T (98.97 %), Micromonospora sagamiensis DSM 43912T and Micromonospora auratinigra JCM 12357T (both 98.97 %). The G+C content of the DNA was 74.5 mol%. DNA–DNA relatedness values among strain PWB-003T and related type strains ranged from 11.3 ± 1.3 to 38.8 ± 1.1 %. On the basis of these observations, strain PWB-003T could be distinguished from its closely related type strains and is considered to represent a novel species of the genus Micromonospora, for which the name Micromonospora fluostatini sp. nov. (type strain PWB-003T = JCM 30529T = PCU 341T = TISTR 2345T) is proposed.

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 Marinomonas ostreistagni sp. nov., isolated from a pearl-oyster culture pond in Sanya, Hainan Province, China

2006 ◽  
Vol 56 (10) ◽  
pp. 2271-2275 ◽  
Author(s):  
Ken W. K. Lau ◽  
Jianping Ren ◽  
Natalie L. M. Wai ◽  
Simon C. L. Lau ◽  
Pei-Yuan Qian ◽  
...  
Keyword(s):  
Marine Bacterium ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Pearl Oyster ◽  
Rrna Gene ◽  
Hainan Province ◽  
Oyster Culture ◽  
Gene Sequence Analysis ◽  
Type Strains

A Gram-negative, aerobic, halophilic, neutrophilic, rod-shaped, non-pigmented, polar-flagellated bacterium, UST010306-043T, was isolated from a pearl-oyster culture pond in Sanya, Hainan Province, China in January 2001. This marine bacterium had an optimum temperature for growth of between 33 and 37 °C. On the basis of 16S rRNA gene sequence analysis, the strain was closely related to Marinomonas aquimarina and Marinomonas communis, with 97.5–97.7 and 97.1 % sequence similarity, respectively. Levels of DNA–DNA relatedness to the type strains of these species were well below 70 %. Analyses of phylogenetic, phenotypic and chemotaxomonic characteristics showed that strain UST010306-043T was distinct from currently established Marinomonas species. A novel species with the name Marinomonas ostreistagni sp. nov. is proposed to accommodate this bacterium, with strain UST010306-043T (=JCM 13672T=NRRL B-41433T) as the type strain.

scholarly journals Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov., isolated from soil

2007 ◽  
Vol 57 (9) ◽  
pp. 2089-2095 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Type Strains

Two Gram-negative, non-motile, pleomorphic bacterial strains, DS-40T and DS-45T, were isolated from a soil sample collected from Dokdo, Korea, and their exact taxonomic positions were investigated by using a polyphasic approach. Strains DS-40T and DS-45T grew optimally at 25 °C and pH 6.5–7.5 in the presence of 0–1.0 % (w/v) NaCl. They contained MK-7 as the predominant menaquinone and possessed iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C contents of strains DS-40T and DS-45T were 36.0 and 36.8 mol%, respectively. Strains DS-40T and DS-45T shared a 16S rRNA gene sequence similarity of 96.7 % and demonstrated a mean DNA–DNA relatedness level of 12 %. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains DS-40T and DS-45T were most closely phylogenetically affiliated with the genus Pedobacter of the family Sphingobacteriaceae. Strains DS-40T and DS-45T exhibited 16S rRNA gene sequence similarity values of 91.4–93.7 and 89.9–91.6 % with respect to the type strains of Pedobacter and Sphingobacterium species, respectively. Phenotypic and chemotaxonomic properties, together with the phylogenetic data, support the assignment of strains DS-40T and DS-45T as two distinct species within the genus Pedobacter. On the basis of phenotypic, phylogenetic and genetic data, strains DS-40T and DS-45T represent two novel species of the genus Pedobacter, for which the names Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov. are proposed, respectively. The respective type strains are DS-40T (=KCTC 12875T=JCM 14593T) and DS-45T (=KCTC 12876T=JCM 14594T).

scholarly journals Gordonia neofelifaecis sp. nov., a cholesterol side-chain-cleaving actinomycete isolated from the faeces of Neofelis nebulosa

2011 ◽  
Vol 61 (1) ◽  
pp. 165-169 ◽  
Author(s):  
Yuchang Liu ◽  
Fanglan Ge ◽  
Guiying Chen ◽  
Wei Li ◽  
Pingmei Ma ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Side Chain ◽  
Rrna Gene ◽  
The Novel ◽  
Nearest Neighbours ◽  
Gene Sequence Analysis ◽  
Neofelis Nebulosa ◽  
Taxonomic Approach ◽  
Type Strains

A cholesterol side-chain-cleaving bacterial strain, AD-6T, was isolated from fresh faeces of a clouded leopard (Neofelis nebulosa) and was studied using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis showed that the novel strain formed a distinct subline within the genus Gordonia, its closest neighbours being the type strains of Gordonia cholesterolivorans, Gordonia sihwensis and Gordonia hydrophobica, with sequence similarity values of 98.2, 97.8 and 97.6 %, respectively. The gyrB gene sequence of strain AD-6T exhibited similarities of 77–91 % with those of the type strains of recognized species of the genus Gordonia, being most similar to the type strains of G. sihwensis, G. hydrophobica and Gordonia hirsuta (91, 87 and 84 % similarity, respectively). The results of whole-cell fatty acid analyses and DNA–DNA relatedness data readily distinguished the new isolate from its nearest neighbours. Strain AD-6T is therefore considered to represent a novel species of the genus Gordonia, for which the name Gordonia neofelifaecis sp. nov. is proposed. The type strain is AD-6T (=NRRL B-59395T=CCTCC AB-209144T).

Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2457-2462 ◽  
Author(s):  
Om Prakash ◽  
Stefan J. Green ◽  
Puja Jasrotia ◽  
Will A. Overholt ◽  
Andy Canion ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Contaminated Aquifer ◽  
Content Type ◽  
Link Type ◽  
Characteristic Features

Bacterial strains 2APBS1T and 116-2 were isolated from the subsurface of a nuclear legacy waste site where the sediments are co-contaminated with large amounts of acids, nitrate, metal radionuclides and other heavy metals. A combination of physiological and genetic assays indicated that these strains represent the first member of the genus Rhodanobacter shown to be capable of complete denitrification. Cells of strain 2APBS1T and 116-2 were Gram-negative, non-spore-forming rods, 3–5 µm long and 0.25–0.5 µm in diameter. The isolates were facultative anaerobes, and had temperature and pH optima for growth of 30 °C and pH 6.5; they were able to tolerate up to 2.0 % NaCl, although growth improved in its absence. Strains 2APBS1T and 116-2 contained fatty acid and quinone (ubiquinone-8; 100 %) profiles that are characteristic features of the genus Rhodanobacter . Although strains 2APBS1T and 116-2 shared high 16S rRNA gene sequence similarity with Rhodanobacter thiooxydans LCS2T (>99 %), levels of DNA–DNA relatedness between these strains were substantially below the 70 % threshold used to designate novel species. Thus, based on genotypic, phylogenetic, chemotaxonomic and physiological differences, strains 2APBS1T and 116-2 are considered to represent a single novel species of the genus Rhodanobacter , for which the name Rhodanobacter denitrificans sp. nov. is proposed. The type strain is 2APBS1T ( = DSM 23569T = JCM 17641T).

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