scholarly journals Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia

2007 ◽  
Vol 57 (6) ◽  
pp. 1310-1314 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Emended Description ◽  
Type Strains

A Gram-negative, motile, aerobic and oval- or rod-shaped bacterial strain, DS-56T, which is phylogenetically closely related to the genus Devosia, was isolated from soil from Dokdo, Korea. Strain DS-56T grew optimally at pH 6.5–7.5 and 25 °C in the presence of 0.5 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain DS-56T joins the cluster comprising Devosia species, at a bootstrap resampling value of 100 %. The levels of 16S rRNA gene sequence similarity between strain DS-56T and the type strains of recognized Devosia species ranged from 95.4 to 96.4 %. Strain DS-56T contained Q-11 as the predominant ubiquinone, unlike Devosia species, which contain Q-10 as the predominant ubiquinone. The novel strain also contained some fatty acids, including branched and hydroxy fatty acids, that are not detected in Devosia species. The DNA G+C content of strain DS-56T was 66.2 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain DS-56T represents a novel species of the genus Devosia, for which the name Devosia insulae sp. nov. is proposed. The type strain is DS-56T (=KCTC 12821T=DSM 17955T).

scholarly journals Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea

2004 ◽  
Vol 54 (5) ◽  
pp. 1799-1803 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Soo-Hwan Yeo ◽  
In-Gi Kim ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sea Water ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Type Strains

Two Gram-negative, motile, non-spore-forming and slightly halophilic rods (strains SW-145T and SW-156T) were isolated from sea water of the Yellow Sea in Korea. Strains SW-145T and SW-156T grew optimally at 37 and 30–37 °C, respectively, and in the presence of 2–6 % (w/v) NaCl. Strains SW-145T and SW-156T were chemotaxonomically characterized as having ubiquinone-9 as the predominant respiratory lipoquinone and C16 : 0, C18 : 1 ω9c, C16 : 1 ω9c and C12 : 0 3-OH as the major fatty acids. The DNA G+C contents of strains SW-145T and SW-156T were 58 and 57 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-145T and SW-156T fell within the evolutionary radiation enclosed by the genus Marinobacter. The 16S rRNA gene sequences of strains SW-145T and SW-156T were 94·8 % similar. Strains SW-145T and SW-156T exhibited 16S rRNA gene sequence similarity levels of 94·3–98·1 and 95·4–97·7 %, respectively, with respect to the type strains of all Marinobacter species. Levels of DNA–DNA relatedness, together with 16S rRNA gene sequence similarity values, indicated that strains SW-145T and SW-156T are members of two species that are distinct from seven Marinobacter species with validly published names. On the basis of phenotypic properties and phylogenetic and genotypic distinctiveness, strains SW-145T (=KCTC 12185T=DSM 16070T) and SW-156T (=KCTC 12184T=DSM 16072T) should be placed in the genus Marinobacter as the type strains of two distinct novel species, for which the names Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov. are 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 Paracoccus fistulariae sp. nov., a lipolytic bacterium isolated from bluespotted cornetfish, Fistularia commersonii

2010 ◽  
Vol 60 (12) ◽  
pp. 2908-2912 ◽  
Author(s):  
Young-Ok Kim ◽  
Hee Jeong Kong ◽  
Sooyeon Park ◽  
So-Jung Kang ◽  
Kyung-Kil Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Type Strains

A Gram-stain-negative, non-motile, non-spore-forming and short rod- or rod-shaped bacterial strain, designated 22-5T, was isolated from a bluespotted cornetfish, Fistularia commersonii, and subjected to taxonomic study. Strain 22-5T grew optimally at 30 °C and in the presence of 2–5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 22-5T belonged to the genus Paracoccus and joined the cluster comprising Paracoccus homiensis DD-R11T and Paracoccus zeaxanthinifaciens ATCC 21588T, with which strain 22-5T exhibited 97.4 and 96.9 % 16S rRNA gene sequence similarity, respectively. Strain 22-5T exhibited 94.0–96.6 % 16S rRNA gene sequence similarity with the other type strains of species of the genus Paracoccus. Strain 22-5T contained Q-10 as the predominant menaquinone and C18 : 1 ω7c as the predominant fatty acid. In this study, P. zeaxanthinifaciens KCTC 22688T also contained Q-10 as the predominant isoprenoid quinone. The DNA G+C content of strain 22-5T was 63.6 mol%. Strain 22-5T exhibited 44 and 32 % DNA–DNA relatedness to P. homiensis KACC 11518T and P. zeaxanthinifaciens KCTC 22688T, respectively. On the basis of phenotypic, phylogenetic and genetic data, strain 22-5T is considered to represent a novel species of the genus Paracoccus, for which the name Paracoccus fistulariae sp. nov. is proposed. The type strain is 22-5T (=KCTC 22803T =CCUG 58401T).

scholarly journals Vibrio olivae sp. nov., isolated from Spanish-style green-olive fermentations

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1895-1901 ◽  
Author(s):  
Helena Lucena-Padrós ◽  
Juan M. González ◽  
Belén Caballero-Guerrero ◽  
José Luis Ruiz-Barba ◽  
Antonio Maldonado-Barragán
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Green Olive

Three isolates originating from Spanish-style green-olive fermentations in a manufacturing company in the province of Seville, Spain, were taxonomically characterized by a polyphasic approach. This included a phylogenetic analysis based on 16S rRNA gene sequences and multi-locus sequence analysis (MLSA) based on pyrH, recA, rpoA, gyrB and mreB genes. The isolates shared 98.0 % 16S rRNA gene sequence similarity with Vibrio xiamenensis G21T. Phylogenetic analysis based on 16S rRNA gene sequences using the neighbour-joining and maximum-likelihood methods showed that the isolates fell within the genus Vibrio and formed an independent branch close to V. xiamenensis G21T. The maximum-parsimony method grouped the isolates to V. xiamenensis G21T but forming two clearly separated branches. Phylogenetic trees based on individual pyrH, recA, rpoA, gyrB and mreB gene sequences revealed that strain IGJ1.11T formed a clade alone or with V. xiamenensis G21T. Sequence similarities of the pyrH, recA, rpoA, gyrB and mreB genes between strain IGJ1.11T and V. xiamenensis G21T were 86.7, 85.7, 97.3, 87.6 and 84.8 %, respectively. MLSA of concatenated sequences showed that strain IGJ1.11T and V. xiamenensis G21T are two clearly separated species that form a clade, which we named Clade Xiamenensis, that presented 89.7 % concatenated gene sequence similarity, i.e. less than 92 %. The major cellular fatty acids (>5 %) of strain IGJ1.11T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Enzymic activity profiles, sugar fermentation patterns and DNA G+C content (52.9 mol%) differentiated the novel strains from the closest related members of the genus Vibrio. The name Vibrio olivae sp. nov. is proposed for the novel species. The type strain is IGJ1.11T ( = CECT 8064T = DSM 25438T).

scholarly journals Chryseobacterium daeguense sp. nov., isolated from wastewater of a textile dye works

2007 ◽  
Vol 57 (6) ◽  
pp. 1355-1359 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Textile Dye ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, rod-shaped bacterial strain, K105T, was isolated from wastewater of a textile dye works in Korea and subjected to a polyphasic taxonomic study. Strain K105T grew optimally at pH 6.5–7.5 and 30–37 °C. It contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 1 ω9c, 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 content was 36.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain K105T belonged to the genus Chryseobacterium. Strain K105T exhibited 16S rRNA gene sequence similarity values of less than 96.9 % to the type strains of recognized Chryseobacterium species. Strain K105T differed from phylogenetically related Chryseobacterium species in several phenotypic properties. On the basis of phenotypic and phylogenetic data, strain K105T (=KCTC 12841T=JCM 14362T) is placed in the genus Chryseobacterium as the type strain of a novel species, for which the name Chryseobacterium daeguense sp. nov. is proposed.

Lysobacter xinjiangensis sp. nov., a moderately thermotolerant and alkalitolerant bacterium isolated from a gamma-irradiated sand soil sample

2011 ◽  
Vol 61 (2) ◽  
pp. 433-437 ◽  
Author(s):  
Ming Liu ◽  
Yufeng Liu ◽  
Yaqiong Wang ◽  
Xuesong Luo ◽  
Junqiang Dai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Sand Soil ◽  
Gamma Irradiated ◽  
Type Strains

A yellow-pigmented bacterial strain, designated RCML-52T, was isolated from an abandoned gold mine in the desert in Xinjiang, China. Strain RCML-52T was Gram-negative, aerobic and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RCML-52T was affiliated with the genus Lysobacter. Strain RCML-52T exhibited <95.6 % 16S rRNA gene sequence similarity to the type strains of all species of the genus Lysobacter. The major fatty acids were iso-C16 : 0 (27.6 %), iso-C15 : 0 (19.1 %), iso-C17 : 1 ω9c (16.4 %), iso-C11 : 0 3-OH (6.5 %) and iso-C11 : 0 (5.3 %). The DNA G+C content was 69.7 mol%. The major isoprenoid quinone was Q-8. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain RCML-52T should be assigned to a novel species of the genus Lysobacter, for which the name Lysobacter xinjiangensis sp. nov. is proposed. The type strain is RCML-52T (=CCTCC AB 208194T =KCTC 22558T).

scholarly journals Brevundimonas lenta sp. nov., isolated from soil

2007 ◽  
Vol 57 (10) ◽  
pp. 2236-2240 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Jung-Sook Lee ◽  
Hyun Woo Oh ◽  
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, Brevundimonas-like bacterial strain, DS-18T, was isolated from soil in Dokdo, Korea, and its exact taxonomic position was investigated by using a polyphasic approach. Strain DS-18T grew optimally at pH 6.5–7.0 and 25 °C without NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-18T belonged to the genus Brevundimonas. Strain DS-18T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The DNA G+C content was 68.7 mol%. Strain DS-18T exhibited levels of 16S rRNA gene sequence similarity of 96.3–98.7 % to the type strains of Brevundimonas species and Mycoplana bullata. Mean DNA–DNA relatedness values between strain DS-18T and the type strains of phylogenetically related Brevundimonas species and M. bullata were in the range 15–32 %. Strain DS-18T differed from Brevundimonas species and M. bullata in several phenotypic characteristics. On the basis of phenotypic, phylogenetic and genetic data, strain DS-18T represents a novel species of the genus Brevundimonas, for which the name Brevundimonas lenta sp. nov. is proposed. The type strain is DS-18T (=KCTC 12871T =JCM 14602T).

scholarly journals Loktanella maricola sp. nov., isolated from seawater of the East Sea in Korea

2007 ◽  
Vol 57 (8) ◽  
pp. 1799-1802 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
East Sea ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, non-motile and rod-shaped Loktanella-like bacterial strain, DSW-18T, was isolated from seawater of the East Sea, Korea, and its exact taxonomic position was investigated by using a polyphasic approach. Strain DSW-18T grew optimally at pH 7.0–8.0 and 25 °C in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 56.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DSW-18T fell within the cluster comprising Loktanella species. The levels of 16S rRNA gene sequence similarity between strain DSW-18T and the type strains of recognized Loktanella species ranged from 94.4 to 98.4 %. The DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain DSW-18T was distinguishable from recognized Loktanella species. On the basis of the phenotypic, phylogenetic and genetic data, strain DSW-18T represents a novel species of the genus Loktanella, for which the name Loktanella maricola sp. nov. is proposed. The type strain is DSW-18T (=KCTC 12863T=JCM 14564T).

scholarly journals Agromyces allii sp. nov., isolated from the rhizosphere of Allium victorialis var. platyphyllum

2007 ◽  
Vol 57 (3) ◽  
pp. 588-593 ◽  
Author(s):  
Seo-Youn Jung ◽  
Soo-Young Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness ◽  
Type Strains

Two Gram-positive, non-motile, yellow-pigmented, slightly curved and rod-shaped bacterial strains, UMS-62T and UMS-101, were isolated from the rhizosphere of Allium victorialis var. platyphyllum, a variety of wild edible greens grown on Ulleung island, Korea. The taxonomic position of the strains was investigated by a polyphasic approach. Strains UMS-62T and UMS-101 grew optimally at 30 °C and at pH 6.5–7.5. The novel strains contained MK-11 and MK-12 as the predominant menaquinones and rhamnose, ribose and galactose as the major cell-wall sugars. The major cellular fatty acids (>10 % of the total fatty acids) were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The DNA G+C contents were 71.1–71.3 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strains UMS-62T and UMS-101 belong to the genus Agromyces. Strains UMS-62T and UMS-101 showed a 16S rRNA gene sequence similarity value of 99.9 % and a mean DNA–DNA relatedness level of 91.1 %. Similarity values between the 16S rRNA gene sequences of the two novel strains and the type strains of recognized Agromyces species ranged from 95.2 to 99.1 %. The levels of DNA–DNA relatedness between the two novel strains and the type strains of five phylogenetically related Agromyces species were in the range of 13.4 to 54.2 %. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain UMS-62T (=KCTC 19181T=JCM 13584T) and strain UMS-101 are classified as representing a novel species in the genus Agromyces, for which the name Agromyces allii sp. nov. is proposed.

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