scholarly journals Yersinia nurmii sp. nov.

2011 ◽  
Vol 61 (10) ◽  
pp. 2368-2372 ◽  
Author(s):  
Anna Murros-Kontiainen ◽  
Maria Fredriksson-Ahomaa ◽  
Hannu Korkeala ◽  
Per Johansson ◽  
Riitta Rahkila ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Yersinia Ruckeri ◽  
Phenotypic Properties ◽  
Broiler Meat ◽  
Dna Reassociation ◽  
The 16S Rrna Gene

This study was set up to identify three Gram-negative, rod-shaped strains originating from broiler meat packaged under a modified atmosphere. A polyphasic taxonomic approach, including multilocus sequence analysis (MLSA) of five genes (16S rRNA, glnA, gyrB, recA and HSP60), DNA–DNA reassociation between the closest phylogenetic neighbours and determination of relevant phenotypic properties, was applied. Phylogenetic analysis of the 16S rRNA gene sequences grouped these strains together and within the genus Yersinia. MLSA of the 16S rRNA gene and four housekeeping genes showed that the strains formed a monophyletic group separate from other Yersinia species in all phylogenetic trees constructed. The strains had a phenotypic profile different from those of other representatives of the genus Yersinia, but most similar to that of Yersinia ruckeri. Typical virulence markers for pathogenic Yersinia were not detected. Based on phylogenetic, phenotypic and DNA–DNA reassociation data, a novel species, Yersinia nurmii sp. nov., is proposed for the isolated strains. The type strain is APN3a-cT ( = DSM 22296T  = LMG 25213T).

scholarly journals Variovorax gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4335-4340 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gossypium Hirsutum ◽  
Dna Hybridization ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
The 16S Rrna Gene

A beige-pigmented bacterial strain (JM-310T), isolated from the healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar ‘DES-119’) in Tallassee (Macon county), Alabama, USA, was studied taxonomically. The isolate produced small rod-shaped cells, which showed a Gram-negative staining behaviour. A comparison of the 16S rRNA gene sequence of the isolate revealed 99.2, 98.8, 98.7, 98.7, 98.1 and 97.6 % similarity to the 16S rRNA gene sequences of the type strains of Variovorax paradoxus, Variovorax boronicumulans, Variovorax ginsengisoli, Variovorax soli, Variovorax defluvii and Variovorax dokdonensis, respectively. In phylogenetic trees based on 16S rRNA gene sequences, strain JM-301T was placed within the monophyletic cluster of Variovorax species. The fatty acid profile of strain JM-310T consisted mainly of the major fatty acids C16 : 0, C10 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH/C16 : 1ω7c/t). The quinone system of strain JM-310T contained predominantly ubiquinone Q-8 and lesser amounts of Q-7 and Q-9. The major polyamine was putrescine and the diagnostic polyamine 2-hydroxyputrescine was detected as well. The polar lipid profile consisted of the major lipids phosphatidylethanolamine, phosphatidylglycerol, diphospatidylglycerol and several unidentified lipids. DNA–DNA hybridization experiments with V. paradoxus LMG 1797T, V. boronicumulans 1.22T, V. soli KACC 11579T and V. ginsengisoli 3165T gave levels of relatedness of < 70 %. These DNA–DNA hybridization results in addition to differential biochemical properties indicate clearly that strain JM-310T is a member of a novel species, for which the name Variovorax gossypii sp. nov. is proposed. The type strain is JM-310T ( = LMG 28869T = CIP 110912T = CCM 8614T).

Winogradskyella litorisediminis sp. nov., isolated from coastal sediment

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1793-1799 ◽  
Author(s):  
Chul-Hyung Kang ◽  
Soo-Young Lee ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Coastal Sediment ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-staining-negative, non-flagellated, non-gliding, aerobic, rod-shaped bacterium, designated DPS-8T, was isolated from coastal sediment of Geoje island in the South Sea, South Korea, and subjected to a polyphasic study. Strain DPS-8T grew optimally at 30 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain DPS-8T joined the clade comprising the type strains of Winogradskyella species with a high bootstrap resampling value of 93.5 %. Phylogenetic trees constructed using maximum-likelihood and maximum-parsimony algorithms revealed that strain DPS-8T belonged to the genus Winogradskyella . Strain DPS-8T exhibited 94.1–96.5 % 16S rRNA gene sequence similarity to the type strains of species of the genus Winogradskyella . Strain DPS-8T contained MK-6 as the predominant menaquinone and iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 1ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The major polar lipids of strain DPS-8T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain DPS-8T was 34.7 mol%. Differential phenotypic properties, together with its phylogenetic distinctiveness, revealed that strain DPS-8T is separate from recognized species of the genus Winogradskyella . On the basis of the data presented, strain DPS-8T is considered to represent a novel species of the genus Winogradskyella , for which the name Winogradskyella litorisediminis sp. nov. is proposed. The type strain is DPS-8T ( = KCTC 32110T = CCUG 62215T).

scholarly journals Isoptericola dokdonensis sp. nov., isolated from soil

2006 ◽  
Vol 56 (12) ◽  
pp. 2893-2897 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Peter Schumann ◽  
So-Jung Kang ◽  
Seo-Youn Jung ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Bacterium Strain ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-positive, non-motile, rod- or coccoid-shaped Isoptericola-like bacterium, strain DS-3T, was isolated from a soil sample from Dokdo, Korea, and its taxonomic position was investigated by a polyphasic approach. The organism grew optimally at 30 °C and pH 7.0–8.0. Strain DS-3T had the peptidoglycan type based on l-lys–d-Asp, and galactose, glucose, rhamnose and ribose as the whole-cell sugars. It contained MK-9(H4) as the predominant menaquinone and anteiso-C15 : 0 and iso-C15 : 0 as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unidentified glycolipids. The DNA G+C content was 74.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-3T was most closely related to members of the genus Isoptericola. Similarity values between the 16S rRNA gene sequences of strain DS-3T and the type strains of Isoptericola species ranged from 98.0 to 98.4 %. DNA–DNA relatedness values (11–23 %) and differential phenotypic properties demonstrated that strain DS-3T was distinguishable from recognized Isoptericola species. On the basis of phenotypic properties and phylogenetic and genetic distinctiveness, strain DS-3T represents a novel species in the genus Isoptericola, for which the name Isoptericola dokdonensis sp. nov. is proposed. The type strain is DS-3T (=KCTC 19128T=CIP 108921T).

Genetic analysis of housekeeping genes of members of the genus Acholeplasma: Phylogeny and complementary molecular markers to the 16S rRNA gene

2007 ◽  
Vol 44 (2) ◽  
pp. 699-710 ◽  
Author(s):  
Dmitriy V. Volokhov ◽  
Alexander A. Neverov ◽  
Joseph George ◽  
Hyesuk Kong ◽  
Sue X. Liu ◽  
...  
Keyword(s):  
Molecular Markers ◽  
16S Rrna ◽  
Genetic Analysis ◽  
16S Rrna Gene ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals Litorivivens lipolytica gen. nov., sp. nov., a lipolytic bacterium isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 141-146 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Novel Genus And Species ◽  
Type Strains

A Gram-stain-negative, flagellated, aerobic and rod-shaped or ovoid bacterial strain, designated HJTF-7T, was isolated from a tidal flat on the South Sea of South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain HJTF-7T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees, based on 16S rRNA gene sequences, showed that strain HJTF-7T joined the cluster comprising the type strains of species of the genera Spongiibacter and Zhongshania . Strain HJTF-7T exhibited 16S rRNA gene sequence similarities of 90.4–92.5 % to the type strains of species of the genera Spongiibacter and Zhongshania and of less than 91.5 % to the type strains of other recognized species. Strain HJTF-7T contained Q-8 as the predominant ubiquinone. The major fatty acids were iso-C17 : 1ω9c, iso-C15 : 0, iso-C17 : 0, iso-C11 : 0 3-OH and C17 : 1ω8c and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The fatty acid and polar lipid profiles of strain HJTF-7T were distinct from those of members of the genera Spongiibacter and Zhongshania . The DNA G+C content of strain HJTF-7T was 55.9 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain HJTF-7T represents a novel genus and species within the class Gammaproteobacteria , for which the name Litorivivens lipolytica gen. nov., sp. nov. is proposed. The type strain of Litorivivens lipolytica is HJTF-7T ( = KCTC 42157T = CECT 8654T).

scholarly journals Lactobacillus hayakitensis sp. nov., isolated from intestines of healthy thoroughbreds

2007 ◽  
Vol 57 (12) ◽  
pp. 2836-2839 ◽  
Author(s):  
Hidetoshi Morita ◽  
Chiharu Shiratori ◽  
Masaru Murakami ◽  
Hideto Takami ◽  
Yukio Kato ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Biochemical Characterization ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Dna Reassociation ◽  
The 16S Rrna Gene

Two strains, KBL13T and GBL13, were isolated as one of intestinal lactobacilli from the faecal specimens from different thoroughbreds of the same farm where they were born in Hokkaido, Japan. They were Gram-positive, facultatively anaerobic, catalase-negative, non-spore-forming and non-motile rods. KBL13T and GBL13 homofermentatively metabolize glucose, and produce lactate as the sole final product from glucose. The 16S rRNA gene sequence, DNA–DNA hybridization, DNA G+C content and biochemical characterization indicated that these two strains, KBL13T and GBL13, belong to the same species. In the representative strain, KBL13T, the DNA G+C content was 34.3 mol%. Lactobacillus salivarius JCM 1231T (=ATCC 11741T; AF089108) is the type strain most closely related to the strain KBL13T as shown in the phylogenetic tree, and the 16S rRNA gene sequence identity showed 96.0 % (1425/1484 bp). Comparative 16S rRNA gene sequence analysis of this strain indicated that the two isolated strains belong to the genus Lactobacillus and that they formed a branch distinct from their closest relatives, L. salivarius, Lactobacillus aviarius, Lactobacillus saerimneri and Lactobacillus acidipiscis. DNA–DNA reassociation experiments with L. salivarius and L. aviarius confirmed that KBL13T represents a novel species, for which the name Lactobacillus hayakitensis sp. nov. is proposed. The type strain is KBL13T (=JCM 14209T=DSM 18933T).

scholarly journals Caenispirillum bisanense gen. nov., sp. nov., isolated from sludge of a dye works

2007 ◽  
Vol 57 (6) ◽  
pp. 1217-1221 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
The 16S Rrna Gene

Two Gram-negative, non-spore-forming, motile and helical-shaped bacterial strains, K92T and K93, were isolated from sludge from a dye works in Korea, and their taxonomic positions were investigated by means of a polyphasic approach. Strains K92T and K93 grew optimally at 37 °C and pH 7.0–8.0 in the presence of 0.5 % (w/v) NaCl. They contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified amino-group-containing lipids that were ninhydrin-positive. Their DNA G+C contents were 70.0 mol%. The 16S rRNA gene sequences of K92T and K93 showed no differences, and the two strains had a mean DNA–DNA relatedness of 93 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains K92T and K93 formed a distinct evolutionary lineage within the Alphaproteobacteria. The 16S rRNA gene sequences of strains K92T and K93 exhibited similarity values of less than 91.5 % with respect to the 16S rRNA gene sequences of other members of the Alphaproteobacteria. The two strains were distinguishable from phylogenetically related genera through differences in several phenotypic properties. On the basis of the phenotypic, phylogenetic and genetic data, strains K92T and K93 represent a novel genus and species, for which the name Caenispirillum bisanense gen. nov., sp. nov. is proposed. The type strain of Caenispirillum bisanense is K92T (=KCTC 12839T=JCM 14346T).

scholarly journals Polaribacter dokdonensis sp. nov., isolated from seawater

2006 ◽  
Vol 56 (6) ◽  
pp. 1251-1255 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strain, DSW-5T, was isolated from seawater off Dokdo, Korea, and subjected to a polyphasic taxonomic study. It grew optimally at 25–28 °C and in the presence of 2 % (w/v) NaCl. Strain DSW-5T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 and iso-C15 : 0 3-OH as the major fatty acids. The major polar lipids detected were phosphatidylethanolamine, three unidentified phospholipids and an amino-group-containing lipid. The DNA G+C content was 30.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DSW-5T was most closely related to the genus Polaribacter. Similarity values between the 16S rRNA gene sequences of strain DSW-5T and the type strains of recognized Polaribacter species were in the range 96.2–96.8 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DSW-5T (=KCTC 12392T=DSM 17204T) was classified in the genus Polaribacter as the type strain of a novel species, for which the name Polaribacter dokdonensis sp. nov. is proposed.

Tenacibaculum aestuarii sp. nov., isolated from a tidal flat sediment in Korea

2006 ◽  
Vol 56 (7) ◽  
pp. 1577-1581 ◽  
Author(s):  
Seo-Youn Jung ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Tidal Flat Sediment ◽  
Total Fatty Acids

A novel Tenacibaculum-like bacterial strain, SMK-4T, was isolated from a tidal flat sediment in Korea. Strain SMK-4T was Gram-negative, pale yellow-pigmented and rod-shaped. It grew optimally at 30–37 °C and in the presence of 2–3 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C16 : 0 3-OH and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids (>10 % of total fatty acids). The DNA G+C content was 33.6 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strain SMK-4T fell within the evolutionary radiation encompassed by the genus Tenacibaculum. Strain SMK-4T exhibited 16S rRNA gene sequence similarity levels of 95.2–98.6 % with respect to the type strains of recognized Tenacibaculum species. DNA–DNA relatedness levels and differential phenotypic properties made it possible to categorize strain SMK-4T as a species that is separate from previously described Tenacibaculum species. On the basis of phenotypic properties and phylogenetic and genetic distinctiveness, strain SMK-4T (=KCTC 12569T=JCM 13491T) should be classified as a novel Tenacibaculum species, for which the name Tenacibaculum aestuarii sp. nov. is proposed.

scholarly journals Roseomonas terrae sp. nov.

2007 ◽  
Vol 57 (11) ◽  
pp. 2485-2488 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Hyun Woo Oh ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, non-motile, coccobacilli-shaped bacterium, DS-48T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by means of a polyphasic study. Strain DS-48T grew optimally at 25 °C and pH 7.0–8.0 in the presence of 0.5 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C18 : 1 2-OH as the major fatty acids. The DNA G+C content was 69.3 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-48T fell within the genus Roseomonas, clustering with Roseomonas lacus TH-G33T (at a bootstrap confidence level of 100 %). The levels of similarity between the 16S rRNA gene sequence of strain DS-48T and those of the type strains of recognized Roseomonas species were in the range 93.2–98.0 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness of DS-48T, revealed that this strain differs from recognized Roseomonas species. On the basis of phenotypic, phylogenetic and genetic data, therefore, strain DS-48T represents a novel species within the genus Roseomonas, for which the name Roseomonas terrae sp. nov. is proposed. The type strain is DS-48T (=KCTC 12874T=JCM 14592T).

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