Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil

2010 ◽  
Vol 60 (11) ◽  
pp. 2577-2582 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Joonhong Park ◽  
Soon-Ae Yoo
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, non-motile, aerobic bacterial strain, designated MJ20T, was isolated from farm soil near Daejeon (South Korea) and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ20T belongs to the family Cytophagaceae, class Sphingobacteria, and was related most closely to Dyadobacter fermentans DSM 18053T (98.9 % sequence similarity), Dyadobacter beijingensis JCM 14200T (98.0 %) and Dyadobacter ginsengisoli KCTC 12589T (96.4 %). The G+C content of the genomic DNA of strain MJ20T was 48.5 mol%. The detection of MK-7 as the predominant menaquinone and a fatty acid profile with summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 0 and C16 : 1 ω5c as major components supported the affiliation of strain MJ20T to the genus Dyadobacter. The new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to D. fermentans DSM 18053T (mean±sd of three determinations, 47±7 %) and D. beijingensis JCM 14200T (38±8 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ20T (=KCTC 22481T =JCM 16232T) should be classified in the genus Dyadobacter as the type strain of a novel species, for which the name Dyadobacter soli sp. nov. is proposed.

scholarly journals Aurantimonas altamirensis sp. nov., a member of the order Rhizobiales isolated from Altamira Cave

2006 ◽  
Vol 56 (11) ◽  
pp. 2583-2585 ◽  
Author(s):  
Valme Jurado ◽  
Juan M. Gonzalez ◽  
Leonila Laiz ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Wide Range ◽  
The Family ◽  
Aurantimonas Coralicida

A bacterial strain, S21BT, was isolated from Altamira Cave (Cantabria, Spain). The cells were Gram-negative, short rods growing aerobically. Comparative 16S rRNA gene sequence analysis revealed that strain S21BT represented a separate subline of descent within the family ‘Aurantimonadaceae’ (showing 96 % sequence similarity to Aurantimonas coralicida) in the order Rhizobiales (Alphaproteobacteria). The major fatty acids detected were C16 : 0 and C18 : 1 ω7c. The G+C content of the DNA from strain S21BT was 71.8 mol%. Oxidase and catalase activities were present. Strain S21BT utilized a wide range of substrates for growth. On the basis of the results of this polyphasic study, isolate S21BT represents a novel species of the genus Aurantimonas, for which the name Aurantimonas altamirensis sp. nov. is proposed. The type strain is S21BT (=CECT 7138T=LMG 23375T).

scholarly journals Shinella daejeonensis sp. nov., a nitrate-reducing bacterium isolated from sludge of a leachate treatment plant

2011 ◽  
Vol 61 (9) ◽  
pp. 2123-2128 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Leonid N. Ten
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Leachate Treatment ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative-staining, motile, rod-shaped, aerobic bacterial strain, designated MJ02T, was isolated from sludge of a leachate treatment plant in Daejeon (South Korea) and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ02T belonged to the family Rhizobiaceae, class Alphaproteobacteria, and was most closely related to Shinella yambaruensis MS4T (97.6 % sequence similarity) and Shinella fusca DC-196T (97.5 %). The G+C content of the genomic DNA of strain MJ02T was 64.3 mol%. The detection of a quinone system with ubiquinone Q-10 as the predominant respiratory lipoquinone and a fatty acid profile with C18 : 1ω7c (45.8 %) and C16 : 0 (21.8 %) as the major components supported the affiliation of strain MJ02T to the genus Shinella. However, strain MJ02T exhibited relatively low levels of DNA–DNA relatedness with respect to S. fusca DSM 21319T (17±7 %) and S. yambaruensis KACC 14483T (12±6 %), showing clearly that the isolate constituted a new genospecies. Strain MJ02T could be clearly differentiated from its phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, strain MJ02T is considered to represent a novel species of the genus Shinella, for which the name Shinella daejeonensis sp. nov. is proposed. The type strain is MJ02T ( = KCTC 22450T = JCM 16236T).

scholarly journals Sphingobacterium daejeonense sp. nov., isolated from a compost sample

2006 ◽  
Vol 56 (9) ◽  
pp. 2031-2036 ◽  
Author(s):  
Kyoung-Ho Kim ◽  
Leonid N. Ten ◽  
Qing-Mei Liu ◽  
Wan-Taek Im ◽  
Sung-Taik Lee
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
The Family

A Gram-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated TR6-04T, was isolated from compost and characterized taxonomically by using a polyphasic approach. The organism grew optimally at 30 °C and at pH 6.5–7.0. The isolate was positive for catalase and oxidase tests but negative for gelatinase, indole and H2S production. Comparative 16S rRNA gene sequence analysis showed that strain TR6-04T fell within the radiation of the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii ATCC 33299T (96.7 % sequence similarity); the similarity to sequences of other species within the family Sphingobacteriaceae was less than 92.0 %. The G+C content of the genomic DNA was 38.7 mol%. The predominant respiratory quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c). These chemotaxonomic data supported the affiliation of strain TR6-04T to the genus Sphingobacterium. However, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain TR6-04T (=KCTC 12579T=LMG 23402T=CCUG 52468T) should be classified as the type strain of a novel species, for which the name Sphingobacterium daejeonense sp. nov. is proposed.

scholarly journals Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field

2010 ◽  
Vol 60 (10) ◽  
pp. 2358-2363 ◽  
Author(s):  
Sathiyaraj Srinivasan ◽  
Myung Kyum Kim ◽  
Gayathri Sathiyaraj ◽  
Vaidyanathan Veena ◽  
Muthusamy Mahalakshmi ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Separate Species ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Physiological And Biochemical

A Gram-negative, rod-shaped, motile bacterium was isolated from the soil of a ginseng field in Daejeon, South Korea, and characterized in order to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that strain DCY34T belonged to the family Sphingomonadaceae, and the highest degree of sequence similarity was found with Sphingopyxis witflariensis W-50T (97.1 %), Sphingopyxis ginsengisoli Gsoil 250T (97.0 %), Sphingopyxis chilensis S37T (96.9 %), Sphingopyxis macrogoltabida IFO 15033T (96.8 %), Sphingopyxis alaskensis RB2256T (96.7 %) and Sphingopyxis taejonensis JSS54T (96.7 %). Chemotaxonomic data revealed that strain DCY34T possessed ubiquinone Q-10 as the predominant respiratory lipoquinone, which is common to members of the genus Sphingopyxis. The predominant fatty acids were C18 : 1 ω7c (27.5 %), summed feature 4 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH; 18.6 %), C16 : 0 (15.6 %) and summed feature 8 (C19 : 1 ω6c and/or unknown 18.864; 15.4 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and an unknown polar lipid. The results of physiological and biochemical tests clearly demonstrated that strain DCY34T represented a separate species and supported its affiliation to the genus Sphingopyxis. Based on these data, the new isolate represents a novel species, for which the name Sphingopyxis panaciterrulae sp. nov. is proposed. The type strain is DCY34T (=KCTC 22112T=JCM 14844T).

scholarly journals Bacillus panaciterrae sp. nov., isolated from soil of a ginseng field

2006 ◽  
Vol 56 (12) ◽  
pp. 2861-2866 ◽  
Author(s):  
Leonid N. Ten ◽  
Sang-Hoon Baek ◽  
Wan-Taek Im ◽  
Qing-Mei Liu ◽  
Zubair Aslam ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Distinct Phylogenetic Lineage

A Gram-positive, non-motile, endospore-forming bacterium, designated Gsoil 1517T, was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized in order to determine its taxonomic position, using a polyphasic approach. It was found to rod-shaped and aerobic or facultatively anaerobic. It grew optimally at 30 °C and at pH 6.5–7.0. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 1517T forms a distinct phylogenetic lineage within the genus Bacillus, being related to Bacillus funiculus JCM 11201T (96.8 %). The strain showed less than 94.3 % sequence similarity with other Bacillus species. The G+C content of the genomic DNA was found to be 47.8 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C15 : 0 (42.4 %), anteiso-C15 : 0 (17.4 %), iso-C14 : 0 (9.7 %) and C16 : 0 (6.0 %). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1517T represents a novel species of the genus Bacillus, for which the name Bacillus panaciterrae sp. nov. is proposed. The type strain is Gsoil 1517T (=KCTC 13929T=CCUG 52470T=LMG 23408T).

scholarly journals Flavisolibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity isolated from soil used for cultivating ginseng

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4868-4872 ◽  
Author(s):  
Yan Zhao ◽  
Qingmei Liu ◽  
Myung-Suk Kang ◽  
Fengxie Jin ◽  
Hongshan Yu ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Active Components ◽  
Respiratory Quinone ◽  
The Family ◽  
Ginseng Cultivation

A Gram-reaction-negative, aerobic, non-motile and rod-shaped bacterial strain designated Gsoil 636T was isolated from soil of a ginseng cultivation field in Pocheon Province, South Korea and its taxonomic position was investigated using a polyphasic approach. Gsoil 636T grew at 18–30 °C and at pH 6.0–8.0 on R2A medium. Gsoil 636T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenoside Rb1 (ones of the dominant active components of ginseng) to F2. On the basis of 16S rRNA gene sequence similarity, Gsoil 636T was shown to belong to the family Chitinophagaceae and to be related to Flavisolibacter ginsengiterrae Gsoil 492T (96.7 % sequence similarity), Flavisolibacter ginsengisoli Gsoil 643T (96.6 %) and Flavisolibacter rigui 02SUJ3T (96.6 %). The G+C content of the genomic DNA was 48.9 %. The predominant respiratory quinone was MK-7 and the major fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. DNA and chemotaxonomic data supported the affiliation of Gsoil 636T to the genus Flavisolibacter. Gsoil 636T could be differentiated genotypically and phenotypically from the species of the genus Flavisolibacter with validly published names. The isolate therefore represents a novel species, for which the name Flavisolibacter ginsenosidimutans sp. nov. is proposed, with the type strain Gsoil 636T (KCTC 22818T = JCM 18197T = KACC 14277T).

Nocardioides ungokensis sp. nov., isolated from lake sediment

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4857-4862 ◽  
Author(s):  
Yan Zhao ◽  
Qingmei Liu ◽  
Myung-Suk Kang ◽  
Fengxie Jin ◽  
Hongshan Yu ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Bacterium Strain

A Gram-reaction-positive, aerobic, coccus- to rod-shaped, non-motile, non-spore-forming bacterium (strain UKS-03T) was isolated from a sediment sample of Ungok Lake in Gochang, Republic of Korea. The taxonomic position of this bacterium was determined in an investigation based on a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain UKS-03T was shown to belong to the family Nocardioidaceae and to be related most closely to Nocardioides ginsengisegetis Gsoil 485T (98.5 % similarity), Nocardioides koreensis MSL-09T (98.4 %) and ‘Nocardioides panaciterrulae’ Gsoil 958 (97.3 %). Strain UKS-03T was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in its cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone, diphosphatidylglycerol and phosphatidylglycerol as the main polar lipids, and iso-C16 : 0, C17 : 1ω8c and C17 : 0 10-methyl as its major fatty acids. The G+C content of the genomic DNA was 71.9 mol%. Mean DNA–DNA relatedness values between strain UKS-03T and N. ginsengisegetis Gsoil 485T, N. koreensis KCTC 19272T and ‘N. panaciterrulae’ Gsoil 958 were 37.5 ± 7.2, 6.8 ± 0.9 and 3.1 ± 0.7 %, respectively. On the basis of the data from this polyphasic taxonomic study, strain UKS-03T represents a novel species of the genus Nocardioides, for which the name Nocardioides ungokensis sp. nov. is proposed. The type strain is UKS-03T ( = KACC 18304T = LMG 28591T).

scholarly journals Myroides marinus sp. nov., a member of the family Flavobacteriaceae, isolated from seawater

2011 ◽  
Vol 61 (4) ◽  
pp. 938-941 ◽  
Author(s):  
Sung-Heun Cho ◽  
Song-Hee Chae ◽  
Wan-Taek Im ◽  
Seung Bum Kim
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
16S Rna ◽  
The Family ◽  
Myroides Odoratimimus ◽  
Bacterium Strain

A Gram-negative, aerobic, non-motile, yellow-pigmented, rod-shaped bacterium (strain JS-08T) isolated from seawater was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis indicated that strain JS-08T belongs to the genus Myroides, a member of the phylum Bacteroidetes. Its closest phylogenetic relative was Myroides odoratimimus JCM 7460T, with which it shared 97.0 % 16S RNA gene sequence similarity. Strain JS-08T contained menaquinone-6 (MK-6) as the predominant menaquinone, and the dominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and a summed feature consisting of iso-C15 : 0 2-OH and/or C16 : 1ω7c. The DNA G+C content of strain JS-08T was 34.2 mol%. Based on phenotypic, genotypic and phylogenetic evidence, it is suggested that strain JS-08T represents a novel species of the genus Myroides, for which the name Myroides marinus sp. nov. is proposed. The type strain is JS-08T ( = KCTC 23023T  = JCM 16529T).

Pusillimonas soli sp. nov., isolated from farm soil

2010 ◽  
Vol 60 (10) ◽  
pp. 2326-2330 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Myoungsoo Chae ◽  
Leonid N. Ten
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, motile, non-spore-forming bacterial strain, designated MJ07T, was isolated from a farm soil and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ07T belongs to the family Alcaligenaceae, class Betaproteobacteria, and is related most closely to Pusillimonas ginsengisoli KCTC 22046T (98.6 % sequence similarity) and Pusillimonas noertemannii BN9T (96.9 %). The levels of 16S rRNA gene sequence similarity between strain MJ07T and members of all other recognized species of the family Alcaligenaceae were below 95.2 %. The G+C content of the genomic DNA of strain MJ07T was 59.4 mol%. The detection of a quinone system with ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown aminolipids as major polar lipids and a fatty acid profile with C16 : 0 (32.0 %), C17 : 0 cyclo (24.7 %) and C19 : 0 cyclo ω8c (11.5 %) as the major components supported the affiliation of strain MJ07T to the genus Pusillimonas. Strain MJ07T exhibited relatively low levels of DNA–DNA relatedness with respect to P. ginsengisoli KCTC 22046T (50±8 %) and P. noertemannii KACC 13183T (18±7 %). On the basis of its phenotypic and genotypic properties together with its phylogenetic distinctiveness, strain MJ07T (=KCTC 22455T =JCM 16386T) should be classified in the genus Pusillimonas as the type strain of a novel species, for which the name Pusillimonas soli sp. nov. is proposed.

scholarly journals Description of Ruminococcus catenae SW178 sp. nov., a new anaerobic species isolated from feral chicken

2019 ◽  
Author(s):  
Supapit Wongkuna ◽  
Sudeep Ghimire ◽  
Surang Chankhamhaengdecha ◽  
Tavan Janvilisri ◽  
Joy Scaria
Keyword(s):  
Sequence Analysis ◽  
South Dakota ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
The 16S Rrna Gene

AbstractA Gram-positive, obligately anaerobic coccobacillus, with the white raised circular colony was isolated from the cecum of feral chickens in Brookings, South Dakota, USA. The 16S rRNA gene sequence analysis suggested that the closest species to strain SW178 was Ruminococcus torques ATCC 27756T (96.94% similarity) that belongs to the family Lachnospiraceae. The genome of strain SW178 is 3.18 Mbp with G+C content of 46.9 mol%. Based on the phylogenetic and phenotypic comparison, we propose that strain SW178 be assigned to the genus Ruminococcus as a novel species, for which the name Ruminococcus catenae is proposed. The type strain is SW178 (= CCOS 1886 T, =DSM 109242T).

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