scholarly journals Description of Klebsiella indica sp. nov., isolated from the surface of tomato

2019 ◽  
Author(s):  
Sukriti Gujarati ◽  
Diptaraj Chaudhari ◽  
Mitesh Khairnar ◽  
Yogesh Shouche ◽  
Praveen Rahi
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Sequence ◽  
Agar Medium ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Strain Nctc ◽  
Distinct Branch

AbstractA novel bacterial strain designated TOUT106T was isolated from the surface of a tomato collected from the local vegetable market in Pune, India. The cells were rod shaped, Gram-stain-negative, encapsulated and non-motile. The strain TOUT106T grows as mucoid and translucent colonies on blood agar medium and the best growth was observed at 28°C and at pH 7.0, and could tolerate up to 2% (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain TOUT106T was placed under Salmonella clade, with close similarity to Salmonella enterica subsp. arizonae strain NCTC 8297T (98.42%). Genome-based phylogenetic analysis revealed that the strain forms a distinct branch within the Klebsiella clade and K. michiganensis DSM25444T and K. oxytoca NBRC105695T were the closest neighbor. The genomic DNA G+C content of strain TOUT106T was 53.53 mol%. The average nucleotide identity of TOUT106T was less 86.4% with closely related members of the family Enterobacteriaceae. The major fatty acids of strain TOUT106T were C16:0, C17:0 cyclo, C14:0 3OH/C16:1 iso, C14:0, C19:0cyclow8c, C18:1 w6c/C18:1 w7c, C12:0 and C16:1 w7c/C16:1 w6c. The strain TOUT106T showed differences in physiological, phenotypic and protein profiles by MALDI-TOF MS to its closest relatives. Based on the phenotypic including chemotaxonomic properties and phylogenetic analysis the strain TOUT106T could be distinguished from the recognized species of the genus Klebsiella, was suggested to represent a novel species of this genus, for which the name Klebsiella indica sp. nov. is proposed. The type strain is TOUT106T (=MCC 2901T).

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 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).

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).

Sphingomonas kyungheensis sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3848-3853 ◽  
Author(s):  
Heung-Min Son ◽  
Jung-Eun Yang ◽  
YongJin Park ◽  
Chang-Kyun Han ◽  
Song-Gun Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Family

A bacterial strain THG-B283T, which has β-glucosidase activity, was isolated from soil of a ginseng field. Cells were Gram-reaction-negative, oxidase- and catalase-positive, aerobic, motile with one polar flagellum and rod-shaped. The strain was subjected to a polyphasic taxonomic study. Strain THG-B283T grew optimally at around pH 7.0, at 25–28 °C and in the absence of NaCl on R2A agar. 16S rRNA gene sequence analysis revealed that strain THG-B283T belongs to the family Sphingomonadaceae and is closely related to Sphingomonas melonis DAPP-PG 224T (98.2 %), S. aquatilis JSS7T (98.1 %), S. insulae DS-28T (97.6 %), S. mali IFO 15500T (97.1 %) and S. pruni IFO 15498T (97.0 %). Strain THG-B283T contained Q-10 as the predominant ubiquinone. The major fatty acids included summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c, C14 : 0 2-OH and C16 : 0. The DNA G+C content was 72.2 mol%. The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipid, diphosphatidylglycerol, an unidentified glycolipid, unidentified aminolipids, an unidentified phospholipid and unidentified lipids. Genomic and chemotaxonomic data supported the affiliation of strain THG-B283T to the genus Sphingomonas . DNA–DNA relatedness between strain THG-B283T and its closest phylogenetic neighbours was below 23 %. On the basis of phenotypic, phylogenetic and genetic data, strain THG-B283T represents a novel species of genus Sphingomonas , for which the name Sphingomonas kyungheensis sp. nov. is proposed. The type strain is THG-B283T ( = KACC 16224T = LMG 26582T).

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).

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).

scholarly journals Polyphasic taxonomic study of strain CCM 2783 resulting in the description of Arthrobacter stackebrandtii sp. nov.

2005 ◽  
Vol 55 (2) ◽  
pp. 805-808 ◽  
Author(s):  
Ludmila Tvrzová ◽  
Peter Schumann ◽  
Cathrin Spröer ◽  
Ivo Sedláček ◽  
Susanne Verbarg ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Taxonomic Study ◽  
Rrna Gene Sequence ◽  
Dna Relatedness ◽  
Arthrobacter Aurescens ◽  
Gene Sequence Analysis

Strain CCM 2783, previously classified as representing Arthrobacter aurescens, was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis and chemotaxonomic characteristics such as peptidoglycan type A3α Lys–Ala2, major menaquinone MK-9(H2) and fatty acid composition confirmed assignment of the strain to the genus Arthrobacter. The results of phylogenetic analysis, DNA–DNA relatedness experiments and physiological and chemotaxonomic characteristics indicate that CCM 2783 differs from its nearest phylogenetic relative Arthrobacter psychrolactophilus and from other recognized Arthrobacter species. Therefore, a novel species, Arthrobacter stackebrandtii sp. nov., is proposed with the type strain CCM 2783T (=DSM 16005T).

scholarly journals Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium

2006 ◽  
Vol 56 (8) ◽  
pp. 1765-1769 ◽  
Author(s):  
Daniel Muller ◽  
Diliana D. Simeonova ◽  
Philippe Riegel ◽  
Sophie Mangenot ◽  
Sandrine Koechler ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Industrial Sludge ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Curved Rods

An arsenite-oxidizing bacterium, designated strain ULPAs1T, was isolated from industrial sludge heavily contaminated with arsenic. Cells of this isolate were Gram-negative, curved rods, motile by means of a polar flagellum. The strain was positive for oxidase and catalase activities, was able to reduce nitrate to nitrite, used acetate, lactate and peptone as organic carbon sources under aerobic conditions and was able to oxidize arsenite (As[III]) to arsenate (As[V]). 16S rRNA gene sequence analysis and the absence of dodecanoic fatty acids suggested that this strain represents a member of the genus Herminiimonas of the family Oxalobacteraceae, order Burkholderiales in the Betaproteobacteria. Genomic DNA–DNA hybridization between strain ULPAs1T and Herminiimonas fonticola S-94T and between strain ULPAs1T and Herminiimonas aquatilis CCUG 36956T revealed levels of relatedness of <10 %, well below the recommended 70 % species cut-off value. Thus, strain ULPAs1T (=CCM 7303T=DSM 17148T=LMG 22961T) is the type strain of a novel species of Herminiimonas, for which the name Herminiimonas arsenicoxydans sp. nov. is proposed.

Amnibacterium kyonggiense gen. nov., sp. nov., a new member of the family Microbacteriaceae

2011 ◽  
Vol 61 (1) ◽  
pp. 155-159 ◽  
Author(s):  
Sun-Jung Kim ◽  
Sang-Seob Lee
Keyword(s):  
New Genus ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Diamino Acid ◽  
Taxonomic Approach

A Gram-positive, non-motile bacterium, designated KSL51201-037T, was isolated from Anyang stream, Republic of Korea, and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain KSL51201-037T belonged to the family Microbacteriaceae of the class Actinobacteria and exhibited 96.9 % gene sequence similarity to Labedella gwakjiensis KSW2-17T, 96.0 % to Leifsonia ginsengi wged11T and 95.9 % to Microterricola viridarii KV-677T. The G+C content of the genomic DNA was 72.7 mol%. Strain KSL51201-037T had l-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, MK-11 and MK-12 as the major menaquinones, anteiso-C15 : 0 (47.8 %) and iso-C16 : 0 (24.0 %) as the major fatty acids and phosphatidylglycerol and three unknown phospholipids as the major polar lipids. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, it is suggested that strain KSL51201-037T represents a novel species of a new genus in the family Microbacteriaceae for which the name Amnibacterium kyonggiense gen. nov., sp. nov. is proposed. The type strain of the type species is KSL51201-037T (=KEMC 51201-037T=JCM 16463T).

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