scholarly journals Sphingomonas vulcanisoli sp. nov., isolated from soil of a lava forest

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3320-3325 ◽  
Author(s):  
Keun Chul Lee ◽  
Kwang Kyu Kim ◽  
Jong-Shik Kim ◽  
Dae-Shin Kim ◽  
Suk-Hyung Ko ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Isoprenoid Quinone ◽  
Gram Stain ◽  
Rrna Gene Sequencing

A Gram-stain-negative, non-motile, yellow-pigmented and rod-shaped bacterial strain, designated SN6-13T, was isolated from soil of the Gotjawal, lava forest, located in Jeju, Republic of Korea. Cells of strain SN6-13T were oxidase- and catalase-positive. The isolate contained Q-10 as the predominant isoprenoid quinone, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the major fatty acids, sym-homospermidine as the major polyamine and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, ninhydrinphosphatidylglycerol and two unidentified aminophospholipids as the polar lipids. The DNA G+C content was 64.6 mol%. In phylogenetic analyses based on 16S rRNA gene sequencing, strain SN6-13T was most closely related to Sphingomonas laterariae LNB2T (95.4 % sequence similarity) and formed a separate lineage in the genus Sphingomonas. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, it is concluded that strain SN6-13T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas vulcanisoli sp. nov. is proposed. The type strain is SN6-13T ( = KCTC 42454T = CECT 8804T).

scholarly journals Mucilaginibacter gotjawali sp. nov., isolated from soil of a lava forest

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 952-958 ◽  
Author(s):  
Keun Chul Lee ◽  
Kwang Kyu Kim ◽  
Mi Kyung Eom ◽  
Jong-Shik Kim ◽  
Dae-Shin Kim ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gram Stain ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

A novel bacterial strain, designated SA3-7T, was isolated from soil of a lava forest located in Jeju, Republic of Korea. Cells of strain SA3-7T were Gram-stain-negative, oxidase- and catalase-positive, non-motile rods and produced creamy white colonies on ten-fold-diluted R2A agar. The isolate contained menaquinone-7 (MK-7) as the predominant isoprenoid quinone and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 43.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain SA3-7T was related most closely to Mucilaginibacter frigoritolerans FT22T (96.7 % sequence similarity) and that it formed a separate lineage in the genus Mucilaginibacter . Combined phenotypic, chemotaxonomic and phylogenetic characteristics supported the conclusion that strain SA3-7T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter gotjawali sp. nov. is proposed; the type strain is SA3-7T ( = KCTC 32515T = CECT 8628T = DSM 29289T).

scholarly journals Halomonas stevensii sp. nov., Halomonas hamiltonii sp. nov. and Halomonas johnsoniae sp. nov., isolated from a renal care centre

2010 ◽  
Vol 60 (2) ◽  
pp. 369-377 ◽  
Author(s):  
Kwang Kyu Kim ◽  
Keun Chul Lee ◽  
Hee-Mock Oh ◽  
Jung-Sook Lee
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Care Centre ◽  
Hybridization Data ◽  
Rrna Gene Sequencing

A total of 14 Halomonas strains were isolated from the blood of two patients and from dialysis machines of a renal care centre. The strains were Gram-negative, halophilic, motile and non-spore-forming rods. They produced cream-coloured colonies and contained Q-9 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. Phylogenetic analysis based on 16S rRNA gene sequencing showed that the 14 isolates were most closely related to Halomonas magadiensis 21 MIT with 98.1–98.9 % sequence similarity and that they formed three separate lineages among themselves. Combined phenotypic and DNA–DNA hybridization data support the conclusion that they represent three novel species of the genus Halomonas, for which the names Halomonas stevensii sp. nov. (type strain S18214T=KCTC 22148T=DSM 21198T), Halomonas hamiltonii sp. nov. (type strain W1025T=KCTC 22154T=DSM 21196T) and Halomonas johnsoniae sp. nov. (type strain T68687T=KCTC 22157T=DSM 21197T) are proposed.

scholarly journals Methanosarcina horonobensis sp. nov., a methanogenic archaeon isolated from a deep subsurface Miocene formation

2011 ◽  
Vol 61 (10) ◽  
pp. 2503-2507 ◽  
Author(s):  
Satoru Shimizu ◽  
Rahul Upadhye ◽  
Yoji Ishijima ◽  
Takeshi Naganuma
Keyword(s):  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Deep Subsurface ◽  
Optimum Ph ◽  
Rrna Gene Sequencing

A methanogenic organism, designated strain HB-1T, from the domain Archaea was isolated from groundwater sampled from a subsurface Miocene formation located in Horonobe, Hokkaido, Japan. The strain grew on methanol, dimethylamine, trimethylamine, dimethylsulfide and acetate but not on monomethylamine, H2/CO2, formate, 2-propanol, 2-butanol or cyclopentanol. Cells were Gram-reaction-negative, non-motile, irregular cocci that were 1.4–2.9 µm in diameter and occurred singly or in pairs. The strain grew at 20–42 °C (optimum 37 °C), at pH 6.0–7.75 (optimum pH 7.0–7.25) and in 0–0.35 M NaCl (optimum 0.1 M). The G+C content of the genomic DNA was 41.4 mol%. 16S rRNA gene sequencing revealed that the strain was a member of the genus Methanosarcina but that it clearly differed from all recognized species of this genus (93.1–97.9 % sequence similarity). The phenotypic and phylogenetic features of strain HB-1T indicate that it represents a novel species of the genus Methanosarcina, for which the name Methanosarcina horonobensis sp. nov. is proposed. The type strain is HB-1T ( = DSM 21571T  = JCM 15518T  = NBRC 102577T).

scholarly journals Leuconostoc durionis sp. nov., a heterofermenter with no detectable gas production from glucose

2005 ◽  
Vol 55 (3) ◽  
pp. 1267-1270 ◽  
Author(s):  
J. J. Leisner ◽  
M. Vancanneyt ◽  
R. Van der Meulen ◽  
K. Lefebvre ◽  
K. Engelbeen ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Gas Production ◽  
Rrna Gene ◽  
Nearest Neighbour ◽  
Sds Page ◽  
Rrna Gene Sequencing

Three lactic acid bacterial (LAB) strains obtained from a Malaysian acid-fermented condiment, tempoyak (made from pulp of the durian fruit), showed analogous but distinct patterns after screening by SDS-PAGE of whole-cell proteins and comparison with profiles of all recognized LAB species. 16S rRNA gene sequencing of one representative strain showed that the taxon belongs phylogenetically to the genus Leuconostoc, with its nearest neighbour being Leuconostoc fructosum (98 % sequence similarity). Biochemical characteristics and DNA–DNA hybridization experiments demonstrated that the strains differ from Leuconostoc fructosum and represent a single, novel Leuconostoc species for which the name Leuconostoc durionis sp. nov. is proposed. The type strain is LMG 22556T (=LAB 1679T=D-24T=CCUG 49949T).

scholarly journals Sutterella stercoricanis sp. nov., isolated from canine faeces

2004 ◽  
Vol 54 (5) ◽  
pp. 1581-1584 ◽  
Author(s):  
Hazel L. Greetham ◽  
Matthew D. Collins ◽  
Glenn R. Gibson ◽  
Catriona Giffard ◽  
Enevold Falsen ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Molecular Genetic ◽  
Gene Sequencing ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Anaerobic Conditions ◽  
Genetic Studies ◽  
Rrna Gene Sequencing

Morphological, biochemical and molecular genetic studies were carried out on an unknown non-spore-forming, Gram-negative, rod-shaped bacterium which was isolated from dog faeces. The bacterium grew under anaerobic conditions, was asaccharolytic, resistant to 20 % (v/v) bile and was oxidase- and urease-negative. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that the unidentified bacterium clustered with Sutterella wadsworthensis, although a sequence divergence of >5 % indicated that the bacterium from dog faeces represented a previously unrecognized subline within the genus. On the basis of the presented findings, a novel species, Sutterella stercoricanis sp. nov., is described. The type strain of Sutterella stercoricanis is 5BAC4T (=CCUG 47620T=CIP 108024T).

scholarly journals Microbacterium paludicola sp. nov., a novel xylanolytic bacterium isolated from swamp forest

2006 ◽  
Vol 56 (3) ◽  
pp. 535-539 ◽  
Author(s):  
Hye Yoon Park ◽  
Kwang Kyu Kim ◽  
Long Jin ◽  
Sung-Taik Lee
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Swamp Forest ◽  
Phenotypic Data ◽  
Cellular Fatty Acids ◽  
Rrna Gene Sequencing

A xylanolytic bacterium, US15T, was isolated from swamp forest soil in Ulsan, Korea. The cells of the novel strain were Gram-positive, non-motile, short-rod-shaped and showed chemotaxonomic properties that were consistent with its classification in the genus Microbacterium. Chemotaxonomic results showed MK-12 and MK-11 as major menaquinones, predominating iso- and anteiso-branched cellular fatty acids, glucose, galactose and mannose as cell-wall sugars, peptidoglycan-type B2β with glycolyl residues and a DNA G+C content of 66·5 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain US15T was closely related to Microbacterium arborescens IFO 3750T, Microbacterium imperiale IFO 12610T and Microbacterium ulmi LMG 20991T (96·9, 96·8 and 96·2 % similarities, respectively), and formed a separate lineage within the genus Microbacterium. Combined genotypic and phenotypic data showed that strain US15T (=DSM 16915T=KCTC 19080T) merits recognition as the type strain of a novel species within the genus Microbacterium, for which the name Microbacterium paludicola sp. nov. is proposed.

scholarly journals Corynebacterium canis sp. nov., isolated from a wound infection caused by a dog bite

2010 ◽  
Vol 60 (11) ◽  
pp. 2544-2547 ◽  
Author(s):  
Guido Funke ◽  
Ralf Englert ◽  
Reinhard Frodl ◽  
Kathryn A. Bernard ◽  
Steffen Stenger
Keyword(s):  
Novel Species ◽  
Molecular Genetic ◽  
Gene Sequencing ◽  
Genetic Data ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gram Stain ◽  
Dog Bite ◽  
Molecular Genetic Data ◽  
Rrna Gene Sequencing

A non-lipophilic, coryneform bacterium isolated from a patient's wound caused by a dog bite was characterized by phenotypic, chemotaxonomic and molecular genetic methods. Chemotaxonomic features suggested assignment of the unknown bacterium to the genus Corynebacterium. The isolate exhibited the following unusual features, which made it possible to phenotypically differentiate it from all other medically relevant corynebacteria: the Gram stain showed some very filamentous rods (>15 μm in length); some cells exhibited branching; colonies were domed and adherent to agar; the micro-organism was positive for pyrazinamidase, β-glucosidase, α-glucosidase and trypsin but negative for β-galactosidase. 16S rRNA gene sequencing and partial rpoB gene sequencing showed that the closest phylogenetic relative, Corynebacterium freiburgense, exhibited more than 1.9 % and 17.9 % divergence with the unknown bacterium, respectively. Based on both phenotypic and molecular genetic data, it is proposed that the isolate should be classified as a novel species, Corynebacterium canis sp. nov., with the type strain 1170T (=CCUG 58627T =DSM 45402T).

scholarly journals Gemella asaccharolytica sp. nov., isolated from human clinical specimens

2010 ◽  
Vol 60 (5) ◽  
pp. 1023-1026 ◽  
Author(s):  
Nurver Ulger-Toprak ◽  
Paula H. Summanen ◽  
Chengxu Liu ◽  
Marie-Claire Rowlinson ◽  
Sydney M. Finegold
Keyword(s):  
Type Strain ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gram Stain ◽  
Biochemical Tests ◽  
Clinical Specimens ◽  
Sequencing Studies ◽  
Taxonomic Methods ◽  
Rrna Gene Sequencing

Three strains of an unidentified Gram-stain-variable, fastidious, catalase-negative, capnophilic, non-spore-forming, coccus-shaped bacterium from human wound specimens were characterized by phenotypic and molecular taxonomic methods. Initially, these strains were anaerobic; with repeated culture, they became aerotolerant. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains were genealogically homogeneous and constituted a novel subline within the genus Gemella. The unknown bacterium was readily distinguished from other Gemella species by biochemical tests. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from clinical specimens be classified as Gemella asaccharolytica sp. nov. The type strain is WAL 1945JT (=ATCC BAA-1630T =CCUG 57045T).

scholarly journals Corynebacterium caspium sp. nov., from a Caspian seal (Phoca caspica)

2004 ◽  
Vol 54 (3) ◽  
pp. 925-928 ◽  
Author(s):  
Matthew D. Collins ◽  
Lesley Hoyles ◽  
Geoffrey Foster ◽  
Enevold Falsen
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Gene Sequencing ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Facultative Anaerobe ◽  
Phenotypic Differences ◽  
Rrna Gene Sequencing ◽  
Caspian Seal

A previously unknown Gram-positive, non-spore-forming, non-lipophilic, catalase-positive, irregular rod-shaped bacterium (M/106/00/5T) was isolated, in mixed culture, from the penis of a Caspian seal (Phoca caspica). The strain was a facultative anaerobe that was able to grow at 22 and 42 °C. Comparative 16S rRNA gene sequencing showed that the organism formed a hitherto unknown subline within the genus Corynebacterium. Sequence divergence values of more than 5 % from other described Corynebacterium species, together with phenotypic differences, showed that the unidentified bacterium represents a previously unrecognized member of this genus. On the basis of phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium isolated from a Caspian seal (strain M/106/00/5T=CCUG 44566T=CIP 107965T) be classified as the type strain of a novel species of the genus Corynebacterium, Corynebacterium caspium sp. nov.

scholarly journals Bacillus infantis sp. nov. and Bacillus idriensis sp. nov., isolated from a patient with neonatal sepsis

2006 ◽  
Vol 56 (11) ◽  
pp. 2541-2544 ◽  
Author(s):  
Kwan Soo Ko ◽  
Won Sup Oh ◽  
Mi Young Lee ◽  
Jang Ho Lee ◽  
Hyuck Lee ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacillus Firmus ◽  
Dna Reassociation ◽  
Microbiological Methods ◽  
Newborn Child ◽  
Rrna Gene Sequencing

Two Gram-positive bacilli, designated as strains SMC 4352-1T and SMC 4352-2T, were isolated sequentially from the blood of a newborn child with sepsis. They could not be identified by using conventional clinical microbiological methods. 16S rRNA gene sequencing and phylogenetic analysis revealed that both strains belonged to the genus Bacillus but clearly diverged from known Bacillus species. Strain SMC 4352-1T and strain SMC 4352-2T were found to be closely related to Bacillus firmus NCIMB 9366T (98.2 % sequence similarity) and Bacillus cibi JG-30T (97.1 % sequence similarity), respectively. They also displayed low DNA–DNA reassociation values (less than 40 %) with respect to the most closely related Bacillus species. On the basis of their polyphasic characteristics, strain SMC 4352-1T and strain SMC 4352-2T represent two novel species of the genus Bacillus, for which the names Bacillus infantis sp. nov. (type strain SMC 4352-1T=KCCM 90025T=JCM 13438T) and Bacillus idriensis sp. nov. (type strain SMC 4352-2T=KCCM 90024T=JCM 13437T) are proposed.

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