scholarly journals Bacillus massiliensis sp. nov., isolated from cerebrospinal fluid

2006 ◽  
Vol 56 (7) ◽  
pp. 1485-1488 ◽  
Author(s):  
Olga O. Glazunova ◽  
Didier Raoult ◽  
Véronique Roux
Keyword(s):  
Cerebrospinal Fluid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Bacillus Sphaericus ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics

An unidentified Gram-negative-staining, aerobic, rod-shaped, spore-forming bacterium was isolated from a sample of cerebrospinal fluid. Based on comparative analysis of 16S rRNA gene sequences and phenotypic characteristics, the novel isolate was included in the Bacillus sphaericus-like group. The isolate was closely related to Bacillus odysseyi and Bacillus silvestris, with 96.2 and 94.4 % 16S rRNA gene sequence similarity, respectively. The major fatty acid was iso-C15 : 0 (48 %). The name Bacillus massiliensis sp. nov. is proposed for the novel isolate, with strain 4400831T (=CIP 108446T=CCUG 49529T) as the type strain.

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).

Gaetbulicola byunsanensis gen. nov., sp. nov., isolated from tidal flat sediment

2010 ◽  
Vol 60 (1) ◽  
pp. 196-199 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Yong-Taek Jung ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences

A Gram-negative, non-motile and pleomorphic bacterial strain, SMK-114T, which belongs to the class Alphaproteobacteria, was isolated from a tidal flat sample collected in Byunsan, Korea. Strain SMK-114T grew optimally at pH 7.0–8.0 and 25–30 °C and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain SMK-114T formed a cluster with Octadecabacter species, with which it exhibited 16S rRNA gene sequence similarity values of 95.2–95.4 %. This cluster was part of the clade comprising Thalassobius species with a bootstrap resampling value of 76.3 %. Strain SMK-114T exhibited 16S rRNA gene sequence similarity values of 95.1–96.3 % to members of the genus Thalassobius. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The DNA G+C content was 60.0 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SMK-114T is considered to represent a novel species in a new genus for which the name Gaetbulicola byunsanensis gen. nov., sp. nov. is proposed. The type strain of Gaetbulicola byunsanensis is SMK-114T (=KCTC 22632T =CCUG 57612T).

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 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 Plantactinospora sonchi sp. nov., an actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.)

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4895-4901 ◽  
Author(s):  
Zhaoxu Ma ◽  
Chongxi Liu ◽  
Jianlong Fan ◽  
Hairong He ◽  
Chuang Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Sonchus Oleraceus

A novel actinobacterium, designated strain NEAU-QY2T, was isolated from the leaves of Sonchus oleraceus L. specimen, collected from Wuchang, Heilongjiang Province, China. A polyphasic study was carried out to establish the taxonomic position of this strain. The organism formed single spores with rough surfaces on substrate mycelia. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-QY2T belonged to the genus Plantactinospora and formed a monophyletic clade with its closest related strains Plantactinospora endophytica YIM 68255T (99.2 % 16S rRNA gene sequence similarity), Plantactinospora veratri NEAU-FHS4T (98.8 %) and Plantactinospora mayteni YIM 61359T (98.7 %), an association that was supported by a bootstrap value of 90 % in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. However, DNA–DNA hybridization values between strain NEAU-QY2T and the three closely related strains were below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA–DNA hybridization results, strain NEAU-QY2T was distinguished from closely related strains and is classified as representing a novel species of the genus Plantactinospora, for which the name Plantactinospora sonchi sp. nov. is proposed. The type strain is NEAU-QY2T ( = CGMCC 4.7216T = JCM 30345T).

scholarly journals Gaetbulibacter aestuarii sp. nov., isolated from shallow coastal seawater, and emended description of the genus Gaetbulibacter

2012 ◽  
Vol 62 (1) ◽  
pp. 150-154 ◽  
Author(s):  
Seong Chan Park ◽  
Han Na Choe ◽  
Keun Sik Baik ◽  
Kang Hyun Lee ◽  
Chi Nam Seong
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Bacterium ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Emended Description ◽  
South Sea

A rod-shaped, yellow and strictly aerobic marine bacterium, designated KYW382T, was isolated from seawater collected from the South Sea, Republic of Korea. Cells were Gram-negative and catalase- and oxidase-positive. The major fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and anteiso-C15 : 0. The DNA G+C content was 32.4 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain KYW382T constituted an evolutionary lineage within the radiation enclosing the members of the genus Gaetbulibacter. The closest neighbour was Gaetbulibacter saemankumensis SMK-12T (96.1 % 16S rRNA gene sequence similarity). A number of phenotypic characteristics distinguished strain KYW382T from the described members of the genus Gaetbulibacter. On the basis of the data presented in this study, strain KYW382T represents a novel species, for which the name Gaetbulibacter aestuarii sp. nov. is proposed. The type strain is KYW382T ( = KCTC 23303T  = JCM 17455T). An emended description of the genus Gaetbulibacter is also given.

scholarly journals Thalassobius maritimus sp. nov., isolated from seawater

2012 ◽  
Vol 62 (1) ◽  
pp. 8-12 ◽  
Author(s):  
Sooyeon Park ◽  
Mi-Hwa Lee ◽  
Jung-Sook Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
The Mean ◽  
Type Strains

A Gram-stain-negative, aerobic, motile, rod-shaped bacterial strain, GSW-M6T, was isolated from seawater of Geoje island, Korea, and was subjected to a polyphasic taxonomic study. Strain GSW-M6T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain GSW-M6T clustered with Thalassobius aestuarii, Thalassobius gelatinovorus and Thalassobius mediterraneus. Strain GSW-M6T exhibited 96.2–96.9 % 16S rRNA gene sequence similarity to the type strains of these three Thalassobius species. Strain GSW-M6T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profiles of strain GSW-M6T and the type strains of the three Thalassobius species were similar, with phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid as common major components. The DNA G+C content of strain GSW-M6T was 57 mol%. The mean level of DNA–DNA relatedness between strain GSW-M6T and the type strain of Thalassobius gelatinovorus was 17 %. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, enabled strain GSW-M6T to be differentiated from recognized species of the genus Thalassobius. On the basis of the data presented, strain GSW-M6T is considered to represent a novel species of the genus Thalassobius, for which the name Thalassobius maritimus sp. nov. is proposed. The type strain is GSW-M6T ( = KCTC 23347T  = CCUG 60021T).

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).

Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1902-1907 ◽  
Author(s):  
Bédis Dridi ◽  
Marie-Laure Fardeau ◽  
Bernard Ollivier ◽  
Didier Raoult ◽  
Michel Drancourt
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Human Faeces ◽  
Link Type

During attempts to obtain novel, human-associated species of the domain Archaea , a coccoid micro-organism, designated strain B10T, was isolated in pure culture from a sample of human faeces collected in Marseille, France. On the basis of its phenotypic characteristics and 16S rRNA and mcrA gene sequences, the novel strain was classified as a methanogenic archaeon. Cells of the strain were non-motile, Gram-staining-positive cocci that were approximately 850 nm in diameter and showed autofluorescence at 420 nm. Cells were lysed by 0.1 % (w/v) SDS. With hydrogen as the electron donor, strain B10T produced methane by reducing methanol. The novel strain was unable to produce methane when hydrogen or methanol was the sole energy source. In an atmosphere containing CO2, strain B10T could not produce methane from formate, acetate, trimethylamine, 2-butanol, 2-propanol, cyclopentanol, 2-pentanol, ethanol, 1-propanol or 2,3-butanediol. Strain B10T grew optimally with 0.5–1.0 % (w/v) NaCl, at pH 7.6 and at 37 °C. It required tungstate-selenite for growth. The complete genome of the novel strain was sequenced; the size of the genome was estimated to be 2.05 Mb and the genomic DNA G+C content was 59.93 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the highest sequence similarities (98.0–98.7 %) were seen between strain B10T and several uncultured, methanogenic Archaea that had been collected from the digestive tracts of a cockroach, a chicken and mammals. In the same analysis, the non-methanogenic ‘Candidatus Aciduliprofundum boonei’ DSM 19572 was identified as the cultured micro-organism that was most closely related to strain B10T (83.0 % 16S rRNA gene sequence similarity). Each of the three treeing algorithms used in the analysis of 16S rRNA gene sequences indicated that strain B10T belongs to a novel order that is distinct from the Thermoplasmatales . The novel strain also appeared to be distinct from Methanosphaera stadtmanae DSM 3091T (72.9 % 16S rRNA gene sequence similarity), another methanogenic archaeon that was isolated from human faeces and can use methanol in the presence of hydrogen. Based on the genetic and phenotypic evidence, strain B10T represents a novel species of a new genus for which the name Methanomassiliicoccus luminyensis gen. nov., sp. nov. is proposed. The type strain of the type species is B10T ( = DSM 24529T = CSUR P135T).

scholarly journals Brevundimonas terrae sp. nov., isolated from an alkaline soil in Korea

2006 ◽  
Vol 56 (12) ◽  
pp. 2915-2919 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Jung-Sook Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
The Mean ◽  
Type Strains

A Gram-negative, rod-shaped, Brevundimonas-like bacterial strain, KSL-145T, was isolated from an alkaline soil in Korea and subjected to a polyphasic taxonomic investigation. Strain KSL-145T grew optimally at pH 7.5–8.0 and 30 °C without NaCl. It was characterized chemotaxonomically as containing Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The DNA G+C content was 61.8 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain KSL-145T fell within the radiation of the cluster comprising Brevundimonas species and Mycoplana bullata. The levels of 16S rRNA gene sequence similarity between strain KSL-145T and the type strains of Brevundimonas species and M. bullata ranged from 95.3 to 98.7 %. The mean DNA–DNA relatedness values between strain KSL-145T and the type strains of Brevundimonas diminuta and M. bullata, the closest phylogenetic relatives, were 26 and 15 %, respectively. Strain KSL-145T could be differentiated from Brevundimonas species and M. bullata by differences in several phenotypic characteristics. On the basis of the phenotypic, phylogenetic and genetic data, strain KSL-145T represents a novel species in the genus Brevundimonas, for which the name Brevundimonas terrae sp. nov. is proposed. The type strain is KSL-145T (=KCTC 12481T=JCM 13476T).

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