Vibrio ulleungensis sp. nov., isolated from Mytilus coruscus

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Yea-Lin Moon ◽  
Jin-Sook Park
Keyword(s):  
Type Species ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Mytilus Coruscus ◽  
Link Type ◽  
Light Yellow ◽  
Rrna Gene Sequencing

A Gram-stain-negative, rod-shaped, motile via polar flagellum, facultatively aerobic, light-yellow, bacterium (designated 188UL20-2T) was isolated from a mussel sample of Mytilus coruscus collected on Ulleung Island, Ulleung-gun, Gyeongsangbuk-do, Republic of Korea. On the basis of 16S rRNA gene sequencing results, strain 188UL20-2T clustered with species of the genus Vibrio and appeared closely related to Vibrio marisflavi DSM 23086T (96.59%), Vibrio variabilis DSM 26147T (96.57%), Vibrio penaeicida DSM 14398T (96.37%) and Vibrio litoralis DSM 17657T (95.97%). The average nucleotide identity and digital DNA–DNA hybridization values between strain 188UL20-2T and its closest related strain were 71.3 and 16.4%, indicating that 188UL20-2T represents a novel species of the genus Vibrio . Growth occurred at 18–37 °C on MA medium in the presence of 1–4% NaCl (w/v) and at pH 5.0–10.0. The DNA G+C content of the genomic DNA was 45.4 mol%, and ubiquinone-8 (Q-8) was the major respiratory quinone. The major cellular fatty acids (>5%) were C16:1 ω6c and/or C16:1 ω7c (summed feature 3), C18:1 ω7c and/or C18:1 ω6c (summed feature 8), C16:0, C16:0 iso, C14:0, C14:0 iso and C12:0. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, unidentified aminophospholipid, unidentified glycolipid and seven unidentified lipids. Physiological and biochemical characteristics indicated that strain 188UL20-2T represents a novel species of the genus Vibrio , for which the name Vibrio ulleungensis sp. nov. is proposed. The type strain is 188UL20-2T (=KACC 22258T=LMG 32202T).

scholarly journals Pseudogulbenkiania gefcensis sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 187-191 ◽  
Author(s):  
Dong-Geol Lee ◽  
Dong-Moon Im ◽  
HeeCheol Kang ◽  
Pyeong Yun ◽  
Sun-Ki Park ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Sequencing Studies ◽  
Major Respiratory Quinone ◽  
Rrna Gene Sequencing

A novel strain, yH16, was isolated on nutrient agar from soil samples collected at KyungHee University, Suwon City, Republic of Korea. Cells of strain yH16T were short rods, Gram-negative-staining, motile and non-spore-forming, with a polar flagellum. Biochemical and molecular characterization revealed that this strain was most similar to Pseudogulbenkiania subflava BP-5T. Further 16S rRNA gene sequencing studies revealed that the new strain clustered with Pseudogulbenkiania subflava BP-5T (95.9 % similarity), Paludibacterium yongneupense 5YN8-15T (95.2 % similarity), Gulbenkiania mobilis E4FC31-5T (94.6 % similarity) and Chromobacterium aquaticum CC-SE-YA-1T (93.9 % similarity). The isolate was able to grow at 25–40 °C, 0.3–2 % NaCl and pH 5.5–7. The DNA G+C content was 65.9±1.0 mol%. The predominant fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16:0. Ubiquinone 8 was the major respiratory quinone. It was evident from the data obtained that the strain should be classified as a novel species of the genus Pseudogulbenkiania . The name proposed for this taxon is Pseudogulbenkiania gefcensis sp. nov., and the type strain is yH16T ( = KCCM 90100T = JCM 17850T).

Chryseobacterium panacisoli sp. nov., isolated from ginseng-cultivation soil with ginsenoside-converting activity

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Dong Ho Keum ◽  
Jun Mo Yeon ◽  
Chan-Seok Yun ◽  
Soon Youl Lee ◽  
Wan-Taek Im
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Active Components ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing ◽  
Ginseng Cultivation

A Gram-stain-negative, non-motile, non-spore-forming, aerobic, rod-shaped and yellow-pigmented bacterium, designated strain Gsoil 183T, was isolated from ginseng-cultivation soil sampled in Pocheon Province, Republic of Korea. This bacterium was characterized to determine its taxonomic position by using a polyphasic approach. Strain Gsoil 183T grew at 10–37 °C and at pH 5.0–9.0 on tryptic soy agar. Strain Gsoil 183T had β-glucosidase activity, which was responsible for its ability to convert ginsenoside Rb1 (one of the dominant active components of ginseng) to F2. Based on 16S rRNA gene sequencing, strain Gsoil 183T clustered with species of the genus Chryseobacterium and appeared to be closely related to Chryseobacterium sediminis LMG 28695T (99.1 % sequence similarity), Chryseobacterium lactis NCTC 11390T (98.6%), Chryseobacterium rhizoplanae LMG 28481T (98.6%), Chryseobacterium oncorhynchi CCUG 60105T (98.5%), Chryseobacterium viscerum CCUG 60103T (98.4%) and Chryseobacterium joostei DSM 16927T (98.3%). Menaquinone MK-6 was the predominant respiratory quinone and the major fatty acids were iso-C15 : 0, iso-C17 : 0-3OH and summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c). The polar lipids were phosphatidylethanolamine, six unidentified glycolipids, five unidentified aminolipids and three unidentified lipids. The G+C content of the genomic DNA was 36.6 mol%. Digital DNA–DNA hybridization between strain Gsoil 183T and the type strains of C. sediminis , C. lactis , C. rhizoplanae , C. oncorhynchi , C. viscerum and C. joostei resulted in values below 70 %. Strain Gsoil 183T could be differentiated genotypically and phenotypically from the recognized species of the genus Chryseobacterium . The isolate therefore represents a novel species, for which the name Chryseobacterium panacisoli sp. nov. is proposed, with the type strain Gsoil 183T (=KACC 15033T=LMG 23397T)

Vibrio caribbeanicus sp. nov., isolated from the marine sponge Scleritoderma cyanea

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1736-1743 ◽  
Author(s):  
Maria Hoffmann ◽  
Steven R. Monday ◽  
Marc W. Allard ◽  
Errol A. Strain ◽  
Paul Whittaker ◽  
...  
Keyword(s):  
Marine Sponge ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

A Gram-negative, oxidase-positive, catalase-negative, facultatively anaerobic, motile, curved rod-shaped bacterium, strain N384T, was isolated from a marine sponge (Scleritoderma cyanea; phylum Porifera) collected from a depth of 795 feet (242 m) off the west coast of Curaçao. On the basis of 16S rRNA gene sequencing, strain N384T was shown to belong to the genus Vibrio , most closely related to Vibrio brasiliensis LMG 20546T (98.8 % similarity), Vibrio nigripulchritudo ATCC 27043T (98.5 %), Vibrio tubiashii ATCC 19109T (98.6 %) and V. sinaloensis DSM 21326T (98.2 %). The DNA G+C content of strain N384T was 41.6 mol%. An analysis of concatenated sequences of five genes (gyrB, rpoA, pyrH, mreB and ftsZ; 4068 bp) demonstrated a clear separation between strain N384T and its closest neighbours and clustered strain N384T into the ‘Orientalis’ clade of vibrios. Phenotypically, the novel species belonged to the arginine dihydrolase-positive, lysine decarboxylase- and ornithine decarboxylase-negative (A+/L−/O−) cluster. The novel species was also differentiated on the basis of fatty acid composition, specifically that the proportions of iso-C13 : 0, iso-C15 : 0, C15 : 0, iso-C16 : 0, C16 : 0, iso-C17 : 0, C17 : 1ω8c and C17 : 0 were significantly different from those found in V. brasiliensis and V. sinaloensis . The results of DNA–DNA hybridization, average nucleotide identity and physiological and biochemical tests further allowed differentiation of this strain from other described species of the genus Vibrio . Collectively, these findings confirm that strain N384T represents a novel Vibrio species, for which the name Vibrio caribbeanicus sp. nov. is proposed, with the type strain N384T ( = ATCC BAA-2122T = DSM 23640T).

scholarly journals Pantoea rodasii sp. nov., Pantoea rwandensis sp. nov. and Pantoea wallisii sp. nov., isolated from Eucalyptus

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1457-1464 ◽  
Author(s):  
Carrie L. Brady ◽  
Ilse Cleenwerck ◽  
Lorinda van der Westhuizen ◽  
Stephanus N. Venter ◽  
Teresa A. Coutinho ◽  
...  
Keyword(s):  
South Africa ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Culture Collection ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

Several Gram-negative-staining, facultatively anaerobic bacterial isolates were obtained from Eucalyptus seedlings showing symptoms of bacterial blight and dieback in Colombia, Rwanda and South Africa. Partial 16S rRNA gene sequencing, together with partial gyrB sequencing, placed the isolates in the genus Pantoea and indicated that they constituted three novel species. Multilocus sequence analysis (MLSA) based on partial sequences of gyrB, rpoB, infB and atpD revealed Pantoea dispersa , Pantoea eucrina and Pantoea cypripedii as their closest phylogenetic relatives. DNA–DNA hybridization studies confirmed the classification of the new isolates as three novel species and phenotypic tests allowed them to be differentiated from their closest phylogenetic neighbours. The names Pantoea rodasii sp. nov. [type strain LMG 26273T = BD 943T (deposited with the Plant Pathogenic and Plant Protecting Bacteria Collection, South Africa) = BCC 581T (deposited with the Bacterial Culture Collection, Forestry and Agricultural Institute, South Africa)], Pantoea rwandensis sp. nov. (type strain LMG 26275T = BD 944T = BCC 571T) and Pantoea wallisii sp. nov. (type strain LMG 26277T = BD 946T = BCC 682T) are proposed.

Gemmobacter megaterium sp. nov., isolated from coastal planktonic seaweeds

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 66-71 ◽  
Author(s):  
Jin-Jin Liu ◽  
Xin-Qi Zhang ◽  
Fang-Tao Chi ◽  
Jie Pan ◽  
Cong Sun ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Sea Salts ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile and aerobic bacterium, designated CF17T, was isolated from coastal planktonic seaweeds, East China Sea. The isolate grew at 18–37 °C (optimum 25–28 °C), pH 6.5–9.0 (optimum 7.0–8.0) and with 0–5 % NaCl (optimum 1–2 %, w/v) and 0.5–10 % sea salts (optimum 2–3 %, w/v). Growth of strain CF17T could be stimulated prominently by supplementing the growth medium with the autoclaved supernatant of a culture of strain CF5, which was isolated from the same sample along with strain CF17T. The cell morphology of strain CF17T was a bean-shaped rod consisting of a swollen end and a long prostheca. The phylogenetic analysis of 16S rRNA gene sequences indicated that strain CF17T clustered with Gemmobacter nectariphilus DSM 15620T within the genus Gemmobacter . The DNA G+C content of strain CF17T was 61.4 mol%. The respiratory quinone was ubiquinone Q-10. The major fatty acids included C18 : 1ω7c and C18 : 0. The polar lipids of strain CF17T consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two uncharacterized phospholipids, one uncharacterized aminolipid, three uncharacterized glycolipids and one uncharacterized lipid. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain CF17T ( = CGMCC 1.11024T = JCM 18498T) is considered to represent a novel species of the genus Gemmobacter , for which the name Gemmobacter megaterium sp. nov. is proposed.

Geobacter luticola sp. nov., an Fe(III)-reducing bacterium isolated from lotus field mud

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 442-448 ◽  
Author(s):  
Samson Viulu ◽  
Kohei Nakamura ◽  
Yurina Okada ◽  
Sakiko Saitou ◽  
Kazuhiro Takamizawa
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Physiological Tests ◽  
Straight Rod

A novel species of Fe(III)-reducing bacterium, designated strain OSK6T, belonging to the genus Geobacter , was isolated from lotus field mud in Japan. Strain OSK6T was isolated using a solid medium containing acetate, Fe(III)-nitrilotriacetate (NTA) and gellan gum. The isolate is a strictly anaerobic, Gram-negative, motile, straight rod-shaped bacterium, 0.6–1.9 µm long and 0.2–0.4 µm wide. The growth of the isolate occurred at 20–40 °C with optima of 30–37 °C and pH 6.5–7.5 in the presence of up to 0.5 g NaCl l−1. The G+C content of the genomic DNA was determined by HPLC to be 59.7 mol%. The major respiratory quinone was MK-8. The major fatty acids were 16 : 1ω7c and 16 : 0. Strain OSK6T was able to grow with Fe(III)-NTA, ferric citrate, amorphous iron (III) hydroxide and nitrate, but not with fumarate, malate or sulfate as electron acceptors. Among examined substrates grown with Fe(III)-NTA, the isolate grew on acetate, lactate, pyruvate and succinate. Analysis of the near full-length 16S rRNA gene sequence revealed that strain OSK6T is closely related to Geobacter daltonii and Geobacter toluenoxydans with 95.6 % similarity to the type strains of these species. On the basis of phylogenetic analysis and physiological tests, strain OSK6T is described as a representative of a novel species, Geobacter luticola sp. nov.; the type strain is OSK6T ( = DSM 24905T = JCM 17780T).

Emendation of the description of the species Corynebacterium propinquum to include strains which produce urease

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2146-2154 ◽  
Author(s):  
Kathryn Bernard ◽  
Ana Luisa Pacheco ◽  
Ian Cunningham ◽  
Navdeep Gill ◽  
Tamara Burdz ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Single Test ◽  
Content Type ◽  
Link Type ◽  
Corynebacterium Pseudodiphtheriticum ◽  
Rrna Gene Sequencing

Corynebacterium propinquum is a Gram-positive rod occasionally recovered from clinical infections which, according to 16S rRNA gene sequencing, is most closely related (>99 % sequence similarity) to Corynebacterium pseudodiphtheriticum . The two species are very similar biochemically, commonly differentiated by a single test, the detection of urease, where strains of C. propinquum are described as being urease-non-producing and strains of C. pseudodiphtheriticum are described as urease-producing. In this study, historical and contemporary strains of C. propinquum and C. pseudodiphtheriticum from this laboratory were definitively characterized, which included use of rpoB sequencing. Urease-producing strains of C. propinquum as well as typical urease-non-producing isolates were identified after rpoB sequencing, with six of these being originally identified as C. pseudodiphtheriticum . Based on these observations, we propose emendation of the description of C. propinquum to include strains which produce urease. MALDI-TOF analysis may be a useful tool to differentiate these taxa. Existing commercial databases should be updated to include urease-positive strains of C. propinquum .

scholarly journals Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov.

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1486-1490 ◽  
Author(s):  
Dominique Clermont ◽  
Laurence Motreff ◽  
Virginie Passet ◽  
José-Carlos Fernandez ◽  
Chantal Bizet ◽  
...  
Keyword(s):  
Type Species ◽  
16S Rrna Gene Sequencing ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Rrna Gene Sequencing

Strains originating from various sources and classified as members of the genus Citrobacter within the family Enterobacteriaceae were characterized by sequencing internal portions of genes rpoB, fusA, pyrG and leuS, 16S rRNA gene sequencing, average nucleotide identity (ANI) of genomic sequences and biochemical tests. Phylogenetic analysis based on the four housekeeping genes showed that the 11 species of the genus Citrobacter with validly published names are well demarcated. Strains CIP 55.13T and CIP 55.9 formed a distinct branch associated with Citrobacter youngae . The ANI between CIP 55.9 and CIP 55.13T was 99.19 %, whereas it was 94.75 % between CIP 55.13T and strain CIP 105016T of the species C. youngae , the most closely related species. Biochemical characteristics consolidated the fact that the two isolates represent a separate species, for which the name Citrobacter pasteurii sp. nov. is proposed. The type strain is CIP 55.13T ( = DSM 28879T = Na 1aT).

Steroidobacter gossypii sp. nov., isolated from cotton field soil

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Rui-Rui Huang ◽  
Xian-Feng Ge ◽  
Xin-Kai Chen ◽  
Shen-Rong Yang ◽  
Cheng Zhen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Novel Species ◽  
Draft Genome ◽  
Cotton Field ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A Gram-negative bacterium, designated S1-65T, was isolated from soil samples collected from a cotton field located in the Xinjiang region of PR China. Results of 16S rRNA gene sequence analysis revealed that strain S1-65T was affiliated to the genus Steroidobacter with its closest phylogenetic relatives being ‘Steroidobacter cummioxidans’ 35Y (98.4 %), ‘ Steroidobacter agaridevorans ’ SA29-B (98.3 %) and Steroidobacter agariperforans KA5-BT (98.3 %). 16S rRNA-directed phylogenetic analysis showed that strain S1-65T formed a unique phylogenetic subclade next to ‘ S. agaridevorans ’ SA29-B and S. agariperforans KA5-BT, suggesting that strain S1-65T should be identified as a member of the genus Steroidobacter . Further, substantial differences between the genotypic properties of strain S1-65T and the members of the genus Steroidobacter , including average nucleotide identity and digital DNA–DNA hybridization, resolved the taxonomic position of strain S1-65T and suggested its positioning as representing a novel species of the genus Steroidobacter . The DNA G+C content of strain S1-65T was 62.5 mol%, based on its draft genome sequence. The predominant respiratory quinone was ubiquinone-8. The main fatty acids were identified as summed feature 3 (C16:1ω6c/C16:1ω7c), C16 : 0 and iso-C15 : 0. In addition, its polar lipid profile was composed of aminophospholipid, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Here, we propose a novel species of the genus Steroidobacter : Steroidobacter gossypii sp. nov. with the type strain S1-65T (=JCM 34287T=CGMCC 1.18736T).

Amorphus suaedae sp. nov., isolated from the root of a tidal flat plant, Suaeda maritima

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3868-3872 ◽  
Author(s):  
Jung Moon Hwang ◽  
Eu Jin Chung ◽  
Jeong Ae Park ◽  
Jae Heon Jeong ◽  
Che Ok Jeon ◽  
...  
Keyword(s):  
Tidal Flat ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Ubiquinone 10

A novel bacterial strain, YC6899T, was isolated from the root of Suaedae maritima growing on a tidal flat of Namhae Island, Korea. Cells were Gram-reaction-negative, rod-shaped, non-motile, slightly halophilic and heterotrophic. Strain YC6899T grew optimally at a salinity of 2–4 %, at 25–37 °C and at pH 6.5–8.0. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that strain YC6899T was closely related to Amorphus orientalis YIM D10T (96.1 % similarity) and Amorphus coralli RS.Sph.026T (95.9 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown aminolipids, an unknown aminophospholipid, an unknown aminoglycolipid, unknown glycolipids and unknown lipids. The major fatty acids of strain YC6899T were C19 : 0 cyclo ω8c and C18 : 1ω7c. The G+C content of the genomic DNA was 61.3 mol%. Strain YC6899T contained ubiquinone-10 (Q-10) as the major respiratory quinone system. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YC6899T represents a novel species within the genus Amorphus , for which the name Amorphus suaedae sp. nov. is proposed. The type strain is YC6899T ( = KACC 14912T = NBRC 107845T).

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