scholarly journals Vibrio litoralis sp. nov., isolated from a Yellow Sea tidal flat in Korea

2007 ◽  
Vol 57 (3) ◽  
pp. 562-565 ◽  
Author(s):  
Young-Do Nam ◽  
Ho-Won Chang ◽  
Ja Ryeong Park ◽  
Hyuk-Yong Kwon ◽  
Zhe-Xue Quan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Arginine Dihydrolase ◽  
Wide Range ◽  
Branching Point

Two Gram-negative, facultatively anaerobic bacterial strains, MANO22DT and MANO22P, were isolated from a tidal flat area of Dae-Chun, Chung-Nam, Korea. The isolates were rod-shaped and were motile by means of one or more polar flagella. They grew at 1–12 % NaCl, 4–45 °C and pH 4.1–8.8 and were oxidase-positive, arginine dihydrolase-negative and sensitive to the vibriostatic agent O/129. The isolates required Na+ for growth, produced acid, but no gas, from d-glucose under anaerobic conditions and utilized a wide range of compounds as sole carbon and energy sources. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains belong to the Gammaproteobacteria and are specifically related to Vibrio species. They were most closely related to Vibrio rumoiensis FERM P-14531T, with which they were found to share 98.65 % 16S rRNA gene sequence similarity. In the phylogenetic tree, the two novel strains comprised a relatively long subline of descent, sharing a branching point with the outlying species V. rumoiensis, and were found to occupy a phylogenetically distant position on the main Vibrio branch. The levels of DNA–DNA hybridization with respect to V. rumoiensis FERM P-14531T, which is their most closely related phylogenetically related Vibrio species, were 7.4 % (MANO22DT) and 3.9 % (MANO22P). Thus, the two novel isolates appear to represent a novel species within the genus Vibrio, for which the name Vibrio litoralis sp. nov. is proposed. The type strain is MANO22DT (=KCTC 12520T=DSM 17657T).

scholarly journals Shewanella affinis sp. nov., isolated from marine invertebrates

2004 ◽  
Vol 54 (4) ◽  
pp. 1089-1093 ◽  
Author(s):  
Elena P. Ivanova ◽  
Olga I. Nedashkovskaya ◽  
Tomoo Sawabe ◽  
Natalia V. Zhukova ◽  
Galina M. Frolova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Marine Invertebrates ◽  
Sequence Similarity ◽  
Tween 20 ◽  
Rrna Gene ◽  
The Novel ◽  
Bacterial Strains ◽  
North West

Four marine bacterial strains, designated KMM 3587T, KMM 3586, KMM 3821 and KMM 3822, were isolated from the sipuncula Phascolosoma japonicum, a common inhabitant of Troitza Bay in the Gulf of Peter the Great (Sea of Japan region), and from an unidentified hydrocoral species collected in Makarov Bay (Iturup Islands), Kuril Islands, North-West Pacific Ocean. The strains were characterized to clarify their taxonomic position. 16S rRNA gene sequences of KMM 3587T and KMM 3586 indicated 99 % similarity to Shewanella colwelliana. Despite such a high level of 16S rRNA gene sequence similarity, DNA–DNA hybridization experiments demonstrated only 45–52 % binding with DNA of S. colwelliana ATCC 39565T. The DNA G+C contents of the novel strains were 45 mol% and the shared level of DNA hybridization was conspecific (81–97 %), indicating that they represent a single genospecies. The novel strains were mesophilic (able to grow at 10–34 °C), neutrophilic and haemolytic, and able to degrade gelatin, casein and Tween 20, 40 and 80, but not starch, agar, elastin, alginate or chitin. The major fatty acids were i13 : 0, i15 : 0, 16 : 0, 16 : 1ω7 and 17 : 1ω8 (68·9 % of total). The major isoprenoid quinones were Q7 (47–62 %) and Q8 (26–47 %). Eicosapentaenoic acid was produced in minor amounts. Based on these data, the strains are assigned to a novel species, Shewanella affinis sp. nov. (type strain KMM 3587T=CIP 107703T=ATCC BAA-642T).

scholarly journals Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa

2006 ◽  
Vol 56 (4) ◽  
pp. 889-893 ◽  
Author(s):  
Cheng-Hui Xie ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Rrna Gene Sequence ◽  
Bacterial Strains

Three yellow-pigmented strains associated with rice plants were characterized by using a polyphasic approach. The nitrogen-fixing abilities of these strains were confirmed by acetylene reduction assay and nifH gene detection. The three strains were found to be very closely related, with 99·9 % 16S rRNA gene sequence similarity and greater than 70 % DNA–DNA hybridization values, suggesting that the three strains represent a single species. 16S rRNA gene sequence analysis indicated that the strains were closely related to Sphingomonas trueperi, with 99·5 % similarity. The chemotaxonomic characteristics (G+C content of the DNA of 68·0 mol%, ubiquinone Q-10 system, 2-OH as the only hydroxy fatty acid and homospermidine as the sole polyamine) were similar to those of members of the genus Sphingomonas. Based on DNA–DNA hybridization values and physiological characteristics, the three novel strains could be differentiated from other recognized species of the genus Sphingomonas. The name Sphingomonas azotifigens sp. nov. is proposed to accommodate these bacterial strains; the type strain is Y39T (=NBRC 15497T=IAM 15283T=CCTCC AB205007T).

scholarly journals Gaetbulibacter saemankumensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat sediment in Korea

2005 ◽  
Vol 55 (5) ◽  
pp. 1845-1849 ◽  
Author(s):  
Seo-Youn Jung ◽  
So-Jung Kang ◽  
Mi-Hwa Lee ◽  
Soo-Young Lee ◽  
Tae-Kwang Oh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Tidal Flat Sediment ◽  
Distinct Evolutionary Lineage ◽  
The Family

Three Gram-negative, yellow-pigmented, rod-shaped bacterial strains, SMK-12T, SMK-36 and SMK-45, were isolated from a tidal flat sediment of the Yellow Sea in Korea, and their taxonomic positions were investigated by a polyphasic approach. The three strains grew optimally at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. They contained MK-6 as the predominant menaquinone. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1, anteiso-C15 : 0, iso-C15 : 0 3-OH and C16 : 1 ω7c and/or iso-C15 : 0 2-OH. The DNA G+C contents of the three strains were 34·7–34·9 mol%. The phylogenetic tree based on 16S rRNA gene sequences revealed that the three strains form one distinct evolutionary lineage supported by a bootstrap value of 100 % within the family Flavobacteriaceae. The three strains exhibited 16S rRNA gene sequence similarity levels of 93·8–94·9 % to the nearest phylogenetic neighbours, the genera Algibacter, Bizionia and Formosa. On the basis of differences in phenotypic characteristics and phylogenetic distinctiveness, strains SMK-12T, SMK-36 and SMK-45 were classified in a novel genus and species, for which the name Gaetbulibacter saemankumensis gen. nov., sp. nov. is proposed. The type strain for the novel species is SMK-12T (=KCTC 12379T=DSM 17032T).

Lactobacillus siliginis sp. nov., isolated from wheat sourdough in South Korea

2006 ◽  
Vol 56 (9) ◽  
pp. 2209-2213 ◽  
Author(s):  
Zubair Aslam ◽  
Wan-Taek Im ◽  
Leonid N. Ten ◽  
Myung-jin Lee ◽  
Kyoung-Ho Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
South Korea ◽  
Dna Hybridization ◽  
Genomic Dna ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Optimum Growth Temperature ◽  
Range Of Values

The taxonomic position of two lactic-acid-producing bacterial strains, isolated from wheat sourdough in South Korea, was studied using a polyphasic approach. Phylogenetic analysis on the basis of 16S rRNA gene sequences and biochemical and physiological characteristics indicated these two strains to be members of the genus Lactobacillus. They had high 16S rRNA gene sequence similarity (98.5 %) with Lactobacillus rossiae DSM 15814T and very low (<94.0 %) similarity with any other recognized species of the genus Lactobacillus. These two strains (designated M1-212T and M2-236) were heterofermentative, facultatively anaerobic, Gram-positive, non-spore-forming, non-motile, short rod-shaped bacteria. The optimum growth temperature for these strains was 30 °C (no growth at 15 or 45 °C) and they were able to tolerate 5 % (w/v) NaCl. The G+C content of the genomic DNA of the two strains was 45.5 mol%, within the range of values reported for the genus Lactobacillus (32–53 mol%). The peptidoglycan was of the A3α (l-lys–d-glu–l-Ala) type. Physiological, biochemical and genotypic data, as well as results of DNA–DNA hybridization of the genomic DNA with one of the closest phylogenetic relatives, L. rossiae DSM 15814T, indicated that the strains represent a novel species of the genus Lactobacillus, for which the name Lactobacillus siliginis sp. nov. is proposed. The type strain is M1-212T (=KCTC 3985T=NBRC 101315T).

scholarly journals Lactobacillus rennini sp. nov., isolated from rennin and associated with cheese spoilage

2006 ◽  
Vol 56 (2) ◽  
pp. 449-452 ◽  
Author(s):  
Empar Chenoll ◽  
M. Carmen Macián ◽  
Rosa Aznar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Bacterial Strains ◽  
Specific Primers ◽  
Lactobacillus Coryniformis

Two bacterial strains, DSM 20253T and DSM 20254, isolated from rennin and regarded as causing cheese spoilage, were deposited in the DSMZ as Lactobacillus sp. by J. Stadhouders. The strains show 99·9 % 16S rRNA gene sequence similarity and have less than 94·3 % similarity with any other species of the genus. Lactobacillus coryniformis is their closest phylogenetic neighbour. DNA–DNA hybridization experiments confirmed that the two strains are members of the same species with separate status within the genus Lactobacillus. The strains are homofermentative lactic acid bacteria and can be phenotypically and genotypically distinguished from their closest relatives. 16S rRNA gene-targeted specific primers were designed to enable PCR detection of the novel species. The name Lactobacillus rennini sp. nov. is proposed for the novel isolates, with strain CECT 5922T (=DSM 20253T) as the type strain.

scholarly journals Sphaerochaeta associata sp. nov., a spherical spirochaete isolated from cultures of Methanosarcina mazei JL01

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4315-4322 ◽  
Author(s):  
Olga Troshina ◽  
Viktoria Oshurkova ◽  
Natalia Suzina ◽  
Andrei Machulin ◽  
Elena Ariskina ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Methanosarcina Mazei ◽  
Wide Range

An anaerobic, saccharolytic bacterial strain designated GLS2T was isolated from aggregates of the psychrotolerant archaeon Methanosarcina mazei strain JL01 isolated from arctic permafrost. Bacterial cells were non-motile, spherical, ovoid and annular with diameter 0.2–4 μm. They were chemoorganoheterotrophs using a wide range of mono-, di- and trisaccharides as carbon and energy sources. The novel isolate required yeast extract and vitamins for growth. The bacteria exhibited resistance to a number of β-lactam antibiotics, rifampicin, streptomycin and vancomycin. Optimum growth was observed between 30 and 34 °C, at pH 6.8–7.5 and with 1–2 g NaCl l− 1. Isolate GLS2T was a strict anaerobe but it tolerated oxygen exposure. On the basis of 16S rRNA gene sequence similarity, strain GLS2T was shown to belong to the genus Sphaerochaeta within the family Spirochaetaceae. Its closest relatives were Sphaerochaeta globosa BuddyT (99.3 % 16S rRNA gene sequence similarity) and Sphaerochaeta pleomorpha GrapesT (95.4 % similarity). The G+C content of DNA was 47.2 mol%. The level of DNA–DNA hybridization between strains GLS2T and BuddyT was 34.7 ± 8.8 %. Major polar lipids were phosphoglycolipids, phospholipids and glycolipids; major fatty acids were C14 : 0, C16 : 0, C16 : 0 3-OH, C16 : 0 dimethyl acetal (DMA), C16 : 1n8 and C16 : 1 DMA; respiratory quinones were not detected. The results of DNA–DNA hybridization, physiological and biochemical tests demonstrated genotypic and phenotypic differentiation of strain GLS2T from the four species of the genus Sphaerochaeta with validly published names that allowed its separation into a new lineage at the species level. Strain GLS2T therefore represents a novel species, for which the name Sphaerochaeta associata sp. nov. is proposed, with the type strain GLS2T ( = DSM 26261T = VKM B-2742T).

scholarly journals Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).

scholarly journals Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2005 ◽  
Vol 55 (2) ◽  
pp. 885-889 ◽  
Author(s):  
In-Gi Kim ◽  
Mi-Hwa Lee ◽  
Seo-Youn Jung ◽  
Jae Jun Song ◽  
Tae-Kwang Oh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Three Gram-variable, rod-shaped bacterial strains, TF-16T, TF-19 and TF-80T, were isolated from a tidal flat of Daepo Beach (Yellow Sea) near Mokpo City, Korea, and their taxonomic positions were investigated by a polyphasic approach. These isolates grew optimally in the presence of 2 % NaCl and at 30 °C. Their peptidoglycan types were based on l-Lys–Gly. The predominant menaquinone detected in the three strains was MK-7. The three strains contained large amounts of the branched fatty acids iso-C17 : 0, anteiso-C13 : 0, iso-C13 : 0 and iso-C15 : 0. The DNA G+C contents of strains TF-16T, TF-19 and TF-80T were 48·6, 48·4 and 48·0 mol%, respectively. The three strains formed a coherent cluster with Exiguobacterium species in a phylogenetic tree based on 16S rRNA gene sequences. They showed closest phylogenetic affiliation to Exiguobacterium aurantiacum, with 16S rRNA gene sequence similarity values of 98·1–98·3 %. The three strains exhibited 16S rRNA gene sequence similarity values of 94·0–94·6 % to the type strains of other Exiguobacterium species. Levels of DNA–DNA relatedness indicated that strains TF-16T and TF-19 and strain TF-80T are members of two species that are separate from E. aurantiacum. On the basis of phenotypic, phylogenetic and genetic data, strains TF-16T and TF-19 and strain TF-80T represent two novel species in the genus Exiguobacterium; the names Exiguobacterium aestuarii sp. nov. (type strain TF-16T=KCTC 19035T=DSM 16306T; reference strain TF-19) and Exiguobacterium marinum sp. nov. (type strain TF-80T=KCTC 19036T=DSM 16307T) are proposed.

scholarly journals Erythrobacter luteolus sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2005 ◽  
Vol 55 (3) ◽  
pp. 1167-1170 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Kook Hee Kang ◽  
Soo-Hwan Yeo ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties

A Gram-negative, non-spore-forming, yellow-pigmented, slightly halophilic bacterial strain, SW-109T, was isolated from a tidal flat of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. This isolate did not produce bacteriochlorophyll a and contained ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c as the major fatty acid. The DNA G+C content was 60·3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SW-109T is phylogenetically affiliated to the genus Erythrobacter of the family Sphingomonadaceae. Strain SW-109T exhibited levels of 16S rRNA gene sequence similarity to the type strains of Erythrobacter species of 94·0–96·3 %, making it possible to categorize strain SW-109T as a species that is separate from previously recognized Erythrobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, SW-109T (=KCTC 12311T=JCM 12599T) was classified as the type strain of a novel Erythrobacter species, for which the name Erythrobacter luteolus sp. nov. is proposed.

scholarly journals Pareuzebyella sediminis gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae, isolated from a tidal flat sediment

2020 ◽  
Author(s):  
Zhaobin Huang ◽  
Xiaomei Wei ◽  
Qiliang Lai ◽  
Shiyong Chen ◽  
Jianjun Yuan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

Two marine bacterial strains, designated S2-4-21T and MT2-5-19, were isolated from two tidal flat sediments of cordgrass Spartina alterniflora and adjacent oyster culture field in Quanzhou bay, China, respectively. Both strains were Gram-staining-negative, rod-shaped, non-flagellated, non-motile, aerobic, had NaCl requirements, and contained carotenoid and flexirubin pigments. The 16S rRNA gene sequence similarity (99.8%), average nucleotide identity value (99.4%) and average amino acid identity (99.3%) between strain S2-4-21T and strain MT2-5-19 strongly supported that they belonged to a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2-4-21T and strain MT2-5-19 formed a monophyletic branch affiliated to the family Flavobacteriaceae , sharing similarities of 94.6% with Euzebyella marina CY01T and E. saccharophila 7SM30T, and of 94.1 and 92.8% with E. algicola MEBiC 12267T and Pseudozobellia thermophile DSM 19858T, respectively. Phylogenomic analysis based on the whole genome sequences supported that the two strains formed a distinct monophyletic clade within Flavobacteriaceae members, which was phylogenetically different from the clades of Euzebyella and Pseudozobellia . The major respiratory quinone was menaquinone MK-6. The major fatty acids (>10%) consisted of C15 : 0 iso, C16 : 0, summed feature 9 (C17 : 1 iso ω9c/C16 : 0 10-methyl) and C17 : 0 iso 3-OH. The polar lipid profiles of strain S2-4-21T and strain MT2-5-19 are identical, including phosphatidylethanolamine, four unidentified aminolipids, and four unidentified lipids. The genomic size was 4.9–5.0 Mb with genomic DNA G+C content of 41.5 mol%. Based on the above characteristics, strains S2-4-21T and MT2-5-19 represented a novel species of a novel genus in the family Flavobacteriaceae . Thus, Pareuzebyella sediminis gen. nov. sp. nov. is proposed with type strain S2-4-21T (=MCCC 1K03818T=KCTC 72152T), and another strain MT2-5-19 (=KCTC 72539=MCCC 1K03874).

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