scholarly journals Humicoccus flavidus gen. nov., sp. nov., isolated from soil

2007 ◽  
Vol 57 (1) ◽  
pp. 56-59 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Seo-Youn Jung ◽  
Tae-Kwang Oh
Keyword(s):  
Fatty Acids ◽  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Diamino Acid

A Gram-positive, non-motile, spherical, non-spore-forming bacterial strain, DS-52T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. It grew optimally at 25 °C and pH 6.0–7.0. Strain DS-52T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and galactose, mannose, xylose and rhamnose as whole-cell sugars. It contained MK-8(H4) and MK-9(H4) as the predominant menaquinones and anteiso-C15 : 0, iso-C15 : 0 and C17 : 0 as major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyldimethylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-52T is most closely related to the genus Nakamurella of the suborder Frankineae. Strain DS-52T exhibited 16S rRNA gene sequence similarity values of 96.5 % to Nakamurella multipartita JCM 9543T and 92.0–93.9 % to other members of the suborder Frankineae. The diagnostic diamino acid type and polar lipid profile of strain DS-52T were the same as those of the genus Nakamurella. However, strain DS-52T could be clearly distinguished from the genus Nakamurella by differences in predominant menaquinones, major fatty acids and cell-wall sugars. Accordingly, based on combined phenotypic, chemotaxonomic and phylogenetic data, strain DS-52T (=KCTC 19127T=CIP 108919T) is proposed as the type strain of a novel species in a new genus, Humicoccus flavidus gen. nov., sp. nov.

Reclassification of Marinococcus albus Hao et al. 1985 as Salimicrobium album gen. nov., comb. nov. and Bacillus halophilus Ventosa et al. 1990 as Salimicrobium halophilum comb. nov., and description of Salimicrobium luteum sp. nov.

2007 ◽  
Vol 57 (10) ◽  
pp. 2406-2411 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
New Genus ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Separate Species ◽  
Diamino Acid

A Gram-positive, non-motile, coccoid-shaped, non-spore-forming halophilic bacterial strain, BY-5T, was isolated from a marine solar saltern in Korea and its taxonomic position was investigated by using a polyphasic approach. The novel strain grew optimally at 37 °C and in the presence of 10 % (w/v) NaCl. Strain BY-5T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone and anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 as the major fatty acids. The DNA G+C content was 47.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BY-5T formed a coherent cluster with Bacillus halophilus and Marinococcus albus. Strain BY-5T exhibited 16S rRNA gene sequence similarity values of 98.7 and 97.4 % to the type strains of B. halophilus and M. albus, respectively. Strain BY-5T was distinguished from B. halophilus and M. albus by several phenotypic properties and DNA–DNA relatedness data. On the basis of the combined chemotaxonomic and phylogenetic data, it is proposed that M. albus, B. halophilus and strain BY-5T should be placed in a new genus as three separate species. Marinococcus albus and Bacillus halophilus are reclassified in a new genus, Salimicrobium gen. nov., as Salimicrobium album comb. nov. and Salimicrobium halophilum comb. nov., respectively. The type species of the new genus is Salimicrobium album. Strain BY-5T (=KCTC 3989T=CIP 108918T) is placed in the genus Salimicrobium as a novel species Salimicrobium luteum sp. nov.

scholarly journals Nocardioides marinus sp. nov.

2007 ◽  
Vol 57 (4) ◽  
pp. 775-779 ◽  
Author(s):  
Dong Han Choi ◽  
Hye Min Kim ◽  
Jae-Hoon Noh ◽  
Byung Cheol Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Diamino Acid ◽  
Ph Range ◽  
Type Strains

A Gram-positive, slightly halophilic, rod-shaped bacterium, designated CL-DD14T, was isolated from seawater of the East Sea, Korea. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CL-DD14T belongs to the genus Nocardioides. Levels of 16S rRNA gene sequence similarity between strain CL-DD14T and the type strains of recognized species of the genus Nocardioides were low (94.1–97.1 %). Strain CL-DD14 T grew over the pH range 6–9 and temperature range 10–40 °C. The strain grew at NaCl concentrations of 0.5–8 % (w/v) with optimum growth at 1–3 % and no growth was observed after 3 weeks on nutrient agar without any salts. It contained ll-diaminopimelic acid as the diamino acid in the cell wall. The major isoprenoid quinone was MK-8(H4) and the major cellular fatty acids were iso-C16 : 0 and 10-methyl C17 : 0. The DNA G+C content was 72.9 mol%. On the basis of phenotypic and phylogenetic data, strain CL-DD14T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides marinus sp. nov. is proposed. The type strain is CL-DD14T (=KCCM 42321T=DSM 18248T).

scholarly journals Brachybacterium phenoliresistens sp. nov., isolated from oil-contaminated coastal sand

2007 ◽  
Vol 57 (11) ◽  
pp. 2674-2679 ◽  
Author(s):  
Jui-Hsing Chou ◽  
Kuan-Yin Lin ◽  
Mei-Chun Lin ◽  
Shih-Yi Sheu ◽  
Yu-Hong Wei ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Sand Sample ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Coastal Sand

A coccoid- to ovoid-shaped, Gram-positive, non-motile bacterial strain, designated phenol-AT, was isolated from an oil-contaminated coastal sand sample collected from Pingtung County, southern Taiwan, and characterized by use of a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Brachybacterium in the family Dermabacteraceae, class Actinobacteria. The closest neighbours were Brachybacterium rhamnosum LMG 19848T (96.9 % 16S rRNA gene sequence similarity), Brachybacterium nesterenkovii DSM 9573T (97.0 %) and Brachybacterium muris C3H-21T (96.3 %). The peptidoglycan type of strain phenol-AT was variation A4γ with meso-diaminopimelic acid as the diagnostic cell-wall diamino acid. The isolate contained MK-7 as the major component of the quinone system. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, and unidentified phospholipids and glycolipids. The predominant fatty acid was anteiso-C15 : 0 (59.5 %); significant amounts of iso-C16 : 0 (9.4 %), iso-C14 : 0 (9.5 %) and anteiso-C17 : 0 (10.8 %) were also present. The isolate was also distinguished from recognized members of the genus Brachybacterium on the basis of several phenotypic and biochemical characteristics. It is evident from the genotypic, chemotaxonomic and phenotypic data that isolate phenol-AT represents a novel species of the genus Brachybacterium, for which the name Brachybacterium phenoliresistens sp. nov. is proposed. The type strain is phenol-AT (=LMG 23707T=BCRC 17589T).

Hoyosella lacisalsi sp. nov., a halotolerant actinobacterium isolated from the Lake Gudzhirganskoe

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Qin Yang ◽  
Pu-Yu Guo ◽  
Elena Y. Abidueva ◽  
Fei-Na Li ◽  
Chun-mei Xue ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Salicornia Europaea ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Mycolic Acids ◽  
Link Type

A Gram-stain-positive, aerobic, non-motile, non-spore-forming and coccus-shaped strain, designated strain G463T, was isolated from the rhizosphere soil of Salicornia europaea L. collected from Lake Gudzhirganskoe in Siberia. Based on 16S rRNA gene phylogeny, strain G463T belonged to the genus Hoyosella , with the highest 16S rRNA gene sequence similarity to Hoyosella altamirensis DSM 45258T (96.1%). The major fatty acids were C17:1 ω8c, C16:0, C15 : 0 and C17:0. The strain contained meso-diaminopimelic acid as the cell-wall diagnostic diamino acid and arabinose, galactose and ribose as the whole-cell sugars. MK-8 and MK-7 were the predominant menaquinones. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, one unidentified phosphoglycolipid, two unidentified glycolipids and several unidentified lipids. Acetyl was the muramyl residue. Mycolic acids (C28–C34) were present. The G+C content of the genomic DNA was 68.3 mol%. Based on its phylogenetic, phenotypic and chemotaxonomic features, strain G463T was considered to represent a novel species of the genus Hoyosella , for which the name Hoyosella lacisalsi sp. nov. is proposed. The type strain is G463T (=JCM 33650T=CGMCC 1.17230T).

scholarly journals Alkalibacillus flavidus sp. nov., isolated from a marine solar saltern

2010 ◽  
Vol 60 (2) ◽  
pp. 434-438 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Yong-Taek Jung ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Marine Solar Saltern ◽  
Phenotypic Properties ◽  
Diamino Acid

A Gram-stain-positive, motile, rod-shaped bacterial strain, ISL-17T, was isolated from a marine solar saltern of the Yellow Sea, Korea, and its taxonomic position was investigated by means of a polyphasic study. Strain ISL-17T grew optimally at pH 8.5–9.0, at 37 °C and in the presence of approximately 10 % (w/v) NaCl. It contained meso-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan, MK-7 as the predominant menaquinone and iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 as the major fatty acids. The DNA G+C content was 48.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-17T fell within the genus Alkalibacillus, clustering with Alkalibacillus salilacus BH163T with a bootstrap resampling value of 100 %. Strain ISL-17T exhibited 98.2 % 16S rRNA gene sequence similarity to A. salilacus BH163T and 95.8–96.5 % similarity to the type strains of the other Alkalibacillus species. The mean DNA–DNA relatedness value between strain ISL-17T and A. salilacus KCTC 3916T was 19 %. The phenotypic properties of strain ISL-17T, together with its phylogenetic and genetic distinctiveness, enable this strain to be differentiated from recognized Alkalibacillus species. On the basis of phenotypic, phylogenetic and genetic data, strain ISL-17T represents a novel species within the genus Alkalibacillus, for which the name Alkalibacillus flavidus sp. nov. is proposed; the type strain is ISL-17T (=KCTC 13258T =CCUG 56753T).

scholarly journals Mariniflexile aquimaris sp. nov., isolated from seawater, and emended description of the genus Mariniflexile Nedashkovskaya et al. 2006

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 539-544 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Polar Lipid Profile ◽  
The Family ◽  
Emended Description

A Gram-staining-negative, non-flagellated, non-gliding and rod-shaped bacterial strain, designated HWR-17T, was isolated from seawater of the Yellow Sea in Korea. Strain HWR-17T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HWR-17T clustered with the two Mariniflexile species in the family Flavobacteriaceae, exhibiting 16S rRNA gene sequence similarity of 97.1–97.2 % to their type strains and less than 95.7 % sequence similarity to other members of the family Flavobacteriaceae. Strain HWR-17T contained MK-6 as the predominant menaquinone and iso-C15 : 0 as the major fatty acid. The polar lipid profile of strain HWR-17T contained phosphatidylethanolamine, an unidentified aminolipid and four unidentified lipids. The DNA G+C content of strain HWR-17T was 35.7 mol% and it exhibited 11 and 10 % DNA–DNA relatedness, respectively, with Mariniflexile gromovii KCTC 12570T and Mariniflexile fucanivorans DSM 18792T. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain HWR-17T is distinguishable from the two recognized Mariniflexile species. On the basis of the data presented, strain HWR-17T is considered to represent a novel species of the genus Mariniflexile, for which the name Mariniflexile aquimaris sp. nov. is proposed. The type strain is HWR-17T ( = KCTC 23346T  = CCUG 60529T). An emended description of the genus Mariniflexile is also proposed.

scholarly journals Aeromicrobium tamlense sp. nov., isolated from dried seaweed

2007 ◽  
Vol 57 (2) ◽  
pp. 337-341 ◽  
Author(s):  
Soon Dong Lee ◽  
Se Jae Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Octadecenoic Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Hexadecanoic Acid ◽  
Phenotypic Data ◽  
Separate Branch

A Gram-positive, non-motile, rod-shaped actinomycete strain, designated SSW1-57T, was isolated from a dried seaweed sample from the coast of Jeju Island, Republic of Korea and subjected to a polyphasic taxonomic study. A neighbour-joining tree based on 16S rRNA gene sequences showed that the organism was related to members of the family Nocardioidaceae and formed a separate branch at the base of a taxon encompassing members of the genus Aeromicrobium, whereas it occupied an intermediate position between Aeromicrobium alkaliterrae–Aeromicrobium marinum and Aeromicrobium erythreum–Aeromicrobium fastidiosum clusters in maximum-parsimony and maximum-likelihood trees. The phylogenetic association of the isolate with the genus Aeromicrobium was supported by the following chemotaxonomic properties: ll-diaminopimelic acid in the peptidoglycan, MK-9(H4) as the major menaquinone and major fatty acids cis-9-octadecenoic acid, hexadecanoic acid, 10-methyl octadecanoic acid and 2-hydroxy hexadecanoic acid. The polar lipid profile contained phosphatidylinositol, diphosphatidylglycerol and phosphatidylglycerol. Levels of 16S rRNA gene sequence similarity between the novel organism and the type strains of the four recognized Aeromicrobium species were in the range 96.5–96.7 %. On the basis of phylogenetic analyses and phenotypic data, it is proposed that the organism should be classified as representing a novel species of the genus Aeromicrobium, with the name Aeromicrobium tamlense sp. nov. The type strain is SSW1-57T (=JCM 13811T=NRRL B-24466T).

scholarly journals Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil

2010 ◽  
Vol 60 (6) ◽  
pp. 1334-1338 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Sooyeon Park ◽  
So-Jung Kang ◽  
Jung-Sook Lee ◽  
Keun Chul Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A Gram-positive, non-motile and rod- or coccoid-shaped bacterial strain, MDN22T, was isolated from a soil sample from Korea. Strain MDN22T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 0–0.5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MDN22T was phylogenetically most closely related to the genera Nocardioides and Marmoricola. In the neighbour-joining phylogenetic tree, strain MDN22T was most closely related to Nocardioides jensenii KCTC 9134T, with which it exhibited 98.3 % 16S rRNA gene sequence similarity. The strain exhibited 93.1–96.9 % and 95.3–95.9 % 16S rRNA gene sequence similarities to the type strains of other species of the genera Nocardioides and Marmoricola, respectively. The chemotaxonomic properties of strain MDN22T were consistent with those of the genus Nocardioides; the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, the predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0 and C17 : 1. The DNA G+C content was 68.7 mol%. DNA–DNA relatedness data and differential phenotypic properties suggested that strain MDN22T could be differentiated from N. jensenii and Nocardioides dubius. On the basis of the data obtained, strain MDN22T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides daedukensis sp. nov., is proposed. The type strain is MDN22T (=KCTC 19601T=CCUG 57505T).

Lacibacterium aquatile gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a freshwater lake

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4797-4804 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yi-Ling Chen ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Link Type ◽  
The Family

A bacterial strain designated LTC-2T was isolated from a freshwater lake in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain LTC-2T were Gram-reaction-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore-forming, slightly curved rods surrounded by a thick capsule and formed creamy white colonies. Growth occurred at 10–37 °C (optimum, 20–30 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0) and with 0–1.0 % NaCl (optimum, 0 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-10 and the DNA G+C content was 58.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, two uncharacterized phospholipids and two uncharacterized aminophospholipids. The major polyamines were putrescine, homospermidine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LTC-2T forms a distinct lineage with respect to closely related genera in the family Rhodospirillaceae , most closely related to the genera Elstera and Dongia , and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera were less than 94 %. On the basis of the genotypic and phenotypic data, strain LTC-2T represents a novel genus and species of the family Rhodospirillaceae , for which the name Lacibacterium aquatile gen. nov., sp. nov. is proposed. The type strain is LTC-2T ( = BCRC 80445T = LMG 26999T = KCTC 32017T).

Yonghaparkia Aerolata sp. nov., a Novel Member of the Genus Yonghaparkia, Isolated From Electronic Waste Associated Bioaerosols

2021 ◽  
Author(s):  
Yimin Pan ◽  
Qiaoqiao Ren ◽  
Lingyun Chen ◽  
Yunxia Jiang ◽  
Jiguo Wu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Electronic Waste ◽  
Draft Genome ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Actinomycete Strain

Abstract A Gram-positive, non-motile, non-spore-forming and short rod-shaped actinomycete strain, designated GA224T, was isolated from an electronic waste associated bioaerosols. The isolate is facultatively anaerobic, which is able to grow at 25–40 ℃ (optimum 37 ℃) and pH 6.5–8.5 (optimum 8.0). The diamino acid in the cell wall of strain GA224T is 2,4-diaminobutyric acid (DAB), while major menaquinone is MK-12. The polar lipid profile is composed of diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, unidentified glycolipids and unidentified lipid. The major cellular fatty acid is anteiso-C15:0 and iso-C16:0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GA224T fell within the genus Yonghaparkia, the highest 16S rRNA gene sequence similarity values (98.60%) being obtained with respect to Yonghaparkia alkaliphile KSL-113T. The draft genome of strain GA224T comprised 2,495,189 bp with a G+C content of 72.17 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain GA224T and phylogenetically related Yonghaparkia species were lower than 95% and 70%, respectively. Based on the phenotypic, chemotaxonomic and genomic data, strain GA224T represents a novel species, for which the name Yonghaparkia aerolata sp. nov. is proposed, with GA224T as the type strain (= GDMCC 1.2165T = JCM 34462T).

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