scholarly journals Marmoricola aequoreus sp. nov., a novel actinobacterium isolated from marine sediment

2007 ◽  
Vol 57 (7) ◽  
pp. 1391-1395 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Initial Ph ◽  
Diamino Acid ◽  
Unknown Phospholipid ◽  
Spherical Cells

A yellow-coloured, marine actinobacterium, designated SST-45T, was isolated from sandy sediment under the surface of a beach and taxonomically characterized by physiological, chemotaxonomic and phylogenetic methods. The cells of the isolate were Gram-positive, aerobic, non-sporulating, non-motile, spherical cells that occurred singly, in pairs, in clusters or as short chains. The isolate grew at 10–37 °C, an initial pH 5.1–12.1 and in the presence of 5 % (w/v) NaCl. The organism possessed ll-2,6-diaminopimelic acid as the diagnostic diamino acid in the cell wall, MK-8(H4) as the major menaquinone, a polar lipid profile including diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown phospholipid, C18 : 1 and C16 : 0 as the major fatty acids, and a DNA G+C content of 72.4 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that the organism was related to members of the genera Marmoricola and Nocardioides. The closest neighbours were Marmoricola aurantiacus DSM 12652T (97.0 % sequence similarity) and Nocardioides jensenii KCTC 9134T (96.7 %). The combination of morphological and chemotaxonomic characters supported the assignment of the isolate to the genus Marmoricola. However, the organism is clearly distinguished phenotypically from the single described species of this genus, Marmoricola aurantiacus. Based on the data obtained, the organism has been assigned as a novel species, for which the name Marmoricola aequoreus sp. nov. is proposed. The type strain is strain SST-45T (=JCM 13812T=NRRL B-24464T).

scholarly journals Antricoccus suffuscus gen. nov., sp. nov., isolated from a natural cave

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4410-4416 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Type Strain ◽  
New Genus ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Diamino Acid ◽  
Unknown Phospholipid

A novel actinobacterium, designated strain C4-31T, was isolated from soil collected from a cave. Cells were aerobic, Gram-reaction-positive, oxidase-negative, catalase-positive and non-motile cocci. Comparison of 16S rRNA gene sequences showed that the organism occupied a distinct phylogenetic position within the suborder Frankineae, with sequence similarity values of less than 93.2 % to members of this suborder. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, an unknown aminophospholipid and an unknown phospholipid. The major fatty acids were iso-C16 : 0, C17 : 1ω6c and C16 : 0. The G+C content of the DNA was 62.8 mol%. On the basis of morphological and chemotaxonomic data as well as phylogenetic evidence, strain C4-31T ( = KCTC 39556T = DSM 100065T) is considered to represent the type strain of a novel species of a new genus in the suborder Frankineae, for which the name Antricoccus suffuscus gen. nov., sp. nov. is proposed.

scholarly journals Prauserella muralis sp. nov., from the indoor environment

2010 ◽  
Vol 60 (2) ◽  
pp. 287-290 ◽  
Author(s):  
Jenny Schäfer ◽  
Karin Martin ◽  
Peter Kämpfer
Keyword(s):  
Indoor Environment ◽  
Sequence Similarity ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Polar Lipid Profile ◽  
Mycolic Acids ◽  
Diamino Acid ◽  
Unknown Phospholipid

A novel Gram-stain-positive, mycelium-forming actinobacterium (05-Be-005T) isolated from the wall of an indoor environment was studied for its taxonomic position. The isolated strain formed a substrate mycelium that fragmented into rod-shaped cells and showed an aerial mycelium on medium M79. On the basis of 16S rRNA gene sequence similarity studies, strain 05-Be-005T was shown to belong to the genus Prauserella, closely related to Prauserella rugosa DSM 43194T (96.6 % similarity), Prauserella alba YIM 90005T (95.9 %) and Prauserella halophila YIM 90001T (95.4 %). The predominant menaquinone was MK-9(H4); whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid of the cell wall and arabinose and galactose as the main sugars. Mycolic acids were absent. The polar lipid profile consisted of the lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylserine and an unknown phospholipid. Major fatty acids C16 : 0 iso, C16 : 0, C17 : 1 ω8c and C17 : 1 ω6c supported the affiliation of strain 05-Be-005T to the genus Prauserella. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain 05-Be-005T from the three known Prauserella species. Strain 05-Be-005T represents a novel Prauserella species, for which we propose the name Prauserella muralis sp. nov., with the type strain 05-Be-005T (=CCUG 57426T =NRRL B-24780T =CCM 7635T=DSM 45305T).

scholarly journals Paenibacillus sputi sp. nov., isolated from the sputum of a patient with pulmonary disease

2010 ◽  
Vol 60 (10) ◽  
pp. 2371-2376 ◽  
Author(s):  
Kwang Kyu Kim ◽  
Keun Chul Lee ◽  
Heekyung Yu ◽  
Sungweon Ryoo ◽  
Youngkil Park ◽  
...  
Keyword(s):  
Pulmonary Disease ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Diamino Acid

Strain KIT 00200-70066-1T was isolated from the sputum of a patient with pulmonary disease. Cells of the strain were Gram-variable, facultatively anaerobic, motile, spore-forming rods and formed colourless to white colonies on tryptic soy agar at 30 °C and pH 7. The pathogenicity of the strain is not known. The strain contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone, anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 as the major fatty acids and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids in the polar lipid profile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Paenibacillus, sharing the highest levels of sequence similarity with Paenibacillus nanensis MX2-3T, Paenibacillus agaridevorans DSM 1355T and Paenibacillus alkaliterrae KSL-134T (95.4, 95.2 and 94.8 %, respectively), and that it occupied a distinct position within this genus. Combined phylogenetic and phenotypic data supported the conclusion that strain KIT 00200-70066-1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus sputi sp. nov. is proposed; the type strain is KIT 00200-70066-1T (=KCTC 13252T =DSM 22699T).

Deinococcus cellulosilyticus sp. nov., isolated from air

2007 ◽  
Vol 57 (8) ◽  
pp. 1685-1688 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Peter Schumann ◽  
Jung-A Son ◽  
Jaeseon Jang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Unknown Phospholipid ◽  
Air Sample

A pink-coloured bacterial strain, 5516J-15T, was isolated from an air sample from Jeju Island, Republic of Korea. The organism was found to have resistance to UV radiation typical of members of the genus Deinococcus, and it was placed within the radiation of the Deinococcus on a phylogenetic tree based on 16S rRNA gene sequences. Strain 5516J-15T shared low 16S rRNA gene sequence similarity (84.5–87.8 %) with Deinococcus species, showing highest sequence similarity to Deinococcus deserti VCD115T (87.8 %) and Deinococcus indicus Wt/1aT (87.8 %). Strain 5516J-15T had type A3β peptidoglycan with l-ornithine, menaquinone 8 (MK-8) as the major quinone and iso-C12 : 0, anteiso-C13 : 0, iso-C16 : 0 and C16 : 0 as the major fatty acids. Its polar lipid profile contained three unknown aminophospholipids, two unknown polar lipids, one unknown phospholipid and one unknown glycolipid. The DNA G+C content of strain 5516J-15T was 61.3 mol%. Based on the phylogenetic and phenotypic data presented, it is proposed that the unknown strain should be classified within a novel species in the genus Deinococcus with the name Deinococcus cellulosilyticus sp. nov. The type strain is 5516J-15T (=KACC 11606T =DSM 18568T).

scholarly journals Lapillicoccus jejuensis gen. nov., sp. nov., a novel actinobacterium of the family Intrasporangiaceae, isolated from stone

2007 ◽  
Vol 57 (12) ◽  
pp. 2794-2798 ◽  
Author(s):  
Soon Dong Lee ◽  
Dong Wan Lee
Keyword(s):  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Straight Chain ◽  
Polar Lipid Profile ◽  
The Family ◽  
Small Stone ◽  
Novel Genus And Species ◽  
Diamino Acid ◽  
The 16S Rrna Gene

A novel, yellow-pigmented actinobacterium was isolated from a small stone collected in Jeju, Republic of Korea. The cells of the organism, designated strain R-Ac013T, were Gram-positive, aerobic, non-motile cocci that occurred singly or in pairs. The strain showed growth at 10–37 °C and pH 4.1–11.1, and tolerated 2 % NaCl. On the basis of the 16S rRNA gene sequence, the organism was phylogenetically related to members of the genera Tetrasphaera (94.6–97.1 % sequence similarity), Terrabacter (96.5 %), Knoellia (96.4 %), Terracoccus (96.4 %), Oryzihumus (96.4 %), Janibacter (96.1–96.4 %) and Intrasporangium (96.2 %). The chemotaxonomic results for the organism were as follows: ll-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan, acetyl-type murein, MK-8(H4) as the major menaquinone, a DNA G+C content of 74.1 mol%, and a polar lipid profile that comprised diphosphatidylglycerol and phosphatidylinositol. The fatty acid profile consisted of iso- and anteiso-methyl-branched, straight-chain saturated and monounsaturated types, the major components being iso-C16 : 0, C17 : 1 ω8c and iso-C15 : 0. The combination of the phenotypic and phylogenetic data revealed that this strain represents a novel genus and species of the family Intrasporangiaceae, for which the name Lapillicoccus jejuensis gen. nov., sp. nov. is proposed. The type strain is strain R-Ac013T (=KCTC 19200T=DSM 18607T).

scholarly journals Brevibacterium sandarakinum sp. nov., isolated from a wall of an indoor environment

2010 ◽  
Vol 60 (4) ◽  
pp. 909-913 ◽  
Author(s):  
Peter Kämpfer ◽  
Jenny Schäfer ◽  
Nicole Lodders ◽  
Hans-Jürgen Busse
Keyword(s):  
Indoor Environment ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Polar Lipid Profile ◽  
Closely Related Species ◽  
Phenotypic Differentiation ◽  
Diamino Acid ◽  
Type Strains

A Gram-stain-positive, rod-shaped, non-endospore-forming, orange-pigmented (coloured) actinobacterium (01-Je-003T) was isolated from the wall of an indoor environment primarily colonized with moulds. On the basis of 16S rRNA gene sequence similarity studies, strain 01-Je-003T was shown to belong to the genus Brevibacterium and was most similar to the type strains of Brevibacterium picturae (98.8 % similarity), Brevibacterium marinum (97.3 %) and Brevibacterium aurantiacum (97.2 %). Chemotaxonomic data [predominant quinone menaquinone MK-8(H2); polar lipid profile consisting of major compounds diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid; characteristic cell-wall diamino acid meso-diaminopimelic acid; polyamine pattern showing major compounds putrescine and cadaverine; major fatty acids anteiso-C15 : 0 and anteiso-C17 : 0] supported the affiliation of strain 01-Je-003T to the genus Brevibacterium. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 01-Je-003T from the two most closely related species, B. picturae and B. marinum. Strain 01-Je-003T therefore represents a novel species, for which the name Brevibacterium sandarakinum sp. nov. is proposed, with the type strain 01-Je-003T (=DSM 22082T =CCM 7649T).

scholarly journals Marmoricola korecus sp. nov.

2011 ◽  
Vol 61 (7) ◽  
pp. 1628-1631 ◽  
Author(s):  
Soon Dong Lee ◽  
Dong Wan Lee ◽  
Young-Hwan Ko
Keyword(s):  
Dna Hybridization ◽  
Volcanic Ash ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Hybridization Data ◽  
Phyletic Line ◽  
Diamino Acid ◽  
Unknown Phospholipid ◽  
Type Strains

A novel actinomycete, designated strain Sco-A36T, was isolated from volcanic ash. Cells were aerobic, Gram-stain-positive, oxidase-negative, catalase-positive, non-motile cocci; colonies were yellow-coloured, smooth, entire and convex. Phylogenetic analysis showed that the organism formed a distinct phyletic line within the radiation of the genus Marmoricola. Its closest phylogenetic neighbours were Marmoricola aurantiacus DSM 12652T (97.9 % 16S rRNA gene sequence similarity), Marmoricola scoriae Sco-D01T (97.9 %), Marmoricola aequoreus SST-45T (97.4 %) and Marmoricola bigeumensis MSL-05T (96.3 %). The diagnostic diamino acid in the cell walls was ll-diaminopimelic acid. The predominant menaquinone was MK-8(H4). The polar lipids contained phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and an unknown phospholipid. The predominant fatty acids were C16 : 0, C17 : 1ω8c, C18 : 1ω9c and C16 : 1ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content of strain Sco-A36T was 71.0 mol%. Levels of DNA–DNA relatedness between the new isolate and the type strains of recognized species of the genus Marmoricola were 4.9–29.2 %. The phenotypic and DNA–DNA hybridization data presented here strongly suggest that strain Sco-A36T represents a novel species of the genus Marmoricola, for which the name Marmoricola korecus sp. nov. is proposed. The type strain is Sco-A36T ( = KCTC 19596T = DSM 22128T).

scholarly journals Actinomadura rupiterrae sp. nov., isolated from cliff soil

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 990-995 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Mycolic Acids ◽  
Hybridization Data ◽  
Actinomycete Strain ◽  
Diamino Acid

A novel actinomycete strain, designated CS5-AC15T, was isolated from a soil sample collected from a cliff on Mara Island, Jeju, Republic of Korea, and subjected to a polyphasic taxonomic analysis. The isolate produced well-developed, yellow substrate mycelium and white aerial mycelium that differentiated into straight or flexuous chains of smooth-surfaced spores. 16S rRNA gene sequence analyses showed that the organism belonged to the family Thermomonosporaceae and formed a tight cluster with the type strain of Actinomadura oligospora (97.4 % sequence similarity). Chemotaxonomic characteristics were consistent with its assignment to the genus Actinomadura in that the isolate had meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall, madurose as the characteristic sugar, N-acetyl type of murein in the peptidoglycan, MK-9(H6) and MK-9(H8) as major menaquinones and a polar lipid profile containing diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown phospholipids. Mycolic acids were not detected. The predominant fatty acids were C16 : 0, C18 : 1ω9c and iso-C16 : 0. The DNA G+C content was 70.9 mol%. DNA relatedness of strain CS5-AC15T and A. oligospora JCM 10648T was 37.9±0.7 %. On the basis of the phenotypic, phylogenetic and DNA–DNA hybridization data, strain CS5-AC15T is assigned to a novel species of the genus Actinomadura, for which the name Actinomadura rupiterrae sp. nov. is proposed (type strain CS5-AC15T  = KCTC 19559T  = DSM 45251T).

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.

scholarly journals Rhodococcus enclensis sp. nov., a novel member of the genus Rhodococcus

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2693-2697 ◽  
Author(s):  
Syed G. Dastager ◽  
Rahul Mawlankar ◽  
Shan-Kun Tang ◽  
Srinivasan Krishnamurthi ◽  
V. Venkata Ramana ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Marine Sediment Sample ◽  
Diamino Acid ◽  
Unknown Phospholipid

A novel actinobacterial strain, designated, NIO-1009T, was isolated from a marine sediment sample collected from Chorao Island, Goa, India. Phylogenetic analysis comparisons based on 16S rRNA gene sequences between strain NIO-1009T and other members of the genus Rhodococcus revealed that strain NIO-1009T had the closest sequence similarity to Rhodococcus kroppenstedtii DSM 44908T and Rhodococcus corynebacterioides DSM 20151T with 99.2 and 99.1 %, respectively. Furthermore, DNA–DNA hybridization results showed that R. kroppenstedtii DSM 44908T and R. corynebacterioides DSM 20151T were 39.5 (3.0 %) and 41.7 (2.0 %) with strain NIO-1009T, respectively, which were well below the 70 % limit for any novel species proposal. Phylogenetically strain NIO-1009T forms a stable clade with and R. kroppenstedtii DSM 44908T and R. corynebacterioides DSM 20151T with 100 % bootstrap values. Strain NIO-1009T contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose and arabinose as the cell wall sugars. The major fatty acids were C16 : 0, C18 : 1ω9c, C16 : 1(ω6c and/or ω7c) and 10-methyl C18 : 0. The only menaquinone detected was MK-8(H2), while the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unknown phospholipid. The G+C content of the genomic DNA was 66.9 mol%. The phenotypic and genotypic data showed that strain NIO-1009T warrants recognition as a novel species of the genus Rhodococcus for which the name Rhodococcus enclensis sp. nov., is proposed; the type strain is NIO-1009T ( = NCIM 5452T = DSM 45688T).

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