scholarly journals Arthrobacter endophyticus sp. nov., an endophytic actinobacterium isolated from root of Salsola affinis C. A. Mey

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2154-2160 ◽  
Author(s):  
Hong-Fei Wang ◽  
Li Li ◽  
Yong-Guang Zhang ◽  
Wael N. Hozzein ◽  
Xing-Kui Zhou ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Rrna Gene ◽  
West China ◽  
North West ◽  
Hybridization Data ◽  
Gram Staining ◽  
Gene Sequence Analysis ◽  
Endophytic Actinobacterium ◽  
Optimum Ph

A Gram-staining-positive, white-coloured, aerobic, non-motile, catalase-positive and oxidase-negative, endophytic actinobacterium, designated strain EGI 6500322T, was isolated from the surface-sterilized root of the halophyte Salsola affinis C. A. Mey collected from Urumqi, Xinjiang province, north-west China. Growth occurred at 5–35 °C (optimum 25–30 °C), at pH 5–10 (optimum pH 7–8) and with 0–13 % NaCl (w/v) (optimum 0–5 %). The predominant menaquinone was MK-9 (93.1 %). The major cellular fatty acids were anteiso-C15:0 (49.5 %) and iso-C15:0 (15.1 %). The cell-wall peptidoglycan contained lysine, alanine and glutamic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unknown phospholipids and one unknown glycolipid. The DNA G+C content of strain EGI 6500322T was 62.0 mol%. Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain EGI 6500322T were identified as Arthrobacter ardleyensis DSM 17432T (98.38 %) and Arthrobacter bergerei DSM 16367T (98.37 %). The DNA–DNA relatedness between strain EGI 6500322T and Arthrobacter ardleyensis DSM 17432T and Arthrobacter bergerei DSM 16367T was 53.4 ± 4.1 % and 30.5 ± 1.7 %, respectively. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA–DNA hybridization data, strain EGI 6500322T should represent a novel species of the genus Arthrobacter, for which the name Arthrobacter endophyticus sp. nov. is proposed. The type strain is EGI 6500322T ( = KCTC 29490T = JCM 30091T).

Saccharopolyspora gloriosae sp. nov., an endophytic actinomycete isolated from the stem of Gloriosa superba L.

2010 ◽  
Vol 60 (5) ◽  
pp. 1147-1151 ◽  
Author(s):  
Sheng Qin ◽  
Hua-Hong Chen ◽  
Hans-Peter Klenk ◽  
Chang-Jin Kim ◽  
Li-Hua Xu ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Yunnan Province ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Gloriosa Superba ◽  
West China ◽  
Phenotypic Differences ◽  
Hybridization Data ◽  
Gene Sequence Analysis ◽  
Actinomycete Strain

A Gram-stain-positive, aerobic actinomycete, strain YIM 60513T, was isolated from the stem of Gloriosa superba L. collected from tropical rainforest at Xishuangbanna, Yunnan Province, south-west China. 16S rRNA gene sequence analysis indicated that strain YIM 60513T belonged to the genus Saccharopolyspora and was closely related to Saccharopolyspora gregorii NCIB 12823T (99.1 % similarity) and Saccharopolyspora cebuensis SPE 10-1T (97.3 % similarity). Data for the predominant quinone [MK-9(H4)], major fatty acids (iso-C16 : 0, anteiso-C17 : 0 and C17 : 1 cis9) and G+C content of the genomic DNA (71.6 mol%) were similar to those for members of the genus Saccharopolyspora. The level of DNA–DNA relatedness between strain YIM 60513T and S. gregorii NCIB 12823T was 43 %. The combination of phylogenetic analysis, phenotypic differences, chemotaxonomic characteristics and DNA–DNA hybridization data supported the view that strain YIM 60513T should be distinguished from S. gregorii NCIB 12823T and S. cebuensis SPE 10-1T. Strain YIM 60513T therefore represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora gloriosae sp. nov. is proposed. The type strain is YIM 60513T (=KCTC 19243T =CCTCC AA 207006T).

Isolation and description of Selenomonas timonae sp. nov., a novel Selenomonas species detected in a gingivitis patient

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Angéline Antezack ◽  
Manon Boxberger ◽  
Mariem Ben Khedher ◽  
Bernard La Scola ◽  
Virginie Monnet-Corti
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
Optimum Ph

A Gram-stain-negative bacterium, designated strain Marseille-Q3039T, was isolated from subgingival dental plaque of a woman with gingivitis in Marseille, France. Strain Marseille-Q3039T was found to be an anaerobic, motile and spore-forming crescent-shaped bacterium that grew at 25–41.5 °C (optimum, 37 °C), pH 5.5–8.5 (optimum, pH 7.5) and salinity of 5.0 g l−1 NaCl. The results of 16S rRNA gene sequence analysis revealed that strain Marseille-Q3039T was closely related to Selenomonas infelix ATCC 43532T (98.42 % similarity), Selenomonas dianae ATCC 43527T (97.25 %) and Centipedia periodontii DSM 2778T (97.19 %). The orthologous average nucleotide identity and digital DNA–DNA hybridization relatedness between strain Q3039T and its closest phylogenetic neighbours were respectively 84.57 and 28.2 % for S. infelix ATCC 43532T and 83.93 and 27.2 % for C. periodontii DSM 2778T. The major fatty acids were identified as C13 : 0 (27.7 %), C15 : 0 (24.4 %) and specific C13 : 0 3-OH (12.3 %). Genome sequencing revealed a genome size of 2 351 779 bp and a G+C content of 57.2 mol%. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3039T represents a novel species of the genus Selenomonas , for which the name Selenomonas timonae sp. nov. is proposed (=CSUR Q3039=CECT 30128).

scholarly journals Halorubrum aquaticum sp. nov., an archaeon isolated from hypersaline lakes

2011 ◽  
Vol 61 (5) ◽  
pp. 1144-1148 ◽  
Author(s):  
M. C. Gutiérrez ◽  
A. M. Castillo ◽  
P. Corral ◽  
M. Kamekura ◽  
A. Ventosa
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Lipid Analysis ◽  
Halophilic Archaea ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Dna Relatedness ◽  
Gene Sequence Analysis ◽  
Nacl Concentration ◽  
Optimum Ph

Two halophilic archaea, strains EN-2T and SH-4, were isolated from the saline lakes Erliannor and Shangmatala, respectively, in Inner Mongolia, China. Cells were strictly aerobic, motile rods. Colonies were red. Strains EN-2T and SH-4 were able to grow at 25–50 °C (optimum 35–40 °C), with 2.5–5.0 M NaCl (optimum 3.4 M NaCl) and at pH 6.0–9.0 (optimum pH 7.5). MgCl2 was not required for growth. Cells lysed in distilled water and the lowest NaCl concentration that prevented cell lysis was 12 % (w/v). On the basis of 16S rRNA gene sequence analysis, strains EN-2T and SH-4 were closely related to Halorubrum cibi B31T (97.9 and 98.0 % similarity, respectively), Hrr. tibetense 8W8T (97.3 and 97.7 %), Hrr. alkaliphilum DZ-1T (96.8 and 97.1 %), Hrr. luteum CGSA15T (96.8 and 97.0 %) and Hrr. lipolyticum 9-3T (96.8 and 97.0 %). DNA–DNA hybridization showed that strains EN-2T and SH-4 did not belong to the same species as any of these strains (≤45 % DNA–DNA relatedness) but that they are members of the same species (>70 % DNA–DNA relatedness). Polar lipid analysis revealed that strains EN-2T and SH-4 contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated diglycosyl diethers and several unidentified glycolipids. The DNA G+C content of both isolates was 62.1 mol%. It was concluded that strains EN-2T and SH-4 represent a novel species of the genus Halorubrum, for which the name Halorubrum aquaticum sp. nov. is proposed. The type strain is EN-2T ( = CECT 7174T  = CGMCC 1.6377T  = JCM 14031T).

scholarly journals Vibrio oceanisediminis sp. nov., a nitrogen-fixing bacterium isolated from an artificial oil-spill marine sediment

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3552-3557 ◽  
Author(s):  
Sang Rim Kang ◽  
Sathiyaraj Srinivasan ◽  
Sang-Seob Lee
Keyword(s):  
Oil Spill ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Gram Staining ◽  
Gene Sequence Analysis

A Gram-staining-negative, halophilic, facultatively anaerobic, motile, rod-shaped and nitrogen-fixing bacterium, designated strain S37T, was isolated from an artificial oil-spill sediment sample from the coast of Taean, South Korea. Cells grew at 10–37 °C and pH 5.0–9.0, with optimal growth at 28 °C and pH 6.0–8.0. Growth was observed with 1–9 % (w/v) NaCl in marine broth, with optimal growth with 3–5 % NaCl, but no growth was observed in the absence of NaCl. According to the results of 16S rRNA gene sequence analysis, strain S37T represents a member of the genus Vibrio of the class Gammaproteobacteria and forms a clade with Vibrio plantisponsor MSSRF60T (97.38 %), Vibrio diazotrophicus ATCC 33466T (97.31 %), Vibrio aestuarianus ATCC 35048T (97.07 %) Vibrio areninigrae J74T (96.76 %) and Vibrio hispanicus LMG 13240T (96.76 %). The major fatty acids were C16 : 0, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The DNA G+C content was 41.9 %. The DNA–DNA hybridization analysis results showed a 30.2 % association value with the closely related type strain V. plantisponsor DSM 21026T. On the basis of phenotypic and chemotaxonomic characteristics, strain S37T represents a novel species of the genus Vibrio, for which the name Vibrio oceanisediminis sp. nov., is proposed with the type strain S37T ( = KEMB 2255-005T = JCM 30409T).

scholarly journals Microbacterium rhizomatis sp. nov., a β-glucosidase-producing bacterium isolated from rhizome of Korean mountain ginseng

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3196-3202 ◽  
Author(s):  
Van-An Hoang ◽  
Yeon-Ju Kim ◽  
Ngoc Lan Nguyen ◽  
Chang Ho Kang ◽  
Jong-Pyo Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Ginseng Root ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gram Staining ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A novel Gram-staining-positive, rod-shaped bacterium, designated DCY100T, was isolated from rhizome of mountain ginseng root in Hwacheon mountain, Gangwon province, Republic of Korea. The 16S rRNA gene sequence analysis showed that strain DCY100T belonged to the genus Microbacterium and was most closely related to Microbacterium ginsengisoli KCTC 19189T (97.9 %), Microbacterium lacus JCM 15575T (97.2 %) and Microbacterium invictum DSM 19600T (97.1 %). The major menaquinones were MK-11 and MK-12. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The major fatty acids (>10.0 %) were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The cell-wall peptidoglycan contained the amino acids ornithine, alanine, glutamic acid and glycine; whole-cell sugars consisted of glucose, galactose, rhamnose and ribose. The DNA G+C content was 63.6 ± 0.7 mol%. The DNA–DNA hybridization relatedness values between strain DCY100T and Microbacterium ginsengisoli KCTC 19189T, Microbacterium lacus JCM 15575T and Microbacterium invictum DSM 19600T were 36.2 ± 0.4, 22.0 ± 3.0 and 15.3 ± 1.8 %, respectively. On the basis of phenotypic, chemotaxonomic and genotypic analyses, the isolate is classified as a representative of a novel species in the genus Microbacterium, for which the name Microbacterium rhizomatis DCY100T is proposed. The type strain is DCY100T ( = KCTC 39529T = JCM 30598T).

scholarly journals Labrys neptuniae sp. nov., isolated from root nodules of the aquatic legume Neptunia oleracea

2007 ◽  
Vol 57 (3) ◽  
pp. 577-581 ◽  
Author(s):  
Yi-Ju Chou ◽  
Geoffrey N. Elliott ◽  
Euan K. James ◽  
Kuan-Yin Lin ◽  
Jui-Hsing Chou ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Root Nodules ◽  
Rrna Gene ◽  
Hybridization Data ◽  
Physiological And Biochemical Characteristics ◽  
Gene Sequence Analysis ◽  
Southern Taiwan ◽  
Physiological And Biochemical ◽  
Fatty Acid Compositions

A bacterium designated strain Liujia-146T was isolated in the Tainan area of southern Taiwan from root nodules of the aquatic legume Neptunia oleracea. 16S rRNA gene sequence analysis indicated that strain Liujia-146T was highly similar to Labrys monachus VKM B-1479T (97.8 %) and Labrys methylaminiphilus JLW10T (95.5 %) and belonged to the order Rhizobiales in the Alphaproteobacteria. On the basis of phylogenetic analysis, DNA–DNA hybridization data, physiological and biochemical characteristics and fatty acid compositions, the organism was shown to belong to the genus Labrys whilst representing a novel species within this genus. We propose to classify strain Liujia-146T (=BCRC 17578T=LMG 23578T) as the type strain of Labrys neptuniae sp. nov.

scholarly journals Brachybacterium zhongshanense sp. nov., a cellulose-decomposing bacterium from sediment along the Qijiang River, Zhongshan City, China

2007 ◽  
Vol 57 (11) ◽  
pp. 2519-2524 ◽  
Author(s):  
Guoxia Zhang ◽  
Guoqu Zeng ◽  
Xiaowei Cai ◽  
Suier Deng ◽  
Huidong Luo ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Insertion Sequence ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Ratio Analysis ◽  
Polyphasic Analysis ◽  
Hybridization Data ◽  
Dna Base ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

A cellulose-decomposing bacterium, strain JBT, was isolated from sediments along the Qijiang River, Zhongshan City, China. Results of morphological, biochemical and chemotaxonomic characterization and 16S rRNA gene sequence analysis revealed that strain JBT belonged to the genus Brachybacterium. Insertion sequence-PCR fingerprinting patterns, DNA base ratio analysis and DNA–DNA hybridization data showed that strain JBT differed from recognized species of the genus Brachybacterium. Based on polyphasic analysis, strain JBT represents a novel species of the genus Brachybacterium, for which the name Brachybacterium zhongshanense sp. nov. is proposed. The type strain is JBT (=LMG 23926T=CGMCC 1.6508T=DSM 18832T).

scholarly journals Bifidobacterium faecale sp. nov., isolated from human faeces

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3134-3139 ◽  
Author(s):  
Jung-Hye Choi ◽  
Kyung Min Lee ◽  
Myung-Ki Lee ◽  
Chang-Jun Cha ◽  
Geun-Bae Kim
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bifidobacterium Adolescentis ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Gene Sequence Analysis

A novel strain, designated strain CU3-7T, was isolated from faeces of a two-week-old baby. The isolate was Gram-staining-positive, anaerobic and rod-shaped. Results from 16S rRNA gene sequence analysis revealed that strain CU3-7T was phylogenetically affiliated with members of the genus Bifidobacterium . Strain CU3-7T showed the highest level of sequence similarity with Bifidobacterium adolescentis KCTC 3216T (98.4 %), followed by Bifidobacterium ruminantium KCTC 3425T (97.9 %). Analysis of hsp60 sequences showed that strain CU3-7T was closely related to B. adolescentis KCTC 3216T (94.0 %) and B. ruminantium KCTC 3425T (92.5 %). The DNA–DNA hybridization values with the closely related strains were all below the cut-off value for species delineation, 17.0 % with B. ruminantium KCTC 3425T and 14.9 % with B. adolescentis KCTC 3216T. Fructose-6-phosphate phosphoketolase activity was detected. The predominant cellular fatty acids were C16 : 0 (27.7 %), C18 : 1ω9c (27.4 %) and C18 : 1ω9c dimethylacetate (15.5 %). The DNA G+C content was 58.6 mol%. On the basis of polyphasic taxonomy, strain CU3-7T should be classified as the type strain of a novel species within the genus Bifidobacterium , for which the name Bifidobacterium faecale sp. nov. is proposed ( = KACC 17904T = JCM 19861T).

scholarly journals Marmoricola scoriae sp. nov., isolated from volcanic ash

2010 ◽  
Vol 60 (9) ◽  
pp. 2135-2139 ◽  
Author(s):  
Dong Wan Lee ◽  
Soon Dong Lee
Keyword(s):  
Dna Hybridization ◽  
Volcanic Ash ◽  
Gene Sequence ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Hybridization Data ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Diamino Acid ◽  
Unknown Phospholipid

A novel Gram-stain-positive, coccoid actinobacterium, designated strain Sco-D01T, was isolated from volcanic ash collected from Oreum (a parasitic volcanic cone) on Jeju Island, Republic of Korea. Cells were aerobic, oxidase-negative and catalase-positive. Colonies were vivid yellow, circular, smooth and convex. The diagnostic diamino acid in the cell wall was ll-diaminopimelic acid. The predominant menaquinone was MK-8(H4). The polar lipids were phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and an unknown phospholipid. The fatty acid profile was represented by large amounts of saturated, unsaturated, 10-methyl and hydroxyl components. The DNA G+C content of strain Sco-D01T was 72.0 mol%. 16S rRNA gene sequence analysis revealed that strain Sco-D01T belonged to the family Nocardioidaceae and formed a distinct sublineage within the radiation of the genus Marmoricola. The level of DNA–DNA relatedness between strain Sco-D01T and its closest phylogenetic relative, Marmoricola aurantiacus DSM 12652T, was 30.2 % (35.4 % in duplicate measurements). On the basis of phenotypic and DNA–DNA hybridization data, strain Sco-D01T is considered to represent a novel species of the genus Marmoricola, for which the name Marmoricola scoriae sp. nov. is proposed. The type strain is Sco-D01T (=KCTC 19597T=DSM 22127T).

scholarly journals Nocardia artemisiae sp. nov., an endophytic actinobacterium isolated from a surface-sterilized stem of Artemisia annua L.

2011 ◽  
Vol 61 (12) ◽  
pp. 2933-2937 ◽  
Author(s):  
Guo-Zhen Zhao ◽  
Jie Li ◽  
Wen-Yong Zhu ◽  
Hans-Peter Klenk ◽  
Li-Hua Xu ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Artemisia Annua ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Physiological And Biochemical Characteristics ◽  
Gene Sequence Analysis ◽  
Endophytic Actinobacterium ◽  
Optimum Ph ◽  
Established Species ◽  
Physiological And Biochemical

A novel actinobacterium, designated YIM 65623T, was isolated from a surface-sterilized stem of Artemisia annua L. Strain YIM 65623T had morphological, biochemical, physiological and chemotaxonomic properties that were consistent with its classification in the genus Nocardia. Growth occurred with 0–7 % (w/v) NaCl (optimum 0–3 %), at pH 5.0–9.0 (optimum pH 6.0) and at 10–37 °C (optimum 20–28 °C). Comparative 16S rRNA gene sequence analysis showed that strain YIM 65623T constituted a distinct sublineage within the genus Nocardia and displayed 94.1–98.2 % sequence similarity to members of established species in the genus Nocardia. However, DNA–DNA relatedness and physiological and biochemical characteristics showed that strain YIM 65623T could be differentiated from its closest phylogenetic relatives. The G+C content of the genomic DNA was 69.6 mol%. It is proposed that strain YIM 65623T be classified as a representative of a novel species, Nocardia artemisiae sp. nov. The type strain is YIM 65623T ( = DSM 45379T  = CCTCC AA 209038T).

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