scholarly journals Phycicoccus ginsenosidimutans sp. nov., isolated from soil of a ginseng field

2011 ◽  
Vol 61 (3) ◽  
pp. 524-528 ◽  
Author(s):  
Liang Wang ◽  
Dong-Shan An ◽  
Feng-Xie Jin ◽  
Sung-Taik Lee ◽  
Wan-Taek Im ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family

A Gram-positive, non-motile, non-spore-forming, aerobic, coccoid-shaped bacterium, designated BXN5-13T, was isolated from the soil of a ginseng field from Baekdu Mountain in Jilin district, China. Strain BXN5-13T grew optimally at 30 °C and pH 6.5–7.5 with 0–2 % (w/v) NaCl. Strain BXN5-13T had β-glucosidase activity that was connected with ginsenoside-converting ability, so that it was able to convert ginsenoside Rb1 to ginsenoside F2. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic relatives of strain BXN5-13T were Phycicoccus aerophilus 5516T-20T (98.4 % 16S rRNA gene sequence similarity), P. bigeumensis MSL-03T (98.3 %), P. dokdonensis DS-8T (97.9 %) and P. jejuensis KSW2-15T (96.9 %). Lower sequence similarity (<97.0 %) was found with the type strains of other recognized species of the family Intrasporangiaceae. The predominant quinone was MK-8(H4). The major fatty acids (>10 %) were iso-C15 : 0, C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The chemotaxonomic data and the high genomic DNA G+C content of strain BXN5-13T (70.8 mol%) supported its affiliation with the genus Phycicoccus. DNA–DNA relatedness between strain BXN5-13T and its closest phylogenetic neighbours was below 16 %. Strain BXN5-13T represents a novel species within the genus Phycicoccus, for which the name Phycicoccus ginsenosidimutans sp. nov. is proposed. The type strain is BXN5-13T (=KCTC 19419T=DSM 21006T=LMG 24462T).

scholarly journals Pseudosphingobacterium domesticum gen. nov., sp. nov., isolated from home-made compost

2007 ◽  
Vol 57 (7) ◽  
pp. 1535-1538 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
M. Fernanda Nobre ◽  
Olga C. Nunes ◽  
Célia M. Manaia
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family

A bacterial strain, DC-186T, isolated from home-made compost, was characterized for its phenotypic and phylogenetic properties. The isolate was a Gram-negative rod that was able to grow at 15–36 °C and pH 5.5–8.0. Strain DC-186T was positive in tests for catalase, oxidase and β-galactosidase activities and aesculin hydrolysis. The predominant fatty acids were the summed feature C16 : 1/iso-C15 : 0 2-OH (42 %) and iso-C15 : 0 (26 %), the major respiratory quinone was menaquinone-7 and the genomic DNA G+C content was 42 mol%. 16S rRNA gene sequence analysis and phenetic characterization indicated that this organism belongs to the phylum Bacteroidetes and revealed its affiliation to the family Sphingobacteriaceae. Of recognized taxa, strain DC-186T was most closely related to Sphingobacterium daejeonense (90 % sequence similarity) based on 16S rRNA gene sequence analysis. The low 16S rRNA gene sequence similarity with other recognized taxa and the identification of distinctive phenetic features for this isolate support the definition of a new genus within the family Sphingobacteriaceae. The name Pseudosphingobacterium domesticum gen. nov., sp. nov. is proposed, with strain DC-186T (=CCUG 54353T=LMG 23837T) as the type strain.

scholarly journals Laceyella tengchongensis sp. nov., a thermophile isolated from soil of a volcano

2010 ◽  
Vol 60 (9) ◽  
pp. 2226-2230 ◽  
Author(s):  
Jing Zhang ◽  
Shu-Kun Tang ◽  
Yu-Qin Zhang ◽  
Li-Yan Yu ◽  
Hans-Peter Klenk ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Morphological Characters ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

A thermophilic strain, designated YIM 10002T, was isolated from a soil sample of Big Empty Volcano in Tengchong county, Yunnan province, south-west China, and a polyphasic approach was used to investigate its taxonomic position. Strain YIM 10002T formed endospores on both aerial and substrate mycelia. Whole-cell hydrolysates contained meso-diaminopimelic acid, ribose, xylose and glucose. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The predominant menaquinone was MK-9. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides, together with some unknown phospholipids. The G+C content of its genomic DNA was 48.6 mol%. All of these chemotaxonomic data together with morphological characters consistently assigned strain YIM 10002T to the genus Laceyella. 16S rRNA gene sequence analysis showed that strain YIM 10002T was most closely related to Laceyella sacchari KCTC 9790T and Laceyella putida KCTC 3666T (99.9 and 98.0 % 16S rRNA gene sequence similarity, respectively). However, strain YIM 10002T showed relatively low DNA–DNA relatedness (34.0 and 39.0 %, respectively) with the above strains. Therefore, strain YIM 10002T represents a novel species of the genus Laceyella, for which the name Laceyella tengchongensis sp. nov. is proposed. The type strain is YIM 10002T (=DSM 45262T =CCTCC AA 208050T).

Pusillimonas soli sp. nov., isolated from farm soil

2010 ◽  
Vol 60 (10) ◽  
pp. 2326-2330 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Myoungsoo Chae ◽  
Leonid N. Ten
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, motile, non-spore-forming bacterial strain, designated MJ07T, was isolated from a farm soil and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ07T belongs to the family Alcaligenaceae, class Betaproteobacteria, and is related most closely to Pusillimonas ginsengisoli KCTC 22046T (98.6 % sequence similarity) and Pusillimonas noertemannii BN9T (96.9 %). The levels of 16S rRNA gene sequence similarity between strain MJ07T and members of all other recognized species of the family Alcaligenaceae were below 95.2 %. The G+C content of the genomic DNA of strain MJ07T was 59.4 mol%. The detection of a quinone system with ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown aminolipids as major polar lipids and a fatty acid profile with C16 : 0 (32.0 %), C17 : 0 cyclo (24.7 %) and C19 : 0 cyclo ω8c (11.5 %) as the major components supported the affiliation of strain MJ07T to the genus Pusillimonas. Strain MJ07T exhibited relatively low levels of DNA–DNA relatedness with respect to P. ginsengisoli KCTC 22046T (50±8 %) and P. noertemannii KACC 13183T (18±7 %). On the basis of its phenotypic and genotypic properties together with its phylogenetic distinctiveness, strain MJ07T (=KCTC 22455T =JCM 16386T) should be classified in the genus Pusillimonas as the type strain of a novel species, for which the name Pusillimonas soli sp. nov. is proposed.

scholarly journals Barnesiella viscericola gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from chicken caecum

2007 ◽  
Vol 57 (2) ◽  
pp. 342-346 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Pham Thi Ngoc Lan ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family

Two bacterial strains isolated from chicken caecum, C46T and C47, were characterized using a polyphasic taxonomic approach that included analysis of the phenotypic and biochemical features, cellular fatty acid profiles, menaquinone profiles and phylogenetic position (using 16S rRNA gene sequence analysis). The 16S rRNA gene sequence analysis showed that these strains belonged to the family Porphyromonadaceae. These strains shared 100 % 16S rRNA gene sequence similarity with each other and were related to Parabacteroides distasonis (showing 86 % sequence similarity). The strains were found to be obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. Growth of the strains was inhibited on medium containing 20 % bile. The major menaquinones of the isolates were MK-11 and MK-12. This menaquinone composition was different from those of other genera of the family Porphyromonadaceae, such as Parabacteroides (in which the predominant menaquinones are MK-9 and MK-10), Porphyromonas (MK-9 and MK-10) and Tannerella (MK-10 and MK-11). This is an important chemotaxonomic characteristic of these micro-organisms. The DNA G+C content of strain C46T is 52.0 mol%. On the basis of these data, strains C46T and C47 represent a novel genus and species, for which the name Barnesiella viscericola gen. nov., sp. nov. is proposed. The type strain of Barnesiella viscericola is C46T (=JCM 13660T=DSM 18177T).

scholarly journals Castellaniella daejeonensis sp. nov., isolated from soil

2010 ◽  
Vol 60 (9) ◽  
pp. 2056-2060 ◽  
Author(s):  
Myungjin Lee ◽  
Hae-Min Jung ◽  
Sung-Geun Woo ◽  
Soon-Ae Yoo ◽  
Leonid N. Ten
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, non-spore-forming, motile, facultatively anaerobic bacterium, designated strain MJ06T, was isolated from oil-contaminated soil and was characterized taxonomically by using a polyphasic approach. Strain MJ06T contained ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine and phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. The G+C content of the genomic DNA of strain MJ06T was 66.2 mol%. The major fatty acids were summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 32.5 %), C16 : 0 (22.8 %) and summed feature 7 (one or more of C18 : 1 ω7c, C18 : 1 ω9t and C18 : 1 ω12t; 14.9 %). Comparative 16S rRNA gene sequence analysis showed that strain MJ06T belonged to the family Alcaligenaceae, class Betaproteobacteria, and joined the evolutionary radiation enclosed by the genus Castellaniella. Levels of 16S rRNA gene sequence similarity between strain MJ06T and its phylogenetically closest relatives, Castellaniella denitrificans NKNTAUT, Castellaniella defragrans 54PinT, Castellaniella ginsengisoli DCY36T and Castellaniella caeni Ho-11T, were 98.6, 98.3, 97.8 and 97.3 %, respectively. Levels of similarity between strain MJ06T and the type strains of all other recognized species in the family Alcaligenaceae were below 95.0 %. Strain MJ06T exhibited relatively low levels of DNA–DNA relatedness with respect to C. defragrans DSM 12141T (52 %), C. denitrificans DSM 11046T (31 %), C. ginsengisoli KCTC 22398T (18 %) and C. caeni KCTC 12197T (15 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ06T is considered to represent a novel species of the genus Castellaniella, for which the name Castellaniella daejeonensis sp. nov. is proposed. The type strain is MJ06T (=KCTC 22454T =JCM 16240T).

scholarly journals Tamaricihabitans halophyticus gen. nov., sp. nov., an endophytic actinomycete of the family Pseudonocardiaceae

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4662-4668 ◽  
Author(s):  
Sheng Qin ◽  
Juan-Luan Bai ◽  
Yu Wang ◽  
Wei-Wei Feng ◽  
Bo Yuan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Mycolic Acids ◽  
The Family

A novel actinomycete strain, designated KLBMP 1356T, was isolated from the root of halophyte Tamarix chinensis Lour. collected from the coastal area of Jiangsu province, PR China. The isolate was characterized using a polyphasic approach. Comparative analysis of the 16S rRNA gene sequence indicated that strain KLBMP 1356T was phylogenetically related to members of the family Pseudonocardiaceae and formed a distinct monophyletic clade between the genera Amycolatopsis (93.1–94.7 % 16S rRNA gene sequence similarity), Prauserella (93.6–95.1 %) and Saccharomonospora (93.2–94.3 %). The isolate displayed long spore chains containing rod-shaped and smooth-surfaced spores. Strain KLBMP 1356T contained meso-diaminopimelic acid as the diagnostic diamino acid, and galactose, arabinose and glucose as the whole-cell sugars. The major menaquinone was MK-9(H4) and the fatty acid profile was characterized by the predominance of iso-C16 : 0, C17 : 1ω8c, C17 : 1ω6c and C17 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, unknown aminophospholipids and an unknown glycolipid. Mycolic acids were not present. The G+C content of the genomic DNA was 67.2 mol%. On the basis of the evidence from this polyphasic study, strain KLBMP 1356T is considered to represent a novel species of a new genus in the family Pseudonocardiaceae, for which the name Tamaricihabitans halophyticus gen. nov., sp. nov. is proposed. The type strain of the type species is KLBMP 1356T ( = DSM 45765T = NBRC 109361T).

scholarly journals Allobacillus halotolerans gen. nov., sp. nov. isolated from shrimp paste

2011 ◽  
Vol 61 (5) ◽  
pp. 1023-1027 ◽  
Author(s):  
Shih-Yi Sheu ◽  
A. B. Arun ◽  
Sing-Rong Jiang ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family

A novel bacterial strain designated B3AT, isolated from shrimp paste, was investigated by a polyphasic taxonomic approach. Cells stained Gram-positive and were aerobic, non-pigmented, sporulating and rod-shaped with a polar flagellum. 16S rRNA gene sequence analysis indicated that strain B3AT belonged to the class Bacilli and was a member of the family Bacillaceae. Strain B3AT shared low levels of 16S rRNA gene sequence similarity (<94.0 %) with members of other genera in the family Bacillaceae and was most closely related to Halalkalibacillus halophilus BH2T (93.8 % sequence similarity). The isolate was able to grow at 20–45 °C, with 0.5–15 % NaCl and at pH 6–9. Menaquinone with seven isoprene units (MK-7) was the major respiratory quinone and 16 : 0 iso, 15 : 0 anteiso and 14 : 0 iso were the major fatty acids. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The characteristic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The DNA G+C content was 45.3 mol%. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and physiological data, strain B3AT represents a novel genus and species in the family Bacillaceae for which the name Allobacillus halotolerans gen. nov., sp. nov. is proposed. The type strain of Allobacillus halotolerans is B3AT ( = BCRC 17939T  = LMG 24826T).

scholarly journals Paenibacillus xinjiangensis sp. nov., isolated from Xinjiang province in China

2006 ◽  
Vol 56 (11) ◽  
pp. 2579-2582 ◽  
Author(s):  
Jee-Min Lim ◽  
Che Ok Jeon ◽  
Dong-Jin Park ◽  
Li-Hua Xu ◽  
Cheng-Lin Jiang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Sequence Similarities

Strain B538T is a Gram-positive, motile, rod-shaped bacterium, which was isolated from Xinjiang province in China. This organism grew optimally at 30–35 °C and pH 8.0–8.5. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B538T belonged to the genus Paenibacillus and chemotaxonomic data (DNA G+C content, 47.0 mol%; major isoprenoid quinone, MK-7; cell wall type, A1γ meso-diaminopimelic acid; major fatty acids, anteiso-C15 : 0 and C16 : 0) supported affiliation of the isolate with the genus Paenibacillus. Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to Paenibacillus glycanilyticus DS-1T, with 16S rRNA gene sequence similarity of 98.1 %; sequence similarities to other members of the genus Paenibacillus used in the phylogenetic tree were less than 96.5 %. The DNA–DNA relatedness between strain B538T and P. glycanilyticus DS-1T was about 8.0 %. On the basis of physiological and molecular properties, strain B538T (=KCTC 3952T=DSM 16970T) is proposed as the type strain of a novel species within the genus Paenibacillus, for which the name Paenibacillus xinjiangensis sp. nov. is proposed.

scholarly journals Bacillus thermolactis sp. nov., isolated from dairy farms, and emended description of Bacillus thermoamylovorans

2011 ◽  
Vol 61 (8) ◽  
pp. 1954-1961 ◽  
Author(s):  
An Coorevits ◽  
Niall A. Logan ◽  
Anna E. Dinsdale ◽  
Gillian Halket ◽  
Patsy Scheldeman ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Emended Description

A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA–DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084T) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization experiments, the remaining 18 isolates (R-6488T, R-28193, R-6491, R-6492, R-7336, R-33367, R-6486, R-6770, R-31288, R-28160, R-26358, R-7632, R-26955, R-26950, R-33520, R-6484, R-26954 and R-7165) represented one single species, most closely related to Bacillus thermoamylovorans (93.9 % 16S rRNA gene sequence similarity), for which the name Bacillus thermolactis is proposed. Cells were Gram-stain-positive, facultatively anaerobic, endospore-forming rods that grew optimally at 40–50 °C. The cell wall peptidoglycan type of strain R-6488T, the proposed type strain, was A1γ based on meso-diaminopimelic acid. Major fatty acids of the strains were C16 : 0 (28.0 %), iso-C16 : 0 (12.1 %) and iso-C15 : 0 (12.0 %). MK-7 was the predominant menaquinone, and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and some unidentified phospholipids. DNA G+C content was 35.0 mol%. Phenotypic properties allowed discrimination from other thermotolerant species of the genus Bacillus and supported the description of the novel species Bacillus thermolactis, with strain R-6488T ( = LMG 25569T  = DSM 23332T) as the proposed type strain.

scholarly journals Lactobacillus hammesii sp. nov., isolated from French sourdough

2005 ◽  
Vol 55 (2) ◽  
pp. 763-767 ◽  
Author(s):  
Rosica Valcheva ◽  
Maher Korakli ◽  
Bernard Onno ◽  
Hervé Prévost ◽  
Iskra Ivanova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Fragment Length Polymorphism ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Different Strains

Twenty morphologically different strains were chosen from French wheat sourdough isolates. Cells were Gram-positive, non-spore-forming, non-motile rods. The isolates were identified using amplified-fragment length polymorphism, randomly amplified polymorphic DNA and 16S rRNA gene sequence analysis. All isolates were members of the genus Lactobacillus. They were identified as representing Lactobacillus plantarum, Lactobacillus paralimentarius, Lactobacillus sanfranciscensis, Lactobacillus spicheri and Lactobacillus sakei. However, two isolates (LP38T and LP39) could be clearly discriminated from recognized Lactobacillus species on the basis of genotyping methods. 16S rRNA gene sequence similarity and DNA–DNA relatedness data indicate that the two strains belong to a novel Lactobacillus species, for which the name Lactobacillus hammesii is proposed. The type strain is LP38T (=DSM 16381T=CIP 108387T=TMW 1.1236T).

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