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).

scholarly journals Description of Herbiconiux flava sp. nov. and emended description of the genus Herbiconiux

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 795-799 ◽  
Author(s):  
Moriyuki Hamada ◽  
Chiaki Komukai ◽  
Tomohiko Tamura ◽  
Lyudmila I. Evtushenko ◽  
Natalia G. Vinokurova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Differences ◽  
Gene Sequence Analysis ◽  
Lipid Pattern

A non-motile and non-endospore-forming rod, strain NBRC 16403T, was isolated from the phyllosphere of a sedge (Carex sp.). 16S rRNA gene sequence analysis indicated that strain NBRC 16403T was closely related to Herbiconiux solani DSM 19813T (98.6 % 16S rRNA gene sequence similarity), Herbiconiux ginsengi wged11T (97.8 %) and Herbiconiux moechotypicola RB-62T (97.8 %). The peptidoglycan (B2γ type) contained d- and l-2,4-diaminobutyric acids, d-alanine, glycine and threo-3-hydroxyglutamic acid, which replaced glutamic acid almost completely. The predominant menaquinones were MK-10 and MK-11. The polar lipid pattern comprised diphosphatidylglycerol, phosphatidylglycerol, three glycolipids and minor amounts of other polar lipids. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0; no cyclohexyl-C17 : 0 was detected. The DNA G+C content was 71.0 mol%. The results of phylogenetic and DNA–DNA relatedness studies, along with phenotypic differences between strain NBRC 16403T and recognized members of the genus Herbiconiux, indicated that the isolate should be assigned to a novel species of the genus Herbiconiux, for which the name Herbiconiux flava sp. nov. is proposed. The type strain is NBRC 16403T ( = VKM Ac-2058T).

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.

Prevotella aurantiaca sp. nov., isolated from the human oral cavity

2010 ◽  
Vol 60 (3) ◽  
pp. 500-503 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Natsuko Suzuki ◽  
Masaaki Okamoto
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

Two anaerobic, pigmented, non-spore-forming, Gram-stain-negative, rod-shaped strains isolated from the human oral cavity, OMA31T and OMA130, were characterized by determining their phenotypic and biochemical features, cellular fatty acid profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that the new isolates belonged to a single species of the genus Prevotella. The two isolates showed 100 % 16S rRNA gene sequence similarity with each other and were most closely related to Prevotella intermedia ATCC 25611T with 96.4 % 16S rRNA gene sequence similarity; the next most closely related strains to the isolates were Prevotella pallens AHN 10371T (96.1 %) and Prevotella falsenii JCM 15124T (95.3 %). Phenotypic and biochemical characteristics of the isolates were the same as those of P. intermedia JCM 12248T, P. falsenii JCM 15124T and Prevotella nigrescens JCM 12250T. The isolates could be differentiated from P. pallens JCM 11140T by mannose fermentation and α-fucosidase activity. Conventional biochemical tests were unable to differentiate the new isolates from P. intermedia, P. falsenii and P. nigrescens. However, hsp60 gene sequence analysis suggested that strain OMA31T was not a representative of P. intermedia, P. pallens, P. falsenii or P. nigrescens. Based on these data, a novel species of the genus Prevotella, Prevotella aurantiaca sp. nov., is proposed, with OMA31T (=JCM 15754T=CCUG 57723T) as the type strain.

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

2011 ◽  
Vol 61 (11) ◽  
pp. 2606-2609 ◽  
Author(s):  
Dong-Shan An ◽  
Liang Wang ◽  
Minseok S. Kim ◽  
Heon-Meen Bae ◽  
Sung-Taik Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Active Components ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

A Gram-reaction-positive, non-motile, non-spore-forming, aerobic rod, designated BXN5-15T, was isolated from the soil of a ginseng field on Baekdu Mountain in China. Strain BXN5-15T grew optimally at 30 °C and pH 6.0–7.0 in the absence of NaCl on R2A agar. Strain BXN5-15T displayed β-glucosidase activity, which allowed it to transform ginsenoside Rb1 (one of the dominant active components of ginseng) via Rd to minor ginsenoside F2. On the basis of 16S rRNA gene sequence analysis, strain BXN5-15T was shown to belong to the genus Solirubrobacter. The closest phylogenetic relatives were Solirubrobacter soli Gsoil 355T (98.4 % 16S rRNA gene sequence similarity) and Solirubrobacter pauli B33D1T (96.4 %). Lower sequence similarities (<96.0 %) were found with all of the other recognized members of the order Solirubrobacterales. The predominant quinone was MK-7(H4). The major fatty acids (>10 %) were C18 : 1ω9c, iso-C16 : 0 and C18 : 3ω6,9,12c. The G+C content of the genomic DNA was 70.6 mol%. DNA−DNA relatedness between strain BXN5-15T and S. soli KCTC 12628T was 23.3 %. On the basis of genotypic, phenotypic and chemotaxonomic data, strain BXN5-15T represents a novel species within the genus Solirubrobacter, for which the name Solirubrobacter ginsenosidimutans sp. nov. is proposed. The type strain is BXN5-15T ( = KACC 20671T  = LMG 24459T).

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).

scholarly journals Chryseobacterium xinjiangense sp. nov., isolated from alpine permafrost

2011 ◽  
Vol 61 (6) ◽  
pp. 1397-1401 ◽  
Author(s):  
Qi Zhao ◽  
Yu Bai ◽  
Gaosen Zhang ◽  
Shan Zhu ◽  
Hongmei Sheng ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Culturable Bacteria ◽  
Rrna Gene Sequence ◽  
Gram Staining ◽  
Gene Sequence Analysis

Strain TSBY 67T was isolated during a study on the phylogenetic diversity of culturable bacteria from alpine permafrost in Tianshan Mountains, China. On the basis of 16S rRNA gene sequence analysis, strain TSBY 67T was closely related to members of the genus Chryseobacterium and exhibited 96.8 % 16S rRNA gene sequence similarity to Chryseobacterium aquaticum 10-46T and Chryseobacterium soldanellicola PSD 1-4T. Strain TSBY 67T grew aerobically, at 4–37 °C, with 0–2 % NaCl and at pH 6–8. Cells were Gram-staining negative, non-motile and non-spore-forming rods. The dominant cellular fatty acids were iso-C15 : 0 (26.9 %), iso-C17 : 0 3-OH (16.1 %) and iso-C17 : 1ω9c (15.4 %). The G+C content of the DNA was 33.5 mol%. Strain TSBY 67T was distinguishable from its closest phylogenetic neighbours by a combination of phenotypic characteristics. Therefore, strain TSBY 67T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium xinjiangense sp. nov. is proposed. The type strain is TSBY 67T ( = NRRL B-51308T = CCTCC AB 207183T).

Kaistia geumhonensis sp. nov. and Kaistia dalseonensis sp. nov., two members of the class Alphaproteobacteria

2011 ◽  
Vol 61 (11) ◽  
pp. 2577-2581 ◽  
Author(s):  
Long Jin ◽  
Kwang Kyu Kim ◽  
Sang-Hoon Baek ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

Two strains, designated B1-1T and B6-8T, were isolated from the Geumho River and the Dalseo Stream in Korea. Comparative 16S rRNA gene sequence analysis showed a clear affiliation of these two bacteria with the class Alphaproteobacteria, their closest relatives being Kaistia adipata KCTC 12095T, Kaistia granuli KCTC 12575T, Kaistia soli KACC 12605T and Kaistia terrae KACC 12910T with 16S rRNA gene sequence similarities of 95.3 –97.7 % to the two novel strains. Strains B1-1T and B6-8T shared a 16S rRNA gene sequence similarity value of 96.1 %. Cells of the two strains were Gram-reaction-negative, aerobic, non-motile, short rods or cocci. The predominant ubiquinone was Q-10. The major fatty acids were C16 : 0, C18 : 1ω7c, C18 : 0 and C19 : 0ω8c cyclo for strain B1-1T and C16 : 0, C18 : 1ω7c, C18 : 0, C18 : 1 2-OH, and C19 : 0ω8c cyclo for strain B6-8T. The G+C contents of the genomic DNA of the strains B1-1T and B6-8T were 61.6 and 66.5 mol%, respectively. Based on the results of this polyphasic study, strains B1-1T ( = KCTC 12849T  = DSM 18799T) and B6-8T ( = KCTC 12850T  = DSM 18800T) represent two novel species of the genus Kaistia, for which the names Kaistia geumhonensis sp. nov. and Kaistia dalseonensis sp. nov. are proposed, respectively.

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 Silvimonas terrae gen. nov., sp. nov., a novel chitin-degrading facultative anaerobe belonging to the ‘Betaproteobacteria’

2005 ◽  
Vol 55 (6) ◽  
pp. 2329-2332 ◽  
Author(s):  
Hee-Chan Yang ◽  
Wan-Taek Im ◽  
Dong-Shan An ◽  
Woo-shin Park ◽  
In S. Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Novel Genus And Species

A taxonomic study was carried out on a bacterial strain, designated KM-45T, isolated from forest soil collected near Daejeon, South Korea. Comparative 16S rRNA gene sequence analysis indicated a clear affiliation of this bacterium to the ‘Betaproteobacteria’ and that it was related most closely to Chitinibacter tainanensis BCRC 17254T, Formivibrio citricus DSM 6150T and Iodobacter fluviatilis ATCC 33051T (92·4, 91·2 and 88·9 % 16S rRNA gene sequence similarity, respectively). Cells were Gram-negative, facultatively anaerobic, motile and rod-shaped. The strain grew well on R2A medium and utilized a broad spectrum of carbon sources. The G+C content of the genomic DNA was 58 mol% and the predominant ubiquinone was Q-8. Major fatty acids were C16 : 0, C16 : 1 ω7c/iso-C15 : 0 2-OH, C18 : 1 ω7c/ω9t/ω12t and C17 : 0 cyclo. On the basis of the evidence presented, it is proposed that strain KM-45T should be placed in a novel genus and species, for which the name Silvimonas terrae gen. nov., sp. nov. is proposed. The type strain is KM-45T (=KCTC 12358T=NBRC 100961T).

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).

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