scholarly journals Reclassification of Lactobacillus ferintoshensis as a later heterotypic synonym of Lactobacillus parabuchneri

2005 ◽  
Vol 55 (5) ◽  
pp. 2195-2198 ◽  
Author(s):  
Marc Vancanneyt ◽  
Katrien Engelbeen ◽  
Marjan De Wachter ◽  
Katrien Vandemeulebroecke ◽  
Ilse Cleenwerck ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Lactobacillus Kefiri

Lactobacillus ferintoshensis has recently been described as a novel species, distinct from its close phylogenetic neighbours Lactobacillus buchneri, Lactobacillus kefiri and Lactobacillus hilgardii. Two highly related species with validly published names, Lactobacillus parakefiri and Lactobacillus parabuchneri, were not considered in the study due to the lack of 16S rRNA gene sequence data at that time. Since the publication of the study, the sequences have become available and have revealed that L. ferintoshensis and L. parabuchneri share 99·7 % 16S rRNA gene sequence similarity. Further genomic and phenotypic data, derived from fluorescent amplified fragment length polymorphism, DNA–DNA hybridization and API 50 CHL analyses, have demonstrated that the species are synonymous.

scholarly journals Fibrisoma limi gen. nov., sp. nov., a filamentous bacterium isolated from tidal flats

2011 ◽  
Vol 61 (6) ◽  
pp. 1418-1424 ◽  
Author(s):  
Manuela Filippini ◽  
Andres Kaech ◽  
Urs Ziegler ◽  
Homayoun C. Bagheri
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The North ◽  
Gram Staining

An orange-pigmented, Gram-staining-negative, non-motile, filament-forming, rod-shaped bacterium (BUZ 3T) was isolated from a coastal mud sample from the North Sea (Fedderwardersiel, Germany) and characterized taxonomically using a polyphasic approach. According to 16S rRNA gene sequence data, it belonged to the family Cytophagaceae, exhibiting low 16S rRNA gene sequence similarity (<90 %) with members of the genera Spirosoma, Rudanella and Fibrella. The DNA G+C content was 52.0 mol%. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 1ω5c and iso-C17 : 0 3-OH. The major polar lipids consisted of phosphatidylethanolamine and several aminolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is proposed that strain BUZ 3T represents a novel genus and species, for which the name Fibrisoma limi gen. nov., sp. nov. is proposed. The type strain is BUZ 3T ( = DSM 22564T  = CCUG 58137T).

scholarly journals Nocardioides iriomotensis sp. nov., an actinobacterium isolated from forest soil

2011 ◽  
Vol 61 (9) ◽  
pp. 2205-2209 ◽  
Author(s):  
Hideki Yamamura ◽  
Shin-ya Ohkubo ◽  
Youji Nakagawa ◽  
Yuumi Ishida ◽  
Moriyuki Hamada ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Forest Soil ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data

An actinomycete strain, designated IR27-S3T, was isolated from a forest soil sample collected from Iriomote Island, Okinawa, Japan. Cells of the isolate were Gram-stain-positive, aerobic, non-sporulating, non-motile coccoids or short rods. The strain grew in the presence of 0–7 % (w/v) NaCl, at pH 6–8 and at 12–37 °C, with optimum growth at 30 °C. Chemotaxonomically, the strain contained ll-diaminopimelic acid as the diagnostic diamino acid and MK-8(H4) as the predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown phospholipid. The major cellular fatty acids were iso-C16 : 0, C17 : 1 cis-9, C15 : 0 and iso-C15 : 0. The DNA G+C content was 73.7 mol%. On the basis of 16S rRNA gene sequence analysis, strain IR27-S3T was closely related to Nocardioides mesophilus MSL-22T (98.1 % 16S rRNA gene sequence similarity), Marmoricola bigeumensis MSL-05T (97.2 %) and Nocardioides jensenii DSM 20641T (96.5 %). On the basis of fatty acid analysis, phylogenetic analysis and phenotypic data, the isolate should be classified in a novel species of the genus Nocardioides, for which the name Nocardioides iriomotensis sp. nov. is proposed. The type strain is IR27-S3T ( = NBRC 105384T  = KACC 14926T).

scholarly journals Alkalimicrobium pacificum gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2453-2458 ◽  
Author(s):  
Gaiyun Zhang ◽  
Yanliu Yang ◽  
Shuang Wang ◽  
Zhilei Sun ◽  
Kailin Jiao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Unidentified Phospholipid ◽  
The Family

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated strain F15T, was isolated from a deep-sea sediment of the western Pacific Ocean. The temperature, pH and NaCl ranges for growth were 4–50 °C, pH 6–11 and 0–10 % (w/v), respectively. Strain F15T showed the highest 16S rRNA gene sequence similarity to Sagittula stellata E-37T (96.4 %), followed by Ponticoccus litoralis CL-GR66T (96.4 %), Antarctobacter heliothermus EL-219T (96.3 %) and Thalassococcus lentus YCS-24T (96.0 %). Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain F15T formed a lineage within the family Rhodobacteraceae of the class Alphaproteobacteria. The polar lipid profile of strain F15T comprised significant amounts of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and one unidentified phospholipid. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 40.2 %), anteiso-C15 : 0 (30.4 %) and anteiso-C17 : 0 (9.7 %). The genomic DNA G+C content of strain F15T was 60.2 mol% and the major respiratory quinone was Q-10. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain F15T is considered to represent a novel species of a new genus within the family Rhodobacteraceae, for which the name Alkalimicrobium pacificum gen. nov., sp. nov. is proposed. The type strain is F15T ( = LMG 28107T = JCM 19851T = CGMCC 1.12763T = MCCC 1A09948T).

Amnibacterium soli sp. nov., an actinobacterium isolated from grass soil

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4750-4753 ◽  
Author(s):  
Long Jin ◽  
Hyung-Gwan Lee ◽  
Hee-Sik Kim ◽  
Chi-Yong Ahn ◽  
Hee-Mock Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

A Gram-stain-positive, aerobic, non-motile, non-spore-forming, short rod-shaped actinobacterium, designated strain PB243T, was isolated from grass soil sampled in Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies showed the isolate was clearly affiliated with the class Actinobacteria , and most closely related to Amnibacterium kyonggiense KEMC 51201-037T, showing 98.8 % 16S rRNA gene sequence similarity. Cells of strain PB243T formed yellow colonies on R2A agar, contained MK-11 and MK-12 as the predominant menaquinones, l-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, and anteiso-C15 : 0 and iso-C16 : 0 among the major fatty acids. The acyl type of the muramic acid was acetyl. The G+C content of the genomic DNA of strain PB243T was 71.5 mol%. Thus, the combined genotypic and phenotypic data supported the conclusion that strain PB243T represents a novel species of the genus Amnibacterium , for which the name Amnibacterium soli sp. nov. is proposed. The type strain is PB243T ( = KCTC 33147T = JCM 19015T).

scholarly journals Kineococcus gypseus sp. nov., isolated from saline sediment

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3703-3708 ◽  
Author(s):  
Qinyuan Li ◽  
Guiding Li ◽  
Xiu Chen ◽  
Fangji Xu ◽  
Yong Li ◽  
...  
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 Data

A novel Gram-stain-positive, aerobic, motile, non-spore-forming coccus-shaped actinomycete, designated strain YIM 121300T, was isolated from alkaline sediment in Yuanjiang, Yunnan province, south-west China. Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain YIM 121300T was affiliated to the genus Kineococcus, and was closely related to Kineococcus aurantiacus IFO 15268T (97.3 % similarity). 16S rRNA gene sequence similarity to other species of the genus Kineococcus was < 97 %. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The whole-cell sugars contained arabinose, galactose, glucose, mannose and ribose. The predominant menaquinone was MK-9(H2). Mycolic acids were not detected. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unknown phospholipid. The predominant fatty acids were anteiso-C15 : 0 and anteiso-C15 : 1 A. The G+C content of the genomic DNA was 75.1 mol%. DNA–DNA relatedness (55 ± 4 % to K. aurantiacus IFO 15268T) and differential phenotypic data demonstrated that strain YIM 121300T was distinguished from all related species of the genus Kineococcus. On the basis of data from the present polyphasic study, the organism should be assigned to a novel species of the genus Kineococcus, for which the name Kineococcus gypseus sp. nov. is proposed. The type strain is YIM 121300T ( = CCTCC AA 2013232T = DSM 27627T).

scholarly journals The genus Listonella MacDonell and Colwell 1986 is a later heterotypic synonym of the genus Vibrio Pacini 1854 (Approved Lists 1980) – a taxonomic opinion

2011 ◽  
Vol 61 (12) ◽  
pp. 3023-3027 ◽  
Author(s):  
Fabiano L. Thompson ◽  
Cristiane C. Thompson ◽  
Graciela M. Dias ◽  
Hiroaki Naka ◽  
Christopher Dubay ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Vibrio Anguillarum ◽  
16S Rrna Gene Sequence ◽  
Published Data ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data

We analysed the taxonomic position of the genus Listonella based on phylogenetic, genomic and phenotypic data. The species of the genus Listonella were nested within the genus Vibrio according to the 16S rRNA gene sequence-based phylogenetic tree. The closest neighbour of Vibrio (Listonella) anguillarum strains LMG 4437T and ATCC 68554 ( = strain 775) was Vibrio ordalii LMG 13544T, with more than 99.5 % 16S rRNA gene sequence similarity. Furthermore, Vibrio (Listonella) pelagius is highly related to Vibrio splendidus. According to average amino acid identity (AAI), multilocus sequence analysis (MLSA) and Karlin genome signature, the closest neighbour of L. anguillarum ATCC 68554 is V. ordalii LMG 13544T, with 95 % AAI, 98 % MLSA and 5 in Karlin. V. anguillarum ATCC 68554 and Vibrio cholerae N16961 had 77 % similarity in AAI, 85 % in MLSA and 14 in the Karlin signature. Phenotypic analyses of previously published data for V. (L.) anguillarum and V. (L.) pelagius revealed that the genus Listonella is extremely similar to the genus Vibrio. V. ordalii and L. anguillarum strains yielded up to 67 % DNA–DNA hybridization. There are only a few phenotypic features that might be used to discriminate these two species: L. anguillarum is positive for the Voges–Proskauer reaction, citrate utilization, starch hydrolysis, lipase activity and acid production from glycerol, sorbitol and trehalose, whereas V. ordalii is negative for these traits. We suggest that the genus Listonella is a later heterotypic synonym of the genus Vibrio and propose to use the names Vibrio anguillarum and Vibrio pelagius in place of Listonella anguillarum and Listonella pelagia, respectively.

scholarly journals Planosporangium mesophilum sp. nov., isolated from rhizosphere soil of Bletilla striata

2011 ◽  
Vol 61 (6) ◽  
pp. 1330-1333 ◽  
Author(s):  
Yan-Ru Cao ◽  
Qian Wang ◽  
Rong-Xian Jin ◽  
Yi Jiang ◽  
Hang-Xian Lai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bletilla Striata

A Gram-stain-positive, non-motile actinomycete, designated strain YIM 48875T, was isolated from rhizosphere soil of Bletilla striata and its taxonomic position was established by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain YIM 48875T belonged to the genus Planosporangium, supported by a bootstrap value of 100 %. Cells of strain YIM 48875T showed two kinds of sporangia, which also supported its classification in the genus Planosporangium. Strain YIM 48875T grew optimally at 28 °C, at pH 6.0–8.0 and in the presence of 2 % (w/v) NaCl. The level of 16S rRNA gene sequence similarity between strain YIM 48875T and Planosporangium flavigriseum YIM 46034T was 98.6 %. Strain YIM 48875T exhibited a quinone system with menaquinones MK-9(H4), MK-9(H6) and MK-9(H8) as the predominant compounds, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol mannoside and the major fatty acids iso-C15 : 0 and iso-C16 : 0; these data were markedly different from those for P. flavigriseum YIM 46034T. The level of DNA–DNA relatedness between strain YIM 48875T and P. flavigriseum YIM 46034T was 45.5 %. It is apparent from the genotypic and phenotypic data that strain YIM 48875T represents a novel species of the genus Planosporangium, for which the name Planosporangium mesophilum sp. nov. is proposed. The type strain is YIM 48875T ( = CCTCC AA 209049T  = KCTC 19779T).

scholarly journals Paraperlucidibaca baekdonensis gen. nov., sp. nov., isolated from seawater

2011 ◽  
Vol 61 (6) ◽  
pp. 1382-1385 ◽  
Author(s):  
Ki-Hoon Oh ◽  
Soo-Young Lee ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Gene Sequence Analysis

A Gram-negative, non-spore-forming, rod-shaped bacterial strain, RL-2T, was isolated from seawater of the East Sea in Korea and was subjected to a polyphasic taxonomic study. Strain RL-2T grew optimally at pH 7.5–8.0, at 20 °C and in the absence of NaCl. Phylogenetic trees based on 16S rRNA gene sequence analysis showed that strain RL-2T forms a cluster with Perlucidibaca piscinae IMCC1704T and various uncultured and unidentified gammaproteobacteria. Strain RL-2T exhibited 16S rRNA gene sequence similarity values of 96.1 % to Perlucidibaca piscinae IMCC1704T and 93.7–99.7 % to the uncultured bacterial clones belonging to the cluster and an unidentified gammaproteobacterium. The fatty acid profile of strain RL-2T was similar to that of Perlucidibaca piscinae IMCC1704T, but the predominant ubiquinone type (Q-11) of strain RL-2T was different from that (Q-8) of Perlucidibaca piscinae IMCC1704T. The DNA G+C content of strain RL-2T was 61.3 mol%. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain RL-2T is considered to represent a novel species of a new genus in the family Moraxellaceae, for which the name Paraperlucidibaca baekdonensis gen. nov., sp. nov. is proposed. The type strain of Paraperlucidibaca baekdonensis is RL-2T ( = KCTC 23145T  = CCUG 59307T).

scholarly journals Amycolatopsis thailandensis sp. nov., a poly(l-lactic acid)-degrading actinomycete, isolated from soil

2011 ◽  
Vol 61 (4) ◽  
pp. 839-843 ◽  
Author(s):  
Atchareeya Chomchoei ◽  
Wasu Pathom-aree ◽  
Akira Yokota ◽  
Chartchai Kanongnuch ◽  
Saisamorn Lumyong
Keyword(s):  
Lactic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Phyletic Line

A novel actinomycete that was capable of degrading poly(l-lactic acid), strain CMU-PLA07T, was isolated from soil in northern Thailand. Strain CMU-PLA07T had biochemical, chemotaxonomic, morphological and physiological properties that were consistent with its classification in the genus Amycolatopsis. 16S rRNA gene sequence analysis showed that the isolate formed a phyletic line within the genus Amycolatopsis. Strain CMU-PLA07T was most similar to Amycolatopsis coloradensis IMSNU 22096T (99.5 % 16S rRNA gene sequence similarity) and Amycolatopsis alba DSM 44262T (99.4 %). However, strain CMU-PLA07T was distinguishable from the type strains of species of the genus Amycolatopsis on the basis of DNA–DNA relatedness and phenotypic data. Therefore, strain CMU-PLA07T is considered to represent a novel species of the genus Amycolatopsis, for which the name Amycolatopsis thailandensis sp. nov. is proposed. The type strain is CMU-PLA07T ( = JCM 16380T = BCC 38279T).

scholarly journals Parapedobacter luteus sp. nov. and Parapedobacter composti sp. nov., isolated from cotton waste compost

2010 ◽  
Vol 60 (8) ◽  
pp. 1849-1853 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Seung-Hee Yoo ◽  
Byung-Yong Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Rrna Gene Sequence ◽  
Phenotypic Data

Two aerobic, Gram-reaction-negative, non-spore-forming bacterial strains, 4M29T and 4M40T, were isolated from cotton composts. The two strains grew in the presence of 0–5 % (w/v) NaCl (optimum growth in the absence of NaCl), at pH 6.0–8.0 (optimum, pH 7.0) and at 15–45 °C (optimum, 30 °C). The strains shared 97.1 % 16S rRNA gene sequence similarity. Strains 4M29T and 4M40T showed the next highest levels of 16S rRNA gene sequence similarity to Parapedobacter koreensis Jip14T (95.6 and 94.4 %, respectively) and Parapedobacter soli DCY14T (95.2 and 93.8 %). The level of DNA–DNA relatedness between strains 4M29T and 4M40T was 38 %. The two strains contained iso-C15 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c) and iso-C17 : 0 3-OH as major fatty acids, MK-7 as the major respiratory quinone, homospermidine as the only polyamine and phosphatidylethanolamine as the major polar lipid. The DNA G+C contents of strains 4M29T and 4M40T were 47.6 and 48.6 mol%, respectively. On the basis of phylogenetic and phenotypic data, strains 4M29T and 4M40T are considered to represent two novel species of the genus Parapedobacter, for which the names Parapedobacter luteus sp. nov. (type strain 4M29T =KACC 10955T =JCM 15977T) and Parapedobacter composti sp. nov. (type strain 4M40T =KACC 10972T =JCM 15978T) are proposed.

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