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 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).

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 Bacillus kribbensis sp. nov., isolated from a soil sample in Jeju, Korea

2007 ◽  
Vol 57 (12) ◽  
pp. 2912-2916 ◽  
Author(s):  
Jee-Min Lim ◽  
Che Ok Jeon ◽  
Jung Ro Lee ◽  
Dong-Jin Park ◽  
Chang-Jin Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Soil Sample ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Phyletic Line

A Gram-positive, endospore-forming bacterium, designated strain BT080T, was isolated from a soil sample in Jeju, Korea. Cells of the isolate were strictly aerobic rods that were motile by means of peritrichous flagella. The strain grew optimally at 30–33 °C and pH 5.5–6.5. Chemotaxonomic data (major isoprenoid quinone, MK-7; DNA G+C content, 43.3 mol%; major fatty acids, anteiso-C15 : 0, iso-C14 : 0, iso-C16 : 0 and iso-C15 : 0) supported the affiliation of the isolate to the genus Bacillus. Comparative 16S rRNA gene sequence analyses showed that strain BT080T formed a distinct phyletic line within the genus Bacillus. The levels of 16S rRNA gene sequence similarity with respect to related Bacillus species were below 96.4 %. On the basis of physiological, biochemical and phylogenetic properties, strain BT080T represents a novel species within the genus Bacillus, for which the name Bacillus kribbensis sp. nov. is proposed. The type strain is BT080T (=KCTC 13934T=DSM 17871T).

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 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 Streptomyces cocklensis sp. nov., a dioxamycin-producing actinomycete

2012 ◽  
Vol 62 (2) ◽  
pp. 279-283 ◽  
Author(s):  
Byung-Yong Kim ◽  
Tiago Domingues Zucchi ◽  
Hans-Peter Fiedler ◽  
Michael Goodfellow
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Gene Sequence Analysis ◽  
Phyletic Line

The taxonomic position of a streptomycete isolated from soil collected from Cockle Park Experimental Farm, Northumberland, UK, was determined by using a polyphasic approach. The organism had chemical and morphological features consistent with its classification in the genus Streptomyces. 16S rRNA gene sequence analysis supported classification of the strain in the genus Streptomyces and showed that it formed a distinct phyletic line loosely associated with members of the Streptomyces yeochonensis clade. It was related most closely to Streptomyces paucisporeus 1413T (98.6 %16S rRNA gene sequence similarity), but could be distinguished from the latter based on the low level of DNA–DNA relatedness (40 %). It was readily distinguished from the type strains of all species assigned to the S. yeochonensis clade based on a combination of phenotypic properties. Strain BK168T ( = KACC 20908T = NCIMB 14704T) should therefore be classified as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces cocklensis sp. nov. is proposed. The organism produces the antibiotic dioxamycin.

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.

scholarly journals Nocardia halotolerans sp. nov., a halotolerant actinomycete isolated from saline soil

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3148-3154 ◽  
Author(s):  
Mahdi Moshtaghi Nikou ◽  
Mohaddaseh Ramezani ◽  
Mohammad Ali Amoozegar ◽  
Mehrnoosh Rasooli ◽  
Sharareh Harirchi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Phenotypic Data

A novel halotolerant actinomycete, strain Chem15T, was isolated from soil around Inche-Broun hypersaline wetland; its taxonomic position was determined based on a polyphasic approach. Strain Chem15T was strictly aerobic and tolerated NaCl up to 12.5 %. The optimum temperature and pH for growth were 28–30 °C and pH 7.0–7.5, respectively. The cell wall of strain Chem15T contained meso-diaminopimelic acid as diamino acid and galactose, arabinose and ribose as whole-cell sugars. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The cellular fatty acids profile consisted of C16 : 0, iso-C18 : 0, C18 : 0 10-methyl and C18 : 1ω9c, and the major respiratory quinone was MK-8(H4cycl). The G+C content of the genomic DNA was 68.0 mol%. The novel strain constituted a distinct phyletic line within the genus Nocardia, based on 16S rRNA gene sequence analysis, and was closely associated with Nocardia sungurluensis DSM 45714T and Nocardia alba DSM 44684T (98.2 and 98.1 % 16S rRNA gene sequence similarity, respectively). However DNA–DNA relatedness and phenotypic data demonstrated that strain Chem15T was clearly different from closely related species of the genus Nocardia. It is concluded that the organism should be classified as a representative of a novel species of the genus Nocardia, for which the name Nocardia halotolerans sp. nov. is proposed. The type strain is Chem15T ( = IBRC-M 10490T = LMG 28544T).

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