scholarly journals Nocardiopsis sinuspersici sp. nov., isolated from sandy rhizospheric soil

2010 ◽  
Vol 60 (10) ◽  
pp. 2346-2352 ◽  
Author(s):  
Javad Hamedi ◽  
Fatemeh Mohammadipanah ◽  
Mathias von Jan ◽  
Gabriele Pötter ◽  
Peter Schumann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A polyphasic taxonomic study of a halotolerant bacterium, isolated from sandy rhizospheric soil in Sarbandar, Persian Gulf, Iran, revealed that strain HM6T represents a novel species within the genus Nocardiopsis. Results of the 16S rRNA gene sequence comparison revealed that strain HM6T clustered with strains of the genus Nocardiopsis, showing the highest degree of 16S rRNA gene sequence similarity to Nocardiopsis quinghaiensis (99.2 %), Nocardiopsis aegyptia (98.5 %) and Nocardiopsis halotolerans (98.3 %). However, DNA–DNA hybridization studies with these type strains revealed less than 39.6 % similarity. Rather than genotypic differences, there are some phenotypic discrepancies between strain HM6T and closely related species of the genus Nocardiopsis. Main morphological and chemotaxonomical features of strain HM6T include: (i) growth characteristics, i.e. the formation of a scant light-yellow to white aerial mycelium and the typical zig-zag form of the hyphae, which fragment during ageing into smooth rod-shaped spores; (ii) the presence of meso-diaminopimelic acid and glucose plus ribose in whole-cell hydrolysates; (iii) the presence of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol, together with three unknown Nocardiopsis-specific phospholipids (close to diphosphatidylglycerol in position) in polar lipid extracts; (iv) the presence of the major menaquinones MK-10(H0), MK-10(H2) and MK-9(H0) in the non-polar fraction; (v) the presence of iso/anteiso-branched plus 10-methyl-branched fatty acids, showing the diagnostic combination for species of the genus Nocardiopsis of iso-16 : 0 (31.1 %), anteiso-17 : 0 (19.2 %), 10-methyl-17 : 0 (5.8 %) and tuberculostearic acid (8.8 %); and (vi) the absence of mycolic acids. Analysis of the 16S rRNA gene sequence revealed that strain HM6T represents a distinct taxon within the genus Nocardiopsis. Based upon genotypic and phenotypic differences from other members of the genus, a novel species, Nocardiopsis sinuspersici sp. nov., is proposed. The type strain is HM6T (=UTMC 00102T =DSM 45277T =CCUG 57624T).

scholarly journals Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil

2010 ◽  
Vol 60 (2) ◽  
pp. 429-433 ◽  
Author(s):  
Kiran Bala ◽  
Pooja Sharma ◽  
Rup Lal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Physiological Tests ◽  
The 16S Rrna Gene

A yellow-pigmented, hexachlorocyclohexane (HCH)-degrading bacterial strain, P25T, was isolated from an HCH dump site located in the northern part of India. Phylogenetic analysis based on the 16S rRNA gene sequence showed that the strain belongs to the genus Sphingobium, as it showed highest sequence similarity to Sphingobium amiense IAM 15006T (97.7 %). The 16S rRNA gene sequence similarity between strain P25T and members of other species of the genus Sphingobium with validly published names ranged from 94.0 to 97.7 %. The DNA–DNA relatedness between strain P25T and Sphingobium amiense IAM 15006T and other related strains was found be less than 30 %, confirming it to represent a novel species. The DNA G+C content of strain P25T was 65 mol%. The polyamine profile showed the presence of spermidine. The predominant cellular fatty acids were summed feature 8 (18 : 1ω7c and/or 18 : 1ω6c; 48.3 %), 16 : 0 (13.7 %) and 14 : 0 2-OH (8.8 %). The polar lipid profile of strain P25T also corresponded to those reported for sphingomonads (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid), supporting its identification as a member of the family Sphingomonadaceae. The results obtained from DNA–DNA hybridization and biochemical and physiological tests clearly distinguished strain P25T from closely related members of the genus Sphingobium. Thus, a novel species of the genus Sphingobium is proposed, Sphingobium quisquiliarum sp. nov. The type strain is P25T (=MTCC 9472T =CCM 7543T).

scholarly journals Oceanobacillus profundus sp. nov., isolated from a deep-sea sediment core

2007 ◽  
Vol 57 (2) ◽  
pp. 409-413 ◽  
Author(s):  
Yoon-Gon Kim ◽  
Dong Han Choi ◽  
Sangmin Hyun ◽  
Byung Cheol Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sediment Core ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A halotolerant, facultatively alkaliphilic bacterium, designated CL-MP28T, was isolated from the surface of a sediment core sample collected at a depth of 2247 m in the Ulleung Basin of the East Sea, Korea. Phylogenetic analysis of the 16S rRNA gene sequence of strain CL-MP28T revealed an affiliation with the genus Oceanobacillus. The sequence similarities between the isolate and type strains of members of the genus Oceanobacillus were in the range 95.0–96.0 %, indicating that strain CL-MP28T represented a novel species within the genus. The strain was found to be Gram-positive, rod-shaped and motile by means of peritrichous flagella and was shown to produce ellipsoidal spores. The strain was strictly aerobic and able to grow with NaCl at concentrations in the range 0–14 % (w/v) at pH 7.5. The strain grew at temperatures of 15–42 °C and at pH 6.5–9.5. The major fatty acids were anteiso-C15 : 0 (64.9 %), anteiso-C17 : 0 (11.9 %) and iso-C16 : 0 (7.7 %). The major isoprenoid quinone was MK-7. The DNA G+C content was 40.2 mol%. According to the 16S rRNA gene sequence, DNA–DNA relatedness and physiological data and the fatty acid composition, CL-MP28T could be assigned to the genus Oceanobacillus, but is distinguishable from the recognized species of this genus. Strain CL-MP28T therefore represents a novel species within the genus Oceanobacillus, for which the name Oceanobacillus profundus sp. nov. is proposed. The type strain is CL-MP28T (=KCCM 42318T=DSM 18246T).

scholarly journals Revised minimal standards for description of new species of the class Mollicutes (division Tenericutes)

2007 ◽  
Vol 57 (11) ◽  
pp. 2703-2719 ◽  
Author(s):  
Daniel R. Brown ◽  
Robert F. Whitcomb ◽  
Janet M. Bradbury
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
The 16S Rrna Gene

Minimal standards for novel species of the class Mollicutes (trivial term, mollicutes), last published in 1995, require revision. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Mollicutes proposes herein revised standards that reflect recent advances in molecular systematics and the species concept for prokaryotes. The mandatory requirements are: (i) deposition of the type strain into two recognized culture collections, preferably located in different countries; (ii) deposition of the 16S rRNA gene sequence into a public database, and a phylogenetic analysis of the relationships among the 16S rRNA gene sequences of the novel species and its neighbours; (iii) deposition of antiserum against the type strain into a recognized collection; (iv) demonstration, by using the combination of 16S rRNA gene sequence analyses, serological analyses and supplementary phenotypic data, that the type strain differs significantly from all previously named species; and (v) assignment to an order, a family and a genus in the class, with an appropriate specific epithet. The 16S rRNA gene sequence provides the primary basis for assignment to hierarchical rank, and may also constitute evidence of species novelty, but serological and supplementary phenotypic data must be presented to substantiate this. Serological methods have been documented to be congruent with DNA–DNA hybridization data and with 16S rRNA gene placements. The novel species must be tested serologically to the greatest extent that the investigators deem feasible against all neighbouring species whose 16S rRNA gene sequences show >0.94 similarity. The investigator is responsible for justifying which characters are most meaningful for assignment to the part of the mollicute phylogenetic tree in which a novel species is located, and for providing the means by which novel species can be identified by other investigators. The publication of the description should appear in a journal having wide circulation. If the journal is not the International Journal of Systematic and Evolutionary Microbiology, copies of the publication must be submitted to that journal so that the name may be considered for inclusion in a Validation List as required by the International Code of Bacteriological Nomenclature (the Bacteriological Code). Updated informal descriptions of the class Mollicutes and some of its constituent higher taxa are available as supplementary material in IJSEM Online.

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 Corynebacterium tapiri sp. nov. and Corynebacterium nasicanis sp. nov., isolated from a tapir and a dog, respectively

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3885-3893 ◽  
Author(s):  
Sandra Baumgardt ◽  
Igor Loncaric ◽  
Peter Kämpfer ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Established Species

Two Gram-stain-positive bacterial isolates, strain 2385/12T and strain 2673/12T were isolated from a tapir and a dog's nose, respectively. The two strains were rod to coccoid-shaped, catalase-positive and oxidase-negative. The highest 16S rRNA gene sequence similarity identified Corynebacterium singulare CCUG 37330T (96.3 % similarity) as the nearest relative of strain 2385/12T and suggested the isolate represented a novel species. Corynebacterium humireducens DSM 45392T (98.7 % 16S rRNA gene sequence similarity) was identified as the nearest relative of strain 2673/12T. Results from DNA–DNA hybridization with the type strain of C. humireducens demonstrated that strain 2673/12T also represented a novel species. Strain 2385/12T showed a quinone system consisting predominantly of menaquinones MK-8(H2) and MK-9(H2) whereas strain 2673/12T contained only MK-8(H2) as predominant quinone. The polar lipid profiles of the two strains showed the major compounds phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. Phosphatidylinositol was identified as another major lipid in 2673/12T whereas it was only found in moderate amounts in strain 2385/12T. Furthermore, moderate to minor amounts of phosphatidylinositol-mannoside, β-gentiobiosyl diacylglycerol and variable counts of several unidentified lipids were detected in the two strains. Both strains contained corynemycolic acids. The polyamine patterns were characterized by the major compound putrescine in strain 2385/12T and spermidine in strain 2673/12T. In the fatty acid profiles, predominantly C18 : 1ω9c and C16 : 0 were detected. The two strains are distinguishable from each other and the nearest related established species of the genus Corynebacterium phylogenetically and phenotypically. In conclusion, two novel species of the genus Corynebacterium are proposed, namely Corynebacterium tapiri sp. nov. (type strain, 2385/12T = CCUG 65456T = LMG 28165T) and Corynebacterium nasicanis sp. nov. (type strain, 2673/12T = CCUG 65455T = LMG 28166T).

scholarly journals Oceanobacillus luteolus sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1495-1500 ◽  
Author(s):  
Min Wu ◽  
Guiqin Yang ◽  
Zhen Yu ◽  
Li Zhuang ◽  
Yingqiang Jin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two Gram-stain-positive, rod-shaped and endospore-forming bacteria, designated WM-1T and WM-4, were isolated from a paddy soil and a forest soil, respectively, in South China. Comparative 16S rRNA gene sequence analyses showed that both strains were members of the genus Oceanobacillus and most closely related to Oceanobacillus chironomi LMG 23627T with pairwise sequence similarity of 96.0 %. The isolates contained menaquinone-7 (MK-7) as the respiratory quinone and anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0 as the major fatty acids (>10 %). Polar lipids consisted of a predominance of diphosphatidylglycerol and moderate to minor amounts of phosphatidylglycerol and phosphatidylinositol. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The DNA G+C content was 38.6–39.2 mol%. The 16S rRNA gene sequence of strain WM-1T displayed 99.7 % similarity to that of strain WM-4, and DNA–DNA hybridization between the two strains showed a relatedness value of 91 %. Based on the results of this polyphasic study, strains WM-1T and WM-4 represent a novel species in the genus Oceanobacillus , for which the name Oceanobacillus luteolus sp. nov. is proposed. The type strain is WM-1T ( = KCTC 33119T = CGMCC 1.12406T).

scholarly journals Kistimonas asteriae gen. nov., sp. nov., a gammaproteobacterium isolated from Asterias amurensis

2010 ◽  
Vol 60 (4) ◽  
pp. 938-943 ◽  
Author(s):  
Eun Ju Choi ◽  
Hak Cheol Kwon ◽  
Young Chang Sohn ◽  
Hyun Ok Yang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Asterias Amurensis ◽  
Light Yellow ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A novel marine bacterium, strain KMD 001T, was isolated from the starfish Asterias amurensis, which inhabits the East Sea of Korea. Strain KMD 001T was aerobic, light-yellow pigmented and Gram-stain-negative. Analyses of the 16S rRNA gene sequence revealed that strain KMD 001T represents a novel lineage within the class Gammaproteobacteria. Strain KMD 001T is closely related to the genera Endozoicomonas and Zooshikella, which belong to the family Hahellaceae and to the order Oceanospirillales. The 16S rRNA gene sequence of strain KMD 001T shows similarities of approximately 91.8–94.6 % with the above-mentioned genera. The DNA G+C content of KMD 001T is 47.6 mol%. It contains Q-9 as the major isoprenoid quinone. The predominant fatty acids were determined to be anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. Strain KMD 001T should be assigned to a novel bacterial genus within the class Gammaproteobacteria based on its phylogenetic, chemotaxonomic and phenotypic characteristics. The name Kistimonas asteriae gen. nov., sp. nov. is proposed. The type strain is KMD 001T (=KCCM 90076T =JCM 15607T).

scholarly journals Nocardia grenadensis sp. nov., isolated from sand of the Caribbean Sea

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 693-697 ◽  
Author(s):  
Peter Kämpfer ◽  
Nicole Lodders ◽  
Iris Grün-Wollny ◽  
Karin Martin ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Caribbean Sea ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Caribbean

A Gram-stain-positive, non-spore-forming bacterium (GW5-5797T) was isolated on soil extract agar from sand collected at a depth of 5 m in the Caribbean Sea near Grenada. 16S rRNA gene sequence analysis and similarity studies showed that strain GW5-5797T belongs to the genus Nocardia, and is most closely related to Nocardia speluncae N2-11T (99.2 % similarity) and Nocardia jinanensis 04-5195T (99.2 %) and more distantly related to Nocardia rhamnosiphila 202GMOT (98.6 %) and other Nocardia species. Strain GW5-5797T could be distinguished from all other recognized Nocardia species by sequence similarity values less than 98.5 %. The peptidoglycan diamino acid was meso-diaminopimelic acid. Strain GW5-5797T exhibited a quinone system with the predominant compounds MK-8(H4ω-cyclo) and MK-8(H2). The polar lipid profile of GW5-5797T consisted of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid, moderate amounts of phosphatidylinositol and a phosphatidylinositol mannoside and minor amounts of several lipids including a second phosphatidylinositol mannoside. The polyamine pattern contained the major compound spermine and moderate amounts of spermidine. The major fatty acids were C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0. These chemotaxonomic traits are in excellent agreement with those of other Nocardia species. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW5-5797T from the most closely related species, showing 16S rRNA gene sequence similarities >98.5 %. Strain GW5-5797T therefore merits separate species status, and we propose the name Nocardia grenadensis sp. nov., with the type strain GW5-5797T ( = CCUG 60970T  = CIP 110294T).

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