scholarly journals Molecular analysis of artisanal Italian cheeses reveals Enterococcus italicus sp. nov.

2004 ◽  
Vol 54 (5) ◽  
pp. 1717-1721 ◽  
Author(s):  
M. Grazia Fortina ◽  
G. Ricci ◽  
D. Mora ◽  
P. L. Manachini
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Enterococcal Species ◽  
Rrna Gene Sequencing ◽  
Enterococcus Italicus

The taxonomic positions of seven atypical Enterococcus strains, isolated from artisanal Italian cheeses, were investigated in a polyphasic study. By using 16S rRNA gene sequencing, DNA–DNA hybridization and intergenic transcribed spacer analysis, as well as by examining the phenotypic properties, the novel isolates were shown to constitute a novel enterococcal species. Their closest relatives are Enterococcus sulfureus and Enterococcus saccharolyticus, having a 16S rRNA gene sequence similarity of 96·7 %. This group of strains can be easily differentiated from the other Enterococcus species by DNA–DNA hybridization and by their phenotypic characteristics: the strains do not grow in 6·5 % NaCl, and they do not produce acid from l-arabinose, melezitose, melibiose, raffinose or ribose. The name Enterococcus italicus sp. nov. is proposed for this species, with strain DSM 15952T (=LMG 22039T) as the type strain.

scholarly journals Prevotella dentasini sp. nov., a black-pigmented species isolated from the oral cavity of donkeys

2010 ◽  
Vol 60 (7) ◽  
pp. 1637-1639 ◽  
Author(s):  
Kazuko Takada ◽  
Kazuhiko Hayashi ◽  
Yutaka Sato ◽  
Masatomo Hirasawa
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Rrna Gene Sequencing

Four strains (NUM 1903T, NUM 1904, NUM 1912 and NUM 1925) that were obligately anaerobic, pigmented, Gram-negative-staining rods were isolated from the oral cavity of donkeys. These strains were analysed using the Rapid ID 32A, API 20A and API ZYM systems, by DNA–DNA hybridization with other related species and by 16S rRNA gene sequencing. 16S rRNA gene sequence analysis showed that each of the new isolates was a member of the genus Prevotella and related to Prevotella multiformis PPPA21T, showing about 93 % sequence similarity. Based on phylogenetic and phenotypic evidence, it is proposed that the four strains are representatives of a novel species, for which the name Prevotella dentasini sp. nov. is proposed. The type strain is NUM 1903T (=JCM 15908T=DSM 22229T).

scholarly journals Chryseobacterium taiwanense sp. nov., isolated from soil in Taiwan

2006 ◽  
Vol 56 (8) ◽  
pp. 1771-1776 ◽  
Author(s):  
Chun-Ju Tai ◽  
Hsiao-Ping Kuo ◽  
Fwu-Ling Lee ◽  
Han-Ken Chen ◽  
Akira Yokota ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Fatty Acid Analysis ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Rrna Gene Sequencing

Among a large collection of Taiwanese soil isolates, a novel Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacterial strain, Soil-3-27T, was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequencing, DNA–DNA hybridization, fatty acid analysis and comparative phenotypic characterization. The 16S rRNA gene sequence analysis indicated that the organism belongs to the genus Chryseobacterium. The organism contains menaquinone MK-6 as the predominant isoprenoid quinone and 15 : 0 iso (43 %), 17 : 1 isoω9c (17.5 %) and 17 : 0 iso 3-OH (16.6 %) as the major fatty acids. Phylogenetically, the closest relatives of strain Soil-3-27T are Chryseobacterium daecheongense, Chryseobacterium defluvii and Chryseobacterium taichungense with 96.7–97.2 % sequence similarity. DNA–DNA hybridization showed relatedness values of 8.5–24.2 % with these species. The DNA G+C content is 36.8 mol%. Strain Soil-3-27T is clearly distinguishable from other Chryseobacterium species and represents a novel species, for which the name Chryseobacterium taiwanense sp. nov. is proposed. The type strain is strain Soil-3-27T (=BCRC 17412T=IAM 15317T=LMG 23355T).

scholarly journals Loktanella koreensis sp. nov., isolated from sea sand in Korea

2006 ◽  
Vol 56 (9) ◽  
pp. 2199-2202 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Seung-Hee Yoo ◽  
Jong-Shik Kim ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sand Sample ◽  
Sea Sand ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Taxonomic Characterization

A bacterial strain, GA2-M3T, isolated from a sea-sand sample in Korea, was subjected to polyphasic taxonomic characterization. Cells of strain GA2-M3T were Gram-negative, non-motile, non-spore-forming and short rod- to ovoid-shaped. Comparative 16S rRNA gene sequencing studies confirmed that the bacterium fell within the radiation of the genus Loktanella. Similarity levels between the 16S rRNA gene sequence of strain GA2-M3T and those of type strains of Loktanella species with validly published names were 93.5–96.1 %; highest sequence similarity was with Loktanella rosea. The G+C content of the genomic DNA of strain GA2-M3T was 60.0 mol% and the predominant ubiquinone was Q-10. Major fatty acids were 18 : 1ω7c, 18 : 0 and 18 : 1ω7c 11-methyl. On the basis of the evidence presented, it is proposed that strain GA2-M3T represents a novel species, for which the name Loktanella koreensis sp. nov. is proposed. The type strain is GA2-M3T (=KACC 11519T=DSM 17925T).

scholarly journals Bacillus horneckiae sp. nov., isolated from a spacecraft-assembly clean room

2010 ◽  
Vol 60 (5) ◽  
pp. 1031-1037 ◽  
Author(s):  
Parag Vaishampayan ◽  
Alexander Probst ◽  
Srinivasan Krishnamurthi ◽  
Sudeshna Ghosh ◽  
Shariff Osman ◽  
...  
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Clean Room ◽  
Rrna Gene Sequencing

Five Gram-stain-positive, motile, aerobic strains were isolated from a clean room of the Kennedy Space Center where the Phoenix spacecraft was assembled. All strains are rod-shaped, spore-forming bacteria, whose spores were resistant to UV radiation up to 1000 J m−2. The spores were subterminally positioned and produced an external layer. A polyphasic taxonomic study including traditional biochemical tests, fatty acid analysis, cell-wall typing, lipid analyses, 16S rRNA gene sequencing and DNA–DNA hybridization studies was performed to characterize these novel strains. 16S rRNA gene sequencing and lipid analyses convincingly grouped these novel strains within the genus Bacillus as a cluster separate from already described species. The similarity of 16S rRNA gene sequences among the novel strains was >99 %, but the similarity was only about 97 % with their nearest neighbours Bacillus pocheonensis, Bacillus firmus and Bacillus bataviensis. DNA–DNA hybridization dissociation values were <24 % to the closest related type strains. The novel strains had a G+C content 35.6±0.5 mol% and could liquefy gelatin but did not utilize or produce acids from any of the carbon substrates tested. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0 and the cell-wall diamino acid was meso-diaminopimelic acid. Based on phylogenetic and phenotypic results, it is concluded that these strains represent a novel species of the genus Bacillus, for which the name Bacillus horneckiae sp. nov. is proposed. The type strain is 1P01SCT (=NRRL B-59162T =MTCC 9535T).

Ochrobactrum pecoris sp. nov., isolated from farm animals

2011 ◽  
Vol 61 (9) ◽  
pp. 2278-2283 ◽  
Author(s):  
Peter Kämpfer ◽  
Bettina Huber ◽  
Hans-Jürgen Busse ◽  
Holger C. Scholz ◽  
Herbert Tomaso ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Ovis Aries ◽  
Farm Animals ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Ochrobactrum Intermedium ◽  
Rrna Gene Sequencing

Two Gram-negative, rod-shaped, non-spore-forming strains, designated 08RB2639T and 08RB2781-1, were isolated from a sheep (Ovis aries) and a domestic boar (Sus scrofa domestica), respectively. By 16S rRNA gene sequencing, the isolates revealed identical sequences and were shown to belong to the Alphaproteobacteria. They exhibited 97.8 % 16S rRNA gene sequence similarity with Ochrobactrum rhizosphaerae PR17T, O. pituitosum CCUG 50899T, O. tritici SCII24T and O. haematophilum CCUG 38531T and 97.4 % sequence similarity with O. cytisi ESC1T, O. anthropi LMG 3331T and O. lupini LUP21T. The recA gene sequences of the two isolates showed only minor differences (99.5 % recA sequence similarity), and strain 08RB2639T exhibited the highest recA sequence similarity with Ochrobactrum intermedium CCUG 24694T (91.3 %). The quinone system was ubiquinone Q-10, with minor amounts of Q-9 and Q-11, the major polyamines were spermidine, putrescine and sym-homospermidine and the major lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine, with moderate amounts of the Ochrobactrum-specific unidentified aminolipid AL2. The major fatty acids (>20 %) were C18 : 1ω7c and C19 : 0 cyclo ω8c. These traits were in excellent agreement with the assignment of the isolates to the genus Ochrobactrum. DNA–DNA relatedness and physiological and biochemical tests allowed genotypic and phenotypic differentiation from other members of the genus Ochrobactrum. Hence, it is concluded that the isolates represent a novel species, for which the name Ochrobactrum pecoris sp. nov. is proposed (type strain 08RB2639T  = DSM 23868T  = CCUG 60088T  = CCM 7822T).

scholarly journals Altererythrobacter ishigakiensis sp. nov., an astaxanthin-producing bacterium isolated from a marine sediment

2011 ◽  
Vol 61 (12) ◽  
pp. 2956-2961 ◽  
Author(s):  
Mitsufumi Matsumoto ◽  
Daisuke Iwama ◽  
Atsushi Arakaki ◽  
Akira Tanaka ◽  
Tsuyoshi Tanaka ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Rrna Gene Sequencing

A Gram-negative, non-motile, non-spore-forming, halophilic rod, designated JPCCMB0017T, was isolated from a marine sediment of the coastal area of Okinawa, Japan. The isolate formed orange–red colonies on marine agar. Bacteriochlorophyll α was absent and sphingoglycolipid 1 and other carotenoids, including astaxanthin, adonixanthin and zeaxanthin, were present. Ubiquinone-10 (Q-10) was the main respiratory quinone and C18 : 1ω7c was the major cellular fatty acid. The G+C content of DNA was 59.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Altererythrobacter in the family Erythrobacteraceae. Strain JPCCMB0017T exhibited 96.8 % 16S rRNA gene sequence similarity with Altererythrobacter marinus H32T. Unlike other members of the genus Altererythrobacter, strain JPCCMB0017T reduced nitrate. On the basis of genotypic and phenotypic data, a novel species is proposed to accommodate this isolate, with the name Altererythrobacter ishigakiensis sp. nov. The type strain is JPCCMB0017T ( = NITE-AP48T = ATCC BAA-2084T = NBRC 107699T).

scholarly journals Blautia faecis sp. nov., isolated from human faeces

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 599-603 ◽  
Author(s):  
Seong-Kyu Park ◽  
Min-Soo Kim ◽  
Jin-Woo Bae
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Dimethyl Acetal ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

A strictly anoxic, Gram-stain-positive, non-motile Blautia -like bacterium, designated strain M25T, was isolated from a human faecal sample. Strain M25T was negative for both catalase and oxidase activity, utilized carbohydrates as fermentable substrates, produced lactate and acetate as the major end products of glucose fermentation in PYG medium, and had a DNA G+C content of 41.6 mol%. Comparative 16S rRNA gene sequencing showed that strain M25T was closely related to Ruminococcus obeum ATCC 29174T (96.40 % 16S rRNA gene sequence similarity) and Blautia glucerasea HFTH-1T (96.17 %) within the family Lachnospiraceae . Straight-chain saturated and monounsaturated cellular fatty acids were also detected, the majority being C14 : 0, C16 : 0 and C16 : 0 dimethyl acetal acids. Based on the phenotypic, genotypic and phylogenetic characteristics presented in this study, strain M25T represents a novel species within the genus Blautia for which the name Blautia faecis sp. nov. is proposed. The type strain is M25T ( = KCTC 5980T = JCM 17205T).

scholarly journals Bizionia echini sp. nov., isolated from a sea urchin

2010 ◽  
Vol 60 (4) ◽  
pp. 928-931 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Marc Vancanneyt ◽  
Seung Bum Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Urchin ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Tween 20 ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Marine Isolate ◽  
Rrna Gene Sequencing

A bacterial strain, designated KMM 6177T, was isolated from the sea urchin Strongylocentrotus intermedius and subjected to a polyphasic taxonomic investigation. The bacterium was found to be heterotrophic, aerobic, non-motile by gliding and orange-pigmented. Comparative phylogenetic analysis based on 16S rRNA gene sequencing placed the marine isolate in the genus Bizionia, a member of the family Flavobacteriaceae, with 16S rRNA gene sequence similarity of 94.9–98.6 % with recognized Bizionia species. Strain KMM 6177T grew at 4–39 °C and with 1–8 % NaCl. It produced alkaline phosphatase, catalase and oxidase and hydrolysed aesculin, gelatin, DNA and Tween 20. The predominant fatty acids were iso-C15 : 1, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and a summed feature (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c). The DNA G+C content was 34.4 mol%. A combination of phylogenetic, genotypic and phenotypic data clearly indicated that strain KMM 6177T represents a novel species in the genus Bizionia, for which the name Bizionia echini sp. nov. is proposed. The type strain is KMM 6177T (=KCTC 22015T=LMG 25220T).

scholarly journals Paenibacillus phoenicis sp. nov., isolated from the Phoenix Lander assembly facility and a subsurface molybdenum mine

2011 ◽  
Vol 61 (6) ◽  
pp. 1338-1343 ◽  
Author(s):  
James N. Benardini ◽  
Parag A. Vaishampayan ◽  
Petra Schwendner ◽  
Elizabeth Swanner ◽  
Youhei Fukui ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Related Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Closely Related Species ◽  
Rrna Gene Sequencing

A novel Gram-positive, motile, endospore-forming, aerobic bacterium was isolated from the NASA Phoenix Lander assembly clean room that exhibits 100 % 16S rRNA gene sequence similarity to two strains isolated from a deep subsurface environment. All strains are rod-shaped, endospore-forming bacteria, whose endospores are resistant to UV radiation up to 500 J m−2. A polyphasic taxonomic study including traditional phenotypic tests, fatty acid analysis, 16S rRNA gene sequencing and DNA–DNA hybridization analysis was performed to characterize these novel strains. The 16S rRNA gene sequencing convincingly grouped these novel strains within the genus Paenibacillus as a separate cluster from previously described species. The similarity of 16S rRNA gene sequences among the novel strains was identical but only 98.1 to 98.5 % with their nearest neighbours Paenibacillus barengoltzii ATCC BAA-1209T and Paenibacillus timonensis CIP 108005T. The menaquinone MK-7 was dominant in these novel strains as shown in other species of the genus Paenibacillus. The DNA–DNA hybridization dissociation value was <45 % with the closest related species. The novel strains had DNA G+C contents of 51.9 to 52.8 mol%. Phenotypically, the novel strains can be readily differentiated from closely related species by the absence of urease and gelatinase and the production of acids from a variety of sugars including l-arabinose. The major fatty acid was anteiso-C15 : 0 as seen in P. barengoltzii and P. timonensis whereas the proportion of C16 : 0 was significantly different from the closely related species. Based on phylogenetic and phenotypic results, it was concluded that these strains represent a novel species of the genus Paenibacillus, for which the name Paenibacillus phoenicis sp. nov. is proposed. The type strain is 3PO2SAT ( = NRRL B-59348T  = NBRC 106274T).

scholarly journals Hafnia paralvei sp. nov., formerly known as Hafnia alvei hybridization group 2

2010 ◽  
Vol 60 (8) ◽  
pp. 1725-1728 ◽  
Author(s):  
Geert Huys ◽  
Margo Cnockaert ◽  
Sharon L. Abbott ◽  
J. Michael Janda ◽  
Peter Vandamme
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Reference Strains ◽  
Sequence Similarities

It has been shown previously, based largely on DNA–DNA hybridizations and partial 16S rRNA gene sequencing, that Hafnia alvei is genotypically heterogeneous and consists of at least two DNA hybridization groups (HGs). In the present study, the taxonomic status of H. alvei HGs 1 and 2 was reassessed. A panel of 24 reference strains and isolates previously assigned to one of the two HGs in H. alvei was subjected to (GTG)5-PCR fingerprinting; this resulted in the delineation of two (GTG)5-PCR clusters in perfect accordance with the respective HG designations. Based on full 16S rRNA gene sequencing of a selection of reference strains, H. alvei HGs 1 and 2 showed internal sequence similarities of 99.8 and 99.5 %, respectively. Between the two groups, sequence similarities ranged from 98.8 to 99.1 %. Mean DNA–DNA hybridization values of 74.7–99.9 % were obtained within each of the two HGs, whereas cross-hybridizations between members of H. alvei HG 1 (including ATCC 13337T) and HG 2 revealed only 32.7–48.7 % DNA–DNA hybridization. Previously published and new phenotypic data revealed that a combination of malonate assimilation and β-glucosidase activity enabled correct assignment of Hafnia isolates to one of the two HGs. Collectively, taxonomic data from this study confirm that H. alvei comprises at least two taxa at the species level, of which HG 1 corresponds to H. alvei sensu stricto because it includes the type strain ATCC 13337T. Strains formerly classified as members of H. alvei HG 2 represent a novel species, for which the name Hafnia paralvei sp. nov. is proposed; ATCC 29927T (=CDC 4510-73T =LMG 24706T), the former reference strain of H. alvei HG 2, is designated the type strain.

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