scholarly journals Enterococcus hermanniensis sp. nov., from modified-atmosphere-packaged broiler meat and canine tonsils

2004 ◽  
Vol 54 (5) ◽  
pp. 1823-1827 ◽  
Author(s):  
Joanna Koort ◽  
Tom Coenye ◽  
Peter Vandamme ◽  
Antti Sukura ◽  
Johanna Björkroth
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Cell Protein ◽  
Rrna Gene ◽  
Modified Atmosphere ◽  
Rrna Gene Sequence ◽  
Protein Patterns ◽  
Broiler Meat

Isolates 302, 334, 356, 377 and 379, detected in modified-atmosphere-packaged broiler meat, together with strains LMG 12317T and LMG 13617, detected in dog tonsils, were analysed in a polyphasic taxonomy study, including numerical analysis of ribopatterns and whole-cell protein patterns, 16S rRNA gene sequence analysis, DNA–DNA hybridization and determination of some phenotypic properties. The results indicated that these isolates represent a novel species in the genus Enterococcus. The isolates showed classical phenotypic reactions for the genus Enterococcus with the exception of not possessing the Lancefield group D antigen. Isolates 334, LMG 12317T and LMG 13617 showed the highest 16S rRNA gene sequence similarity (98·3–99·0 %) to the Enterococcus pallens type strain. In the distance matrix tree based on 16S rRNA gene sequences, the three isolates were located in the Enterococcus avium group with E. pallens as their closest phylogenetic neighbour. Numerical analyses of whole-cell protein patterns and HindIII/EcoRI ribotypes placed all seven isolates together in a single cluster separated from the E. avium group reference strains. The DNA–DNA hybridization level between strains 334 and LMG 12317T was 93·5 %, confirming that they represent the same species. Low hybridization levels (12–30 %) were, by contrast, obtained with the E. pallens and Enterococcus raffinosus type strains. The name Enterococcus hermanniensis sp. nov. is proposed, with strain LMG 12317T (=CCUG 48100T) as the type strain.

scholarly journals Bacillus herbersteinensis sp. nov.

2005 ◽  
Vol 55 (5) ◽  
pp. 2119-2123 ◽  
Author(s):  
Monika Wieser ◽  
Hanna Worliczek ◽  
Peter Kämpfer ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Wall Painting ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Cell Protein ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Protein Patterns

Two bacterial strains, designated D-1,5aT and D-1,5b, were isolated from a medieval wall painting in the chapel of Castle Herberstein, Styria (Austria). The Gram-positive, heterotrophic, aerobic, spore-forming rods showed nearly identical whole-cell protein patterns, identical genomic fingerprints and identical physiological profiles, demonstrating their relationship at the species level. Both strains contained meso-diaminopimelic acid in their peptidoglycan, possessed a quinone system comprising menaquinone MK-7 and had fatty acid profiles in which C15 : 0 iso and C15 : 0 anteiso were predominant. The 16S rRNA gene sequence of D-1,5aT showed the highest similarity (99·5 %) to the sequence of Bacillus sp. LMG 20243, and Bacillus flexus IFO 15715T was the next most closely related established species (96·5 %). Other type strains, such as Bacillus fastidiosus DSM 91T, Bacillus indicus SD/3T, Bacillus cibi JG-30T, Bacillus megaterium IAM 13418T, Bacillus cohnii DSM 6308T, Bacillus bataviensis LMG 21833T and Bacillus soli LMG 21838T, shared 96·0–96·1 % 16S rRNA gene sequence similarity with D-1,5aT. The combination of physiological and chemotaxonomic traits distinguishes the two strains from those species sharing the highest sequence similarities (96·0–96·5 %). On the basis of these characteristics and the phylogenetic position of strain D-1,5aT (=DSM 16534T=CCM 7228T), this strain is assigned as the type strain of a novel species of the genus Bacillus, for which the name Bacillus herbersteinensis sp. nov. is proposed.

scholarly journals Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

scholarly journals Loktanella atrilutea sp. nov., isolated from seawater in Japan

2007 ◽  
Vol 57 (9) ◽  
pp. 1966-1969 ◽  
Author(s):  
Shoichi Hosoya ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sanriku Coast ◽  
Type Strains

A Gram-negative, rod-shaped bacterium, IG8T, was isolated from seawater off the Sanriku coast, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IG8T represented a separate lineage within the genus Loktanella; the highest 16S rRNA gene sequence similarity values were found with the type strains of Loktanella salsilacus (98.6 %) and Loktanella fryxellensis (98.4 %). DNA–DNA hybridization values between strain IG8T and the type strains of L. salsilacus (27.9–36.1 %) and L. fryxellensis (11.3–31.0 %) were clearly below 70 %, the generally accepted limit for species delineation. The DNA G+C content of strain IG8T was 66.3 mol%. On the basis of DNA–DNA hybridization, some biochemical characteristics and 16S rRNA gene sequence comparison, it is proposed that the isolate represents a novel species, Loktanella atrilutea sp. nov. The type strain is IG8T (=IAM 15450T=NCIMB 14280T).

Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2684-2689 ◽  
Author(s):  
V. Venkata Ramana ◽  
P. Shalem Raj ◽  
L. Tushar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two strains (JA643T and JA755) of Gram-stain-negative, facultatively anaerobic phototrophic, bacteria capable of growth at low temperatures (10–15 °C) were isolated from freshwater streams from different geographical regions of India. Both strains contain bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid (PL), unidentified amino lipids (AL1–AL6, AL9) and an unidentified lipid (L1) were the polar lipids present in both strains. The major cellular fatty acid was C18 : 1ω7c (76–79 % of the total). Bacteriohopane derivatives (BHD1,2), unidentified hopanoids (UH1–5), diplopterol (DPL) and diploptene (DPE) were the major hopanoids of both strains. The DNA G+C content was 64.2–64.5 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that both strains are closely related to the genus Rhodomicrobium and clustered with Rhodomicrobium vannielii DSM 162T (99 % sequence similarity). However, both strains exhibited only 46.1 % DNA–DNA hybridization with R. vannielii DSM 162T. Strains JA643T and JA755 shared >99 % 16S rRNA gene sequence similarity and were >85 % related on the basis of DNA–DNA hybridization; they are therefore considered to represent a novel species in the genus Rhodomicrobium , for which the name Rhodomicrobium udaipurense sp. nov. is proposed. The type strain is JA643T ( = KCTC 15219T = NBRC 109057T).

Transfer of Wautersia numazuensis to the genus Cupriavidus as Cupriavidus numazuensis comb. nov.

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 208-211 ◽  
Author(s):  
Lourdes Martínez-Aguilar ◽  
Jesús Caballero-Mellado ◽  
Paulina Estrada-de los Santos
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Phylogenetic analysis of the 16S rRNA gene sequences of strains TE26T and K6 belonging to Wautersia numazuensis Kageyama et al. 2005 showed the strains to be deeply intermingled among the species of the genus Cupriavidus . The comparison showed that strain TE26T was closely related to the type strains of Cupriavidus pinatubonensis (99.1 % 16S rRNA gene sequence similarity), C. basilensis (98.7 %), C. necator (98.7 %) and C. gilardii (98.0 %). However, DNA–DNA hybridization experiments (less than 20 % relatedness) demonstrated that strain TE26T is different from these Cupriavidus species. A comparative phenotypic and chemotaxonomic analysis (based on fatty acid profiles) in combination with the 16S rRNA gene sequence phylogenetic analysis and the DNA–DNA hybridization results supported the incorporation of Wautersia numazuensis into the genus Cupriavidus as Cupriavidus numazuensis comb. nov.; the type strain is TE26T ( = LMG 26411T  = DSM 15562T  = CIP 108892T).

scholarly journals Burkholderia bannensis sp. nov., an acid-neutralizing bacterium isolated from torpedo grass (Panicum repens) growing in highly acidic swamps

2011 ◽  
Vol 61 (7) ◽  
pp. 1645-1650 ◽  
Author(s):  
Tomoko Aizawa ◽  
Pisoot Vijarnsorn ◽  
Mutsuyasu Nakajima ◽  
Michio Sunairi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Cell Protein ◽  
Rrna Gene ◽  
Good Growth ◽  
Rrna Gene Sequence ◽  
Panicum Repens

Two strains of acid-neutralizing bacteria, E25T and E21, were isolated from torpedo grass (Panicum repens) growing in highly acidic swamps (pH 2–4) in actual acid sulfate soil areas of Thailand. Cells of the strains were Gram-negative, aerobic, non-spore-forming rods, 0.6–0.8 µm wide and 1.6–2.1 µm long. The strains showed good growth at pH 4.0–8.0 and 17–37 °C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone and C16 : 0, C17 : 0 cyclo and C18 : 1ω7c as the major fatty acids. Their fatty acid profiles were similar to those reported for other Burkholderia species. The DNA G+C content of the strains was 65 mol%. On the basis of 16S rRNA gene sequence similarity, the strains were shown to belong to the genus Burkholderia. Although the calculated 16S rRNA gene sequence similarity of E25T to strain E21 and the type strains of Burkholderia unamae, B. tropica, B. sacchari, B. nodosa and B. mimosarum was 100, 98.7, 98.6, 97.6, 97.4 and 97.3 %, respectively, strains E25T and E21 formed a group that was distinct in the phylogenetic tree; the DNA–DNA relatedness of E25T to E21 and B. unamae CIP 107921T, B. tropica LMG 22274T, B. sacchari LMG 19450T, B. nodosa LMG 23741T and B. mimosarum LMG 23256T was 90, 42, 42, 42, 45 and 35 %, respectively. The results of physiological and biochemical tests including whole-cell protein pattern analysis allowed phenotypic differentiation of these strains from previously described Burkholderia species. Therefore, strains E25T and E21 represent a novel species, for which the name Burkholderia bannensis sp. nov. is proposed. The type strain is E25T ( = NBRC 103871T  = BCC 36998T).

Weissella fabaria sp. nov., from a Ghanaian cocoa fermentation

2010 ◽  
Vol 60 (9) ◽  
pp. 1999-2005 ◽  
Author(s):  
Katrien De Bruyne ◽  
Nicholas Camu ◽  
Luc De Vuyst ◽  
Peter Vandamme
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Cell Protein ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Two lactic acid bacteria, strains 257T and 252, were isolated from traditional heap fermentations of Ghanaian cocoa beans. 16S rRNA gene sequence analysis of these strains allocated them to the genus Weissella, showing 99.5 % 16S rRNA gene sequence similarity towards Weissella ghanensis LMG 24286T. Whole-cell protein electrophoresis, fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and biochemical tests confirmed their unique taxonomic position. DNA–DNA hybridization experiments towards their nearest phylogenetic neighbour demonstrated that the two strains represent a novel species, for which we propose the name Weissella fabaria sp. nov., with strain 257T (=LMG 24289T =DSM 21416T) as the type strain. Additional sequence analysis using pheS gene sequences proved useful for identification of all Weissella–Leuconostoc–Oenococcus species and for the recognition of the novel species.

scholarly journals Paenibacillus sophorae sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sophora japonica

2011 ◽  
Vol 61 (4) ◽  
pp. 767-771 ◽  
Author(s):  
Hao-Jie Jin ◽  
Jing Lv ◽  
San-Feng Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sophora Japonica ◽  
Type Strains

A nitrogen-fixing bacterium, designated strain S27T, was isolated from rhizosphere soil of Sophora japonica. Phylogenetic analysis based on a fragment of the nifH gene and the full-length 16S rRNA gene sequence revealed that strain S27T is a member of the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between strain S27T and Paenibacillus durus DSM 1735T (97.3 %), Paenibacillus sabinae DSM 17841T (96.9 %), Paenibacillus forsythiae DSM 17842T (96.7 %) and Paenibacillus zanthoxyli DSM 18202T (96.6 %). However, DNA–DNA hybridization values between strain S27T and the four type strains were 37.64 %, 23.12 %, 25.6 % and 34.99 %, respectively. Levels of 16S rRNA gene sequence similarity between strain S27T and the type strains of other recognized members of the genus Paenibacillus were below 96.5 %. The DNA G+C content of strain S27T was 46.0 mol%. The major fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. On the basis of its phenotypic characteristics and DNA–DNA hybridization results, strain S27T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sophorae sp. nov. is proposed. The type strain is S27T ( = CGMCC 1.10238T  = DSM 23020T).

scholarly journals Chromohalobacter japonicus sp. nov., a moderately halophilic bacterium isolated from a Japanese salty food

2007 ◽  
Vol 57 (10) ◽  
pp. 2262-2266 ◽  
Author(s):  
Cristina Sánchez-Porro ◽  
Hiroko Tokunaga ◽  
Masao Tokunaga ◽  
Antonio Ventosa
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Moderately Halophilic ◽  
Salty Food ◽  
Moderately Halophilic Bacterium

A Gram-negative, non-spore-forming, rod-shaped, motile bacterium, designated strain 43T, was isolated from a Japanese salty food and then subjected to a polyphasic taxonomic study. Strain 43T is moderately halophilic, growing at NaCl concentrations in the range 5–25 % (w/v), with optimum growth between 7.5 and 12.5 % (w/v) NaCl. Growth occurs at temperatures from 15 to 42 °C (optimally at 28–37 °C) and at pH 5.5–9.0 (optimally at pH 7.0–8.0). A phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain 43T belongs to the genus Chromohalobacter. The closest relatives were Chromohalobacter canadensis ATCC 43984T (99.3 % 16S rRNA gene sequence similarity), Chromohalobacter beijerinckii ATCC 19372T (99.1 %), Chromohalobacter sarecensis LV4T (98.3 %), Chromohalobacter nigrandesensis LTS-4NT (97.9 %) and Chromohalobacter marismortui ATCC 17056T (97.9 %). The DNA G+C content was 62.9 mol%, which is within the range described for the genus Chromohalobacter. DNA–DNA hybridization studies between strain 43T and C. canadensis CECT 5385T and C. beijerinckii DSM 7218T showed 38 and 49 % relatedness, respectively; lower DNA–DNA hybridization percentages were obtained with respect to other related Chromohalobacter species. The major fatty acids of strain 43T were C16 : 0, C19 : 0 cyclo ω8c and C12 : 0 3-OH. Overall, the phenotypic, genotypic and phylogenetic results demonstrated that strain 43T represents a novel species within the genus Chromohalobacter. The name Chromohalobacter japonicus sp. nov. is proposed, with strain 43T (=CECT 7219T =CCM 7416T) as the type strain.

scholarly journals Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water

2007 ◽  
Vol 57 (11) ◽  
pp. 2629-2635 ◽  
Author(s):  
Margarita Gomila ◽  
Botho Bowien ◽  
Enevold Falsen ◽  
Edward R. B. Moore ◽  
Jorge Lalucat
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains

Three Gram-negative, rod-shaped, non-spore-forming bacteria (strains CCUG 52769T, CCUG 52770 and CCUG 52771) isolated from haemodialysis water were characterized taxonomically, together with five strains isolated from industrial waters (CCUG 52428, CCUG 52507, CCUG 52575T, CCUG 52590 and CCUG 52631). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these isolates belonged to the class Betaproteobacteria and were related to the genus Pelomonas, with 16S rRNA gene sequence similarities higher than 99 % with the only species of the genus, Pelomonas saccharophila and to Pseudomonas sp. DSM 2583. The type strains of Mitsuaria chitosanitabida and Roseateles depolymerans were their closest neighbours (97.9 and 97.3 % 16S rRNA gene sequence similarity, respectively). Phylogenetic analysis was also performed for the internally transcribed spacer region and for three genes [hoxG (hydrogenase), cbbL/cbbM (Rubisco) and nifH (nitrogenase)] relevant for the metabolism of the genus Pelomonas. DNA–DNA hybridization, major fatty acid composition and phenotypical analyses were carried out, which included the type strain of Pelomonas saccharophila obtained from different culture collections (ATCC 15946T, CCUG 32988T, DSM 654T, IAM 14368T and LMG 2256T), as well as M. chitosanitabida IAM 14711T and R. depolymerans CCUG 52219T. Results of DNA–DNA hybridization, physiological and biochemical tests supported the conclusion that strains CCUG 52769, CCUG 52770 and CCUG 52771 represent a homogeneous phylogenetic and genomic group, including strain DSM 2583, clearly differentiated from the industrial water isolates and from the Pelomonas saccharophila type strain. On the basis of phenotypic and genotypic characteristics, these strains belong to two novel species within the genus Pelomonas, for which the names Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are proposed. The type strains of Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are CCUG 52769T (=CECT 7234T) and CCUG 52575T (=CECT 7233T), respectively.

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