scholarly journals Reclassification of Enterococcus flavescens Pompei et al. 1992 as a later synonym of Enterococcus casseliflavus (ex Vaughan et al. 1979) Collins et al. 1984 and Enterococcus saccharominimus Vancanneyt et al. 2004 as a later synonym of Enterococcus italicus Fortina et al. 2004

2006 ◽  
Vol 56 (2) ◽  
pp. 413-416 ◽  
Author(s):  
Sabri M. Naser ◽  
Marc Vancanneyt ◽  
Bart Hoste ◽  
Cindy Snauwaert ◽  
Katrien Vandemeulebroecke ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Single Species ◽  
Alpha Subunit ◽  
Rrna Gene ◽  
Taxonomic Relatedness ◽  
Analysis Scheme ◽  
Enterococcus Casseliflavus ◽  
Enterococcus Italicus

The taxonomic relatedness between the species Enterococcus casseliflavus and Enterococcus flavescens and between Enterococcus italicus and Enterococcus saccharominimus was investigated. Literature data had already indicated the synonymy between E. casseliflavus and E. flavescens, but this observation had not been formally published. Additional evidence that the two taxa represent a single species was provided by comparison of the partial sequences for three housekeeping genes, phenylalanyl-tRNA synthase alpha subunit (pheS), RNA polymerase alpha subunit (rpoA) and the alpha subunit of ATP synthase (atpA). Additional genomic data derived from DNA–DNA hybridization demonstrated that the two species are synonymous. For E. italicus and E. saccharominimus, two recently described taxa, a high 16S rRNA gene sequence similarity of >99 % and analogous phenotypic features indicated a close taxonomic relatedness. The same multilocus sequence analysis scheme for the three housekeeping genes was also applied for E. italicus and E. saccharominimus and indicated possible conspecificity, an observation that was also confirmed by a high DNA–DNA hybridization value (⩾78 %). Data from the present study led to the proposal that E. flavescens should be reclassified as a later synonym of E. casseliflavus and that E. saccharominimus should be reclassified as a later synonym of E. italicus.

Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis)

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3823-3828 ◽  
Author(s):  
Chokchai Kittiwongwattana ◽  
Chitti Thawai
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Low Levels ◽  
Sequence Similarity Analysis ◽  
Ph Range

A Gram-stain-negative, rod-shaped bacterium was isolated and designated strain L6-8T during a study of endophytic bacterial communities in lesser duckweed (Lemna aequinoctialis). Cells of strain L6-8T were motile with peritrichous flagella. The analysis of the nearly complete 16S rRNA gene sequence indicated that strain L6-8T was phylogenetically related to species of the genus Rhizobium . Its closest relatives were Rhizobium borbori DN316T (97.6 %), Rhizobium oryzae Alt 505T (97.3 %) and Rhizobium pseudoryzae J3-A127T (97.0 %). The sequence similarity analysis of housekeeping genes recA, glnII, atpD and gyrB showed low levels of sequence similarity (<91.5 %) between strain L6-8T and other species of the genus Rhizobium with validly published names. The pH range for growth was 4.0–9.0 (optimum 6.0–7.0), and the temperature range for growth was 20–45 °C (optimum 30 °C). Strain L6-8T tolerated NaCl up to 2 % (w/v) (optimum 1 % NaCl). The predominant components of cellular fatty acids were C19 : 0 cyclo ω8c (31.32 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 25.39 %) and C16 : 0 (12.03 %). The DNA G+C content of strain L6-8T was 60.4 mol% (T m). nodC and nifH were not amplified in strain L6-8T. DNA–DNA relatedness between strain L6-8T and R. borbori DN316T, R. oryzae Alt505T and R. pseudoryzae J3-A127T was between 11.2 and 18.3 %. Based on the sequence similarity analyses, phenotypic, biochemical and physiological characteristics and DNA–DNA hybridization, strain L6-8T could be readily distinguished from its closest relatives and represents a novel species of the genus Rhizobium , for which the name Rhizobium paknamense sp. nov. is proposed. The type strain is L6-8T ( = NBRC 109338T = BCC 55142T).

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 Gemella parahaemolysans sp. nov. and Gemella taiwanensis sp. nov., isolated from human clinical specimens

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2060-2065 ◽  
Author(s):  
Wei-Chun Hung ◽  
Hsiao-Jan Chen ◽  
Jui-Chang Tsai ◽  
Sung-Pin Tseng ◽  
Tai-Fen Lee ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

Four Gram-staining-positive, catalase-negative, coccoid isolates, designated NTUH_1465T, NTUH_2196, NTUH_4957 and NTUH_5572T, were isolated from human specimens. The four isolates displayed more than 99.6 % 16S rRNA gene sequence similarity with Gemella haemolysans ATCC 10379T, and 96.7 to 98.6 % similarity with Gemella sanguinis ATCC 700632T, Gemella morbillorum ATCC 27824T or Gemella cuniculi CCUG 42726T. However, phylogenetic analysis of concatenated sequences of three housekeeping genes, groEL, rpoB and recA, suggested that the four isolates were distinct from G. haemolysans ATCC 10379T and other species. Isolates NTUH_2196, NTUH_4957 and NTUH_5572T clustered together and formed a stable monophyletic clade. DNA–DNA hybridization values among strains NTUH_1465T and NTUH_5572T and their phylogenetically related neighbours were all lower than 49 %. The four isolates could be distinguished from G. haemolysans and other species by phenotypic characteristics. Based on the phylogenetic and phenotypic results, two novel species Gemella parahaemolysans sp. nov. (type strain NTUH_1465T = BCRC 80365T = JCM 18067T) and Gemella taiwanensis sp. nov. (type strain NTUH_5572T = BCRC 80366T = JCM 18066T) are proposed.

Lonsdalea quercina subsp. populi subsp. nov., isolated from bark canker of poplar trees

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2309-2313 ◽  
Author(s):  
Tímea Tóth ◽  
Tamás Lakatos ◽  
András Koltay
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type ◽  
Poplar Trees ◽  
Distinct Lineage

Seven Gram-negative bacterial strains were isolated from oozing bark canker of poplar (Populus×euramericana) trees in Hungary. They showed high (>98.3 %) 16S rRNA gene sequence similarity to Lonsdalea quercina ; however, they differed from this species in several phenotypic characteristics. Multilocus sequence analysis based on three housekeeping genes (gyrB, atpD and infB) revealed, and DNA–DNA hybridization analysis confirmed, that this group of bacterial strains forms a distinct lineage within the species Lonsdalea quercina . A detailed study of phenotypic and physiological characteristics confirmed the separation of isolates from poplars from other subspecies of L. quercina ; therefore, a novel subspecies, Lonsdalea quercina subsp. populi, type strain NY060T ( = DSM 25466T = NCAIM B 02483T), is proposed.

scholarly journals Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov.

2007 ◽  
Vol 57 (12) ◽  
pp. 2729-2737 ◽  
Author(s):  
Richard A. Albert ◽  
Julieta Archambault ◽  
Melissa Lempa ◽  
Beth Hurst ◽  
Christine Richardson ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Sequence Similarity ◽  
Single Species ◽  
Rrna Gene ◽  
New Taxon ◽  
Clear Cut ◽  
Close Relationship ◽  
Chemotaxonomic Markers ◽  
Sequence Similarities

A polyphasic study was undertaken to clarify the taxonomic position of endospore-forming strains 433-D9, 433-E17 and 121-X1. BOX-PCR-generated fingerprints indicated that they may be members of a single species. 16S rRNA gene sequence similarity demonstrated that a representative of this group, 433-D9, is affiliated closely with Bacillus arvi DSM 16317T (100 %), Bacillus arenosi DSM 16319T (99.8 %) and Bacillus neidei NRRL BD-87T (97.1 %). Sequence similarities revealed Bacillus pycnus NRRL NRS-1691T and several Kurthia species as the next nearest relatives. DNA–DNA hybridization results showed that strain 433-D9 is a member of B. arvi. Detection of l-Lys–d-Asp-based peptidoglycan in strain 433-D9, B. arvi DSM 16317T and B. arenosi DSM 16319T was in agreement with their close relationship, but differentiated these strains from B. neidei NRRL BD-87T and B. pycnus NRRL NRS-1691T, for which l-Lys–d-Glu was reported. A similar quinone system was detected in strains 433-D9, 433-E17, 121-X1, B. arvi DSM 16317T, B. arenosi DSM 16319T and B. neidei NRRL BD-87T. This system, unusual for bacilli, consisted of the major compound menaquinone MK-8 (69–80 %) and moderate amounts of MK-7 (19–30 %). This observation was in contrast to the predominance of MK-7 of the closest relative B. pycnus NRRL NRS-1691T, as also reported for representatives of the closely related non-endospore-forming genus Kurthia. Strains 433-D9, B. arvi DSM 16317T and B. arenosi DSM 16319T exhibited homogeneous and discriminative polar lipid profiles and fatty acid profiles consisting of major acids i-C15 : 0 and ai-C15 : 0 and moderate amounts of i-C17 : 1 ω10c and i-C17 : 1 I/ai-C17 : 1 B that discriminated them from closely related strains such as B. neidei NRRL BD-87T. On the basis of clear-cut discriminative chemotaxonomic markers, we propose strains 433-D9, 433-E17 and 121-X1, B. arvi DSM 16317T, B. arenosi DSM 16319T and B. neidei NRRL BD-87T to be reclassified within a separate genus. For this new taxon, we propose the name Viridibacillus gen. nov., and we propose the reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov. (the type species of Viridibacillus, with the type strain DSM 16317T =LMG 22165T), Viridibacillus arenosi comb. nov. (type strain DSM 16319T =LMG 22166T) and Viridibacillus neidei comb. nov. (type strain NRRL BD-87T =DSM 15031T =JCM 11077T).

Sunxiuqinia elliptica gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment in a sea cucumber farm

2011 ◽  
Vol 61 (12) ◽  
pp. 2885-2889 ◽  
Author(s):  
Lingyun Qu ◽  
Fengling Zhu ◽  
Xuguang Hong ◽  
Wei Gao ◽  
Junhui Chen ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Sea Cucumber ◽  
New Genus ◽  
Sequence Similarity ◽  
Single Species ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Major Respiratory Quinone

Three novel aerobic, elliptic bacteria, designated DQHS4T, DQHS8 and DQHS15, were isolated from sediment of a seashore pond for sea cucumber culture in Jimo, Qingdao, on the east coast of China. Cells were Gram-, oxidase- and catalase-negative. All three strains grew at 15–42 °C, pH 5–9 and NaCl concentrations between 0.5 and 10 %. DNA–DNA hybridization experiments revealed high (>85 %) relatedness among the three novel isolates and suggested that the strains constitute a single species. Comparative 16S rRNA gene sequence analysis indicated that these bacteria had less than 90 % similarity to all described species of the phylum Bacteroidetes; the closest relative of the three isolates was Prolixibacter bellariivorans F2T, sharing only 89.6 % sequence similarity. The major cellular fatty acids were iso-C17 : 0 3-OH (19.8–20.0 %), iso-C15 : 0 (16.9–17.3 %), anteiso-C17 : 1 B and/or iso-C17 : 1 I (7.4–8.7 %), C17 : 0 2-OH (8.4 %), anteiso-C15 : 0 (8.2–8.6 %) and C17 : 1ω6c (5.6–6.0 %). The major respiratory quinone was menaquinone-7 (MK-7) and the DNA G+C content was 41.8–43.5 mol%. Based on the distinct phylogenetic position and the combination of genotypic, phenotypic and chemotaxonomic characteristics, these three strains were considered to represent a novel species of a new genus in the phylum Bacteroidetes, for which the name Sunxiuqinia elliptica gen. nov., sp. nov. is proposed. The type strain of Sunxiuqinia elliptica is DQHS4T ( = CGMCC 1.9156T  = NCCB 100301T  = LMG 25367T).

scholarly journals Vibrio gallicus sp. nov., isolated from the gut of the French abalone Haliotis tuberculata

2004 ◽  
Vol 54 (3) ◽  
pp. 843-846 ◽  
Author(s):  
Tomoo Sawabe ◽  
Karin Hayashi ◽  
Jun Moriwaki ◽  
Fabiano L. Thompson ◽  
Jean Swings ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Vibrio Fischeri ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Rrna Gene ◽  
Vibrio Salmonicida ◽  
Carbon Compounds ◽  
Haliotis Tuberculata

Five alginolytic, facultatively anaerobic, non-motile bacteria were isolated from the gut of the abalone Haliotis tuberculata. Phylogenetic analyses based on 16S rDNA data indicated that these strains are related to Vibrio wodanis, Vibrio salmonicida, Vibrio logei and Vibrio fischeri (but with <97 % 16S rRNA gene sequence similarity). DNA–DNA hybridization and fluorescence amplified fragment length polymorphism fingerprinting demonstrated that the five strains constituted a single species that was different from all currently known vibrios. The name Vibrio gallicus sp. nov. (type strain, CIP 107863T=LMG 21878T=HT2-1T; DNA G+C content, 43·6–44·3 mol%) is proposed for this novel taxon. Several phenotypic features were disclosed that discriminated V. gallicus from other Vibrio species: V. gallicus can be differentiated from Vibrio halioticoli on the basis of four traits (β-galactosidase test and assimilation of three carbon compounds) and from Vibrio superstes by 16 traits.

scholarly journals Morganella psychrotolerans sp. nov., a histamine-producing bacterium isolated from various seafoods

2006 ◽  
Vol 56 (10) ◽  
pp. 2473-2479 ◽  
Author(s):  
Jette Emborg ◽  
Paw Dalgaard ◽  
Peter Ahrens
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Morganella Morganii ◽  
Protein Encoding ◽  
Type Strains ◽  
The 16S Rrna Gene

Mesophilic Morganella morganii (n=6) and psychrotolerant M. morganii-like isolates from various seafoods (n=13), as well as clinical M. morganii isolates (n=3), were characterized by using a polyphasic approach including multi-locus sequencing. Based on the phylogenetic analysis, the 22 strains were divided into two distinct groups comprising mesophilic and psychrotolerant isolates, respectively. This classification was supported by DNA–DNA hybridization studies, whereby a psychrotolerant isolate (strain U2/3T) showed 41.0 and 17.8 % relatedness to the type strains of the mesophilic species Morganella morganii subsp. morganii (strain LMG 7874T) and Morganella morganii subsp. sibonii (strain DSM 14850T), respectively. Analysis of the 16S rRNA gene sequences showed a similarity of 98.6 % between mesophilic and psychrotolerant isolates. However, fragments of seven protein-encoding housekeeping genes (atpD, dnaN, gyrB, hdc, infB, rpoB and tuf) all showed less than 90.9 % sequence similarity between the two groups. The psychrotolerant isolates grew at 0–2 °C and also differed from the mesophilic M. morganii isolates with respect to growth at 37 °C and in 8.5 % (w/v) NaCl and fermentation of d-galactose. The psychrotolerant strains appear to represent a novel species, for which the name Morganella psychrotolerans sp. nov. is proposed. The type strain is U2/3T (=LMG 23374T=DSM 17886T).

scholarly journals Rubritalea halochordaticola sp. nov., a carotenoid-producing verrucomicrobial species isolated from a marine chordate

2011 ◽  
Vol 61 (7) ◽  
pp. 1515-1520 ◽  
Author(s):  
Jaewoo Yoon ◽  
Satoru Matsuda ◽  
Kyoko Adachi ◽  
Hiroaki Kasai ◽  
Akira Yokota
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Sea Squirt ◽  
Cell Biomass ◽  
Taxonomic Approach

A Gram-negative-staining, obligately aerobic, non-motile, rod-shaped and chemoheterotrophic bacterium, designated strain MN1-1006T, was isolated from an ascidian (sea squirt) sample, and was studied using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the new isolate shared approximately 93–99% sequence similarity with recognized species of the genus Rubritalea within the phylum ‘Verrucomicrobia’. DNA–DNA hybridization values between strain MN1-1006T and Rubritalea squalenifaciens HOact23T and Rubritalea sabuli YM29-052T were 57% and 14.5%, respectively. Strain MN1-1006T produced carotenoid compounds that rendered the cell biomass a reddish pink colour. The strain also contained squalene. The cell-wall peptidoglycan of the novel strain contained muramic acid and meso-diaminopimelic acid. The DNA G+C content of strain MN1-1006T was 51.4 mol%. The major cellular fatty acids were iso-C14:0, iso-C16:0 and anteiso-C15:0. The major isoprenoid quinone was MK-9. On the basis of these data, it was concluded that strain MN1-1006T represents a novel species of the genus Rubritalea, for which the name Rubritalea halochordaticola sp. nov. is proposed. The type strain is MN1-1006T ( = KCTC 23186T = NBRC 107102T).

scholarly journals Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field

2006 ◽  
Vol 56 (7) ◽  
pp. 1531-1534 ◽  
Author(s):  
Reiji Tanaka ◽  
Satoshi Kawaichi ◽  
Hiroshi Nishimura ◽  
Yoshihiko Sako
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Thermophilic Bacterium ◽  
Hydrothermal Field ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Optimum Ph ◽  
Kagoshima Prefecture ◽  
Bacterium Strain

A novel thermophilic bacterium, strain KW1T, was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52–78 °C (optimum, 70 °C), pH 5–8 (optimum, pH 7) and 0–4.5 % NaCl (optimum, 1.0 %). The novel isolate was a strictly aerobic heterotroph that utilized complex proteinaceous substrates as well as a variety of carboxylic acids and amino acids. The G+C content of the genomic DNA was 70.8 mol%. Analysis of 16S rRNA gene sequences indicated that strain KW1T is closely related to Thermaerobacter subterraneus C21T (98.4 % sequence similarity). However, the DNA–DNA hybridization value for strain KW1T and T. subterraneus ATCC BAA-137T was below 46 %. On the basis of the molecular and physiological traits of strain KW1T, it represents a novel species of the genus Thermaerobacter, for which the name Thermaerobacter litoralis sp. nov. is proposed. The type strain is KW1T (=JCM 13210T=DSM 17372T).

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