scholarly journals Microbacterium xylanilyticum sp. nov., a xylan-degrading bacterium isolated from a biofilm

2005 ◽  
Vol 55 (5) ◽  
pp. 2075-2079 ◽  
Author(s):  
Kwang Kyu Kim ◽  
Hye Yoon Park ◽  
Wooshin Park ◽  
In S. Kim ◽  
Sung-Taik Lee
Keyword(s):  
Dna Hybridization ◽  
Membrane Bioreactor ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Degrading Bacterium ◽  
Chemotaxonomic Markers ◽  
Rrna Gene Sequencing

A novel xylan-degrading bacterium, S3-ET, was isolated from the biofilm of a membrane bioreactor. The cells of this strain were Gram-positive, non-motile, non-spore-forming rods, produced primary branches and formed yellow colonies on nutrient agar. The strain had chemotaxonomic markers that were consistent with classification in the genus Microbacterium, i.e. MK-12, MK-11 and MK-13 as the major menaquinones, predominant iso- and anteiso-branched cellular fatty acids, glucose and galactose as the cell-wall sugars, peptidoglycan-type B2β with glycolyl residues and a DNA G+C content of 69·7 mol%. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that strain S3-ET is most similar to Microbacterium hominis IFO 15708T and Microbacterium foliorum DSM 12966T (97·6 and 97·4 % sequence similarity, respectively), and that it forms a separate lineage with M. hominis in the genus Microbacterium. DNA–DNA hybridization results and phenotypic properties showed that strain S3-ET could be distinguished from all known Microbacterium species and represented a novel species, for which the name Microbacterium xylanilyticum sp. nov. is proposed; the type strain is S3-ET (=DSM 16914T=KCTC 19079T).

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 Fontibacillus panacisegetis sp. nov., isolated from soil of a ginseng field

2011 ◽  
Vol 61 (2) ◽  
pp. 369-374 ◽  
Author(s):  
Keun Chul Lee ◽  
Kwang Kyu Kim ◽  
Mi Kyung Eom ◽  
Mi Jeong Kim ◽  
Jung-Sook Lee
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Hybridization Data ◽  
The Family ◽  
Rrna Gene Sequencing

A facultatively anaerobic, endospore-forming bacterium, designated strain P11-6T, was isolated from soil of a ginseng field located in Geumsan County, Republic of Korea. Cells of strain P11-6T were Gram-stain-negative, catalase-negative, motile rods and produced semi-translucent, circular, white colonies on tryptic soy agar. The isolate contained MK-7 as the only menaquinone and anteiso-C15 : 0 as the major fatty acid. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown aminophosphoglycolipid, an unknown aminophospholipid, two unknown phospholipids, three unknown glycolipids and three unknown lipids were detected in the polar lipid profile. The DNA G+C content of strain P11-6T was 41.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain P11-6T was most closely related to Fontibacillus aquaticus GPTSA 19T (97.2 % sequence similarity) and that it formed a separate lineage with F. aquaticus in the family Paenibacillaceae. Combined phenotypic and DNA–DNA hybridization data supported the conclusion that strain P11-6T represents a novel species in the genus Fontibacillus, for which the name Fontibacillus panacisegetis sp. nov. is proposed; the type strain is P11-6T (=KCTC 13564T =CECT 7605T).

scholarly journals Halomonas stevensii sp. nov., Halomonas hamiltonii sp. nov. and Halomonas johnsoniae sp. nov., isolated from a renal care centre

2010 ◽  
Vol 60 (2) ◽  
pp. 369-377 ◽  
Author(s):  
Kwang Kyu Kim ◽  
Keun Chul Lee ◽  
Hee-Mock Oh ◽  
Jung-Sook Lee
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Care Centre ◽  
Hybridization Data ◽  
Rrna Gene Sequencing

A total of 14 Halomonas strains were isolated from the blood of two patients and from dialysis machines of a renal care centre. The strains were Gram-negative, halophilic, motile and non-spore-forming rods. They produced cream-coloured colonies and contained Q-9 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. Phylogenetic analysis based on 16S rRNA gene sequencing showed that the 14 isolates were most closely related to Halomonas magadiensis 21 MIT with 98.1–98.9 % sequence similarity and that they formed three separate lineages among themselves. Combined phenotypic and DNA–DNA hybridization data support the conclusion that they represent three novel species of the genus Halomonas, for which the names Halomonas stevensii sp. nov. (type strain S18214T=KCTC 22148T=DSM 21198T), Halomonas hamiltonii sp. nov. (type strain W1025T=KCTC 22154T=DSM 21196T) and Halomonas johnsoniae sp. nov. (type strain T68687T=KCTC 22157T=DSM 21197T) are proposed.

scholarly journals Rhodococcus triatomae sp. nov., isolated from a blood-sucking bug

2005 ◽  
Vol 55 (4) ◽  
pp. 1575-1579 ◽  
Author(s):  
A. F. Yassin
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Mycolic Acids ◽  
Blood Sucking ◽  
Taxonomic Methods ◽  
Rrna Gene Sequencing

Two bacterial isolates, strains IMMIB RIV-085T and IMMIB RIV-095, isolated from a blood-sucking bug of the genus Triatoma, were characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and mycolic acids consistent with the genus Rhodococcus. Comparative 16S rRNA gene sequencing showed that the two isolates are genealogically highly related (100 % sequence similarity) and constitute a new subline within the genus Rhodococcus, with Rhodococcus corynebacteroides and Rhodococcus rhodnii as their nearest phylogenetic neighbours (98·4 and 98·3 % sequence similarity, respectively). However, DNA–DNA hybridization experiments demonstrated unambiguously that the isolates are genealogically distinct from R. corynebacteroides and R. rhodnii (32 and 43 % relatedness, respectively). The isolates could be distinguished from their phylogenetic relatives and other members of the genus Rhodococcus by means of biochemical tests. On the basis of both phenotypic and phylogenetic evidence, it is proposed that these isolates be classified as a novel species, Rhodococcus triatomae sp. nov. The type strain is strain IMMIB RIV-085T (=CCUG 50202T=DSM 44892T).

scholarly journals Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium

2005 ◽  
Vol 55 (1) ◽  
pp. 405-408 ◽  
Author(s):  
Raúl Rivas ◽  
Pedro F. Mateos ◽  
Eustoquio Martínez-Molina ◽  
Encarna Velázquez
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Sequence Similarity ◽  
Hydrolytic Enzymes ◽  
16S Rrna Gene Sequencing ◽  
Gas Production ◽  
Rrna Gene ◽  
Hybridization Data ◽  
Paenibacillus Illinoisensis ◽  
Rrna Gene Sequencing

During a search for xylan-degrading micro-organisms, a sporulating bacterium was recovered from xylan-containing agar plates exposed to air in a research laboratory (Salamanca University, Spain). The airborne isolate (designated strain XIL14T) was identified by 16S rRNA gene sequencing as representing a Paenibacillus species most closely related to Paenibacillus illinoisensis JCM 9907T (99·3 % sequence similarity) and Paenibacillus pabuli DSM 3036T (98 % sequence similarity). Phenotypic, chemotaxonomic and DNA–DNA hybridization data indicated that the isolate belongs to a novel species of the genus Paenibacillus. Cells of strain XIL14T were motile, sporulating, rod-shaped, Gram-positive and facultatively anaerobic. The predominant cellular fatty acids were anteiso-C15 : 0 and C16 : 0. The DNA G+C content of strain XIL14T was 50·5 mol%. Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. Catalase was positive and oxidase was negative. The airborne isolate produced a variety of hydrolytic enzymes, including xylanases, amylases, gelatinase and β-galactosidase. DNA–DNA hybridization levels between strain XIL14T and P. illinoisensis DSM 11733T and P. pabuli DSM 3036T were 43·3 and 36·3 %, respectively. According to the data obtained, strain XIL14T is considered to represent a novel species for which the name Paenibacillus xylanilyticus sp. nov. is proposed (=LMG 21957T=CECT 5839T).

scholarly journals Leuconostoc durionis sp. nov., a heterofermenter with no detectable gas production from glucose

2005 ◽  
Vol 55 (3) ◽  
pp. 1267-1270 ◽  
Author(s):  
J. J. Leisner ◽  
M. Vancanneyt ◽  
R. Van der Meulen ◽  
K. Lefebvre ◽  
K. Engelbeen ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Gas Production ◽  
Rrna Gene ◽  
Nearest Neighbour ◽  
Sds Page ◽  
Rrna Gene Sequencing

Three lactic acid bacterial (LAB) strains obtained from a Malaysian acid-fermented condiment, tempoyak (made from pulp of the durian fruit), showed analogous but distinct patterns after screening by SDS-PAGE of whole-cell proteins and comparison with profiles of all recognized LAB species. 16S rRNA gene sequencing of one representative strain showed that the taxon belongs phylogenetically to the genus Leuconostoc, with its nearest neighbour being Leuconostoc fructosum (98 % sequence similarity). Biochemical characteristics and DNA–DNA hybridization experiments demonstrated that the strains differ from Leuconostoc fructosum and represent a single, novel Leuconostoc species for which the name Leuconostoc durionis sp. nov. is proposed. The type strain is LMG 22556T (=LAB 1679T=D-24T=CCUG 49949T).

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 Streptococcus dentapri sp. nov., isolated from the wild boar oral cavity

2010 ◽  
Vol 60 (4) ◽  
pp. 820-823 ◽  
Author(s):  
Kazuko Takada ◽  
Kazuhiko Hayashi ◽  
Yutaka Sato ◽  
Masatomo Hirasawa
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phylogenetic Studies ◽  
Streptococcus Equi ◽  
Sequencing Studies ◽  
Streptococcal Species ◽  
Rrna Gene Sequencing

Four Gram-stain-positive, catalase-negative, coccoid-shaped isolates were obtained from the oral cavities of wild boars and characterized by phenotypic and phylogenetic studies. On the results of biochemical tests, the organisms were tentatively identified as a streptococcal species. Comparative 16S rRNA gene sequencing studies confirmed that the organisms are members of the genus Streptococcus, with Streptococcus equi subsp. equi ATCC 33398T as their closest phylogenetic relative (94.7 % similarity). DNA–DNA hybridization analysis showed that the isolates displayed less than 10 % relatedness to Streptococcus equi subsp. equi DSM 20561T. From the phylogenetic and phenotypic evidence, the four isolates represent a novel species of the genus Streptococcus, for which the name Streptococcus dentapri sp. nov. (type strain NUM 1529T =JCM 15752T =DSM 21999T) is proposed.

scholarly journals Leuconostoc pseudoficulneum sp. nov., isolated from a ripe fig

2006 ◽  
Vol 56 (6) ◽  
pp. 1375-1381 ◽  
Author(s):  
Lélia Chambel ◽  
Ivo M. Chelo ◽  
Líbia Zé-Zé ◽  
Luis G. Pedro ◽  
Mário A. Santos ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Protein Profiling ◽  
Cell Protein ◽  
Rrna Gene ◽  
Dot Blot ◽  
Distinct Cluster ◽  
Carbohydrate Fermentation ◽  
Rrna Gene Sequencing

Six strains of lactic acid bacteria (LAB) were isolated from a ripe fig. These strains constituted a highly homogeneous, but distinct, cluster that was separate from other LAB species in a polyphasic approach including dot-blot DNA–DNA hybridization, SDS-PAGE whole-cell protein profiling, carbohydrate fermentation ability, growth characteristics, enzymic profiling, pulsed-field gel electrophoresis macrorestriction analysis and RFLPs. Phylogenetic analysis based on 16S rRNA gene sequencing positioned a representative strain, LC51T, in a distinct line of descent within the recently described clade comprising Leuconostoc ficulneum, Leuconostoc fructosum and Leuconostoc durionis; L. ficulneum was its closest neighbour (98 % sequence similarity). DNA–DNA hybridization values and chemotaxonomic and biochemical characteristics, including enzymic profiles detected with API ZYM microtubes, confirmed that this group of strains is distinct from L. ficulneum and represents a novel species within the genus Leuconostoc. Taking into account the common origin and phylogenetic proximity, the name Leuconostoc pseudoficulneum sp. nov. is proposed. Strain LC51T (=DSM 15468T=CECT 5759T) is the type strain; the DNA G+C content of this strain is 44.5 mol%.

scholarly journals Mucilaginibacter gotjawali sp. nov., isolated from soil of a lava forest

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 952-958 ◽  
Author(s):  
Keun Chul Lee ◽  
Kwang Kyu Kim ◽  
Mi Kyung Eom ◽  
Jong-Shik Kim ◽  
Dae-Shin Kim ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gram Stain ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

A novel bacterial strain, designated SA3-7T, was isolated from soil of a lava forest located in Jeju, Republic of Korea. Cells of strain SA3-7T were Gram-stain-negative, oxidase- and catalase-positive, non-motile rods and produced creamy white colonies on ten-fold-diluted R2A agar. The isolate contained menaquinone-7 (MK-7) as the predominant isoprenoid quinone and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 43.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain SA3-7T was related most closely to Mucilaginibacter frigoritolerans FT22T (96.7 % sequence similarity) and that it formed a separate lineage in the genus Mucilaginibacter . Combined phenotypic, chemotaxonomic and phylogenetic characteristics supported the conclusion that strain SA3-7T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter gotjawali sp. nov. is proposed; the type strain is SA3-7T ( = KCTC 32515T = CECT 8628T = DSM 29289T).

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