scholarly journals Lactobacillus floricola sp. nov., lactic acid bacteria isolated from mountain flowers

2011 ◽  
Vol 61 (6) ◽  
pp. 1356-1359 ◽  
Author(s):  
Shinji Kawasaki ◽  
Kana Kurosawa ◽  
Madoka Miyazaki ◽  
Chisato Yagi ◽  
Yoritaka Kitajima ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
Significant Relationships ◽  
Lactobacillus Kefiri

Five strains (Ryu1-2T, Gon2-9, Ryu4-3, Nog8-1 and Aza1-1) of lactic acid bacteria were isolated from flowers in mountainous areas in Japan, Oze National Park, Iizuna mountain and the Nikko area. The five isolates were found to share almost identical (99.6–100 % similar) 16S rRNA gene sequences and were therefore deemed to belong to the same species. These isolates exhibited low levels of 16S rRNA gene sequence similarity to known lactic acid bacteria; the closest recognized relatives to strain Ryu1-2T were the type strains of Lactobacillus hilgardii (92.8 % similarity), Lactobacillus kefiri (92.7 %), Lactobacillus composti (92.6 %) and Lactobacillus buchneri (92.4 %). Comparative analyses of rpoA and pheS gene sequences demonstrated that the novel isolates did not show significant relationships to other Lactobacillus species. The strains were Gram-stain-positive, catalase-negative and homofermentative. The isolates utilized a narrow range of carbohydrates as sources of carbon and energy, including glucose and fructose. On the basis of phenotypic characteristics and phylogenetic data, these isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillus floricola sp. nov. is proposed. The type strain is Ryu1-2T ( = NRIC 0774T  = JCM 16512T  = DSM 23037T).

scholarly journals Lactobacillus ozensis sp. nov., isolated from mountain flowers

2011 ◽  
Vol 61 (10) ◽  
pp. 2435-2438 ◽  
Author(s):  
Shinji Kawasaki ◽  
Kana Kurosawa ◽  
Madoka Miyazaki ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Anaerobic Growth ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
Significant Relationships ◽  
Lactobacillus Kefiri ◽  
Better Than

Five strains (Mizu2-1T, Gon2-7, Koba6-1, Koyu2-2 and Miya2-2) of lactic acid bacteria (LAB) were isolated from flowers in Oze National Park, Japan, using anaerobic cultivation. The five isolates were found to share identical 16S rRNA gene sequences. The isolates exhibited low levels of 16S rRNA gene sequence similarity to known LAB; the closest recognized relatives of strain Mizu2-1T were the type strains of Lactobacillus kunkeei (94.9 %), Lactobacillus kefiri (94.1 %) and Lactobacillus buchneri (93.9 %). Comparative analyses of rpoA and pheS gene sequences demonstrated that the novel isolates did not show significant relationships to other Lactobacillus species. The strains were Gram-stain-positive, catalase-negative and heterofermentative. Anaerobic growth was better than aerobic growth. The isolates utilized a narrow range of carbohydrates as sources of carbon and energy, including glucose and fructose. On the basis of phenotypic characteristics and phylogenetic data, the isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillus ozensis sp. nov. is proposed. The type strain is Mizu2-1T ( = JCM 17196T  = DSM 23829T).

scholarly journals Vibrio olivae sp. nov., isolated from Spanish-style green-olive fermentations

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1895-1901 ◽  
Author(s):  
Helena Lucena-Padrós ◽  
Juan M. González ◽  
Belén Caballero-Guerrero ◽  
José Luis Ruiz-Barba ◽  
Antonio Maldonado-Barragán
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Green Olive

Three isolates originating from Spanish-style green-olive fermentations in a manufacturing company in the province of Seville, Spain, were taxonomically characterized by a polyphasic approach. This included a phylogenetic analysis based on 16S rRNA gene sequences and multi-locus sequence analysis (MLSA) based on pyrH, recA, rpoA, gyrB and mreB genes. The isolates shared 98.0 % 16S rRNA gene sequence similarity with Vibrio xiamenensis G21T. Phylogenetic analysis based on 16S rRNA gene sequences using the neighbour-joining and maximum-likelihood methods showed that the isolates fell within the genus Vibrio and formed an independent branch close to V. xiamenensis G21T. The maximum-parsimony method grouped the isolates to V. xiamenensis G21T but forming two clearly separated branches. Phylogenetic trees based on individual pyrH, recA, rpoA, gyrB and mreB gene sequences revealed that strain IGJ1.11T formed a clade alone or with V. xiamenensis G21T. Sequence similarities of the pyrH, recA, rpoA, gyrB and mreB genes between strain IGJ1.11T and V. xiamenensis G21T were 86.7, 85.7, 97.3, 87.6 and 84.8 %, respectively. MLSA of concatenated sequences showed that strain IGJ1.11T and V. xiamenensis G21T are two clearly separated species that form a clade, which we named Clade Xiamenensis, that presented 89.7 % concatenated gene sequence similarity, i.e. less than 92 %. The major cellular fatty acids (>5 %) of strain IGJ1.11T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Enzymic activity profiles, sugar fermentation patterns and DNA G+C content (52.9 mol%) differentiated the novel strains from the closest related members of the genus Vibrio. The name Vibrio olivae sp. nov. is proposed for the novel species. The type strain is IGJ1.11T ( = CECT 8064T = DSM 25438T).

Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1902-1907 ◽  
Author(s):  
Bédis Dridi ◽  
Marie-Laure Fardeau ◽  
Bernard Ollivier ◽  
Didier Raoult ◽  
Michel Drancourt
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Human Faeces ◽  
Link Type

During attempts to obtain novel, human-associated species of the domain Archaea , a coccoid micro-organism, designated strain B10T, was isolated in pure culture from a sample of human faeces collected in Marseille, France. On the basis of its phenotypic characteristics and 16S rRNA and mcrA gene sequences, the novel strain was classified as a methanogenic archaeon. Cells of the strain were non-motile, Gram-staining-positive cocci that were approximately 850 nm in diameter and showed autofluorescence at 420 nm. Cells were lysed by 0.1 % (w/v) SDS. With hydrogen as the electron donor, strain B10T produced methane by reducing methanol. The novel strain was unable to produce methane when hydrogen or methanol was the sole energy source. In an atmosphere containing CO2, strain B10T could not produce methane from formate, acetate, trimethylamine, 2-butanol, 2-propanol, cyclopentanol, 2-pentanol, ethanol, 1-propanol or 2,3-butanediol. Strain B10T grew optimally with 0.5–1.0 % (w/v) NaCl, at pH 7.6 and at 37 °C. It required tungstate-selenite for growth. The complete genome of the novel strain was sequenced; the size of the genome was estimated to be 2.05 Mb and the genomic DNA G+C content was 59.93 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the highest sequence similarities (98.0–98.7 %) were seen between strain B10T and several uncultured, methanogenic Archaea that had been collected from the digestive tracts of a cockroach, a chicken and mammals. In the same analysis, the non-methanogenic ‘Candidatus Aciduliprofundum boonei’ DSM 19572 was identified as the cultured micro-organism that was most closely related to strain B10T (83.0 % 16S rRNA gene sequence similarity). Each of the three treeing algorithms used in the analysis of 16S rRNA gene sequences indicated that strain B10T belongs to a novel order that is distinct from the Thermoplasmatales . The novel strain also appeared to be distinct from Methanosphaera stadtmanae DSM 3091T (72.9 % 16S rRNA gene sequence similarity), another methanogenic archaeon that was isolated from human faeces and can use methanol in the presence of hydrogen. Based on the genetic and phenotypic evidence, strain B10T represents a novel species of a new genus for which the name Methanomassiliicoccus luminyensis gen. nov., sp. nov. is proposed. The type strain of the type species is B10T ( = DSM 24529T = CSUR P135T).

scholarly journals Streptococcus pharyngis sp. nov., a novel streptococcal species isolated from the respiratory tract of wild rabbits

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2903-2907 ◽  
Author(s):  
Ana I. Vela ◽  
Encarna Casas-Díaz ◽  
Santiago Lavín ◽  
Lucas Domínguez ◽  
Jose F. Fernández-Garayzábal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Molecular Genetic ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences

Four isolates of an unknown Gram-stain-positive, catalase-negative coccus-shaped organism, isolated from the pharynx of four wild rabbits, were characterized by phenotypic and molecular genetic methods. The micro-organisms were tentatively assigned to the genus Streptococcus based on cellular morphological and biochemical criteria, although the organisms did not appear to correspond to any species with a validly published name. Comparative 16S rRNA gene sequencing confirmed their identification as members of the genus Streptococcus, being most closely related phylogenetically to Streptococcus porcorum 682-03T (96.9  % 16S rRNA gene sequence similarity). Analysis of rpoB and sodA gene sequences showed divergence values between the novel species and S. porcorum 682-03T (the closest phylogenetic relative determined from 16S rRNA gene sequences) of 18.1 and 23.9  %, respectively. The novel bacterial isolate could be distinguished from the type strain of S. porcorum by several biochemical characteristics, such as the production of glycyl-tryptophan arylamidase and α-chymotrypsin, and the non-acidification of different sugars. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be assigned to a novel species of the genus Streptococcus, and named Streptococcus pharyngis sp. nov. The type strain is DICM10-00796BT ( = CECT 8754T = CCUG 66496T).

scholarly journals ‘Candidatus Phytoplasma americanum’, a phytoplasma associated with a potato purple top wilt disease complex

2006 ◽  
Vol 56 (7) ◽  
pp. 1593-1597 ◽  
Author(s):  
Ing-Ming Lee ◽  
Kristi D. Bottner ◽  
Gary Secor ◽  
Viviana Rivera-Varas
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Biological Properties ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Distinct Lineage ◽  
Potato Purple Top

Potato purple top wilt (PPT) is a devastating disease that occurs in various regions of North America and Mexico. At least three distinct phytoplasma strains belonging to three different phytoplasma groups (16SrI, 16SrII and 16SrVI) have been associated with this disease. A new disease with symptoms similar to PPT was recently observed in Texas and Nebraska, USA. Two distinct phytoplasma strain clusters were identified. One belongs to the 16SrI phytoplasma group, subgroup A, and the other is a novel phytoplasma that is most closely related to, and shares 96.6 % 16S rRNA gene sequence similarity with, a member of group 16SrXII. Phylogenetic analysis of 16S rRNA gene sequences of the novel PPT-associated phytoplasma strains, previously described ‘Candidatus Phytoplasma’ organisms and other distinct unnamed phytoplasmas indicated that the novel phytoplasma, termed American potato purple top wilt (APPTW) phytoplasma, represents a distinct lineage and shares a common ancestor with stolbur phytoplasma, ‘Candidatus Phytoplasma australiense’, ‘Candidatus Phytoplasma japonicum’, ‘Candidatus Phytoplasma fragariae’, bindweed yellows phytoplasma (IBS), ‘Candidatus Phytoplasma caricae’ and ‘Candidatus Phytoplasma graminis’. On the basis of unique 16S rRNA gene sequences and biological properties, it is proposed that the APPTW phytoplasma represents ‘Candidatus Phytoplasma americanum’, with APPTW12-NE as the reference strain.

scholarly journals Rhizobium helianthi sp. nov., isolated from the rhizosphere of sunflower

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4455-4460 ◽  
Author(s):  
Xuexin Wei ◽  
Shouwei Yan ◽  
Dai Li ◽  
Huancheng Pang ◽  
Yuyi Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
The Novel ◽  
Gene Sequences ◽  
Physiological And Biochemical Characteristics ◽  
Physiological And Biochemical

A Gram-stain-negative, non-spore-forming, rod-shaped and aerobic bacterium, designated Xi19T, was isolated from a soil sample collected from the rhizosphere of sunflower (Helianthus annuus) in Wuyuan county of Inner Mongolia, China and was characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate was related to species of the genus Rhizobium, sharing the greatest 16S rRNA gene sequence similarity with Rhizobium rhizoryzae J3-AN59T (98.4 %), followed by Rhizobium pseudoryzae J3-A127T (97.4 %). There were low similarities ( < 91 %) between the atpD, recA and glnII gene sequences of the novel strain and those of members of the genus Rhizobium. DNA–DNA hybridization values between strain Xi19T and the most related strain Rhizobium rhizoryzae J3-AN59T were low. The major cellular fatty acids of strain Xi19T were C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c. Q-10 was identified as the predominant ubiquinone and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content of strain Xi19T was 60.2 mol%. On the basis of physiological and biochemical characteristics, coupled with genotypic data obtained in this work, strain Xi19T represents a novel species of the genus Rhizobium, for which the name Rhizobium helianthi is proposed. The type strain is Xi19T ( = CGMCC 1.12192T = KCTC 23879T).

scholarly journals Paenibacillus zanthoxyli sp. nov., a novel nitrogen-fixing species isolated from the rhizosphere of Zanthoxylum simulans

2007 ◽  
Vol 57 (4) ◽  
pp. 873-877 ◽  
Author(s):  
Yuchao Ma ◽  
Jian Zhang ◽  
Sanfeng Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

Five endospore-forming, nitrogen-fixing strains were isolated from rhizosphere soils of Zanthoxylum simulans planted in Beijing, China. Phylogenetic analysis based on full-length 16S rRNA gene sequences revealed that the five strains formed a distinct cluster within the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between these novel strains and Paenibacillus azotofixans ATCC 35681T (97.8–98.5 % similarity) and Paenibacillus stellifer DSM 14472T (95.4–96.3 %). Levels of 16S rRNA gene sequence similarity between the novel isolates and other species of the genus Paenibacillus were less than 95.0 %. Levels of 16S rRNA gene sequence similarity among the isolates were more than 98.0 %. DNA–DNA relatedness between the five novel isolates and P. azotofixans ATCC 35681T was 45.50–47.45 % and relatedness among the five novel strains was 95.8–99.6 %. A significant feature of the novel strains that differentiated them from P. azotofixans and other Paenibacillus species was that none of the novel strains could produce acid or gas from the following various carbohydrates: glucose, sucrose, lactose, fructose, glycerol, xylose, maltose, d-sorbitol, sodium succinate, sodium citrate, glycine or l-aspartate. Anteiso-branched C15 : 0 was the major fatty acid component (36.59 %) of novel strain JH29T. On the basis of phenotypic properties, 16S rRNA gene sequences, DNA G+C content, DNA–DNA hybridization, chemotaxonomic properties and the nifH gene sequence, the five novel strains form a very homogeneous group which is different from other related species within the genus Paenibacillus. Therefore, the five novel strains are considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus zanthoxyli sp. nov. is proposed. The type strain is JH29T (=CCBAU 10243T=DSM 18202T).

scholarly journals Bradymonas sediminis gen. nov., sp. nov., isolated from coastal sediment, and description of Bradymonadaceae fam. nov. and Bradymonadales ord. nov.

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1542-1549 ◽  
Author(s):  
Zong-Jie Wang ◽  
Qian-Qian Liu ◽  
Li-Hua Zhao ◽  
Zong-Jun Du ◽  
Guan-Jun Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Coastal Sediment ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

A novel Gram-stain-negative, rod-shaped, gliding, facultatively anaerobic, oxidase-negative and catalase-positive bacterium, designated FA350T, was isolated from coastal sediment from Xiaoshi Island, Weihai, China. Strain FA350T showed growth on modified nutrient agar supplemented with 0.1 % d-(+)-trehalose and with distilled water replaced by seawater. Optimal growth occurred at 33 °C and pH 8.5 with 4 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FA350T belongs to a novel bacterial order in the class Deltaproteobacteria , and the most closely related type strains belong to the order Desulfuromonadales , with 85.1–85.6 % 16S rRNA gene sequence similarity. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol and two unknown phospholipids. Major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω10c and menaquinone MK-7 was the sole respiratory quinone. The DNA G+C content of strain FA350T was 60.3 mol%. The isolate and closely related environmental clones formed a novel order-level clade in the class Deltaproteobacteria . Comparative analysis of 16S rRNA gene sequences and characterization indicated that strain FA350T may represent a novel order of the Deltaproteobacteria . Here, we propose the name Bradymonas sediminis gen. nov., sp. nov. to accommodate strain FA350T. The type strain of Bradymonas sediminis is FA350T ( = DSM 28820T = CICC 10904T); Bradymonadales ord. nov. and Bradymonadaceae fam. nov. are also proposed to accommodate the novel taxon.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

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