Zygosaccharomyces sapae sp. nov., isolated from Italian traditional balsamic vinegar

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 364-371 ◽  
Author(s):  
Lisa Solieri ◽  
Tikam Chand Dakal ◽  
Paolo Giudici
Keyword(s):  
Phylogenetic Analysis ◽  
Novel Species ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Internal Transcribed Spacers ◽  
Rrna Gene ◽  
The Novel ◽  
Balsamic Vinegar ◽  
A Chain ◽  
26S Rrna

Fourteen yeast isolates were recovered from two traditional balsamic vinegar (TBV) samples collected in the provinces of Modena and Reggio Emilia, Italy. Microsatellite-primed-PCR (MSP-PCR) was used to de-replicate the isolate collection into two representative strains, ABT301T and ABT601. Phylogenetic analysis based on the D1/D2 domains of the 26S rRNA gene indicated that these strains represented a distinct species of the genus Zygosaccharomyces, closely related to Zygosaccharomyces rouxii and Zygosaccharomyces mellis. Physiological and morphological tests supported the recognition of a novel taxon of halotolerant, osmotolerant, non-psychrotolerant and maltose-fermentation-negative yeasts showing a chain or star-shaped pattern of budding cells, which remained attached to each other. Morphological observations offered evidence of ascospore formation. A novel species, Zygosaccharomyces sapae sp. nov., is proposed to accommodate these strains, with strain ABT301T ( = CBS 12607T = MUCL 54092T) as the type strain. Based on D1/D2 domain phylogenetic analysis, the novel strains shared the highest sequence similarity (100 %) with Zygosaccharomyces sp. strain NCYC 3042, previously isolated from sugar [James, S. A., Bond, C. J., Stratford, M. & Roberts, I. N. (2005). FEMS Yeast Res 5, 747–755]. However, based on phylogenetic (internal transcribed spacers, ITS), PCR fingerprinting and physiological analyses, marked differences were observed between the novel species and strain NCYC 3042, and these results are discussed in more detail.

scholarly journals Lactobacillus paracollinoides sp. nov., isolated from brewery environments

2004 ◽  
Vol 54 (1) ◽  
pp. 115-117 ◽  
Author(s):  
Koji Suzuki ◽  
Wataru Funahashi ◽  
Masahiro Koyanagi ◽  
Hiroshi Yamashita
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Dna Relatedness ◽  
Beer Spoilage

Three novel strains isolated from brewery environments are described. These strains were Gram-positive, facultatively anaerobic, heterofermentative rods that did not exhibit catalase activity. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that these strains belong to the genus Lactobacillus and are most closely related to Lactobacillus collinoides (approximately 99 % similarity). The novel strains could be differentiated from L. collinoides on the basis of DNA–DNA relatedness, differences in beer-spoilage ability and the inability to utilize d-fructose. These isolates represent a novel species, for which the name Lactobacillus paracollinoides sp. nov. is proposed. The type strain is LA2T (=DSM 15502T=JCM 11969T).

scholarly journals Altererythrobacter namhicola sp. nov. and Altererythrobacter aestuarii sp. nov., isolated from seawater

2011 ◽  
Vol 61 (4) ◽  
pp. 709-715 ◽  
Author(s):  
Seong Chan Park ◽  
Keun Sik Baik ◽  
Han Na Choe ◽  
Chae Hong Lim ◽  
Ho Jun Kim ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
The Family ◽  
South Sea ◽  
Ubiquinone 10 ◽  
Pigmented Bacteria

Two non-motile, orange- or yellow-pigmented bacteria, designated strains KYW48T and KYW147T, were isolated from seawater collected from the South Sea, Republic of Korea. Cells of both strains were Gram-reaction-negative, aerobic and catalase- and oxidase-positive. The major fatty acids of strain KYW48T were C18 : 1ω7c (35.3 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) (22.7 %), C17 : 1ω6c (19.8 %), C14 : 0 2-OH (7.4 %) and C16 : 0 (5.9 %), and those of strain KYW147T were C18 : 1ω7c (36.0 %), summed feature 3 (18.3 %), C16 : 0 (14.7 %), 11-methyl C18 : 1ω7c (10.7 %), C16 : 0 2-OH (9.1 %) and C18 : 1ω9c (8.0 %). The predominant isoprenoid quinone of both strains was ubiquinone 10 (Q-10). The DNA G+C contents of strains KYW48T and KYW147T were 63.8 and 67.2 mol%, respectively. A phylogenetic tree based on 16S rRNA gene sequences showed that strains KYW48T and KYW147T were grouped with the members of the family Erythrobacteraceae and formed a distinct clade with the members of the genus Altererythrobacter (<95.7 % sequence similarity). On the basis of the evidence presented in this study, the novel species Altererythrobacter namhicola sp. nov. (type strain KYW48T  = KCTC 22736T  = JCM 16345T) and Altererythrobacter aestuarii sp. nov. (type strain KYW147T  = KCTC 22735T  = JCM 16339T) are proposed.

scholarly journals Lactobacillus farraginis sp. nov. and Lactobacillus parafarraginis sp. nov., heterofermentative lactobacilli isolated from a compost of distilled shochu residue

2007 ◽  
Vol 57 (4) ◽  
pp. 708-712 ◽  
Author(s):  
Akihito Endo ◽  
Sanae Okada
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Dna Relatedness ◽  
Clear Separation ◽  
Micro Organisms

Five strains of lactic acid bacteria were isolated from a compost of distilled shochu residue in Japan. The isolates were separated into two groups on the basis of 16S rRNA gene sequence similarity, and two subclusters were formed that comprised micro-organisms closely related to Lactobacillus buchneri, L. diolivorans, L. hilgardii, L. kefiri, L. parabuchneri and L. parakefiri. DNA–DNA relatedness results revealed that the isolates could be separated into two groups, and these groups correlated well with the subclusters generated using the phylogenetic analysis. Moreover, the levels of DNA–DNA relatedness showed clear separation of the two groups from their phylogenetic relatives. Therefore, the two groups represent two novel species, for which the names Lactobacillus farraginis sp. nov. (type strain NRIC 0676T=JCM 14108T=DSM 18382T) and Lactobacillus parafarraginis sp. nov. (type strain NRIC 0677T=JCM 14109T=DSM 18390T) are proposed.

scholarly journals Neisseria oralis sp. nov., isolated from healthy gingival plaque and clinical samples

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1323-1328 ◽  
Author(s):  
William J. Wolfgang ◽  
Teresa V. Passaretti ◽  
Reashma Jose ◽  
Jocelyn Cole ◽  
An Coorevits ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
23S Rrna ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type

A polyphasic analysis was undertaken of seven independent isolates of Gram-negative cocci collected from pathological clinical samples from New York, Louisiana, Florida and Illinois and healthy subgingival plaque from a patient in Virginia, USA. The 16S rRNA gene sequence similarity among these isolates was 99.7–100 %, and the closest species with a validly published name was Neisseria lactamica (96.9 % similarity to the type strain). DNA–DNA hybridization confirmed that these isolates are of the same species and are distinct from their nearest phylogenetic neighbour, N. lactamica . Phylogenetic analysis of 16S and 23S rRNA gene sequences indicated that the novel species belongs in the genus Neisseria . The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω7c. The cellular fatty acid profile, together with other phenotypic characters, further supports the inclusion of the novel species in the genus Neisseria . The name Neisseria oralis sp. nov. (type strain 6332T  = DSM 25276T  = LMG 26725T) is proposed.

Lactobacillus odoratitofui sp. nov., isolated from stinky tofu brine

2010 ◽  
Vol 60 (12) ◽  
pp. 2903-2907 ◽  
Author(s):  
Shiou-Huei Chao ◽  
Masae Sasamoto ◽  
Yuko Kudo ◽  
Junji Fujimoto ◽  
Ying-Chieh Tsai ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Positive Staining ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Dna Reassociation ◽  
Type Strains

Three Gram-positive-staining strains isolated from fermented stinky tofu brine were rod-shaped, non-motile, asporogenous, facultatively anaerobic, heterofermentative and did not exhibit catalase activity. Comparative analyses of 16S rRNA, rpoA and pheS gene sequences demonstrated that the novel strains were members of the genus Lactobacillus. On the basis of 16S rRNA gene sequence similarity, the type strains of Lactobacillus collinoides (98.6 %), Lactobacillus paracollinoides (98.6 %) and Lactobacillus similis (99.6 %) were the closest neighbours. However, DNA–DNA reassociation values with these strains were less than 10 %. The phenotypic and genotypic features demonstrated that these isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillus odoratitofui sp. nov. is proposed. The type strain is YIT 11304T (=JCM 15043T =BCRC 17810T =DSM 19909T).

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).

scholarly journals Pelagicoccus croceus sp. nov., a novel marine member of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’ isolated from seagrass

2007 ◽  
Vol 57 (12) ◽  
pp. 2874-2880 ◽  
Author(s):  
Jaewoo Yoon ◽  
Naoya Oku ◽  
Satoru Matsuda ◽  
Hiroaki Kasai ◽  
Akira Yokota
Keyword(s):  
Cell Wall ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Antibiotic Susceptibility Test ◽  
The Family ◽  
Lactam Antibiotic

An obligately aerobic, spherical, non-motile, pale-yellow pigmented bacterium was isolated from a piece of leaf of seagrass, Enhalus acoroides (L.f.) Royle, grown in Okinawa, Japan and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the novel isolate N5FB36-5T shared approximately 96–98 % sequence similarity with the species of the genus Pelagicoccus of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’. The DNA–DNA relatedness values of strain N5FB36-5T with Pelagicoccus mobilis 02PA-Ca-133T and Pelagicoccus albus YM14-201T were below 70 %, which is accepted as the phylogenetic definition of a novel species. β-Lactam antibiotic susceptibility test and amino acid analysis of the cell wall hydrolysates indicated the absence of muramic acid and diaminopimelic acid in the cell walls, which suggested that this strain lacks an ordinary Gram-negative type of peptidoglycan in the cell wall. The DNA G+C content of strain N5FB36-5T was 51.6 mol%; MK-7 was the major menaquinone; and the presence of C16 : 0, C16 : 1 ω7c and anteiso-C15 : 0 as the major cellular fatty acids supported the identification of the novel isolate as a member of the genus Pelagicoccus. On the basis of polyphasic taxonomic data, it was concluded that this strain should be classified as a novel species of the genus Pelagicoccus, for which the name Pelagicoccus croceus sp. nov. is proposed. The type strain is N5FB36-5T (=MBIC08282T=KCTC 12903T).

scholarly journals Polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and rivers

2010 ◽  
Vol 60 (1) ◽  
pp. 166-173 ◽  
Author(s):  
Martin W. Hahn ◽  
Elke Lang ◽  
Ulrike Brandt ◽  
Heinrich Lünsdorf ◽  
Qinglong L. Wu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Natural Environments ◽  
The Novel ◽  
Free Living ◽  
Monophyletic Cluster ◽  
Freshwater Habitats

Five heterotrophic, aerobic, catalase- and oxidase-positive, non-motile strains were characterized from freshwater habitats located in Austria, France, Uganda, P. R. China and New Zealand. The strains shared 16S rRNA gene similarities of ≥99.3 %. The novel strains grew on NSY medium over a temperature range of 10–35 °C (two strains also grew at 5 °C and one strain grew at 38 °C) and a NaCl tolerance range of 0.0–0.3 % (four strains grew up to 0.5 % NaCl). The predominant fatty acids were C16 : 0, C18 : 1 ω7c, C12 : 0 3-OH, and summed feature 3 (including C16 : 1 ω7c). The DNA G+C content of strain MWH-MoIso2T was 44.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the five new strains formed a monophyletic cluster closely related to Polynucleobacter necessarius (96–97 % sequence similarity). This cluster also harboured other isolates as well as environmental sequences which have been obtained from several habitats. Investigations with taxon-specific FISH probes demonstrated that the novel bacteria dwell as free-living, planktonic cells in freshwater systems. Based on the revealed phylogeny and pronounced chemotaxonomic differences to P. necessarius (presence of >7 % C12 : 0 3-OH and absence of C12 : 0 and C12 : 0 2-OH), the new strains are suggested to represent a novel species, for which the name Polynucleobacter cosmopolitanus sp. nov. is proposed. The type strain is MWH-MoIso2T (=DSM 21490T=CIP 109840T=LMG 25212T). The novel species belongs to the minority of described species of free-living bacteria for which both in situ data from their natural environments and culture-based knowledge are available.

scholarly journals Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov.

2011 ◽  
Vol 61 (3) ◽  
pp. 518-523 ◽  
Author(s):  
P. Kämpfer ◽  
N. Lodders ◽  
E. Falsen
Keyword(s):  
New Genus ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Fatty Acid Profiles ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Biochemical Tests ◽  
The Family

Three bacterial strains, designated CCUG 51397T, CCUG 53736 and CCUG 53920, isolated from water samples taken at different locations in southern Sweden were studied to determine their taxonomic position using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences showed that these bacteria had <93 % sequence similarity to all described species of the genera Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Chitinophaga. The three organisms grouped most closely with Sediminibacterium salmoneum NJ-44T but showed only 92.5 % sequence similarity to this strain, the only recognized species of this genus. The fatty acid profiles showed large amounts of iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G with smaller amounts of iso-C15 : 0 3-OH, iso-C16 : 0 3-OH and other fatty acids, which differentiated the novel strains from related genera. Biochemical tests performed on strains CCUG 51397T, CCUG 53736 and CCUG 53920 also gave different results from those of Sediminibacterium salmoneum NJ-44T and other related genera. Based on this evidence, strains CCUG 51397T, CCUG 53736 and CCUG 53920 represent a novel species of a new genus, for which the name Hydrotalea flava gen. nov., sp. nov. is proposed. The type strain of Hydrotalea flava is CCUG 51397T (=CCM 7760T). A formal allocation of the genera Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Chitinophaga to the family Chitinophagaceae fam. nov. is also proposed.

scholarly journals Geobacillus lituanicus sp. nov.

2004 ◽  
Vol 54 (6) ◽  
pp. 1991-1995 ◽  
Author(s):  
Nomeda Kuisiene ◽  
Juozas Raugalas ◽  
Donaldas Chitavichius
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequence Analysis ◽  
Pcr Rflp ◽  
Group 5

Obligately thermophilic, aerobic, proteolytic, endospore-forming strain N-3T was isolated from a high-temperature oilfield in Lithuania. 16S rRNA gene sequence analysis placed this strain in genetic group 5 of the endospore formers. Geobacillus thermoleovorans appeared to be the closest phylogenetic neighbour (99·4 % sequence similarity). The G+C content of strain N-3T was 52·5 mol% and matched the range established for the genus Geobacillus. Studies of DNA–DNA relatedness and morphological and physiological analyses enabled strain N-3T to be described as a member of the genus Geobacillus, but could not assign this strain to any other known species of this genus. Results of this polyphasic study allowed characterization of strain N-3T as a novel species in the genus Geobacillus – Geobacillus lituanicus sp. nov. This species can be distinguished from G. thermoleovorans and Geobacillus stearothermophilus on the basis of 16S rRNA gene PCR-RFLP assays with the restriction endonucleases AluI, HaeIII and TaqI. The type strain of the novel species is N-3T (=DSM 15325T=VKM B-2294T).

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