Discrimination of the Lactobacillus acidophilus group using sequencing, species-specific PCR and SNaPshot mini-sequencing technology based on the recA gene.

Background: To clearly identify specific species and subspecies of the Lactobacillus acidophilus group using phenotypic and genotypic (16S rDNA sequence analysis) techniques alone is difficult. The aim of this study was to use the recA gene for species discrimination in the L. acidophilus group, as well as to develop a species-specific primer and single nucleotide polymorphism primer based on the recA gene sequence for species and subspecies identification.

Rapid identification of Lactobacillus plantarum group using the SNaPshot minisequencing assay.

This study used SNaPshot minisequencing for species identification within the Lactobacillus plantarum group. A SNaPshot minisequencing assay using dnaK as a target gene was developed, and five SNP primers were designed by analysing the conserved regions of the dnaK sequences. The specificity of the minisequencing assay was evaluated using 35 strains of L.

Application of the SNaPshot minisequencing assay to species identification in the Lactobacillus casei group.

This study used group-specific PCR combined with SNaPshot minisequencing for species identification within the Lactobacillus casei group. The L. casei group-specific PCR primer pair was designed using the rpoA gene sequence.

The dnaK gene as a molecular marker for the classification and discrimination of the Lactobacillus casei group.

It is hard to accurately identify specific species of the Lactobacillus casei group using phenotypic techniques alone. Some strains of this species group are considered to be probiotic and are widely applied in the food industry. In this study, we compared the use of two phylogenetic markers, the 16S rRNA and dnaK genes, for species discrimination of the members of the L.

Rhodotorula taiwanensis sp. nov., a novel yeast species from a plant in Taiwan.

A novel anamorphic yeast strain, A1-01(T), belonging to the genus Rhodotorula was isolated from a plant in Taiwan and analysed morphologically, physiologically and phylogenetically. Neither ballistoconidia nor sexual reproduction was observed. Sequence analysis of the 26S rRNA gene and the ITS region indicate that Rhodosporidium sphaerocarpum is the most closely related species, with 14 and 24 nucleotide substitutions, respectively.

Sympodiomycopsis kandeliae sp. nov., a basidiomycetous anamorphic fungus from mangroves, and reclassification of Sympodiomycopsis lanaiensis as Jaminaea lanaiensis comb. nov.

Three ustilaginomycetous anamorphic strains were isolated from flowers of Kandelia candel in mangrove forests of Taiwan. Phylogenetic analyses based on the combined sequences of internal transcribed spacer 1 (ITS1)-5.8S-ITS2 and the D1/D2 domain of the large-subunit (LSU) rDNA indicated that the closest recognized species was Sympodiomycopsis paphiopedili.

Rapid discrimination and classification of the Lactobacillus plantarum group based on a partial dnaK sequence and DNA fingerprinting techniques.

The Lactobacillus plantarum group comprises five very closely related species. Some species of this group are considered to be probiotic and widely applied in the food industry. In this study, we compared the use of two different molecular markers, the 16S rRNA and dnaK gene, for discriminating phylogenetic relationships amongst L.

Pseudomonas taiwanensis sp. nov., isolated from soil.

A novel Gram-negative, rod-shaped, motile, non-spore-forming bacterial strain, CMS(T), isolated from soil was characterized using phenotypic and molecular taxonomic methods. 16S rRNA gene sequence analysis revealed that the organism belongs phylogenetically to the genus Pseudomonas. Pseudomonas monteilii, P.

Lactobacillus taiwanensis sp. nov., isolated from silage.

Strain FIRDI 006T, isolated from silage cattle feed, was characterized by using phenotypic and molecular taxonomic methods. The strain was a homofermentative lactic acid bacterium; the cells stained Gram-positive and were catalase-negative, non-motile, facultatively anaerobic rods. 16S rRNA gene sequence analysis revealed that the strain belongs phylogenetically to the genus Lactobacillus and can be placed within the Lactobacillus acidophilus-delbrueckii group.

Pseudozyma pruni sp. nov., a novel ustilaginomycetous anamorphic fungus from flowers in Taiwan.

Two ustilaginomycetous anamorphic strains were isolated from flowers in Taiwan. Phylogenetic analysis based on the combined rRNA gene sequence of internal transcribed spacer 1 (ITS1)-5.8S-ITS2 and large-subunit D1/D2 domains indicated that the closest recognized species was Pseudozyma fusiformata.

The beta-tubulin gene as a molecular phylogenetic marker for classification and discrimination of the Saccharomyces sensu stricto complex.

The Saccharomyces sensu stricto complex comprises seven very closely related species. In this study, we compared the use of two different phylogenetic markers, the 26S rDNA and beta-tubulin genes, for discriminating phylogenetic relationships among Saccharomyces sensu stricto strains using sequencing as well as RFLP methods. The average sequence similarity for the beta-tubulin gene (90.

Paenibacillus taichungensis sp. nov., from soil in Taiwan.

Among a large collection of Taiwanese soil isolates, a novel Gram-variable, rod-shaped, motile, endospore-forming bacterial strain, strain V10537(T), was subjected to a polyphasic study including 16S rRNA and gyrB gene sequence analysis, DNA-DNA hybridization experiments, cell wall peptidoglycan type, cellular fatty acid composition analysis and comparative phenotypic characterization. 16S rRNA gene sequence analysis indicated that the organism belonged to the genus Paenibacillus. Strain V10537(T) possessed meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan.

A novel specific DNA marker in Saccharomyces bayanus for species identification of the Saccharomyces sensu stricto complex.

This study was based on RAPD fingerprinting for species identification of the Saccharomyces sensu stricto complex. 40 random primers were used for RAPD analysis. The results showed that one of these primers, OPT-18, produced a 974 bp species-specific band, which was only found in the tested S.

Bacillus velezensis is a later heterotypic synonym of Bacillus amyloliquefaciens.

Strain BCRC 14193, isolated from soil, shared more than 99 % 16S rRNA gene sequence similarity with Bacillus amyloliquefaciens BCRC 11601(T) and Bacillus velezensis BCRC 17467(T). This strain was previously identified as B. amyloliquefaciens, based on DNA-DNA hybridization, but its DNA relatedness value with B.

Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group.

The Bacillus subtilis group comprises eight closely related species that are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, the gyrB gene, which encodes the subunit B protein of DNA gyrase, was selected as an alternative phylogenetic marker. To determine whether gyrB gene sequence analysis could be used for phylogenetic analysis and species identification of members of the B.

Reclassification of Bacillus axarquiensis Ruiz-Garcia et al. 2005 and Bacillus malacitensis Ruiz-Garcia et al. 2005 as later heterotypic synonyms of Bacillus mojavensis Roberts et al. 1994.

The Bacillus subtilis group encompasses the taxa Bacillus subtilis subsp. subtilis, B. licheniformis, B.

Paenibacillus taiwanensis sp. nov., isolated from soil in Taiwan.

Among a large collection of Taiwanese soil isolates, a novel Gram-variable, rod-shaped, motile and endospore-forming bacterial strain, designated G-soil-2-3(T), was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequence analysis, DNA-DNA hybridization experiments, fatty acid analysis and comparative phenotypic characterization. 16S rRNA gene sequence analysis indicated that the organism belongs within the genus Paenibacillus.

Polyphasic approach to the taxonomy of the Rhizopus stolonifer group.

Phylogenetic analysis of Rhizopus strains based on the D1/D2 region of LSU rDNA sequences yielded a phylogram with four well-supported clades. The R. microsporus clade concurs with classification obtained by traditional methods.

Chryseobacterium taiwanense sp. nov., isolated from soil in Taiwan.

Among a large collection of Taiwanese soil isolates, a novel Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacterial strain, Soil-3-27(T), was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequencing, DNA-DNA hybridization, fatty acid analysis and comparative phenotypic characterization. The 16S rRNA gene sequence analysis indicated that the organism belongs to the genus Chryseobacterium.

Sporobolomyces diospyroris sp. nov., Sporobolomyces lophatheri sp. nov. and Sporobolomyces pyrrosiae sp. nov., three new species of ballistoconidium-forming yeasts in the Agaricostilbum lineage isolated from plants in Taiwan.

Three strains of xylose-lacking and ubiquinone-10-having ballistoconidium-forming yeasts isolated from plant leaves collected in Taiwan were found to represent respective new species. In phylogenetic trees constructed based on the nucleotide sequences of 18S rDNA and D1/D2 domain of 26S rDNA, they were located in the Agaricostilbum lineage (Agaricostilbum/Bensingtonia cluster). Since the taxonomic properties of these species coincide with those of the genus Sporobolomyces, they are described as Sporobolomyces diospyroris sp.

Two new ballistoconidium-forming yeast species, Bullera melastomae and Bullera formosana, found in Taiwan.

Two yeast strains, the cells of which contained xylose and Q-10 as the major ubiquinone, were isolated from a plant leaf collected in Taiwan. These yeasts were found to represent two new species of the genus Bullera in the Hymenomycetes. Identification was based on the sequence analysis of the 18S rDNA, the internal transcribed spacer (ITS) regions and the D1/D2 domain of 26S rDNA.

Chitinibacter tainanensis gen. nov., sp. nov., a chitin-degrading aerobe from soil in Taiwan.

Five strains with strong chitinolytic activity were isolated from a soil sample collected from southern Taiwan. The strains shared more than 92% DNA-DNA similarity, indicating membership of the same genospecies. This close relationship was supported by high similarities in fatty acid composition and biochemical characteristics.

Sporobolomyces magnisporus sp. nov., a new yeast species in the Erythrobasidium cluster isolated from plants in Taiwan.

Two strains of yeasts that contain Q-10 as the major ubiquinone, lack cellular xylose and produce large bilaterally symmetrical ballistoconidia were isolated from plants collected in a protected subtropical rain forest in Taiwan and were found to represent a new species. The taxonomic properties of this species coincide with the genus Sporobolomyces, so it is described as Sporobolomyces magnisporus sp. nov.