Rapid identification of Lactobacillus plantarum group using the SNaPshot minisequencing assay

Bioresource Collection and Research Center, Food Industry Research and Development Institute, P.O. Box 246, Hsinchu 30099, Taiwan, ROC.
Systematic and Applied Microbiology (Impact Factor: 3.28). 06/2011; 34(8):586-9. DOI: 10.1016/j.syapm.2011.02.006
Source: PubMed


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. plantarum group species. The results showed that the SNaPshot minisequencing assay was able to unambiguously and simultaneously discriminate strains belonging to the species L. plantarum subsp. plantarum, L. plantarum subsp. argentoratensis, Lactobacillus paraplantarum, Lactobacillus pentosus and Lactobacillus fabifermentans. In conclusion, a rapid, accurate and cost-effective assay was successfully developed for species identification of the members of the L. plantarum group.

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    • "Three SNaPshot mini-sequencing assays had been described to identify Lactobacillus spp. The first was developed for a rapid identification of the different species of Lactobacillus plantarum group (Huang et al. 2011b) and the second for Lactobacillus casei group (Huang et al. 2011a). In 2012, a mini-sequencing scheme targeting recA gene was suggested for identification of the L. delbrueckii subsp. "
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    ABSTRACT: Practical schemes based on single nucleotide polymorphisms (SNP) have been proposed as alternatives to simplify and replace the molecular methodologies based on the extensive sequencing analysis of genes. SNaPshot mini-sequencing has been progressively experienced during the last decade and represents a fast and robust strategy to analyze critical polymorphisms. Such assays have been proposed to characterize some bacteria and microbial eukaryotes, and its feasibility was now reviewed in the present manuscript. The mini-sequencing schemes showed high discriminatory power and competence for identification of microorganisms, but some specificity errors were still found, particularly for species of the Burkholderia cepacia complex and mycobacteria. SNP assays designed for other goals, e.g., comparison of strains, detection of serotypes, virulence, epidemic, and phylogenetic-related subgroups of isolates, can be very useful by facilitating the investigation of large collections of isolates. The next-generation of SNP assays might consider the inclusion of large number of markers to fully characterize microbial taxonomy and strains; nevertheless, these new technologies are still prone to errors and can largely benefit from integration with well-established mini-sequencing assays. Newly proposed molecular tools should be systematically tested in collections of isolates with high indexes of diversity and guarantee interlaboratorial validation.
    Full-text · Article · Feb 2015 · Applied Microbiology and Biotechnology
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    • "Lactobacillus strain identification was confirmed using polymerase chain reaction (PCR) amplification of 16 S rRNA coding sequences. Methods described by Chagnaud et al. (2001) and Huang et al. (2011) were referred. "
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    ABSTRACT: This study investigated the survival of encapsulated potential probiotic Lactobacillus plantarum which isolated from fermented cocoa beans. κ-carrageenan was used to encapsulate the probiotic. Encapsulation techniques such as emulsification, freeze-drying or extrusion were adopted to encapsulate the probiotic. Freeze-drying and extrusion methods showed higher (p < 0.05) efficiency (89.48 ± 3.21 and 92.26 ± 1.45%, respectively) in encapsulating the probiotic compared to the emulsification method (82.19 ± 0.71% efficiency). Freeze-dried encapsulated probiotic L. plantarum was selected for further survival analysis as greater amount of beads were produced compared to the extrusion method. Freeze-dried probiotic was found to have significantly (p < 0.05) higher tolerance to acid at pH 2 with higher survival percentage compared to non-encapsulated probiotic. However, freeze-drying encapsulation was proven not to enhance the resistance of the probiotic to bile salt as evidenced by the one log colony reduction as for the non-encapsulated probiotic. Further modification of freeze-drying encapsulation technique is needed to enhance the survival of the encapsulated potential probiotic L. plantarum toward bile salt in the future.
    Full-text · Article · Jun 2013 · Food Science and Technology International
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    ABSTRACT: 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. The average sequence similarity for the recA gene among type strains was 80.0%, and most members of the L. acidophilus group could be clearly distinguished. The species-specific primer was designed according to the recA gene sequencing, which was employed for polymerase chain reaction with the template DNA of Lactobacillus strains. A single 231-bp species-specific band was found only in L. delbrueckii. A SNaPshot mini-sequencing assay using recA as a target gene was also developed. The specificity of the mini-sequencing assay was evaluated using 31 strains of L. delbrueckii species and was able to unambiguously discriminate strains belonging to the subspecies L. delbrueckii subsp. bulgaricus. The phylogenetic relationships of most strains in the L. acidophilus group can be resolved using recA gene sequencing, and a novel method to identify the species and subspecies of the L. delbrueckii and L. delbrueckii subsp. bulgaricus was developed by species-specific polymerase chain reaction combined with SNaPshot mini-sequencing. Copyright © 2012 Society of Chemical Industry.
    No preview · Article · Oct 2012 · Journal of the Science of Food and Agriculture
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