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

Molecular and Cellular Probes

Volumn 25, Issue 4, 2011, Pages 153-157

  Huang, Chien Hsun ^a   Chang, Mu Tzu ^b   Huang, Mu Chiou ^b   Lee, Fwu Ling ^a  

^a FOOD INDUSTRY RESEARCH AND DEVELOPMENT INSTITUTE   (Taiwan)

^b NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

Author keywords

Group specific PCR; Lactobacillus casei group; SNaPshot minisequencing; SNP; Species identification

Indexed keywords

HEAT SHOCK PROTEIN 70;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BACTERIAL STRAIN; CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; GENE SEQUENCE; LACTOBACILLUS; LACTOBACILLUS CASEI; LACTOBACILLUS PARACASEI; LACTOBACILLUS RHAMNOSUS; LACTOBACILLUS ZEAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SINGLE NUCLEOTIDE POLYMORPHISM; SINGLE STRAND CONFORMATION POLYMORPHISM; SPECIES IDENTIFICATION;

DNA PRIMERS; DNA, BACTERIAL; LACTOBACILLUS CASEI; LACTOBACILLUS RHAMNOSUS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

LACTOBACILLUS; LACTOBACILLUS CASEI; LACTOBACILLUS PARACASEI; LACTOBACILLUS RHAMNOSUS;

EID: 79959801039     PISSN: 08908508     EISSN: 10961194     Source Type: Journal    
DOI: 10.1016/j.mcp.2011.03.002     Document Type: Article

References (30)

1. Felis G.E., Dellaglio F. Taxonomy of Lactobacilli and Bifidobacteria. Curr Issues Intest Microbiol 2007, 8:44-61.
2. Collins M.D., Phillips B.A., Zanoni P. Deoxyribonucleic acid homology studies of Lactobacillus casei, Lactobacillus paracasei sp. nov., subsp. paracasei and subsp. tolerans, and Lactobacillus rhamnosus sp. nov., comb. nov. Int J Syst Bacteriol 1989, 39:105-108.
3. Dicks L.M., Du Plessis E.M., Dellaglio F., Lauer E. Reclassification of Lactobacillus casei subsp. casei ATCC 393 and Lactobacillus rhamnosus ATCC 15820 as Lactobacillus zeae nom. rev., designation of ATCC 334 as the Neotype of L. casei subsp. casei, and Rejection of L. casei subsp. casei, and rejection of the name Lactobacillus paracasei. Int J Syst Bacteriol 1996, 46:337-340.
4. Holzapfel W.H., Haberer P., Geisen R., Bjorkroth J., Schillinger U. Taxonomy and important features of probiotic microorganisms in food and nutrition. Am J Clin Nutr 2001, 73:365S-373S.
5. Baken K.A., Ezendam J., Gremmer E.R., de Klerk A., Pennings J.L., Matthee B., et al. Evaluation of immunomodulation by Lactobacillus casei Shirota: immune function, autoimmunity and gene expression. Int J Food Microbiol 2006, 112:8-18.
6. Salminen S. Functional dairy foods with Lactobacillus strain GG. Nutr Rev 1996, 54:99-101.
7. Salminen S., Isolauri E., Salminen E. Clinical uses of probiotics for stabilizing the gut mucosal barrier: successful strains for future challenges. Antonie Leeuwenhoek 1996, 70:347-358.
8. Verdenelli M.C., Ghelfi F., Silvi S., Orpianesi C., Cecchini C., Cresci A. Probiotic properties of Lactobacillus rhamnosus and Lactobacillus paracasei isolated from human faeces. Eur J Nutr 2009, 48:355-363.
9. Boyd M.A., Antonio M.A.D., Hillier S.L. Comparison of API 50 CH strips to whole-chromosomal DNA probes for identification of Lactobacillus species. J Clin Microbiol 2005, 43:5309-5311.
10. Bringel F., Castioni A., Olukoya D.K., Felis G.E., Torriani S., Dellaglio F. Lactobacillus plantarum subsp. argentoratensis subsp. nov., isolated from vegetable matrices. Int J Syst Evol Microbiol 2005, 55:1629-1634.
11. Charteris W.P., Kelly P.M., Morelli L., Collins J.K. Quality control Lactobacillus strains for use with the API 50CH and API ZYM systems at 37° C. J Basic Microbiol 2001, 41:541-551.
12. Ahrne S., Molin G., Stahl S. Plasmids in Lactobacillus strains isolated from meat and meat products. Syst Appl Microbiol 1989, 11:320-325.
13. Petti C.A., Polage C.R., Schreckenberger P. The role of 16S rRNA gene sequencing in identification of microorganisms misidentified by conventional methods. J Clin Microbiol 2005, 43:6123-6125.
14. Janda J.M., Abbott S.L. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 2007, 45:2761-2764.
15. McCartney A.L. Application of molecular biological methods for studying probiotics and the gut flora. Br J Nutr 2002, 88:29-37.
16. Huang C.H., Lee F.L. The dnaK gene as a molecular marker for the classification and discrimination of the Lactobacillus casei group. Antonie Leeuwenhoek 2011, 99:319-327.
17. Quintans B., Alvarez-Iglesias V., Salas A., Phillips C., Lareu M.V., Carracedo A. Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing. Forensic Sci Int 2004, 140:241-257.
18. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25:4876-4882.
19. Schillinger U., Yousif N.M., Sesar L., Franz C.M. Use of group-specific and RAPD-PCR analyses for rapid differentiation of Lactobacillus strains from probiotic yogurts. Curr Microbiol 2003, 47:453-456.
20. Netzer W.J., Hartl F.U. Protein folding in the cytosol: chaperonin-dependent and -independent mechanisms. Trends Biochem Sci 1998, 23:68-73.
21. Gogarten J.P. Which is the most conserved group of proteins? Homology-orthology, paralogy, xenology, and the fusion of independent. J Mol Evol 1994, 39:541-543.
22. Dalmasso A., Civera T., Bottero M.T. Multiplex primer-extension assay for identification of six pathogenic vibrios. Int J Food Microbiol 2009, 129:21-25.
23. Dalmasso A., Rantsiou K., Cocolin L., Bottero M.T. Development of a biomolecular assay for the identification of Listeria at species level. Foodborne Pathog Dis 2010, 7:565-571.
24. Ferri L., Perrin E., Campana S., Tabacchioni S., Taccetti G., Cocchi P., et al. Application of multiplex single nucleotide primer extension (mSNuPE) to the identification of bacteria: the Burkholderia cepacia complex case. J Microbiol Meth 2010, 80:251-256.
25. Wang H., Yue J., Han M., Yang J., Zhao Y. Rapid method for identification of six common species of Mycobacteria based on multiplex SNP analysis. J Clin Microbiol 2010, 48:247-250.
26. Scott J.C., Koylass M.S., Stubberfield M.R., Whatmore A.D. Multiplex assay based on single-nucleotide polymorphisms for rapid identification of Brucella isolates at the species level. Appl Environ Microbiol 2007, 73:7331-7337.
27. Delbes C., Ali-Mandjee L., Montel M.C. Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses. Appl Environ Microbiol 2007, 73:1882-1891.
28. Chen H., Lim C.K., Lee Y.K., Chan Y.N. Comparative analysis of the genes encoding 23S-5S rRNA intergenic spacer regions of Lactobacillus casei-related strains. Int J Syst Evol Microbiol 2000, 50:471-478.
29. Diancourt L., Passet V., Chervaux C., Garault P., Smokvina T., Brisse S. Multilocus sequence typing of Lactobacillus casei reveals a clonal population structure with low levels of homologous recombination. Appl Environ Microbiol 2007, 73:6601-6611.
30. Walter J., Tannock G.W., Tilsala-Timisjarvi A., Rodtong S., Loach D.M., Munro K., et al. Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers. Appl Environ Microbiol 2000, 66:297-303.