Comparison of Molecular Techniques with other Methods for Identification and Enumeration of Probiotics in Fermented Milk Products

REFERENCES

• Aarts, H., Hakemulder, L. and Van Hoef, A. (1999). Genomic typing of Listeria monocytogenes strains by automated laser fluorescence analysis of amplified fragment length polymorphism fingerprint patterns. Int. J. Food Microbiol. 49:95–102.
   PubMed Web of Science ®Google Scholar
• Andrighetto, C., De Dea, P., Lombardi, A., Neviani, E., Rossetti, L. and Giraffa, G. (1998). Molecular identification and cluster analysis of homofermentative thermophilic lactobacilli isolated from dairy products. Res. Microbiol. 149:631–643.
   PubMed Web of Science ®Google Scholar
• Anonymous. (2003). codex standard for fermented milks. Codex Stan 243-2003. Retrieved September 1, 2006, Available from http://www.codexalimentarius.net/download/standards/400/CXS_243e.pdf. Accessed November 2013.
   Google Scholar
• Antonishyn, N., McDonald, R., Chan, E., Horsman, G., Woodmansee, C., Falk, P. and Mayhall, C. (2000). Evaluation of fluorescence-based amplified fragment length polymorphism analysis for molecular typing in hospital epidemiology: Comparison with pulsed-field gel electrophoresis for typing strains of vancomycin-resistant Enterococcus faecium. J. Clin. Microbiol. 38:4058–4065.
   PubMed Web of Science ®Google Scholar
• Aquilanti, L., Dell’Aquila, L., Zannini, E., Zocchetti, A. and Clementi, F. (2006). Resident lactic acid bacteria in raw milk Canestrato Pugliese cheese. Lett. Appl. Microbiol. 43:161–167.
   PubMed Web of Science ®Google Scholar
• Armstrong, D.W. and He, L. (2001a). Determination of cell viability in single or mixed samples using capillary electrophoresis laser-induced fluorescence microfluidic systems. Anal. Chem. 73:4551–4557.
   PubMed Web of Science ®Google Scholar
• Armstrong, D.W. and Schneiderheinze, J.M. (2000). Rapid identification of the bacterial pathogens responsible for urinary tract infections using direct injection CE. Anal. Chem. 72:4474–4476.
   PubMed Web of Science ®Google Scholar
• Armstrong, D.W., Schneiderheinze, J.M., Kullman, J.P. and He, L. (2001b). Rapid CE microbial assays for consumer products that contain active bacteria. FEMS. Microbiol. Lett. 194:33–37.
   PubMed Web of Science ®Google Scholar
• Armstrong, D.W., Schulte, G., Schneiderheinze, J.M. and Westenberg, D.J. (1999). Separating microbes in the manner of molecules. 1. Capillary electrokinetic approaches. Anal. Chem. 71:5465–5469.
   PubMed Web of Science ®Google Scholar
• Baele, M., Baele, P., Vaneechoutte, M., Storms, V., Butaye, P., Devriese, L., Verschraegen, G., Gillis, M. and Haesebrouck, F. (2000). Application of tDNA-PCR for the identification of enterococci. J. Clin. Microbiol. 38:4201–4207.
   PubMed Web of Science ®Google Scholar
• Baele, M., Storms, V., Haesebrouck, F., Devriese, L., Gillis, M., Verschraegen, G., De Baere, T. and Vaneechoutte, M. (2001). Application and evaluation of the interlaboratory reproducibility of tRNA intergenic length polymorphism (tDNA-PCR) for identification of species of the genus Streptococcus. J. Clin. Microbiol. 39:1436–1442.
   PubMed Web of Science ®Google Scholar
• Baele, M., Vaneechoutte, M., Verhelst, R., Vancanneyt, M., Devriese, L. and Haesebrouck, F. (2002). Identification of Lactobacillus species using tDNA-PCR. J. Microbiol. Methods. 50:263–271.
   PubMed Web of Science ®Google Scholar
• Bahaka, D., Neut, C., Khattabi, A., Monget, D. and Gavini, F. (1993). Phenotypic and genomic analyses of human strains belonging or related to Bifidobacterium longum, Bifidobacterium infantis, and Bifidobacterium breve. Int. J. Syst. Evol. Microbiol. 43:565–573.
   Google Scholar
• Berthier, F. and Ehrlich, S. (1998). Rapid species identification within two groups of closely related lactobacilli using PCR primers that target the 16S/23S rRNA spacer region. FEMS. Microbiol. Lett. 161:97–106.
   PubMed Web of Science ®Google Scholar
• Bouton, Y., Guyot, P., Beuvier, E., Tailliez, P. and Grappin, R. (2002). Use of PCR-based methods and PFGE for typing and monitoring homofermentative lactobacilli during Comté cheese ripening. Int. J. Food Microbiol. 76:27–38.
   PubMed Web of Science ®Google Scholar
• Cancilla, M., Powell, I., Hillier, A. and Davidson, B. (1992). Rapid genomic fingerprinting of Lactococcus lactis strains by arbitrarily primed polymerase chain reaction with 32P and fluorescent labels. Appl. Environ. Microbiol. 58:1772–1775.
   PubMed Web of Science ®Google Scholar
• Charteris, W., Kelly, P., Morelli, L. and Collins, J. (1997). Selective detection, enumeration and identification of potentially probiotic Lactobacillus and Bifidobacterium species in mixed bacterial populations. Int. J. Food Microbiol. 35:1–27.
   PubMed Web of Science ®Google Scholar
• Chen, H., Lim, C., Lee, Y. and Chan, Y. (2000). Comparative analysis of the genes encoding 23S-5S rRNA intergenic spacer regions of Lactobacillus casei-related strains. Int. J. Syst. Evol. Microbiol. 50:471–478.
   PubMed Web of Science ®Google Scholar
• Cocolin, L., Innocente, N., Biasutti, M. and Comi, G. (2004). The late blowing in cheese: A new molecular approach based on PCR and DGGE to study the microbial ecology of the alteration process. Int. J. Food Microbiol. 90:83–91.
   PubMed Web of Science ®Google Scholar
• Coeuret, V., Dubernet, S., Bernardeau, M., Gueguen, M. and Vernoux, J. (2003). Isolation, characterisation and identification of lactobacilli focusing mainly on cheeses and other dairy products. Le Lait. 83:269–306.
   Google Scholar
• Collado, C.M. and Hernández, M. (2007). Identification and differentiation of Lactobacillus, Streptococcus and Bifidobacterium species in fermented milk products with bifidobacteria. Microbiol. Res. 162:86–92.
   PubMed Web of Science ®Google Scholar
• Collado, M., Moreno, Y., Cobo, J. and Hernández, M. (2006). Microbiological evaluation and molecular characterization of bifidobacteria strains in commercial fermented milks. Eur. Food Res. Tech. 222:112–117.
   Web of Science ®Google Scholar
• Corich, V., Mattiazzi, A., Soldati, E., Carraro, A. and Giacomini, A. (2005). Sau-PCR, a novel amplification technique for genetic fingerprinting of microorganisms. Appl. Environ. Microbiol. 71:6401–6406.
   PubMed Web of Science ®Google Scholar
• Daud Khaled, A., Neilan, B., Henriksson, A. and Conway, P. (1997). Identification and phylogenetic analysis of Lactobacillus using multiplex RAPD PCR. FEMS. Microbiol. Lett. 153:191–197.
   PubMed Web of Science ®Google Scholar
• De Gheldre, Y., Maes, N., Presti, F., Etienne, J. and Struelens, M. (2001). Rapid identification of clinically relevant Legionella spp. by analysis of transfer DNA intergenic spacer length polymorphism. J. Clin. Microbiol. 39:162–169.
   PubMed Web of Science ®Google Scholar
• De Gheldre, Y., Vandamme, P., Goossens, H. and Struelens, M. (1999). Identification of clinically relevant viridans streptococci by analysis of transfer DNA intergenic spacer length polymorphism. Int. J. Syst. Evol. Microbiol. 49:1591–1598.
   Google Scholar
• De las Rivas, B., Marcobal, A. and Munoz, R. (2006). Development of a multilocus sequence typing method for analysis of Lactobacillus plantarum strains. Microbiol. 152:85–93.
   PubMed Web of Science ®Google Scholar
• Delgado, S. and Mayo, B. (2004). Phenotypic and genetic diversity of Lactococcus lactis and Enterococcus spp. strains isolated from Northern Spain starter-free farmhouse cheeses. Int. J. Food Microbiol. 90:309–319.
   PubMed Web of Science ®Google Scholar
• Drake, M., Small, C., Spence, K. and Swanson, B. (1996a). Differentiation of Lactobacillus helveticus strains using molecular typing methods. Food Res. Int. 29:451–455.
   Web of Science ®Google Scholar
• Drake, M., Small, C., Spence, K. and Swanson, B. (1996b). Rapid detection and identification of Lactobacillus spp. in dairy products by using the polymerase chain reaction. J. Food Prot. 59:1031–1036.
   PubMed Web of Science ®Google Scholar
• Du Plessis, E.M. and Dicks, L.M. T. (1995). Evaluation of random amplified polymorphic DNA (RAPD)-PCR as a method to differentiate Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus johnsonii. Curr. Microbiol. 31:114–118.
   PubMed Web of Science ®Google Scholar
• Dubernet, S., Desmasures, N. and Guéguen, M. (2002). A PCR based method for identification of lactobacilli at the genus level. FEMS. Microbiol. Lett. 214:271–275.
   PubMed Web of Science ®Google Scholar
• Ehrenstein, B., Bernards, A., Dijkshoorn, L., Gerner-Smidt, P., Towner, K., Bouvet, P., Daschner, F. and Grundmann, H. (1996). Acinetobacter species identification by using tRNA spacer fingerprinting. J. Clin. Microbiol. 34:2414–2420.
   PubMed Web of Science ®Google Scholar
• Ercolini, D. (2004). PCR-DGGE fingerprinting: Novel strategies for detection of microbes in food. J. Microbiol. Methods. 56:297–314.
   PubMed Web of Science ®Google Scholar
• Ercolini, D., Moschetti, G., Blaiotta, G. and Coppola, S. (2001). The potential of a polyphasic PCR-DGGE approach in evaluating microbial diversity of natural whey cultures for water-buffalo Mozzarella cheese production: Bias of culture-dependent and culture-independent analyses. Syst. Appl. Microbiol. 24:610–617.
   PubMed Web of Science ®Google Scholar
• FAO/WHO. (2002). Guidelines for the evaluation of probiotics in food. Retrieved August 23, 2006, Available from /ftp://ftp.fao.org/es/esn/ food/wgreport2.pdf. Accessed March 2012.
   Google Scholar
• Fasoli, S., Marzotto, M., Rizzotti, L., Rossi, F., Dellaglio, F. and Torriani, S. (2003). Bacterial composition of commercial probiotic products as evaluated by PCR-DGGE analysis. Int. J. Food Microbiol. 82:59–70.
   PubMed Web of Science ®Google Scholar
• Felske, A., Akkermans, A. and De Vos, W. (1998). Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints. Appl. Environ. Microbiol. 64:4581–4587.
   PubMed Web of Science ®Google Scholar
• Flekna, G., Stefanic, P., Wagner, M., Smulders, F., Mozina, S. and Hein, I. (2007). Insufficient differentiation of live and dead Campylobacter jejuni and Listeria monocytogenes cells by ethidium monoazide (EMA) compromises EMA/real-time PCR. Res. Microbiol. 158:405–412.
   PubMed Web of Science ®Google Scholar
• Friedrich, U. and Lenke, J. (2006). Improved enumeration of lactic acid bacteria in mesophilic dairy starter cultures by using multiplex quantitative real-time PCR and flow cytometry-fluorescence in situ hybridization. Appl. Environ. Microbiol. 72:4163–4171.
   PubMed Web of Science ®Google Scholar
• Fujisawa, T., Benno, Y., Yaeshima, T. and Mitsuoka, T. (1992). Taxonomic study of the Lactobacillus acidophilus group, with recognition of Lactobacillus gallinarum sp. nov. and Lactobacillus johnsonii sp. nov. and synonymy of Lactobacillus acidophilus group A3 (Johnson et al. 1980) with the type strain of Lactobacillus amylovorus (Nakamura 1981). Int. J. Syst. Evol. Microbiol. 42:487–491.
   Google Scholar
• Furet, J., Quénée, P. and Tailliez, P. (2004). Molecular quantification of lactic acid bacteria in fermented milk products using real-time quantitative PCR. Int. J. Food Microbiol. 97:197–207.
   PubMed Web of Science ®Google Scholar
• Gancheva, A., Pot, B., Vanhonacker, K., Hoste, B. and Kersters, K. (1999). A polyphasic approach towards the identification of strains belonging to Lactobacillus acidophilus and related species. Syst. Appl. Microbiol. 22:573–585.
   PubMed Web of Science ®Google Scholar
• García-Cayuela, T., Tabasco, R., Pelaez, C. and Requena, T. (2009). Simultaneous detection and enumeration of viable lactic acid bacteria and bifidobacteria in fermented milk by using propidium monoazide and real-time PCR. Int. Dairy J. 19:405–409.
   Web of Science ®Google Scholar
• Gatti, M., Trivisano, C., Fabrizi, E., Neviani, E. and Gradini, F. (2004). Biodiversity among Lactobacillus helveticus strains isolated from different natural whey starter cultures as revealed by classification trees. Appl. Environ. Microbiol. 70:182–190.
   PubMed Web of Science ®Google Scholar
• Giraffa, G., Lazzi, C., Gatti, M., Rossetti, L., Mora, D. and Neviani, E. (2003). Molecular typing of Lactobacillus delbrueckii of dairy origin by PCR-RFLP of protein-coding genes. Int. J. Food Microbiol. 82:163–172.
   PubMed Web of Science ®Google Scholar
• Giraffa, G. and Neviani, E. (2000). Molecular identification and characterization of food-associated lactobacilli. Ital. J. Food Sci. 12:403–423.
   Web of Science ®Google Scholar
• Grand, M., Küffer, M. and Baumgartner, A. (2003). A Quantitative analysis and molecular identification of Bifidobacteria strains in probiotic milk products. Eur. Food Res. Tech. 217:90–92.
   Web of Science ®Google Scholar
• Grifoni, A., Bazzicalupo, M., Di Serio, C., Fancelli, S. and Fani, R. (1995). Identification of Azospirillum strains by restriction fragment length polymorphism of the 16S rDNA and of the histidine operon. FEMS. Microbiol. Lett. 127:85–91.
   PubMed Web of Science ®Google Scholar
• Guarneri, T., Rossetti, L. and Giraffa, G. (2001). Rapid identification of Lactobacillus brevis using the polymerase chain reaction. Lett. Appl. Microbiol. 33:377–381.
   PubMed Web of Science ®Google Scholar
• Gueimonde, M., Delgado, S., Mayo, B., Ruas-Madiedo, P., Margolles, A. and De los Reyes-Gavilán, C. (2004). Viability and diversity of probiotic Lactobacillus and Bifidobacterium populations included in commercial fermented milks. Food Res. Int. 37:839–850.
   Web of Science ®Google Scholar
• Gurtler, V. and Stanisich, V. (1996). New approaches to typing and identification of bacteria using the 16S–23S rDNA spacer region. Microbiol. 142:3–16.
   PubMed Web of Science ®Google Scholar
• Hamilton-Miller, J., Shah, S. and Winkler, J. (1999). Public health issues arising from microbiological and labelling quality of foods and supplements containing probiotic microorganisms. Public Health Nutr. 2:223–229.
   PubMed Web of Science ®Google Scholar
• Heilig, H., Zoetendal, E., Vaughan, E., Marteau, P., Akkermans, A. and de Vos, W. (2002). Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA. Appl. Environ. Microbiol. 68:114–123.
   PubMed Web of Science ®Google Scholar
• Hein, I., Lehner, A., Rieck, P., Klein, K., Brandl, E. and Wagner, M. (2001). Comparison of different approaches to quantify Staphylococcus aureus cells by real-time quantitative PCR and application of this technique for examination of cheese. Appl. Environ. Microbiol. 67:3122–3126.
   PubMed Web of Science ®Google Scholar
• Hertel, C., Ludwig, W., Pot, B., Kersters, K. and Schleifer, K. (1993). Differentiation of lactobacilli occurring in fermented milk products by using oligonucleotide probes and electrophoretic protein profiles. Syst. Appl. Microbiol. 16:463–467.
   Web of Science ®Google Scholar
• Hjertén, S., Elenbring, K., Kilár, F., Liao J.L., Chen, A.J. C., Siebert, C.J. and Zhu, M.D. (1987). Carrier-free zone electrophoresis, displacement electrophoresis and isoelectric focusing in a high-performance electrophoresis apparatus. J. Chromatogr. A. 403:47–61.
   PubMed Web of Science ®Google Scholar
• Izco, J., Tormo, M., Harris, A., Tong, P. and Jimenez-Flores, R. (2003). Optimization and validation of a rapid method to determine citrate and inorganic phosphate in milk by capillary electrophoresis. J. Dairy Sci. 86:86–95.
   PubMed Web of Science ®Google Scholar
• Janssen, P., Coopman, R., Huys, G., Swings, J., Bleeker, M., Vos, P., Zabeau, M. and Kersters, K. (1996). Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy. Microbiol. 142:1881–1893.
   PubMed Web of Science ®Google Scholar
• Jokovic, N., Nikolic, M., Begovic, J., Jovcic, B., Savic, D. and Topisirovic, L. (2008). A survey of the lactic acid bacteria isolated from Serbian artisanal dairy product kajmak. Int. J. Food Microbiol. 127:305–311.
   PubMed Web of Science ®Google Scholar
• Justé, A., Thomma, B. and Lievens, B. (2008). Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes. Food Microbiol. 25:745–761.
   PubMed Web of Science ®Google Scholar
• Kailasapathy, K. and Chin, J. (2000). Survival and therapeutic potential of probiotic organisms with reference to Lactobacillus acidophilus and Bifidobacterium spp. Immun. Cell Biol. 78:80–88.
   PubMed Web of Science ®Google Scholar
• Kandler, O. and Weiss, N. (1986). Genus Lactobacillus Beijerinck 1901, 212 AL. Bergey's Manual. Syst. Bacteriol. 2:1209–1234.
   Google Scholar
• Kao, Y., Liu, Y. and Shyu, Y. (2007). Identification of Lactobacillus spp. in probiotic products by real-time PCR and melting curve analysis. Food Res. Int. 40:71–79.
   Web of Science ®Google Scholar
• Klein, G., Pack, A., Bonaparte, C. and Reuter, G. (1998). Taxonomy and physiology of probiotic lactic acid bacteria. Int. J. Food Microbiol. 41:103–125.
   PubMed Web of Science ®Google Scholar
• Kłodzińiska, E., Dahm, H., Rózycki, H., Szeliga, J., Jackowski, M. and Buszewski, B. (2006). Rapid identification of Escherichia coli and Helicobacter pylori in biological samples by capillary zone electrophoresis. J. Sep. Sci. 29:1180–1187.
   PubMed Web of Science ®Google Scholar
• Kwon, H., Yang, E., Yeon, S., Kang, B. and Kim, T. (2004). Rapid identification of probiotic Lactobacillus species by multiplex PCR using species specific primers based on the region extending from 16S rRNA through 23S rRNA. FEMS. Microbiol. Lett. 239:267–275.
   PubMed Web of Science ®Google Scholar
• Lick, S. (2003). Typing systems for lactobacilli. Milchwissenschaft. 58:256–260.
   Web of Science ®Google Scholar
• Ligor, M., Jarmalaviciene, R., Szumski, M., Maruška, A. and Buszewski, B. (2008). Determination of volatile and non volatile products of milk fermentation processes using capillary zone electrophoresis and solid phase microextraction coupled to gas chromatography. J. Sep. Sci. 31:2707–2713.
   PubMed Web of Science ®Google Scholar
• Lim, O., Suntornsuk, W. and Suntornsuk, L. (2009). Capillary zone electrophoresis for enumeration of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus in yogurt. J. Chromatogr. B. 877:710–718.
   PubMed Web of Science ®Google Scholar
• Ludwig, W. and Schleifer, K. (1999). Phylogeny of bacteria beyond the 16S rRNA standard. ASM News. 65:752–757.
   Google Scholar
• Ludwig, W. and Schleifer, K. (2000). How quantitative is quantitative PCR with respect to cell counts? Syst. Appl. Microbiol. 23:556–562.
   PubMed Web of Science ®Google Scholar
• Maes, N., De Gheldre, Y., De Ryck, R., Vaneechoutte, M., Meugnier, H., Etienne, J. and Struelens, M. (1997). Rapid and accurate identification of Staphylococcus species by tRNA intergenic spacer length polymorphism analysis. J. Clin. Microbiol. 35:2477–2481.
   PubMed Web of Science ®Google Scholar
• Mainville, I., Robert, N., Lee, B. and Farnworth, E. (2006). Polyphasic characterization of the lactic acid bacteria in kefir. Syst. Appl. Microbiol. 29:59–68.
   PubMed Web of Science ®Google Scholar
• Manzano, M., Cocolin, L., Cantoni, C. and Comi, G. (2000). Temperature gradient gel electrophoresis of the amplified product of a small 16S rRNA gene fragment for the identification of Listeria species isolated from food. J. Food Prot. 63:659–661.
   PubMed Web of Science ®Google Scholar
• Masco, L., Huys, G., De Brandt, E., Temmerman, R. and Swings, J. (2005). Culture-dependent and culture-independent qualitative analysis of probiotic products claimed to contain bifidobacteria. Int. J. food Microbiol. 102:221–230.
   PubMed Web of Science ®Google Scholar
• McClelland, M., Petersen, C. and Welsh, J. (1992). Length polymorphisms in tRNA intergenic spacers detected by using the polymerase chain reaction can distinguish streptococcal strains and species. J. Clin. Microbiol. 30:1499–1504.
   PubMed Web of Science ®Google Scholar
• McLauchlin, J., Ripabelli, G., Brett, M. and Threlfall, E. (2000). Amplified fragment length polymorphism (AFLP) analysis of Clostridium perfringens for epidemiological typing. Int. J. Food Microbiol. 56:21–28.
   PubMed Web of Science ®Google Scholar
• Meile, L., Ludwig, W., Rueger, U., Gut, C., Kauffmann, P., Dasen, G., Wenger, S. and Teuber, M. (1997). Bifidobacterium lactis sp. nov., a moderately oxygen tolerant species isolated from fermented milk. Syst. Appl. Microbiol. 20:57–64.
   Web of Science ®Google Scholar
• Miteva, V., Abadjieva, A. and Stefanova, T. (1992). M13 DNA fingerprinting, a new tool for classification and identification of Lactobacillus spp. J. Appl. Microbiol. 73:349–354.
   Web of Science ®Google Scholar
• Mortazavian, A.M., Ehsani, M.R., Azizi, A., Razavi, S.H., Mousavi, S.M., Sohrabvandi, S. and Reinheimer, J.A. (2008). Viability of calcium-alginate-microencapsulated probiotic bacteria in Iranian yogurt drink (Doogh) during refrigerated storage and under simulated gastrointestinal conditions. Aust. J. Dairy Tech. 63:24–29.
   Google Scholar
• Mortazavian, A., Ehsani, M., Mousavi, S., Reinheimer, J., Emamdjomeh, Z. and Sohrabvandi, S. (2005). Preliminary investigation on the combined effect of heat treatment and incubation temperature on the viability of the probiotic microorganisms in freshly made yoghurt. Int. J. Dairy Tech. 59:8–11.
   Web of Science ®Google Scholar
• Mortazavian, A.M. and Sohrabvandi, S. (2006). Probiotics and Food Probiotic Products; Based on Dairy Probiotic Products. Eta Publication, Tehran.
   Google Scholar
• Moschetti, G., Blaiotta, G., Aponte, M., Mauriello, G., Villani, F. and Coppola, S. (1997). Genotyping of Lactobacillus delbrueckii subsp. bulgaricus and determination of the number and forms of rrn opérons in L. delbrueckii and its subspecies. Res. Microbiol. 148:501–510.
   PubMed Web of Science ®Google Scholar
• Murray, A., Hollibaugh, J. and Orrego, C. (1996). Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl. Environ. Microbiol. 62:2676–2680.
   PubMed Web of Science ®Google Scholar
• Muyzer, G. and Smalla, K. (1998). Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek. 73:127–141.
   PubMed Web of Science ®Google Scholar
• Neeley, E., Phister, T. and Mills, D. (2005). Differential real-time PCR assay for enumeration of lactic acid bacteria in wine. Appl. Environ. Microbiol. 71:8954–8957.
   PubMed Web of Science ®Google Scholar
• Nikolic, M., Terzic-Vidojevic, A., Jovcic, B., Begovic, J., Golic, N. and Topisirovic, L. (2008). Characterization of lactic acid bacteria isolated from Bukuljac, a homemade goat's milk cheese. Int. J. Food Microbiol. 122:162–170.
   PubMed Web of Science ®Google Scholar
• Nocker, A. and Camper, A. (2006a). Selective removal of DNA from dead cells of mixed bacterial communities by use of ethidium monoazide. Appl. Environ. Microbiol. 72:1997–2004.
   PubMed Web of Science ®Google Scholar
• Nocker, A., Cheung, C. and Camper, A. (2006b). Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. J. Microbiol. Methods. 67:310–320.
   PubMed Web of Science ®Google Scholar
• Nocker, A., Sossa, K. and Camper, A. (2007b). Molecular monitoring of disinfection efficacy using propidium monoazide in combination with quantitative PCR. J. Microbiol. Methods. 70:252–260.
   PubMed Web of Science ®Google Scholar
• Nocker, A., Sossa-Fernandez, P., Burr, M. and Camper, A. (2007a). Use of propidium monoazide for live/dead distinction in microbial ecology. Appl. Environ. Microbiol. 73:5111–5117.
   PubMed Web of Science ®Google Scholar
• Nogva, H., Dromtorp, S., Nissen, H. and Rudi, K. (2003). Ethidium monoazide for DNA-based differentiation of viable and dead bacteria by 50-nuclease PCR. Biotechniques. 34:804–813.
   PubMed Web of Science ®Google Scholar
• Nour, M. (1998). 16S–23S and 23S–5S intergenic spacer regions of lactobacilli: Nucleotide sequence, secondary structure and comparative analysis. Res. Microbiol. 149:433–448.
   PubMed Web of Science ®Google Scholar
• O’Riordan, K. and Fitzgerald, G. (1997). Determination of genetic diversity within the genus Bifidobacterium and estimation of chromosomal size. FEMS. Microbiol. Lett. 156:259–264.
   PubMed Web of Science ®Google Scholar
• Omar, N. and Ampe, F. (2000). Microbial community dynamics during production of the Mexican fermented maize dough pozol. Appl. Environ. Microbiol. 66:3664–3673.
   PubMed Web of Science ®Google Scholar
• Ortu, S., Felis, G., Marzotto, M., Deriu A., Molicotti, P., Sechi, L., Dellaglio, F. and Zanetti, S. (2007). Identification and functional characterization of Lactobacillus strains isolated from milk and Gioddu, a traditional Sardinian fermented milk. Int. Dairy J. 17:1312–1320.
   Web of Science ®Google Scholar
• Ouadghiri, M., Amar, M., Vancanneyt, M. and Swings, J. (2005). Biodiversity of lactic acid bacteria in Moroccan soft white cheese (Jben). FEMS. Microbiol. Lett. 251:267–271.
   PubMed Web of Science ®Google Scholar
• Ouwehand, A., Salminen, S. and Isolauri, E. (2002). Probiotics: An overview of beneficial effects. Antonie van Leeuwenhoek. 82:279–289.
   PubMed Web of Science ®Google Scholar
• Palenzuela, B., Simonet, B.M., Garcia, R.M., Rios, A. and Valcarcel, M. (2004). Monitering of bacterial contamination in food samples using capillary zone electrophoresis. Anal. Chem. 76:3012–3017.
   PubMed Web of Science ®Google Scholar
• Palys, T., Nakamura, L. and Cohan, F. (1997). Discovery and classification of ecological diversity in the bacterial world: The role of DNA sequence data. Int. J. Syst. Evol. Microbiol. 47:1145–1156.
   Google Scholar
• Pan, Y. and Breidt, F. (2007). Enumeration of viable Listeria monocytogenes cells by real-time PCR with propidium monoazide and ethidium monoazide in the presence of dead cells. Appl. Environ. Microbiol. 73:8028–8031.
   PubMed Web of Science ®Google Scholar
• Pfetsch, A. and Welsch, T. (1997). Determination of the electrophoretic mobility of bacteria and their separation by capillary zone electrophoresis. Fresenius J. Anal. Chem. 359198201
   Google Scholar
• Piraino, P., Ricciardi, A., Salzano, G., Zotta, T. and Parente, E. (2006). Use of unsupervised and supervised artificial neural networks for the identification of lactic acid bacteria on the basis of SDS-PAGE patterns of whole cell proteins. J. Microbiol. Methods. 66:336–346.
   PubMed Web of Science ®Google Scholar
• Piraino, P., Zotta, T., Ricciardi, A. and Parente, E. (2005). Discrimination of commercial Caciocavallo cheeses on the basis of the diversity of lactic microflora and primary proteolysis. Int. Dairy J. 15:1138–1149.
   Web of Science ®Google Scholar
• Pot, B., Ludwig, W., Kersters, K. and Schleifer, K. (1994). Taxonomy of lactic acid bacteria. In: Bacteriocins of Lactic acid Bacteria. Microbiology, Genetics and Applications Chapter 2, pp. 13–90. De Vuyst, L. and Vandamme, E.J. Eds., Blackie Academic & Professional, London.
   Google Scholar
• Powell, S., Ferguson, S., Bowman, J. and Snape, I. (2006). Using real-time PCR to assess changes in the hydrocarbon-degrading microbial community in Antarctic soil during bioremediation. Microbiol. Ecol. 52:523–532.
   Web of Science ®Google Scholar
• Randazzo, C.L., Caggia, C. and Neviani, E. (2009). Application of molecular approaches to study lactic acid bacteria in artisanal cheeses. J. Microbiol. Methods. 78:1–9.
   PubMed Web of Science ®Google Scholar
• Reutera, G., Kleinb, G. and Goldberga, M. (2002). Identification of probiotic cultures in food samples. Food Res. Int. 35:117–124.
   Web of Science ®Google Scholar
• Rodriguez, M.A., Lantz, A.W. and Armstrong, D.W. (2006). Capillary electrophoretic method for the detection of bacterial contamination. Anal. Chem. 78:4759–4767.
   PubMed Web of Science ®Google Scholar
• Rossi, F., Torriani, S. and Dellaglio, F. (1998). Identification and clustering of dairy propionibacteria by RAPD-PCR and CGE-REA methods. J. Appl. Microbiol. 85:956–964.
   PubMed Web of Science ®Google Scholar
• Roy, D. (2001). Media for the isolation and enumeration of bifidobacteria in dairy products. Int. J. Food Microbiol. 69:167–182.
   PubMed Web of Science ®Google Scholar
• Roy, D. (2005). Technological aspects related to the use of bifidobacteria in dairy products. Le Lait. 85:39–56.
   Google Scholar
• Roy, D., Ward, P. and Champagne, G. (1996). Differentiation of bifidobacteria by use of pulsed-field gel electrophoresis and polymerase chain reaction. Int. J. Food Microbiol. 29:11–29.
   PubMed Web of Science ®Google Scholar
• Rudi, K., Moen, B., Dromtorp, S. and Holck, A. (2005a). Use of ethidium monoazide and PCR in combination for quantification of viable and dead cells in complex samples. Appl. Environ. Microbiol. 71:1018–1024.
   PubMed Web of Science ®Google Scholar
• Rudi, K., Naterstad, K., Drømtorp, S. and Holo, H. (2005b). Detection of viable and dead Listeria monocytogenes on gouda like cheeses by real time PCR. Lett. Appl. Microbiol. 40:301–306.
   PubMed Web of Science ®Google Scholar
• Salzano, G., Moschetti, G., Villani, F., Pepe, O., Mauriello, G. and Coppola, S. (1994). Genotyping of Streptococcus thermophilus evidenced by restriction analysis of ribosomal DNA. Res. Microbiol. 145:651–658.
   PubMed Web of Science ®Google Scholar
• Samona, A. and Robinson, R. (1994). Effect of yogurt cultures on the survival of bifidobacteria in fermented milks. Int. J. Dairy Tech. 47:58–60.
   Web of Science ®Google Scholar
• Schillinger, U. (1999). Isolation and identification of lactobacilli from novel-type probiotic and mild yoghurts and their stability during refrigerated storage. Int. J. Food Microbiol. 47:79–87.
   PubMed Web of Science ®Google Scholar
• Schleifer, K. and Ludwig, W. (1996). Phylogeny of the genus Lactobacillus and related genera. Syst. Appl. Microbiol. 18:461–467.
   Web of Science ®Google Scholar
• Schneiderheinze, J.M., Armstrong, D.W., Schulte, G. and Westenberg, D.J. (2000). High efficiency separation of microbial aggregates using capillary electrophoresis. FEMS. Microbiol. Lett. 189:39–44.
   PubMed Web of Science ®Google Scholar
• Silva, J., Carvalho, A., Duarte, G., Lopes, Z., Domingues, P., Teixeira, P. and Gibbs, P. (2003). Characterisation of enterococci strains isolated from an artisanal Portuguese cheese. Milchwissenschaft. 58:389–392.
   Web of Science ®Google Scholar
• Sohier, D., Coulon, J. and Lonvaud-Funel, A. (1999). Molecular identification of Lactobacillus hilgardii and genetic relatedness with Lactobacillus brevis. Int. J. Syst. Evol. Microbiol. 49:1075–1081.
   Google Scholar
• Sohrabvandi, S., Razavi, S.H., Mousavi, S.M. and Mortazavian, A.M. (2010). Viability of probiotic bacteria in low alcohol- and non- alcoholic beer during refrigerated storage. Phillip Agric. Scientist. 93:24–28.
   Google Scholar
• Song, Y., Kato, N., Liu, C., Matsumiya, Y., Kato, H. and Watanabe, K. (2000). Rapid identification of 11 human intestinal Lactobacillus species by multiplex PCR assays using group-and species-specific primers derived from the 16S–23S rRNA intergenic spacer region and its flanking 23S rRNA. FEMS. Microbiol. Lett. 187:167–173.
   PubMed Web of Science ®Google Scholar
• Song, Y., Kato, N., Matsumiya, Y., Liu, C., Kato, H. and Watanabe, K. (1999). Identification of and hydrogen peroxide production by fecal and vaginal lactobacilli isolated from Japanese women and newborn infants. J. Clin. Microbiol. 37:3062–3064.
   PubMed Web of Science ®Google Scholar
• Švec, P., Vancanneyt, M., Seman, M., Snauwaert, C., Lefebvre, K., Sedláek, I. and Swings, J. (2005). Evaluation of (GTG)5 PCR for identification of Enterococcus spp. FEMS. Microbiol. Lett. 247:59–63.
   PubMed Web of Science ®Google Scholar
• Tabasco, R., Paarup, T., Janer, C., Pelez, C. and Requena, T. (2007). Selective enumeration and identification of mixed cultures of Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, L. acidophilus, L. paracasei subsp. paracasei and Bifidobacterium lactis in fermented milk. Int. Dairy J. 17:1107–1114.
   Web of Science ®Google Scholar
• Tailliez, P., Quénée, P. and Chopin, A. (1996). Estimation de la diversité parmi les souches de la collection CNRZ: Application de la RAPD à un groupe de lactobacilles. Le Lait. 76:147–158.
   Google Scholar
• Temmerman, R., Scheirlinck, I., Huys, G. and Swings, J. (2003). Culture-independent analysis of probiotic products by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 69:220–226.
   PubMed Web of Science ®Google Scholar
• Terzic-Vidojevic, A., Vukasinovic, M., Veljovic, K., Ostojic, M. and Topisirovic, L. (2007). Characterization of microflora in homemade semi-hard white Zlatar cheese. Int. J. Food Microbiol. 114:36–42.
   PubMed Web of Science ®Google Scholar
• Theunissen, J., Britz, T., Torriani, S. and Witthuhn, R. (2005). Identification of probiotic microorganisms in South African products using PCR-based DGGE analysis. Int. J. Food Microbiol. 98:11–21.
   PubMed Web of Science ®Google Scholar
• Tilsala-Timisjärvi, A. and Alatossava, T. (1997). Development of oligonucleotide primers from the 16S-23S rRNA intergenic sequences for identifying different dairy and probiotic lactic acid bacteria by PCR. Int. J. Food Microbiol. 35:49–56.
   PubMed Web of Science ®Google Scholar
• Torriani, S., Clementi, F., Vancanneyt, M., Hoste, B., Dellaglio, F. and Kersters, K. (2001). Differentiation of Lactobacillus plantarum, L. pentosus and L. paraplantarum species by RAPD-PCR and AFLP. Syst. Appl. Microbiol. 24:554–560.
   PubMed Web of Science ®Google Scholar
• Torriani, S., Van Reenen, C., Klein, G., Reuter, G., Dellaglio, F. and Dicks, L. (1996). Lactobacillus curvatus subsp. curvatus subsp. nov. and Lactobacillus curvatus subsp. melibiosus subsp. nov. and Lactobacillus sake subsp. sake subsp. nov. and Lactobacillus sake subsp. carnosus subsp. nov., New Subspecies of Lactobacillus curvatus Abo-Elnaga and Kandler 1965 and Lactobacillus sake Katagiri, Kitahara, and Fukami 1934 (Klein et al. 1996, Emended Descriptions), Respectively. Int. J. Syst. Evol. Microbiol. 46:1158–1163.
   Google Scholar
• Torriani, S., Zapparoli, G. and Dellaglio, F. (1999). Use of PCR-based methods for rapid differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. Appl. Environ. Microbiol. 65:4351–4356.
   PubMed Web of Science ®Google Scholar
• Tsakalidou, E., Manolopoulou, E., Kabaraki, E., Zoidou, E., Pot, B., Kersters, K. and Kalantzopoulos, G. (1994). The combined used of whole-cell protein extracts for the identification (SDS-PAGE) and enzyme activity screening of lactic acid bacteria isolated from traditional greek dairy products. Syst. Appl. Microbiol. 17:444–458.
   Web of Science ®Google Scholar
• Vallejo-Cordoba, B., Mazorra-Manzano, M. and González-Córdova, A. (2004). New Capillary Electrophoresis Method for the Determination of Furosine in Dairy Products. J. Agric. Food Chem. 52:5787–5790.
   PubMed Web of Science ®Google Scholar
• Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K. and Swings, J. (1996). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Molecular Biol. Rev. 60:407–438.
   Google Scholar
• Vaneechoutte, M., Boerlin, P., Tichy, H., Bannerman, E., Jager, B. and Bille, J. (1998). Comparison of PCR-based DNA fingerprinting techniques for the identification of Listeria species and their use for atypical Listeria isolates. Int. J. Syst. Evol. Microbiol. 48:127–139.
   Google Scholar
• Vaneechoutte, M., Rossau, R., De Vos, P., Gillis, M., Janssens, D., Paepe, N., De Rouck, A., Fiers, T., Claeys, G. and Kersters, K. (1992). Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA). FEMS. Microbiol. Lett. 93:227–233.
   Web of Science ®Google Scholar
• Vaughan, E.E., Heilig, H.G. H. J. , Zoetendal, E.G. , Satokari, R., Collins, J.K. , Akkermans, A.D. L. and Vos, W.M. d. (1999). Molecular approaches to study probiotic bacteria. Trends. Food Sci. Tech. 10:400–404.
   Web of Science ®Google Scholar
• Ventura, M., Canchaya, C., Van Sinderen, D., Fitzgerald, G. and Zink, R. (2004). Bifidobacterium lactis DSM 10140: Identification of the atp (atpBEFHAGDC) operon and analysis of its genetic structure, characteristics, and phylogeny. Appl. Environ. Microbiol. 70:3110–3121.
   PubMed Web of Science ®Google Scholar
• Versalovic, J., Koeuth, T. and Lupski, R. (1991). Distribution of repetitive DNA sequences in eubacteria and application to finerpriting of bacterial enomes. Nucleic Acids Res. 19:6823–6831.
   PubMed Web of Science ®Google Scholar
• Villani, F., Moschetti, G., Blaiotta, G. and Coppola, S. (1997). Characterization of strains of Leuconostoc mesenteroides by analysis of soluble whole-cell protein pattern, DNA fingerprinting and restriction of ribosomal DNA. J. Appl. Microbiol. 82:578–588.
   PubMed Web of Science ®Google Scholar
• Vincent, D., Roy, D., Mondou, F. and Déry, C. (1998). Characterization of bifidobacteria by random DNA amplification. Int. J. Food Microbiol. 43:185–193.
   PubMed Web of Science ®Google Scholar
• Vos, P., Hogers, R., Bleeker, M., Reijans, M., Lee, T., Hornes, M., Friters, A., Pot, J., Paleman, J. and Kuiper, M. (1995). AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res. 23:4407–4414.
   PubMed Web of Science ®Google Scholar
• Walter, J., Tannock, G., Tilsala-Timisjarvi, A., Rodtong, S., Loach, D., Munro, K. and Alatossava, T. (2000). Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers. Appl. Environ. Microbiol. 66:297–303.
   PubMed Web of Science ®Google Scholar
• Ward, L. and Timmins, M. (1999). Differentiation of Lactobacillus casei, Lactobacillus paracasei and Lactobacillus rhamnosus by polymerase chain reaction. Lett. Appl. Microbiol. 29:90–92.
   PubMed Web of Science ®Google Scholar
• Welsh, J. and McClelland, M. (1991). Genomic fingerprints produced by PCR with consensus tRNA gene primers. Nucleic Acids Res. 19:861–866.
   PubMed Web of Science ®Google Scholar
• Wiedmann-al-Ahmad, M., Tichy, H. and Schon, G. (1994). Characterization of Acinetobacter type strains and isolates obtained from wastewater treatment plants by PCR fingerprinting. Appl. Environ. Microbiol. 60:4066–4071.
   PubMed Web of Science ®Google Scholar
• Williams, J., Kubelik, A., Livak, K., Rafalski, J. and Tingey, S. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18:6531–6535.
   PubMed Web of Science ®Google Scholar
• Wouters, J., Ayad, E., Hugenholtz, J. and Smit, G. (2002). Microbes from raw milk for fermented dairy products. Int. Dairy J. 12:91–109.
   Web of Science ®Google Scholar
• Yu, L. and Li, S. (2005). Electrophoretic Behavior Study of Bacteria of Pseudomonas aeruginosa, Edwardsiella tarda and Enteropathogenic Escherichia coli by Capillary Electrophoresis with UV and Fluorescence Detection. Chromatographia. 62:401–407.
   Web of Science ®Google Scholar
• Zamfir, M., Vancanneyt, M., Makras, L., Vaningelgem, F., Lefebvre, K., Pot, B., Swings, J. and De Vuyst, L. (2006). Biodiversity of lactic acid bacteria in Romanian dairy products. Syst. Appl. Microbial. 29:487–495.
   PubMed Web of Science ®Google Scholar
• Zoetendal, E., Akkermans, A. and De Vos, W. (1998). Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 64:3854–3859.
   PubMed Web of Science ®Google Scholar