___

• References Albenzio M, Corbo MR, Rehman SU, Fox PF, De Angelis M, Corsetti A, Sevi A, Gobbetti M. 2001. Microbiological and biochemical characteristics of Canestrato Pugliese cheese made from rawmilk, pasteurized milk or by heating the curd in hot whey. International Journal of Food Microbiology. 67:35-48.
• Alegría A, Szczesny P, Mayo B, Bardowski J, Kowalczyk M. 2012. Biodiversity in Oscypek, a traditional Polish cheese, determined by culture-dependent and-independent approaches. Applied and Environmetal Microbiology. 78:1890-1898.
• Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology. Reviews. 59:143- 169.
• Amann R, Fuchs BM, Behrens S. 2001. The identification of microorganisms by fluorescence in situ hybridization. Current Opinion Biotechnology. 12:231-236.
• Ampe F, Ben Omar N, Moizan C, Wacher C, Guyot JP. 1999. Polyphasic study of the spatial distribution of microorganisms in Mexican pozol, a fermented maize dough, demonstrates the need for cultivation-independent methods to investigate traditional fermentations. Applied and Environmental Microbiology. 65:5464-5473.
• Ampe F, Miambi E. 2000. Cluster analysis, richness and biodiversity indexes derived from denaturing gradyan gel electrophoresis fingerprints of bacterial communities demonstrates that traditional maize fermentations are driven by the transformation process. International Journal of Food Microbiology. 60:91-97.
• Baruzzi F, Morea M, Matarante A, Cocconcelli PS. 2000. Changes in the Lactobacillus community during Ricotta Forte cheese natural fermentation. Journal of Applied Microbiology. 89:807-814.
• ben Omar N, Ampe F. 2000. Microbial community dynamics during production of the Mexican fermented maize dough pozol. Applied and Environmental Microbiology. 66:3664- 3673.
• Bouton Y, Guyot P, Beuvir E, Tailliez P, Grappin R. 2002. Use of PCR based method and PFGE for typing and monitoring homofermentative lactobacilli during Comtè cheese ripening. International Journal of Food Microbiology. 76:27- 38.
• Böttger EC. 1989. Rapid determination of bacterial ribosomal RNA sequences by direct sequencing of enzymatically amplified DNA. FEMS Microbiology Letter. 53:171-176.
• Callon C, Millet L, Montel MC. 2004. Diversity of lactic acid bacteria isolated from AOC Salers cheese. Journal of Dairy Research. 71:231-44.
• Cocconcelli PS, Parisi MG, Senini L, Bottazzi V. 1997. Use of RAPD and 16S rDNA sequencing for the study of Lactobacillus population dynamics in natural whey culture. Letters in Applied Microbiology. 25:8-12.
• Cocolin L, Rantsiou K, Iacumin L, Urso R, Cantoni C, Comi G. 2004. Study of the ecology of fresh sausages and characterization of populations of lactic acid bacteria by molecular methods. Applied and Environmental Microbiology. 70:1883-1894.
• Coppola S, Blaiotta G, Ercolini D, Moschetti G. 2001. Molecular evaluation of microbial diversity occurring in different types of Mozzarella cheese. Journal of Applied Microbiology. 90:414-420.
• Corroler D, Magin I, Desmasures N, Guèguen M. 1998. An ecological study of lactococci isolated from raw milk in the Camembert cheese registered designation of origin area. Applied Environmental Microbiology. 64:4729-4735.
• Dasen A, Berthier F, Grappin R, Williams AG, Banks J. 2003. Genotypic and phenotypic characterization of the dynamics of the lactic acid bacterial population of adjunct-containing Cheddar cheese manufactured from raw and microfiltered pasteurised milk. Journal of Applied Microbiology. 94:595- 607.
• De Candia S, De Angelis M, Dunlea E, Minervini F, McSweeney PLH, Faccia M, Gobbetti M. 2007. Molecular identification and typing of natural whey starter cultures and microbiological properties of related traditional Mozzarella cheeses. International. Journal of Food Microbiology. 119:182-191.
• Delbes C, Montel MC. 2005. Design and application of a Staphylococcus specific Single Strand Conformation Polymophism-PCR analysis to monitor Staphylococcus population diversity and dynamics during production of raw milk cheese. Letters in Applied Microbiology. 41:169-174.
• Dellaglio F, Felis GE, Castioni A, Torriani S, Germond JE. 2005. Lactobacillus delbrueckii subsp. indicus subsp. nov., isolated from Indian dairy products. International Journal of Systematic and Evolutionary Microbiology. 55:401-4.
• Desmasures N, Mangin I, Corroler D, Guèguen M. 1998. Characterization of lactococci isolated from milk produced in the Camembert region of Normandy. Journal of Applied Microbiology . 85:999-1005.
• Dolci P, Alessandria V, Zeppa G, Rantsiou K, Cocolin L. 2008a. Microbiological characterization of artisanal Raschera PDO cheese: analysis of its indigenous lactic acid bacteria. Food Microbiology. 25:392-399.
• Duineveld BM, Rosado AS, van Elsas JD, van Veen JA. 1998. Analysis of the dynamics of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradyan gel electrophoresis and substrate utilization patterns. Applied and Environmental Microbiology. 64:4950-4957.
• Duthoit F, Godon JJ, Montel MC. 2003. Bacterial community dynamics during production of registered designation of origin salers cheese as evaluated by 16S rRNA gene singlestrand conformation polymorphism analysis. Applied and Environmental Microbiology. 69:3840-3848.
• El-Baradei G, Delacroix-Buchet A, Ogier JC. 2007. Biodiversity of Bacterial Ecosystems in Traditional Egyptian Domiati Cheese. Applied and Environmental Microbiology. 73: 1248-1255.
• Ercolini D, Hill PJ, Dodd ERC. 2003. Bacterial community structure and location in stilton cheese. Applied and Environmental Microbiology. 69:3540-3548.
• Ercolini D, De Filippis F, La Storia A, Iacono M. 2012. A “remake” of the microbiota involved in the production of water buffalo mozzarella cheese by high throughput sequencing. Applied and Environmental Microbiology. 78:8142-8145.
• Flórez, A.B. and Mayo, B. 2006. PCR-DGGE as a tool for characterizing dominant microbial populations in the Spanish blue--veined Cabrales cheese. International Dairy Journal 16: 1205-1210.
• Fasoli S, Marzotto M, Rizzotti L, Rossi F, Dellaglio F, Torriani, S. 2003. Bacterial composition of commercial probiotic products as evaluated by PCR-DGJE analysis, International Journal of Food Microbiology. 82:59-70.
• Fortina MG, Ricci G, Acquati A, Zeppa, G, Gandini A, Manichini PL. 2003. Genetic characterization of some lactic acid bacteria occurring in an artisanal protected denomination origin (PDO) Italian cheese, the Toma piemontese. Food Microbiology. 20:397-404.
• Foschino R, Nucera D, Volponi G, Picozzi C, Ortoffi M, Bottero MT. 2008. Comparison of Lactococcus garvieae strains isolated in northern Italy from dairy products and fishes through molecular typing. Journal of Applied Microbiology . 105:652-662.
• Friedrich U, Lenke J. 2006. Improved enumeration of lactic acid bacteria in mesophilic dairy starter cultures by using multiplex quantitative real-time PCR and flow cytometryfluorescence in situ hybridization. Applied and Environmental Microbiology. 72:4163-4171.
• Gevers D, Huys G, Swings J. 2001. Applicability of rep-PCR fingerprinting for differentiation of Lactobacillus species. FEMS Microbiology Letter. 205:31-36.
• Giraffa G, Neviani E. 2000. Molecular identification and characterisation of food-associated lactobacilli. Italian Journal of Food Science. 4:403-423.
• Giraffa G, Lazzi C, Gatti M, Rossetti L, Mora D, Neviani E. 2003. Molecular typing of Lactobacillus delbrueckii of dairy origin by PCR-RFLP of protein coding genes, International Journal of Food Microbiology. 82:163-172.
• Giovannoni SJ, Britschgi TB, Moyer CL, Field KG. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature (London) 345:60-63.
• Harmsen, D, Karch H. 2004. How close is close enough? Not the tree of live but a living tree is of major importance for 16S rDNA based microbial species identification. American Society of Microbiology News. 70:19-24.
• Head IM, Saunders JR, Pickup RW. 1998. Microbial evolution, diversity, and ecology, a decade of ribosomal analysis of uncultivated microorganisms. Microbiology Ecology. 35:1- 21.
• Heilig GHJ, Zoetendal EG, Vaughan EE, Marteau P, Akkermans ADL, de Vos WM. 2002. Molecular diversity of Lactobacillus spp., and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA. Applied and Environmental Microbiology. 68:114-123.
• Holzapfel WH, Haberer P, Geisen R, Bjorkroth J, Schillinger U. 2001. Taxonomy and important features of probiotic microorganisms in food and nutrition. American Journal of Clinical Nutrition. 73:365-373.
• Humblot C, Guyot JP. 2009. Pyrosequencing of tagged 16S rRNA gene amplicons for rapid deciphering of the microbiomes of fermented foods such as pearl millet slurries. Applied and Environmental Microbiology. 75:4354-4361.
• Janssen P, Coopman R, Huys G, Swings J, Bleeker M, Vos P, Zabeau M, Kersters K. 1996. Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy. Journal of General Microbiology. 142:1881- 1893.
• Leite AMO, Mayo B, Rachid CTCC, Peixoto RS, Silva JT, Paschoalin VMF, Delgado S, 2012. Assessment of the microbial diversity of Brazilian kefir grains by PCR-DGGE and pyrosequencing analysis. Food Microbiology. 31:215- 221.
• Lortal S, Rouault A, Guezenec S, Gautier M. 1997. Lactobacillus helviticus: Strain typing and genomic size estimation by pulsed field gel electrophoresis. Current of Microbiology. 34:180-5.
• Ludwig W, Schleifer KH. 1994. Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiology Reviewers. 15:155-173.
• Masoud W, Takamiya M, Vogensen FK, Lillevang S, Al-Soud WA, Sørensen SJ, Jakobsen M. 2011. Characterization of bacterial populations in Danish raw milk cheese made with different starter cultures by denaturing gradient gel electrophoresis and pyrosequencing. International Dairy Journal. 21:142-148.
• McCartney AL. 2002. Application of molecular biological methods for studying probiotics and the gut flora, British Journal of Nutrition. 88:29-S37.
• Mohammed M, Abd El-Aziz H, Omran N, Anwar S, Awad S, El-Soda M. 2009. Rep-PCR characterization and biochemical selection of lactic acid bacteria isolated from the Delta area of Egypt. International Journal of Food Microbiology. 128:417-423.
• Morea M, Baruzzi F, Cappa F, Cocconcelli PS. 1998. Molecular characterization of the Lactobacillus community in traditional processing of mozzarella cheese. International Journal of Food Microbiology .43:53-60.
• Morea M, Baruzzi F, Cocconcelli PS. 1999. Molecular and physiological characterization of dominant bacterial populations in traditional mozzarella cheese processing. Journal of Applied Microbiology. 87:574-582.
• Moschetti G, Blaiotta G, Aponte M, Catzeddu P, Villani F, Deiana P, Coppola S. 1998. Random amplified polymorphic DNA and amplified ribosomal DNA spacer polymorphism: powerful methods to differentiate Streptococcus thermophilus strains. Journal of Applied Microbiology. 85: 25-36.
• Moter A, Göbel UB. 2000. Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. Journal of Microbiology Methods. 41:85-112.
• Mounier J, Monnet C, Jacques N, Antoinette A, Irlinger F. 2009. Assessment of the microbial diversity at the surface of Livarot cheese using culture-dependent and independent approaches. International Journal of Food Microbiology. 133:31-7.
• Mullis KB. 1990. "The unusual origin of the polymerase chain reaction". Scientific American. 262(4): 56-61, 64-5.
• Muyzer G, De Waal EC, Uitterlinden AG. 1993. Profiling of complex microbial populations by denaturing gradyan gel electrophoresis analysis of polymerase chain reactionamplified genes coding for 16S rRNA. Applied and Environmental Microbiology. 59:695-700.
• Ogier JC, Son O, Gruss A, Tailliez P, Delacroix-Buchet A. 2002. Identification of the bacterial microflora in dairy products by temporal temperature gradient gel electrophoresis. Applied and Environmental Microbiology. 68:3691-3701.
• Olive DM, Bean P. 1999. Principles and applications of methods for DNA-based typing of microbal organisms. Journal of Clinical Microbiology. 37:1661-1669.
• Olsen KN, Brockmann E, Molin S. 2007. Quantification of Leuconostoc populations in mixed dairy starter cultures using fluorescence in situ hybridization. Journal of Applied Microbiology. 103:855-863.
• Oneca M, Irigoyen A, Ortigosa M, Torre P. 2003. PCR and RAPD identification of L. plantarum strains isolated from ovine milk and cheese. Geographical distribution of strains. FEMS Microbiology Letter. 227:271-277.
• Quigley L, O'Sullivan O, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD. 2012. High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheese. Applied and Environmental Microbiology. 78:5717-5723.
• Rigottier-Gois L, Le Bourhis AG, Gramet G, Rochet V, Doré J. 2003. Fluorescent hybridisation combined with flow cytometry and hybridisation of total RNA to analyse the composition of microbial communities in human faeces using 16S rRNA probes. FEMS Microbiology Ecology. 43:237-245.
• Rossetti L, Giraffa G. 2005. Rapid identification of dairy lactic acid bacteria by M13-generated, RAPD-PCR fingerprint databases. Journal of Microbiological Methods. 63:135-144.
• Roy D, Ward P, Champagne G. 1996. Differentiation of bifidobacteria by use of pulsed-field gel electrophoresis and polymerase chain reaction. International Journal of Food Microbiology. 29:11-29.
• Roy D, Ward P, Vincent D, Mondou F. 2000. Molecular identification of potentially probiotic lactobacilli. Current Microbiology. 40:40-46.
• Saarela M, Mogensen G, Fonden R, Matto J, Mattila-Sandholm T. 2000. Probiotic bacteria: safety, functional and technological properties. Journal of Biotechnology. 84:197- 215.
• Sánchez I, Seseña S, Poveda JM, Cabezas L, Palop L. 2006. Genetic diversity, dynamics and activity of Lactobacillus community involved in traditional processing of artisanal Manchego cheese. International Journal of Food Microbiology. 107:265-273.
• Temmerman R, Huys G, Swings J. 2004. Identification of lactic acid bacteria, culture-dependent and culture independent methods. Trends in Food Science & Technology. 15:348- 359.
• Tynkkynen S, Satokari R, Saarela M, Mattila-Sandholm T, Saxelin M. 1999. Comparison of ribotyping, randomly amplified polymorphic DNA Analysis, and pulsed-field gel electrophoresis in typing of Lactobacillus rhamnosus and L. casei strains. Applied Environmental Microbiology. 65:3908-14.
• Walter J, Hertel C, Tannock GW, Lis CM, Munro K. 2001. Hammes W.P., Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradyan gel electrophoresis. Applied and Environmental Microbiology. 67:2578-2585.
• Ward DM, Weller R, Bateson MM. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature. 345:63-65.
• Ventura M, Zink R. 2002. Specific identification and molecular typing analysis of Lactobacillus johnsonii by using PCRbased methods and pulsed-field gel electrophoresis. FEMS Microbiology Letter. 217:141-54.
• Vlkova E, Rada V, Trojanova I. 2004. Enumeration, Isolation and Identification of Bifidobacteria from dairy products. Acta Agriculturae Slovenica. 84:31-36.