Gıda Fermantasyonlarındaki Mikrobiyal Floranın Araştırılmasına Yönelik Nükleik Asit Bazlı Yaklaşımlar

Amann, Rudolf I., Lee Krumholz, and David A. Stahl. "Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology." Journal of bacteriology 172.2 (1990): 762-770.

Amann, Rudolf, Fuchs, Bernhard M., Behrens, Sebastian “The identification of microorganisms by fluorescence in situ hybridisation”. Current opinion in biotechnology, (2001), 12(3), 231-236.

Behjati, Sam, and Patrick S. Tarpey. "What is next generation sequencing?." Archives of Disease in Childhood-Education and Practice 98.6 (2013): 236-238.

Bhagwat, Arvind A. "Simultaneous detection of Escherichia coli O157: H7, Listeria monocytogenes and Salmonella strains by real-time PCR." International journal of food microbiology 84.2 (2003): 217-224.

Barata, A., M. Malfeito-Ferreira, and V. Loureiro. "The microbial ecology of wine grape

berries." International journal of food microbiology 153.3 (2012): 243-259.

Björkroth ,K. Johanna, Geisen, Rolf, Schillinger, Ulrich, Weiss, Norbert, De Vos, Paul, Holzapfel,Wilhelm H., Korkeala, Hannu J., Vandamme, Peter "Characterization of Leuconostoc gasicomitatum sp. nov., associated with spoiled raw tomato-marinated broiler meat strips packaged under modified- atmosphere conditions." Applied and Environmental Microbiology 66.9 (2000): 3764-3772.17

Bokulich, Nicholas A., Joseph, Lucy C. M., Allen,Greg, Benson,Andrew K.and Mills David A."Next- generation sequencing reveals significant bacterial diversity of botrytized wine." PloS one 7.5 (2012):e36357

Brettschneider, Reinhold. "RFLP analysis." Molecular tools for screening biodiversity. Springer, Dordrecht, 1998. 85-95.

Carlsson, Mats, and Nicolas Beldiceanu. "Dispensation order generation for pyrosequencing." Proceedings of the second conference on Asia-Pacific bioinformatics-Volume 29. Australian Computer Society, Inc., 2004.

Chial, Heidi. "DNA Fingerprinting Using Amplified Fragment Length Polymorphisms (AFLP)." (2008).

Cocolin, Luca, Paola Dolci, and Kalliopi Rantsiou. "Biodiversity and dynamics of meat fermentations: the contribution of molecular methods for a better comprehension of a complex ecosystem." Meat Science 89.3 (2011): 296-302.

Cocolin, L., et al. "Development of a rapid method for the identification of Lactobacillus spp. İsolated from naturally fermented Italian sausages using a polymerase chain reaction–temperature gradient gel electrophoresis." Letters in Applied Microbiology 30.2 (2000): 126-129.

Coppola, S., et al. "Molecular evaluation of microbial diversity occurring in different types ofMozzarella cheese." Journal of Applied Microbiology 90.3 (2001): 414-420.

Boylston, Terri D., Vinderola, Celso G., Ghoddusi, Hamid B. and Reinheimer,Jorge A. "Incorporation of bifidobacteria into cheeses: challenges and rewards." International Dairy Journal14.5 (2004): 375-387.

Dijkshoorn, L., B. M. Ursing, and J. B. Ursing. "Strain, clone and species: comments on three basic concepts of bacteriology." Journal of medical microbiology 49.5 (2000): 397-401.

Ehrmann, Matthias A., and Rudi F. Vogel. "Molecular taxonomy and genetics of sourdough lactic acid bacteria." Trends in Food Science & Technology 16.1-3 (2005): 31-42.

Eid, John, Fehr, Adrian, Gray, Jeremy, Luong, Khai, Lyle, John, Otto, Geoff, Peluso, Paul, Rank,

David, Baybayan, Primo, Bettman, Brad, Bibillo, Arkadiusz, Bjornson, Keith, Chaudhuri, Bidhan,Christians, Frederick, Cicero, Ronald, Clark, Sonya, Dalal, Ravindra, deWinter, Alex, Dixon, John,Foquet, Mathieu, Gaertner, Alfred, Hardenbol, Paul, Heiner, Cheryl, Hester, Kevin, Holden, David,Kearns, Gregory, Kong, Xiangxu, Kuse, Ronald, Lacroix, Yves, Lin, Steven, Lundquist, Paul, Ma,Congcong, Marks, Patrick, Maxham, Mark, Murphy, Devon, Park, Insil, Pham, Thang, Phillips,Michael, Roy, Joy, Sebra, Robert, Shen, Gene, Sorenson, Jon, Tomaney, Austin, Travers, Kevin,Trulson, Mark, Vieceli, John, Wegener, Jeffrey, Wu, Dawn, Yang, Alicia, Zaccarin, Denis, Zhao, Peter,Zhong, Frank, Korlach, Jonas and Turner, Stephen "Real-time DNA sequencing from single polymerase molecules." Science 323.5910 (2009): 133-138.

Eisenstein, Michael. "Oxford Nanopore announcement sets sequencing sector abuzz." (2012): 295.

El Baradei, Laila. Do parallel structures resolve the problems of the Egyptian government bureaucracy. Egyptian Center for Economic Studies, 2006.

Ercolini D, Mauriello G, Blaiotta G, Moschetti G and Coppola S."PCR–DGGE fingerprints ofmicrobial succession during a manufacture of traditional water buffalo mozzarella cheese." Journal of Applied Microbiology 96.2 (2004): 263-270.

Ermolaeva, Olga, Rastogi, Mohit, Pruitt, Kim D., Schuler, Gregory D., Bittner, Michael L., Chen,Yidong, Simon, Richard, Meltzer, Paul, Trent, Jeffrey M. and Boguski, Mark S. "Data management and analysis for gene expression arrays." Nature genetics 20.1 (1998): 19.

Esteve-Zarzoso, Braulio, Belloch, Carmela and Querol, Amparo "Identification of yeasts by RFLP analysis of the 5.8 S rRNA gene and the two ribosomal internal transcribed spacers." International Journal of Systematic and evolutionary microbiology 49.1 (1999): 329-337.

Falsen, Enevold, Pascual, Christina, Sjödén, Berit, Ohlén, Maria, and Collins, Matthew D. "Phenotypic and phylogenetic characterization of a novel Lactobacillus species from human sources: description of Lactobacillus iners sp. nov." International Journal of Systematic and Evolutionary Microbiology 49.1 (1999): 217-221.

Fasoli, Sara, Marta,Marzotto, Rizzotti,Lucia, Rossi, Franca, Dellaglio, Franco and Torrian, Sandra"Bacterial composition of commercial probiotic products as evaluated by PCR-DGGE analysis." International Journal of Food Microbiology 82.1 (2003): 59-70.

Flórez, Ana Belén, Susana Delgado, and Baltasar Mayo. "Antimicrobial susceptibility of lactic acid bacteria isolated from a cheese environment." Canadian journal of microbiology 51.1 (2005): 51-58.

Friedrich, Udo, and Jan Lenke. "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." Applied and environmental microbiology 72.6 (2006): 4163-4171.18

Giovannetti, Luciana, and Stefano Ventura. "Application of total DNA restriction pattern analysis to identification and differentiation of bacterial strains." Diagnostic bacteriology protocols. Humana Press, 1995. 165-179.

Gish, Gerald, and Fritz Eckstein. "DNA and RNA sequence determination based on phosphorothioate chemistry." Science240.4858 (1988): 1520-1522.

Grimont, Francine . "DNA fingerprinting." Nucleic acid techniques in bacterial systematics (1991):249-276.

Hanna, Scott E., Christopher J. Connor, and Hua H. Wang. "Real‐time polymerase chain reaction for the food microbiologist: technologies, applications, and limitations." Journal of food science 70.3 (2005): R49-R53.

Heilig, Hans G.H.J., Zoetendal, Erwin G., Elaine Vaughan, E. Philippe, Marteau, Akkermans, Antoon D.L. and De Vos, Willem M. "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 68.1 (2002): 114-123.

Hernán-Gómez, S., Espinosa, J. C., and Ubeda, J. F., Characterization of wine yeasts by temperature gradient gel electrophoresis (TGGE). FEMS Microbiology Letters, 2000, 193(1), 45-50.

Huang, Chien-Hsun, Chang,Mu-Tzu, Hu, Mu-Chiouang and Lee,Fwu-Ling. "Application of the SNaPshot minisequencing assay to species identification in the Lactobacillus casei group." Molecular and cellular probes 25.4 (2011): 153-157..

Huse, Susan M, Huber, Julie A, Morrison, Hilary G, Sogin, Mitchell L., and Welch, Mark David "Accuracy and quality of massively parallel DNA pyrosequencing." Genome biology 8.7 (2007): R143.

Jany, Jean-Luc, and Georges Barbier. "Culture-independent methods for identifying microbial communities in cheese." Food microbiology 25.7 (2008): 839-848.

KARACA, Mehmet, and A. Naci ONUS. "Array Gen Ekspresyon Teknolojisi ve Bitkisel Üretimde Kullanımı." alatarım (2004): 5.

Kasianowicz, John J., Brandin, Eric, Branton, Daniel, and Deamer, David W. "Characterization of individual polynucleotide molecules using a membrane channel." Proceedings of the National Academy of Sciences 93.24 (1996): 13770-13773.

KIRAN, Fadime, and Özlem osmanağaoğlu. "Laktik asit bakterilerinin (LAB) identifikasyonunda/tiplendirmesinde kullanılan moleküler yöntemler." Erciyes Üniversitesi Fen Bilimleri Enstitüsü Fen Bilimleri Dergisi” 27.1 (2011): 62-74.

Loman, Nicholas J., Joshua Quick, and Jared T. Simpson. "A complete bacterial genome assembled de novo using only nanopore sequencing data." Nature methods 12.8 (2015): 733.

Moter, Annette, and Ulf B. Göbel. "Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms." (2000): 85-112.

Nam, Young-Do, Sung-Hun Yi, and Seong-Il Lim. "Bacterial diversity of cheonggukjang, a traditional Korean fermented food, analyzed by barcoded pyrosequencing." Food Control 28.1 (2012): 135-142.

Ogier, Jean-Claude, Son, Olivier, Gruss, Alexandra, Tailliez, Patrick, Delacroix-Buchet, Agnes "Identification of the bacterial microflora in dairy products by temporal temperature gradient gel electrophoresis." Applied and Environmental Microbiology 68.8 (2002): 3691-3701.

43. Olsen, K. N., E. Brockmann, and Søren Molin. "Quantification of Leuconostoc populations in mixed dairy starter cultures using fluorescence in situ hybridization." Journal of applied microbiology 103.4 (2007): 855-863.

44. Pray, Leslie A. "The biotechnology revolution: PCR and the use of reverse transcriptase to clone expressed genes." Nat Educ 1.1 (2008): 94.

Quigley, Lisa, O'Sullivan, Orla, Beresford, Tom P., Ross, R. Paul, Fitzgerald, Gerald F. And Cotter, Paul D., "Molecular approaches to analysing the microbial composition of raw milk and raw milk cheese." International journal of food microbiology 150.2-3 (2011): 81-94.

Rantsiou, Kalliopi, and Luca Cocolin. "New developments in the study of the microbiota of naturally fermented sausages as determined by molecular methods: a review." International Journal of Food Microbiology 108.2 (2006): 255-267.

Rigottier-Gois, Lionel, Rochet, Violaine, Garrec, Nathalie, Suau, Antonia and Dore, Joel. "Enumeration of Bacteroides species in human faeces by fluorescent in situ hybridisation combined with flow cytometry using 16S rRNA probes." Systematic and applied microbiology 26.1 (2003): 110.

Ronaghi, Mostafa, Mathias Uhlén, and Pål Nyrén. "A sequencing method based on real-time pyrophosphate." Science 281.5375 (1998): 363-365.

Sabatea, Josep, Cano, Josep, Esteve-Zarzoso, Braulio and Guillamón, Josè M. "Isolation and identification of yeasts associated with vineyard and winery by RFLP analysis of ribosomal genes and mitochondrial DNA." Microbiological research 157.4 (2002): 267-274.19

Sanger, Frederick, Steven Nicklen, and Alan R. Coulson. "DNA sequencing with chain-terminating inhibitors." Proceedings of the national academy of sciences 74.12 (1977): 5463-5467.

Sofu, Aytül. "Analyses of Dynamics in Dairy Products and Identification of Lactic Acid Bacteria Population by Molecular Methods." Turkish Journal of Agriculture-Food Science and Technology 5.1 (2017): 6-13.

Stoddart, David, Heron, Andrew J., Mikhailova, Ellina, Maglia, Giovanni and Bayley Hagan "Single- nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore." Proceedings of the National Academy of Sciences 106.19 (2009): 7702-7707.

Tamang, Jyotı P., Thapa, Namrata, Tamang, Buddhıman, Raı, Arun, Chettrı, Rajen "Microorganisms in fermented foods and beverages." Health benefits of fermented foods and beverages. CRC Press.Taylor & Francis Group, New York (USA), 2015. 1-110.

Vlkova, Eva, Bujňáková, Dobroslava, Kmeť, Vladimír. "Enumeration, isolation, and identification of bifidobacteria from infant feces." Folia microbiologica 49.2 (2004): 209-212.

Walter, Jens, et al. "Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis." Applied and environmental microbiology 67.6 (2001): 2578-2585.

Welsh, John, and Michael McClelland. "Fingerprinting genomes using PCR with arbitrary

primers." Nucleic acids research 18.24 (1990): 7213-7218.

Williams, John G.K., Kubelik, Anne R., Livak, Kenneth J., Rafalski, J.Antoni, Tingey, Scott V.

"DNA polymorphisms amplified by arbitrary primers are useful as genetic markers." Nucleic acid research 18.22 (1990): 6531-6535.

Niessen L, Luo J, Denschlag C, Vogel RF. The application of loop-mediated isothermal amplification (LAMP) in food testing for bacterial pathogens and fungal contaminants. Food Microbiol. 36: 191-206 (2013)

Yan L, Zhou J, Zheng Y, Gamson AS, Roembke BT, Nakayama S, Sintim HO. Isothermal amplified detection of DNA and RNA. Mol. BioSyst. 10: 970-1003 (2014)

Zhao X, Lin CW, Wang J, Oh DH. Advances in rapid detection methods for food-borne pathogens. J. Microbiol. Biotechnol. 24: 297-312 (2014)

Saharan P, Dhingolia S, Khatri P, Duhan JS, Gahlawat SK. Loop mediated isothermal amplification (LAMP) based detection of bacteria: A Review. Afr. J. Biotechnol. 13: 1920-1928 (2014)

Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase

T. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28: e63 (2000)

Wang F, Jiang L, Yang Q, Prinyawiwatkul W, Ge B. Rapid and specific detection of Escherichia coli serogroups O26, O45, O103, O111, O121, O145, and O157 in ground beef, beef trim, and produce by loop-mediated isothermal amplification. Appl. Environ. Microb.78: 2727-2736 (2012)

Shao Y, Zhu S, Jin C, Chen F. Development of multiplex loop-mediated isothermal amplification-RFLP (mLAMP-RFLP) to detect Salmonella spp. And Shigella spp. in milk. Int. J. Food Microbiol. 148: 75-79 (2011)

Yamazaki W, Kumeda Y, Uemura R, Misawa N. Evaluation of a loop mediated isothermal amplification assay for rapid and simple detection of Vibrio parahaemolyticus in naturally contaminated seafood samples. Food Microbiol. 28: 1238-1241 (2011

Nagamine K, Hase T, Notomi T. Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol. Cell Probe. 16: 223-229 (2002)

Kuchta T, Knutsson R, Fiore A, Kudirkiene E, Höhl A, Horvatek Tomic D, Gotcheva V, Pöpping B, Scaramagli S, To Kim A, Wagner M, De Medici D. A decade with nucleic acid-based microbiological methods in safety control of foods. Lett. Appl. Microbiol. 59: 263-271 (2014)

Song T, Toma C, Nakasone N, Iwanaga M. Sensitive and rapid detection of Shigella and enteroinvasive Escherichia coli by a loop-mediated isothermal amplification method. FEMS Microbiol. Lett. 243: 259-263 (2005)

FakruddinM, Mannan KSB, Chowdhury A, Mazumdar RM, Hossain MN, Islam S, Chowdhury MA. Nucleic acid amplification: Alternative methods of polymerase chain reaction. J. Pharm. Bioall. Sci. 5: 245-252 (2013)

Fakruddin M, Chowdhury A. Pyrosequencing: An alternative to traditional sanger sequencing. Am. J. Biochem. Biotechnol. 8: 14-20 (2012)

Fakruddin M, Mazumdar RM, Chowdhury A, Hossain MN, Mannan KS. Pyrosequencing-prospects and applications. Int. J. Life Sci. Pharm. Res. 2: 65- 76 (2012)

Compton J. Nucleic acid sequence-based amplification. Nature 350: 91-92 (1991)

Jean J, Blais B, Darveau A, Fliss I. Detection of hepatitis A virus by the nucleic acid sequence-based amplification (NASBA) technique and comparison with RT-PCR. Appl. Environ. Microb. 67: 5593-5600 (2001)

Greene SR, Moe C, Jaykus LA, Cronin M, Grosso L, van Aarle P. Evaluation of the nuclisens basic kit assay for detection of norwalkvirus rna in stool specimens. J. Virol. Methods 108: 123-131 (2003)

Piette JC, Huraux JM. Comparative evaluation of hepatitis C virus RN quantitation by branched DNA NASBA, and monitor assays. Hepatology 29: 528-535 (1999)

Amagliani G, Omiccioli E, del Campo A, Bruce IJ, Brandi G, Magnani M. Development of a magnetic capture hybridization-PCR assay for Listeria monocytogenes direct detection in milk samples. J. Appl. Microbiol. 100: 375- 378 (2006)

Souii A, Ben Nejma M, Elfray Rhim A, Mastouri M, Bel Hadj Jrad B, Makhlouf M, Nour M. Molecular Identification of 4 Salmonella Serovars isolated from food in Tunisia based on the sequence of the ribosomal RNA genes. Afr. J. Microbiol. Res. 6: 6454-6461 (2012)

Jothikumar N, Griffiths MW. Rapid detection of Escherichia coli O157:H7 with multiplex real-time PCR assays. Appl. Environ. Microb. 68: 3169-3171 (2002)

Krascsenicsová K, Piknová L, Kaclíková E, Kuchta T. Detection of Salmonella enterica in food using two-step enrichment and real-time polymerase chain reaction. Lett. Appl. Microbiol. 46: 483-487 (2008)

Fakruddin M, Mazumdar RM, Chowdhury A, Mannan KSB. Nucleic acid sequence based amplification (NASBA)-prospects and applications. Int. J. Life Sci. Pharm. Res. 2: 106-121 (2012)

McHugh TD, Pope CF, Ling CL, Patel S, Billington OJ, Gosling RD, Lipman MC, Gillespie SH. Prospective evaluation of BDProbeTec strand displacement amplification (SDA) system for diagnosis of tuberculosis in non-respiratory and respiratory samples. J. Med. Microbiol. 53: 1215-1219 (2004)

Walker GT, Fraiser MS, Schram JL, Little MC, Nadeau JG, Malinowski DP. Strand displacement amplification - An isothermal, in vitro DNA amplification technique. Nucleic Acids Res. 20: 1691-1696 (1992)

Römpler H, Dear PH, Krause J, Meyer M, Rohland N, Schöneberg T, Spriggs H, Stiller M, Hofreiter M. Multiplex amplification of ancient DNA. Nat. Protoc. 1: 720-728 (2006)

Rosenfield SI, Jaykus LA. A multiplex reverse transcription polymerase chain reaction method for the detection of food-borne viruses. J. Food Protect. 62: 1210-1214 (1999)

Fratamico PM, Bagi LK, Cray WC, Jr Narang N, Yan X, Medina M, Liu Y. Detection by multiplex real-time polymerase chain reaction assays and isolation of Shiga toxin-producing Escherichia coli serogroups O26, O45, O103, O111, O121, and O145 in ground beef. Foodborne Pathog. Dis. 8: 601-607 (2011)

Fakruddin M, Mazumdar RM, Chowdhury A, Mannan KSB. Nucleic acid sequence based amplification (NASBA)-prospects and applications. Int. J. Life Sci. Pharm. Res. 2: 106-121 (2012)

Jean J, D’Souza DH, Jaykus LA. Multiplex nucleic acid sequence-based amplification for simultaneous detection of several enteric viruses in model ready-to-eat foods. Appl. Environ. Microb. 70: 6603-6610 (2004)

Niessen L, Luo J, Denschlag C, Vogel RF. The application of loop-mediated isothermal amplification (LAMP) in food testing for bacterial pathogens and fungal contaminants. Food Microbiol. 36: 191-206 (2013)

Lunel F, Cresta P, Vitour D, Payan C, Dumont B, Frangeul L, Reboul D, Brault C, Piette JC, Huraux JM. Comparative evaluation of hepatitis C virus RNA quantitation by branched DNA NASBA, and monitor assays. Hepatology 29:528-535 (1999)

Daniel J. O’Sullivan, Linda Giblin1, Paul L. H. McSweeney, Jeremiah J. Sheehan1 and Paul D. Cotter. Nucleic acid-based approaches to investigate microbial-related cheese quality defects. Front. Microbiol.,Sec. Food Microbiology (2013)

Amira Souii, Manel Ben M’hadheb-Gharbi, and Jawhar Gharbi. Nucleic Acid-based Biotechnologies for Food-borne Pathogen Detection Using Routine Time-intensive Culture-based Methods and Fast Molecular Diagnostics. Food Sci. Biotechnol. (2006)

Amann, Rudolf I., Lee Krumholz, and David A. Stahl. "Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology." Journal of bacteriology 172.2 (1990): 762-770.

Amann, Rudolf, Fuchs, Bernhard M., Behrens, Sebastian “The identification of microorganisms by fluorescence in situ hybridisation”. Current opinion in biotechnology, (2001), 12(3), 231-236.

Behjati, Sam, and Patrick S. Tarpey. "What is next generation sequencing?." Archives of Disease in Childhood-Education and Practice 98.6 (2013): 236-238.

Bhagwat, Arvind A. "Simultaneous detection of Escherichia coli O157: H7, Listeria monocytogenes and Salmonella strains by real-time PCR." International journal of food microbiology 84.2 (2003): 217-224.

Barata, A., M. Malfeito-Ferreira, and V. Loureiro. "The microbial ecology of wine grape

berries." International journal of food microbiology 153.3 (2012): 243-259.

Björkroth ,K. Johanna, Geisen, Rolf, Schillinger, Ulrich, Weiss, Norbert, De Vos, Paul, Holzapfel,Wilhelm H., Korkeala, Hannu J., Vandamme, Peter "Characterization of Leuconostoc gasicomitatum sp. nov., associated with spoiled raw tomato-marinated broiler meat strips packaged under modified- atmosphere conditions." Applied and Environmental Microbiology 66.9 (2000): 3764-3772.17

Bokulich, Nicholas A., Joseph, Lucy C. M., Allen,Greg, Benson,Andrew K.and Mills David A."Next- generation sequencing reveals significant bacterial diversity of botrytized wine." PloS one 7.5 (2012):e36357

Brettschneider, Reinhold. "RFLP analysis." Molecular tools for screening biodiversity. Springer, Dordrecht, 1998. 85-95.

Carlsson, Mats, and Nicolas Beldiceanu. "Dispensation order generation for pyrosequencing." Proceedings of the second conference on Asia-Pacific bioinformatics-Volume 29. Australian Computer Society, Inc., 2004.

Chial, Heidi. "DNA Fingerprinting Using Amplified Fragment Length Polymorphisms (AFLP)." (2008).

Cocolin, Luca, Paola Dolci, and Kalliopi Rantsiou. "Biodiversity and dynamics of meat fermentations: the contribution of molecular methods for a better comprehension of a complex ecosystem." Meat Science 89.3 (2011): 296-302.

Cocolin, L., et al. "Development of a rapid method for the identification of Lactobacillus spp. İsolated from naturally fermented Italian sausages using a polymerase chain reaction–temperature gradient gel electrophoresis." Letters in Applied Microbiology 30.2 (2000): 126-129.

Coppola, S., et al. "Molecular evaluation of microbial diversity occurring in different types ofMozzarella cheese." Journal of Applied Microbiology 90.3 (2001): 414-420.

Boylston, Terri D., Vinderola, Celso G., Ghoddusi, Hamid B. and Reinheimer,Jorge A. "Incorporation of bifidobacteria into cheeses: challenges and rewards." International Dairy Journal14.5 (2004): 375-387.

Dijkshoorn, L., B. M. Ursing, and J. B. Ursing. "Strain, clone and species: comments on three basic concepts of bacteriology." Journal of medical microbiology 49.5 (2000): 397-401.

Ehrmann, Matthias A., and Rudi F. Vogel. "Molecular taxonomy and genetics of sourdough lactic acid bacteria." Trends in Food Science & Technology 16.1-3 (2005): 31-42.

Eid, John, Fehr, Adrian, Gray, Jeremy, Luong, Khai, Lyle, John, Otto, Geoff, Peluso, Paul, Rank,

David, Baybayan, Primo, Bettman, Brad, Bibillo, Arkadiusz, Bjornson, Keith, Chaudhuri, Bidhan,Christians, Frederick, Cicero, Ronald, Clark, Sonya, Dalal, Ravindra, deWinter, Alex, Dixon, John,Foquet, Mathieu, Gaertner, Alfred, Hardenbol, Paul, Heiner, Cheryl, Hester, Kevin, Holden, David,Kearns, Gregory, Kong, Xiangxu, Kuse, Ronald, Lacroix, Yves, Lin, Steven, Lundquist, Paul, Ma,Congcong, Marks, Patrick, Maxham, Mark, Murphy, Devon, Park, Insil, Pham, Thang, Phillips,Michael, Roy, Joy, Sebra, Robert, Shen, Gene, Sorenson, Jon, Tomaney, Austin, Travers, Kevin,Trulson, Mark, Vieceli, John, Wegener, Jeffrey, Wu, Dawn, Yang, Alicia, Zaccarin, Denis, Zhao, Peter,Zhong, Frank, Korlach, Jonas and Turner, Stephen "Real-time DNA sequencing from single polymerase molecules." Science 323.5910 (2009): 133-138.

Eisenstein, Michael. "Oxford Nanopore announcement sets sequencing sector abuzz." (2012): 295.

El Baradei, Laila. Do parallel structures resolve the problems of the Egyptian government bureaucracy. Egyptian Center for Economic Studies, 2006.

Ercolini D, Mauriello G, Blaiotta G, Moschetti G and Coppola S."PCR–DGGE fingerprints ofmicrobial succession during a manufacture of traditional water buffalo mozzarella cheese." Journal of Applied Microbiology 96.2 (2004): 263-270.

Ermolaeva, Olga, Rastogi, Mohit, Pruitt, Kim D., Schuler, Gregory D., Bittner, Michael L., Chen,Yidong, Simon, Richard, Meltzer, Paul, Trent, Jeffrey M. and Boguski, Mark S. "Data management and analysis for gene expression arrays." Nature genetics 20.1 (1998): 19.

Esteve-Zarzoso, Braulio, Belloch, Carmela and Querol, Amparo "Identification of yeasts by RFLP analysis of the 5.8 S rRNA gene and the two ribosomal internal transcribed spacers." International Journal of Systematic and evolutionary microbiology 49.1 (1999): 329-337.

Falsen, Enevold, Pascual, Christina, Sjödén, Berit, Ohlén, Maria, and Collins, Matthew D. "Phenotypic and phylogenetic characterization of a novel Lactobacillus species from human sources: description of Lactobacillus iners sp. nov." International Journal of Systematic and Evolutionary Microbiology 49.1 (1999): 217-221.

Fasoli, Sara, Marta,Marzotto, Rizzotti,Lucia, Rossi, Franca, Dellaglio, Franco and Torrian, Sandra"Bacterial composition of commercial probiotic products as evaluated by PCR-DGGE analysis." International Journal of Food Microbiology 82.1 (2003): 59-70.

Flórez, Ana Belén, Susana Delgado, and Baltasar Mayo. "Antimicrobial susceptibility of lactic acid bacteria isolated from a cheese environment." Canadian journal of microbiology 51.1 (2005): 51-58.

Friedrich, Udo, and Jan Lenke. "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." Applied and environmental microbiology 72.6 (2006): 4163-4171.18

Giovannetti, Luciana, and Stefano Ventura. "Application of total DNA restriction pattern analysis to identification and differentiation of bacterial strains." Diagnostic bacteriology protocols. Humana Press, 1995. 165-179.

Gish, Gerald, and Fritz Eckstein. "DNA and RNA sequence determination based on phosphorothioate chemistry." Science240.4858 (1988): 1520-1522.

Grimont, Francine . "DNA fingerprinting." Nucleic acid techniques in bacterial systematics (1991):249-276.

Hanna, Scott E., Christopher J. Connor, and Hua H. Wang. "Real‐time polymerase chain reaction for the food microbiologist: technologies, applications, and limitations." Journal of food science 70.3 (2005): R49-R53.

Heilig, Hans G.H.J., Zoetendal, Erwin G., Elaine Vaughan, E. Philippe, Marteau, Akkermans, Antoon D.L. and De Vos, Willem M. "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 68.1 (2002): 114-123.

Hernán-Gómez, S., Espinosa, J. C., and Ubeda, J. F., Characterization of wine yeasts by temperature gradient gel electrophoresis (TGGE). FEMS Microbiology Letters, 2000, 193(1), 45-50.

Huang, Chien-Hsun, Chang,Mu-Tzu, Hu, Mu-Chiouang and Lee,Fwu-Ling. "Application of the SNaPshot minisequencing assay to species identification in the Lactobacillus casei group." Molecular and cellular probes 25.4 (2011): 153-157..

Huse, Susan M, Huber, Julie A, Morrison, Hilary G, Sogin, Mitchell L., and Welch, Mark David "Accuracy and quality of massively parallel DNA pyrosequencing." Genome biology 8.7 (2007): R143.

Jany, Jean-Luc, and Georges Barbier. "Culture-independent methods for identifying microbial communities in cheese." Food microbiology 25.7 (2008): 839-848.

KARACA, Mehmet, and A. Naci ONUS. "Array Gen Ekspresyon Teknolojisi ve Bitkisel Üretimde Kullanımı." alatarım (2004): 5.

Kasianowicz, John J., Brandin, Eric, Branton, Daniel, and Deamer, David W. "Characterization of individual polynucleotide molecules using a membrane channel." Proceedings of the National Academy of Sciences 93.24 (1996): 13770-13773.

KIRAN, Fadime, and Özlem osmanağaoğlu. "Laktik asit bakterilerinin (LAB) identifikasyonunda/tiplendirmesinde kullanılan moleküler yöntemler." Erciyes Üniversitesi Fen Bilimleri Enstitüsü Fen Bilimleri Dergisi” 27.1 (2011): 62-74.

Loman, Nicholas J., Joshua Quick, and Jared T. Simpson. "A complete bacterial genome assembled de novo using only nanopore sequencing data." Nature methods 12.8 (2015): 733.

Moter, Annette, and Ulf B. Göbel. "Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms." (2000): 85-112.

Nam, Young-Do, Sung-Hun Yi, and Seong-Il Lim. "Bacterial diversity of cheonggukjang, a traditional Korean fermented food, analyzed by barcoded pyrosequencing." Food Control 28.1 (2012): 135-142.

Ogier, Jean-Claude, Son, Olivier, Gruss, Alexandra, Tailliez, Patrick, Delacroix-Buchet, Agnes "Identification of the bacterial microflora in dairy products by temporal temperature gradient gel electrophoresis." Applied and Environmental Microbiology 68.8 (2002): 3691-3701.

43. Olsen, K. N., E. Brockmann, and Søren Molin. "Quantification of Leuconostoc populations in mixed dairy starter cultures using fluorescence in situ hybridization." Journal of applied microbiology 103.4 (2007): 855-863.

44. Pray, Leslie A. "The biotechnology revolution: PCR and the use of reverse transcriptase to clone expressed genes." Nat Educ 1.1 (2008): 94.

Quigley, Lisa, O'Sullivan, Orla, Beresford, Tom P., Ross, R. Paul, Fitzgerald, Gerald F. And Cotter, Paul D., "Molecular approaches to analysing the microbial composition of raw milk and raw milk cheese." International journal of food microbiology 150.2-3 (2011): 81-94.

Rantsiou, Kalliopi, and Luca Cocolin. "New developments in the study of the microbiota of naturally fermented sausages as determined by molecular methods: a review." International Journal of Food Microbiology 108.2 (2006): 255-267.

Rigottier-Gois, Lionel, Rochet, Violaine, Garrec, Nathalie, Suau, Antonia and Dore, Joel. "Enumeration of Bacteroides species in human faeces by fluorescent in situ hybridisation combined with flow cytometry using 16S rRNA probes." Systematic and applied microbiology 26.1 (2003): 110.

Ronaghi, Mostafa, Mathias Uhlén, and Pål Nyrén. "A sequencing method based on real-time pyrophosphate." Science 281.5375 (1998): 363-365.

Sabatea, Josep, Cano, Josep, Esteve-Zarzoso, Braulio and Guillamón, Josè M. "Isolation and identification of yeasts associated with vineyard and winery by RFLP analysis of ribosomal genes and mitochondrial DNA." Microbiological research 157.4 (2002): 267-274.19

Sanger, Frederick, Steven Nicklen, and Alan R. Coulson. "DNA sequencing with chain-terminating inhibitors." Proceedings of the national academy of sciences 74.12 (1977): 5463-5467.

Sofu, Aytül. "Analyses of Dynamics in Dairy Products and Identification of Lactic Acid Bacteria Population by Molecular Methods." Turkish Journal of Agriculture-Food Science and Technology 5.1 (2017): 6-13.

Stoddart, David, Heron, Andrew J., Mikhailova, Ellina, Maglia, Giovanni and Bayley Hagan "Single- nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore." Proceedings of the National Academy of Sciences 106.19 (2009): 7702-7707.

Tamang, Jyotı P., Thapa, Namrata, Tamang, Buddhıman, Raı, Arun, Chettrı, Rajen "Microorganisms in fermented foods and beverages." Health benefits of fermented foods and beverages. CRC Press.Taylor & Francis Group, New York (USA), 2015. 1-110.

Vlkova, Eva, Bujňáková, Dobroslava, Kmeť, Vladimír. "Enumeration, isolation, and identification of bifidobacteria from infant feces." Folia microbiologica 49.2 (2004): 209-212.

Walter, Jens, et al. "Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis." Applied and environmental microbiology 67.6 (2001): 2578-2585.

Welsh, John, and Michael McClelland. "Fingerprinting genomes using PCR with arbitrary

primers." Nucleic acids research 18.24 (1990): 7213-7218.

Williams, John G.K., Kubelik, Anne R., Livak, Kenneth J., Rafalski, J.Antoni, Tingey, Scott V.

"DNA polymorphisms amplified by arbitrary primers are useful as genetic markers." Nucleic acid research 18.22 (1990): 6531-6535.

Niessen L, Luo J, Denschlag C, Vogel RF. The application of loop-mediated isothermal amplification (LAMP) in food testing for bacterial pathogens and fungal contaminants. Food Microbiol. 36: 191-206 (2013)

Yan L, Zhou J, Zheng Y, Gamson AS, Roembke BT, Nakayama S, Sintim HO. Isothermal amplified detection of DNA and RNA. Mol. BioSyst. 10: 970-1003 (2014)

Zhao X, Lin CW, Wang J, Oh DH. Advances in rapid detection methods for food-borne pathogens. J. Microbiol. Biotechnol. 24: 297-312 (2014)

Saharan P, Dhingolia S, Khatri P, Duhan JS, Gahlawat SK. Loop mediated isothermal amplification (LAMP) based detection of bacteria: A Review. Afr. J. Biotechnol. 13: 1920-1928 (2014)

Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase

T. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28: e63 (2000)

Wang F, Jiang L, Yang Q, Prinyawiwatkul W, Ge B. Rapid and specific detection of Escherichia coli serogroups O26, O45, O103, O111, O121, O145, and O157 in ground beef, beef trim, and produce by loop-mediated isothermal amplification. Appl. Environ. Microb.78: 2727-2736 (2012)

Shao Y, Zhu S, Jin C, Chen F. Development of multiplex loop-mediated isothermal amplification-RFLP (mLAMP-RFLP) to detect Salmonella spp. And Shigella spp. in milk. Int. J. Food Microbiol. 148: 75-79 (2011)

Yamazaki W, Kumeda Y, Uemura R, Misawa N. Evaluation of a loop mediated isothermal amplification assay for rapid and simple detection of Vibrio parahaemolyticus in naturally contaminated seafood samples. Food Microbiol. 28: 1238-1241 (2011

Nagamine K, Hase T, Notomi T. Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol. Cell Probe. 16: 223-229 (2002)

Kuchta T, Knutsson R, Fiore A, Kudirkiene E, Höhl A, Horvatek Tomic D, Gotcheva V, Pöpping B, Scaramagli S, To Kim A, Wagner M, De Medici D. A decade with nucleic acid-based microbiological methods in safety control of foods. Lett. Appl. Microbiol. 59: 263-271 (2014)

Song T, Toma C, Nakasone N, Iwanaga M. Sensitive and rapid detection of Shigella and enteroinvasive Escherichia coli by a loop-mediated isothermal amplification method. FEMS Microbiol. Lett. 243: 259-263 (2005)

FakruddinM, Mannan KSB, Chowdhury A, Mazumdar RM, Hossain MN, Islam S, Chowdhury MA. Nucleic acid amplification: Alternative methods of polymerase chain reaction. J. Pharm. Bioall. Sci. 5: 245-252 (2013)

Fakruddin M, Chowdhury A. Pyrosequencing: An alternative to traditional sanger sequencing. Am. J. Biochem. Biotechnol. 8: 14-20 (2012)

Fakruddin M, Mazumdar RM, Chowdhury A, Hossain MN, Mannan KS. Pyrosequencing-prospects and applications. Int. J. Life Sci. Pharm. Res. 2: 65- 76 (2012)

Compton J. Nucleic acid sequence-based amplification. Nature 350: 91-92 (1991)

Jean J, Blais B, Darveau A, Fliss I. Detection of hepatitis A virus by the nucleic acid sequence-based amplification (NASBA) technique and comparison with RT-PCR. Appl. Environ. Microb. 67: 5593-5600 (2001)

Greene SR, Moe C, Jaykus LA, Cronin M, Grosso L, van Aarle P. Evaluation of the nuclisens basic kit assay for detection of norwalkvirus rna in stool specimens. J. Virol. Methods 108: 123-131 (2003)

Piette JC, Huraux JM. Comparative evaluation of hepatitis C virus RN quantitation by branched DNA NASBA, and monitor assays. Hepatology 29: 528-535 (1999)

Amagliani G, Omiccioli E, del Campo A, Bruce IJ, Brandi G, Magnani M. Development of a magnetic capture hybridization-PCR assay for Listeria monocytogenes direct detection in milk samples. J. Appl. Microbiol. 100: 375- 378 (2006)

Souii A, Ben Nejma M, Elfray Rhim A, Mastouri M, Bel Hadj Jrad B, Makhlouf M, Nour M. Molecular Identification of 4 Salmonella Serovars isolated from food in Tunisia based on the sequence of the ribosomal RNA genes. Afr. J. Microbiol. Res. 6: 6454-6461 (2012)

Jothikumar N, Griffiths MW. Rapid detection of Escherichia coli O157:H7 with multiplex real-time PCR assays. Appl. Environ. Microb. 68: 3169-3171 (2002)

Krascsenicsová K, Piknová L, Kaclíková E, Kuchta T. Detection of Salmonella enterica in food using two-step enrichment and real-time polymerase chain reaction. Lett. Appl. Microbiol. 46: 483-487 (2008)

Fakruddin M, Mazumdar RM, Chowdhury A, Mannan KSB. Nucleic acid sequence based amplification (NASBA)-prospects and applications. Int. J. Life Sci. Pharm. Res. 2: 106-121 (2012)

McHugh TD, Pope CF, Ling CL, Patel S, Billington OJ, Gosling RD, Lipman MC, Gillespie SH. Prospective evaluation of BDProbeTec strand displacement amplification (SDA) system for diagnosis of tuberculosis in non-respiratory and respiratory samples. J. Med. Microbiol. 53: 1215-1219 (2004)

Walker GT, Fraiser MS, Schram JL, Little MC, Nadeau JG, Malinowski DP. Strand displacement amplification - An isothermal, in vitro DNA amplification technique. Nucleic Acids Res. 20: 1691-1696 (1992)

Römpler H, Dear PH, Krause J, Meyer M, Rohland N, Schöneberg T, Spriggs H, Stiller M, Hofreiter M. Multiplex amplification of ancient DNA. Nat. Protoc. 1: 720-728 (2006)

Rosenfield SI, Jaykus LA. A multiplex reverse transcription polymerase chain reaction method for the detection of food-borne viruses. J. Food Protect. 62: 1210-1214 (1999)

Fratamico PM, Bagi LK, Cray WC, Jr Narang N, Yan X, Medina M, Liu Y. Detection by multiplex real-time polymerase chain reaction assays and isolation of Shiga toxin-producing Escherichia coli serogroups O26, O45, O103, O111, O121, and O145 in ground beef. Foodborne Pathog. Dis. 8: 601-607 (2011)

Fakruddin M, Mazumdar RM, Chowdhury A, Mannan KSB. Nucleic acid sequence based amplification (NASBA)-prospects and applications. Int. J. Life Sci. Pharm. Res. 2: 106-121 (2012)

Jean J, D’Souza DH, Jaykus LA. Multiplex nucleic acid sequence-based amplification for simultaneous detection of several enteric viruses in model ready-to-eat foods. Appl. Environ. Microb. 70: 6603-6610 (2004)

Niessen L, Luo J, Denschlag C, Vogel RF. The application of loop-mediated isothermal amplification (LAMP) in food testing for bacterial pathogens and fungal contaminants. Food Microbiol. 36: 191-206 (2013)

Lunel F, Cresta P, Vitour D, Payan C, Dumont B, Frangeul L, Reboul D, Brault C, Piette JC, Huraux JM. Comparative evaluation of hepatitis C virus RNA quantitation by branched DNA NASBA, and monitor assays. Hepatology 29:528-535 (1999)

Daniel J. O’Sullivan, Linda Giblin1, Paul L. H. McSweeney, Jeremiah J. Sheehan1 and Paul D. Cotter. Nucleic acid-based approaches to investigate microbial-related cheese quality defects. Front. Microbiol.,Sec. Food Microbiology (2013)

Amira Souii, Manel Ben M’hadheb-Gharbi, and Jawhar Gharbi. Nucleic Acid-based Biotechnologies for Food-borne Pathogen Detection Using Routine Time-intensive Culture-based Methods and Fast Molecular Diagnostics. Food Sci. Biotechnol. (2006)