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Chapter 5 : Milk and Dairy Products

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Abstract:

Dairy-associated microbes are important determinants of food quality and safety and are essential for the production of fermented dairy products. Built upon over 130 years of dairy food microbiology research, this chapter focuses on the microbial ecology and systems biology of dairy products from the perspective of culture-independent metagenomics research. Recent studies have provided new perspectives on the microbial composition in raw and processed fluid milk from bovine, goat, and other animal sources and the introduction and succession of those microbes on the farm and at processing facilities. Also discussed are microbiotas in cheese and cheese-associated environments. The diversity of cheese varieties is possible because of those microorganisms and the metabolic processes they perform. The bacteria contained in milk and found on processing equipment, as well as starter cultures, bacteriophages, enzymes and other ingredients, and production and ripening conditions, have interconnected effects, resulting in different cheese varieties with distinct organoleptic properties. Lastly, the microbial composition of other fermented dairy products is presented, including fermented milk beverages such as kefir, yogurt, koumiss, kurut, nunu, and tarag. High-throughput “-omics” approaches have revolutionized our understanding of the ecology and molecular capacities of dairy-associated microbes. With continued methodological and technical advances, these methods will propel improvements in dairy quality and safety assurance and will accelerate a fundamental understanding of complex microbial ecosystems.

Citation: Xue Z, Marco M. 2019. Milk and Dairy Products, p 103-123. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch5
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Figure 5.1

Sources and factors influencing milk and dairy product microbial composition, as well as genomics-based methods for determining microbiological variation in dairy products.

Citation: Xue Z, Marco M. 2019. Milk and Dairy Products, p 103-123. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch5
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Image of Figure 5.2
Figure 5.2

Steps in cheese manufacturing with the greatest influence on microbial populations.

Citation: Xue Z, Marco M. 2019. Milk and Dairy Products, p 103-123. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch5
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References

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1. Walsh AM, Crispie F, Claesson MJ, Cotter PD . 2017. Translating omics to food microbiology. Annu Rev Food Sci Technol 8 : 113 134[CrossRef].[PubMed]
2. O'Flaherty S, Klaenhammer TR . 2011. The impact of omic technologies on the study of food microbes. Annu Rev Food Sci Technol 2 : 353 371[CrossRef].[PubMed]
3. Mardis ER . 2017. DNA sequencing technologies: 2006–2016. Nat Protoc 12 : 213 218[CrossRef].[PubMed]
4. Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A . 2001. The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res 11 : 731 753[CrossRef].[PubMed]
5. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P . 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315 : 1709 1712[CrossRef].[PubMed]
6. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ . 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci USA 103 : 12115 12120[CrossRef].[PubMed]
7. Downes A . 1879. Diphtheria and milk-supply. BMJ 1 : 148[CrossRef].[PubMed]
8. Oglesby RP . 1880. Typhoid fever and milk. BMJ 1 : 89 90[CrossRef].[PubMed]
9. United States Department of Agriculture . 2017. Dairy: world markets and trade. https://www.fas.usda.gov/data/dairy-world-markets-and-trade. Accessed 28 September 2017.
10. Vacheyrou M, Normand AC, Guyot P, Cassagne C, Piarroux R, Bouton Y . 2011. Cultivable microbial communities in raw cow milk and potential transfers from stables of sixteen French farms. Int J Food Microbiol 146 : 253 262[CrossRef].[PubMed]
11. Zucali M, Bava L, Colombini S, Brasca M, Decimo M, Morandi S, Tamburini A, Crovetto GM . 2015. Management practices and forage quality affecting the contamination of milk with anaerobic spore-forming bacteria. J Sci Food Agric 95 : 1294 1302[CrossRef].[PubMed]
12. Vissers MM, Driehuis F, Te Giffel MC, De Jong P, Lankveld JM . 2007. Quantification of the transmission of microorganisms to milk via dirt attached to the exterior of teats. J Dairy Sci 90 : 3579 3582[CrossRef].[PubMed]
13. Miller RA, Kent DJ, Boor KJ, Martin NH, Wiedmann M . 2015. Different management practices are associated with mesophilic and thermophilic spore levels in bulk tank raw milk. J Dairy Sci 98 : 4338 4351[CrossRef].[PubMed]
14. Garnier L, Valence F, Pawtowski A, Auhustsinava-Galerne L, Frotté N, Baroncelli R, Deniel F, Coton E, Mounier J . 2017. Diversity of spoilage fungi associated with various French dairy products. Int J Food Microbiol 241 : 191 197[CrossRef].[PubMed]
15. Monsallier F, Verdier-Metz I, Agabriel C, Martin B, Montel MC . 2012. Variability of microbial teat skin flora in relation to farming practices and individual dairy cow characteristics. Dairy Sci Technol 92 : 265 278[CrossRef].
16. Verdier-Metz I, Gagne G, Bornes S, Monsallier F, Veisseire P, Delbès-Paus C, Montel MC . 2012. Cow teat skin, a potential source of diverse microbial populations for cheese production. Appl Environ Microbiol 78 : 326 333[CrossRef].[PubMed]
17. Doyle CJ, Gleeson D, O'Toole PW, Cotter PD . 2016. Impacts of seasonal housing and teat preparation on raw milk microbiota: a high-throughput sequencing study. Appl Environ Microbiol 83 : e02694-16.[PubMed]
18. Addis MF, Tanca A, Uzzau S, Oikonomou G, Bicalho RC, Moroni P . 2016. The bovine milk microbiota: insights and perspectives from -omics studies. Mol Biosyst 12 : 2359 2372[CrossRef].[PubMed]
19. Rainard P . 2017. Mammary microbiota of dairy ruminants: fact or fiction? Vet Res (Faisalabad) 48 : 25[CrossRef].[PubMed]
20. Young W, Hine BC, Wallace OAM, Callaghan M, Bibiloni R . 2015. Transfer of intestinal bacterial components to mammary secretions in the cow. PeerJ 3 : e888[CrossRef].[PubMed]
21. Bhatt VD, Ahir VB, Koringa PG, Jakhesara SJ, Rank DN, Nauriyal DS, Kunjadia AP, Joshi CG . 2012. Milk microbiome signatures of subclinical mastitis-affected cattle analysed by shotgun sequencing. J Appl Microbiol 112 : 639 650[CrossRef].[PubMed]
22. Dolci P, De Filippis F, La Storia A, Ercolini D, Cocolin L . 2014. rRNA-based monitoring of the microbiota involved in Fontina PDO cheese production in relation to different stages of cow lactation. Int J Food Microbiol 185 : 127 135[CrossRef].[PubMed]
23. Doyle CJ, Gleeson D, O'Toole PW, Cotter PD . 2017. High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions. Int J Food Microbiol 255 : 1 6[CrossRef].[PubMed]
24. O'Connell A, McParland S, Ruegg PL, O'Brien B, Gleeson D . 2015. Seasonal trends in milk quality in Ireland between 2007 and 2011. J Dairy Sci 98 : 3778 3790.[PubMed]
25. Kuehn JS, Gorden PJ, Munro D, Rong R, Dong Q, Plummer PJ, Wang C, Phillips GJ . 2013. Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis. PLoS One 8 : e61959[CrossRef].[PubMed]
26. Oikonomou G, Bicalho ML, Meira E, Rossi RE, Foditsch C, Machado VS, Teixeira AG, Santisteban C, Schukken YH, Bicalho RC . 2014. Microbiota of cow's milk; distinguishing healthy, sub-clinically and clinically diseased quarters. PLoS One 9 : e85904[CrossRef].[PubMed]
27. Rodrigues MX, Lima SF, Canniatti-Brazaca SG, Bicalho RC . 2017. The microbiome of bulk tank milk: characterization and associations with somatic cell count and bacterial count. J Dairy Sci 100 : 2536 2552[CrossRef].[PubMed]
28. Falentin H, Rault L, Nicolas A, Bouchard DS, Lassalas J, Lamberton P, Aubry JM, Marnet PG, Le Loir Y, Even S . 2016. Bovine teat microbiome analysis revealed reduced alpha diversity and significant changes in taxonomic profiles in quarters with a history of mastitis. Front Microbiol 7 : 480[CrossRef].[PubMed]
29. Ganda EK, Bisinotto RS, Lima SF, Kronauer K, Decter DH, Oikonomou G, Schukken YH, Bicalho RC . 2016. Longitudinal metagenomic profiling of bovine milk to assess the impact of intramammary treatment using a third-generation cephalosporin. Sci Rep 6 : 37565[CrossRef].[PubMed]
30. Ganda EK, Gaeta N, Sipka A, Pomeroy B, Oikonomou G, Schukken YH, Bicalho RC . 2017. Normal milk microbiome is reestablished following experimental infection with Escherichia coli independent of intramammary antibiotic treatment with a third-generation cephalosporin in bovines. Microbiome 5 : 74[CrossRef].[PubMed]
31. Zhang R, Huo W, Zhu W, Mao S . 2015. Characterization of bacterial community of raw milk from dairy cows during subacute ruminal acidosis challenge by high-throughput sequencing. J Sci Food Agric 95 : 1072 1079[CrossRef].[PubMed]
32. Kable ME, Srisengfa Y, Laird M, Zaragoza J, McLeod J, Heidenreich J, Marco ML . 2016. The core and seasonal microbiota of raw bovine milk in tanker trucks and the impact of transfer to a milk processing facility. mBio 7 : e00836-16[CrossRef].[PubMed]
33. Aldrete-Tapia A, Escobar-Ramírez MC, Tamplin ML, Hernández-Iturriaga M . 2014. High-throughput sequencing of microbial communities in Poro cheese, an artisanal Mexican cheese. Food Microbiol 44 : 136 141[CrossRef].[PubMed]
34. Raats D, Offek M, Minz D, Halpern M . 2011. Molecular analysis of bacterial communities in raw cow milk and the impact of refrigeration on its structure and dynamics. Food Microbiol 28 : 465 471[CrossRef].[PubMed]
35. Fricker M, Skånseng B, Rudi K, Stessl B, Ehling-Schulz M . 2011. Shift from farm to dairy tank milk microbiota revealed by a polyphasic approach is independent from geographical origin. Int J Food Microbiol 145( Suppl 1) : S24 S30[CrossRef].[PubMed]
36. Hantsis-Zacharov E, Halpern M . 2007. Culturable psychrotrophic bacterial communities in raw milk and their proteolytic and lipolytic traits. Appl Environ Microbiol 73 : 7162 7168[CrossRef].[PubMed]
37. Weisbecker A . 2007. A legal history of raw milk in the United States. J Environ Health 69 : 62 63.[PubMed]
38. Bradley J, Pickering LK, Jereb J . 2008. Advise families against giving children unpasteurized milk. AAP News 29: 29 30.
39. Codex Alimentarius . 2004. Code of hygienic practice for milk and milk products. CAC/RCP 57-2004. World Health Organization, Geneva, Switzerland.
40. 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 cheeses. Appl Environ Microbiol 78 : 5717 5723[CrossRef].[PubMed]
41. Hotchkiss JH, Werner BG, Lee EYC . 2006. Addition of carbon dioxide to dairy products to improve quality: a comprehensive review. Compr Rev Food Sci Food Saf 5 : 158 168[CrossRef].
42. Lo R, Turner MS, Weeks M, Bansal N . 2016. Culture-independent bacterial community profiling of carbon dioxide treated raw milk. Int J Food Microbiol 233 : 81 89[CrossRef].[PubMed]
43. Skapetas B, Bampidis V . 2016. Goat production in the world: present situation and trends. Livest Res Rural Dev 18 : 725.
44. Ribeiro AC, Ribeiro SDA . 2010. Specialty products made from goat milk. Small Rumin Res 89 : 225 233[CrossRef].
45. Tsakalidou E . 2012. Microbiota of goat's milk and goat's milk cheese, p 39 42. In Proceedings of the First Asia Dairy Goat Conference.
46. McInnis EA, Kalanetra KM, Mills DA, Maga EA . 2015. Analysis of raw goat milk microbiota: impact of stage of lactation and lysozyme on microbial diversity. Food Microbiol 46 : 121 131[CrossRef].[PubMed]
47. Li L, Renye JA Jr, Feng L, Zeng Q, Tang Y, Huang L, Ren D, Yang P . 2016. Characterization of the indigenous microflora in raw and pasteurized buffalo milk during storage at refrigeration temperature by high-throughput sequencing. J Dairy Sci 99 : 7016 7024[CrossRef].[PubMed]
48. Catozzi C, Sanchez Bonastre A, Francino O, Lecchi C, De Carlo E, Vecchio D, Martucciello A, Fraulo P, Bronzo V, Cuscó A, D'Andreano S, Ceciliani F . 2017. The microbiota of water buffalo milk during mastitis. PLoS One 12 : e0184710[CrossRef].[PubMed]
49. Ercolini D, De Filippis F, La Storia A, Iacono M . 2012. “Remake” by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese. Appl Environ Microbiol 78 : 8142 8145[CrossRef].[PubMed]
50. Guo HY, Pang K, Zhang XY, Zhao L, Chen SW, Dong ML, Ren FZ . 2007. Composition, physiochemical properties, nitrogen fraction distribution, and amino acid profile of donkey milk. J Dairy Sci 90 : 1635 1643[CrossRef].[PubMed]
51. Salimei E, Fantuz F . 2012. Equid milk for human consumption. Int Dairy J 24 : 130 142[CrossRef].
52. Soto del Rio MLD, Dalmasso A, Civera T, Bottero MT . 2017. Characterization of bacterial communities of donkey milk by high-throughput sequencing. Int J Food Microbiol 251 : 67 72[CrossRef].[PubMed]
53. Li Z, Wright AG, Yang Y, Si H, Li G . 2017. Unique bacteria community composition and co-occurrence in the milk of different ruminants. Sci Rep 7 : 40950[CrossRef].[PubMed]
54. Salque M, Bogucki PI, Pyzel J, Sobkowiak-Tabaka I, Grygiel R, Szmyt M, Evershed RP . 2013. Earliest evidence for cheese making in the sixth millennium BC in northern Europe. Nature 493 : 522 525[CrossRef].[PubMed]
55. Fox PF, Guinee TP, Cogan TM, McSweeney PLH . 2017. Fundamentals of Cheese Science, 2nd ed, p 27 69. Springer, Boston, MA.
56. Albus WR . 1928. A strain of Clostridium welchii causing abnormal gassy fermentations in Emmenthal or Swiss cheese. J Bacteriol 15 : 203 206.[PubMed]
57. Fox PF, Guinee TP, Cogan TM, McSweeney PLH . 2017. Fundamentals of Cheese Science, 2nd ed, p 11 25. Springer, Boston, MA.
58. Delcenserie V, Taminiau B, Delhalle L, Nezer C, Doyen P, Crevecoeur S, Roussey D, Korsak N, Daube G . 2014. Microbiota characterization of a Belgian protected designation of origin cheese, Herve cheese, using metagenomic analysis. J Dairy Sci 97 : 6046 6056[CrossRef].[PubMed]
59. Wolfe BE, Button JE, Santarelli M, Dutton RJ . 2014. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158 : 422 433[CrossRef].[PubMed]
60. Fox PF, Guinee TP, Cogan TM, McSweeney PLH . 2017. Fundamentals of Cheese Science, 2nd ed, p 121 183. Springer, Boston, MA.
61. Alessandria V, Ferrocino I, De Filippis F, Fontana M, Rantsiou K, Ercolini D, Cocolin L . 2016. Microbiota of an Italian Grana-like cheese during manufacture and ripening, unraveled by 16S rRNA-based approaches. Appl Environ Microbiol 82 : 3988 3995[CrossRef].[PubMed]
62. Parente E, Guidone A, Matera A, De Filippis F, Mauriello G, Ricciardi A . 2016. Microbial community dynamics in thermophilic undefined milk starter cultures. Int J Food Microbiol 217 : 59 67[CrossRef].[PubMed]
63. Erkus O, de Jager VC, Spus M, van Alen-Boerrigter IJ, van Rijswijck IM, Hazelwood L, Janssen PW, van Hijum SA, Kleerebezem M, Smid EJ . 2013. Multifactorial diversity sustains microbial community stability. ISME J 7 : 2126 2136[CrossRef].[PubMed]
64. Frantzen CA, Kot W, Pedersen TB, Ardö YM, Broadbent JR, Neve H, Hansen LH, Dal Bello F, Østlie HM, Kleppen HP, Vogensen FK, Holo H . 2017. Genomic characterization of dairy associated Leuconostoc species and diversity of Leuconostocs in undefined mixed mesophilic starter cultures. Front Microbiol 8 : 132[CrossRef].[PubMed]
65. Masoud W, Vogensen FK, Lillevang S, Abu Al-Soud W, Sørensen SJ, Jakobsen M . 2012. The fate of indigenous microbiota, starter cultures, Escherichia coli, Listeria innocua and Staphylococcus aureus in Danish raw milk and cheeses determined by pyrosequencing and quantitative real time (qRT)-PCR. Int J Food Microbiol 153 : 192 202[CrossRef].[PubMed]
66. De Pasquale I, Di Cagno R, Buchin S, De Angelis M, Gobbetti M . 2014. Microbial ecology dynamics reveal a succession in the core microbiota involved in the ripening of pasta filata caciocavallo pugliese cheese. Appl Environ Microbiol 80 : 6243 6255[CrossRef].[PubMed]
67. Masoud W, Takamiya M, Vogensen FK, Lillevang S, Al-Soud WA, Sørensen SJ, Jakobsen M . 2011. Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing. Int Dairy J 21 : 142 148[CrossRef].
68. Johansen P, Vindeløv J, Arneborg N, Brockmann E . 2014. Development of quantitative PCR and metagenomics-based approaches for strain quantification of a defined mixed-strain starter culture. Syst Appl Microbiol 37 : 186 193[CrossRef].[PubMed]
69. Smid EJ, Erkus O, Spus M, Wolkers-Rooijackers JCM, Alexeeva S, Kleerebezem M . 2014. Functional implications of the microbial community structure of undefined mesophilic starter cultures. Microb Cell Fact 13( Suppl 1) : S2[CrossRef].[PubMed]
70. de Vos WM . 2011. Systems solutions by lactic acid bacteria: from paradigms to practice. Microb Cell Fact 10( Suppl 1) : S2[CrossRef].[PubMed]
71. Spus M, Li M, Alexeeva S, Wolkers-Rooijackers JC, Zwietering MH, Abee T, Smid EJ . 2015. Strain diversity and phage resistance in complex dairy starter cultures. J Dairy Sci 98 : 5173 5182[CrossRef].[PubMed]
72. Gobbetti M, De Angelis M, Di Cagno R, Mancini L, Fox PF . 2015. Pros and cons for using non-starter lactic acid bacteria (NSLAB) as secondary/adjunct starters for cheese ripening. Trends Food Sci Technol 45 : 167 178[CrossRef].
73. De Filippis F, Genovese A, Ferranti P, Gilbert JA, Ercolini D . 2016. Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Sci Rep 6 : 21871[CrossRef].[PubMed]
74. Burns P, Cuffia F, Milesi M, Vinderola G, Meinardi C, Sabbag N, Hynes E . 2012. Technological and probiotic role of adjunct cultures of non-starter lactobacilli in soft cheeses. Food Microbiol 30 : 45 50[CrossRef].[PubMed]
75. Pino A, Van Hoorde K, Pitino I, Russo N, Carpino S, Caggia C, Randazzo CL . 2017. Survival of potential probiotic lactobacilli used as adjunct cultures on Pecorino Siciliano cheese ripening and passage through the gastrointestinal tract of healthy volunteers. Int J Food Microbiol 252 : 42 52[CrossRef].[PubMed]
76. Barrangou R, Horvath P, . 2011. Lactic acid bacteria defenses against phages, p 459 478. In Tsakalidou E, Papadimitriou K (ed), Stress Responses of Lactic Acid Bacteria. Springer, Boston, MA.[CrossRef]
77. Szczepankowska AK, Górecki RK, Kołakowski P, Bardowski JK, . 2013. Lactic acid bacteria resistance to bacteriophage and prevention techniques to lower phage contamination in dairy fermentation. In Kongo M (ed), Lactic Acid Bacteria, R & D for Food, Health and Livestock Purposes. Intech Open, London, UK.[CrossRef]
78. Marcó MB, Moineau S, Quiberoni A . 2012. Bacteriophages and dairy fermentations. Bacteriophage 2 : 149 158[CrossRef].[PubMed]
79. Garneau JE, Moineau S . 2011. Bacteriophages of lactic acid bacteria and their impact on milk fermentations. Microb Cell Fact 10( Suppl 1) : S20[CrossRef].[PubMed]
80. Winter C, Bouvier T, Weinbauer MG, Thingstad TF . 2010. Trade-offs between competition and defense specialists among unicellular planktonic organisms: the “killing the winner” hypothesis revisited. Microbiol Mol Biol Rev 74 : 42 57[CrossRef].[PubMed]
81. Muhammed MK, Kot W, Neve H, Mahony J, Castro-Mejía JL, Krych L, Hansen LH, Nielsen DS, Sørensen SJ, Heller KJ, van Sinderen D, Vogensen FK . 2017. Metagenomic analysis of dairy bacteriophages: extraction method and pilot study on whey samples derived from using undefined and defined mesophilic starter cultures. Appl Environ Microbiol 83 : e00888-17[CrossRef].[PubMed]
82. Guidone A, Zotta T, Matera A, Ricciardi A, De Filippis F, Ercolini D, Parente E . 2016. The microbiota of high-moisture mozzarella cheese produced with different acidification methods. Int J Food Microbiol 216 : 9 17[CrossRef].[PubMed]
83. Faccia M, Trani A, Di Luccia A . 2009. Short communication: relationships between milk quality and acidification in the production of table Mozzarella without starters. J Dairy Sci 92 : 4211 4217[CrossRef].[PubMed]
84. Fox PF, Guinee TP, Cogan TM, McSweeney PLH . 2017. Fundamentals of Cheese Science, 2nd ed, p 1 10. Springer, Boston, MA.
85. Cardinali F, Osimani A, Taccari M, Milanović V, Garofalo C, Clementi F, Polverigiani S, Zitti S, Raffaelli N, Mozzon M, Foligni R, Franciosi E, Tuohy K, Aquilanti L . 2017. Impact of thistle rennet from Carlina acanthifolia All. subsp. acanthifolia on bacterial diversity and dynamics of a specialty Italian raw ewes’ milk cheese. Int J Food Microbiol 255 : 7 16[CrossRef].[PubMed]
86. Bokulich NA, Mills DA . 2013. Facility-specific “house” microbiome drives microbial landscapes of artisan cheesemaking plants. Appl Environ Microbiol 79 : 5214 5223[CrossRef].[PubMed]
87. Erkus O, de Jager VCL, Geene RT, van Alen-Boerrigter I, Hazelwood L, van Hijum SA, Kleerebezem M, Smid EJ . 2016. Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening. Int J Food Microbiol 228 : 1 9[CrossRef].[PubMed]
88. Stellato G, De Filippis F, La Storia A, Ercolini D . 2015. Coexistence of lactic acid bacteria and potential spoilage microbiota in a dairy processing environment. Appl Environ Microbiol 81 : 7893 7904[CrossRef].[PubMed]
89. Calasso M, Ercolini D, Mancini L, Stellato G, Minervini F, Di Cagno R, De Angelis M, Gobbetti M . 2016. Relationships among house, rind and core microbiotas during manufacture of traditional Italian cheeses at the same dairy plant. Food Microbiol 54 : 115 126[CrossRef].
90. Schön K, Schornsteiner E, Dzieciol M, Wagner M, Müller M, Schmitz-Esser S . 2016. Microbial communities in dairy processing environment floor-drains are dominated by product-associated bacteria and yeasts. Food Control 70 : 210 215[CrossRef].
91. O'Sullivan DJ, Cotter PD, O'Sullivan O, Giblin L, McSweeney PLH, Sheehan JJ . 2015. Temporal and spatial differences in microbial composition during the manufacture of a continental-type cheese. Appl Environ Microbiol 81 : 2525 2533[CrossRef].[PubMed]
92. Riquelme C, Câmara S, Dapkevicius ML, Vinuesa P, da Silva CCG, Malcata FX, Rego OA . 2015. Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food). Int J Food Microbiol 192 : 86 94[CrossRef].[PubMed]
93. Monnet C, Dugat-Bony E, Swennen D, Beckerich JM, Irlinger F, Fraud S, Bonnarme P . 2016. Investigation of the activity of the microorganisms in a Reblochon-style cheese by metatranscriptomic analysis. Front Microbiol 7 : 536[CrossRef].[PubMed]
94. Dugat-Bony E, Garnier L, Denonfoux J, Ferreira S, Sarthou AS, Bonnarme P, Irlinger F . 2016. Highlighting the microbial diversity of 12 French cheese varieties. Int J Food Microbiol 238 : 265 273[CrossRef].[PubMed]
95. Fox PF, Guinee TP, Cogan TM, McSweeney PLH . 2017. Fundamentals of Cheese Science, 2nd ed, p 333 390. Springer, Boston, MA.
96. Levante A, De Filippis F, La Storia A, Gatti M, Neviani E, Ercolini D, Lazzi C . 2017. Metabolic gene-targeted monitoring of non-starter lactic acid bacteria during cheese ripening. Int J Food Microbiol 257 : 276 284[CrossRef].[PubMed]
97. Escobar-Zepeda A, Sanchez-Flores A, Quirasco Baruch M . 2016. Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota. Food Microbiol 57 : 116 127[CrossRef].[PubMed]
98. Porcellato D, Skeie SB . 2016. Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese. Int Dairy J 61 : 182 188[CrossRef].
99. Dugat-Bony E, Straub C, Teissandier A, Onésime D, Loux V, Monnet C, Irlinger F, Landaud S, Leclercq-Perlat MN, Bento P, Fraud S, Gibrat JF, Aubert J, Fer F, Guédon E, Pons N, Kennedy S, Beckerich JM, Swennen D, Bonnarme P . 2015. Overview of a surface-ripened cheese community functioning by meta-omics analyses. PLoS One 10 : e0124360[CrossRef].[PubMed]
100. Lessard MH, Viel C, Boyle B, St-Gelais D, Labrie S . 2014. Metatranscriptome analysis of fungal strains Penicillium camemberti and Geotrichum candidum reveal cheese matrix breakdown and potential development of sensory properties of ripened Camembert-type cheese. BMC Genomics 15 : 235[CrossRef].[PubMed]
101. 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. Appl Environ Microbiol 78 : 1890 1898[CrossRef].[PubMed]
102. Fuka MM, Wallisch S, Engel M, Welzl G, Havranek J, Schloter M . 2013. Dynamics of bacterial communities during the ripening process of different Croatian cheese types derived from raw ewe's milk cheeses. PLoS One 8 : e80734[CrossRef].[PubMed]
103. De Pasquale I, Calasso M, Mancini L, Ercolini D, La Storia A, De Angelis M, Di Cagno R, Gobbetti M . 2014. Causal relationship between microbial ecology dynamics and proteolysis during manufacture and ripening of protected designation of origin (PDO) cheese Canestrato Pugliese. Appl Environ Microbiol 80 : 4085 4094[CrossRef].[PubMed]
104. Puniya A, Kumar S, Puniya M, Malik R, . 2017. Fermented milk and dairy products: an overview, p 3 24. In Puniya AK (ed), Fermented Milk and Dairy Products. CRC Press, Boca Raton, FL.
105. Lopitz-Otsoa F, Rementeria A, Elguezabal N, Garaizar J . 2006. Kefir: a symbiotic yeasts-bacteria community with alleged healthy capabilities. Rev Iberoam Micol 23 : 67 74[CrossRef].[PubMed]
106. Guzel-Seydim ZB, Kok-Tas T, Greene AK, Seydim AC . 2011. Review: functional properties of kefir. Crit Rev Food Sci Nutr 51 : 261 268[CrossRef].[PubMed]
107. Bourrie BC, Willing BP, Cotter PD . 2016. The microbiota and health promoting characteristics of the fermented beverage kefir. Front Microbiol 7 : 647[CrossRef].[PubMed]
108. Rosa DD, Dias MMS, Grześkowiak LM, Reis SA, Conceição LL, Peluzio MDCG . 2017. Milk kefir: nutritional, microbiological and health benefits. Nutr Res Rev 30 : 82 96[CrossRef].[PubMed]
109. Witthuhn RC, Schoeman T, Britz TJ . 2005. Characterisation of the microbial population at different stages of kefir production and kefir grain mass cultivation. Int Dairy J 15 : 383 389[CrossRef].
110. Kesmen Z, Kacmaz N . 2011. Determination of lactic microflora of kefir grains and kefir beverage by using culture-dependent and culture-independent methods. J Food Sci 76 : M276 M283[CrossRef].[PubMed]
111. Leite AM, Leite DC, Del Aguila EM, Alvares TS, Peixoto RS, Miguel MA, Silva JT, Paschoalin VM . 2013. Microbiological and chemical characteristics of Brazilian kefir during fermentation and storage processes. J Dairy Sci 96 : 4149 4159[CrossRef].[PubMed]
112. Diosma G, Romanin DE, Rey-Burusco MF, Londero A, Garrote GL . 2014. Yeasts from kefir grains: isolation, identification, and probiotic characterization. World J Microbiol Biotechnol 30 : 43 53[CrossRef].[PubMed]
113. Zanirati DF, Abatemarco M Jr, Sandes SHC, Nicoli JR, Nunes AC, Neumann E . 2015. Selection of lactic acid bacteria from Brazilian kefir grains for potential use as starter or probiotic cultures. Anaerobe 32 : 70 76[CrossRef].[PubMed]
114. Dobson A, O'Sullivan O, Cotter PD, Ross P, Hill C . 2011. High-throughput sequence-based analysis of the bacterial composition of kefir and an associated kefir grain. FEMS Microbiol Lett 320 : 56 62[CrossRef].[PubMed]
115. Marsh AJ, O'Sullivan O, Hill C, Ross RP, Cotter PD . 2013. Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources. PLoS One 8 : e69371[CrossRef].[PubMed]
116. Nalbantoglu U, Cakar A, Dogan H, Abaci N, Ustek D, Sayood K, Can H . 2014. Metagenomic analysis of the microbial community in kefir grains. Food Microbiol 41 : 42 51[CrossRef].[PubMed]
117. Leite AMO, Mayo B, Rachid CT, 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 Microbiol 31 : 215 221[CrossRef].[PubMed]
118. Garofalo C, Osimani A, Milanović V, Aquilanti L, De Filippis F, Stellato G, Di Mauro S, Turchetti B, Buzzini P, Ercolini D, Clementi F . 2015. Bacteria and yeast microbiota in milk kefir grains from different Italian regions. Food Microbiol 49 : 123 133[CrossRef].[PubMed]
119. Korsak N, Taminiau B, Leclercq M, Nezer C, Crevecoeur S, Ferauche C, Detry E, Delcenserie V, Daube G . 2015. Short communication: evaluation of the microbiota of kefir samples using metagenetic analysis targeting the 16S and 26S ribosomal DNA fragments. J Dairy Sci 98 : 3684 3689[CrossRef].[PubMed]
120. Walsh AM, Crispie F, Kilcawley K, O'Sullivan O, O'Sullivan MG, Claesson MJ, Cotter PD . 2016. Microbial succession and flavor production in the fermented dairy beverage kefir. mSystems 1 : e00052-16[CrossRef].[PubMed]
121. Zamberi NR, Mohamad NE, Yeap SK, Ky H, Beh BK, Liew WC, Tan SW, Ho WY, Boo SY, Chua YH, Alitheen NB . 2016. 16S metagenomic microbial composition analysis of kefir grain using MEGAN and BaseSpace. Food Biotechnol 30 : 219 230[CrossRef].
122. Zhong Z, Hou Q, Kwok L, Yu Z, Zheng Y, Sun Z, Menghe B, Zhang H . 2016. Bacterial microbiota compositions of naturally fermented milk are shaped by both geographic origin and sample type. J Dairy Sci 99 : 7832 7841[CrossRef].[PubMed]
123. Oki K, Dugersuren J, Demberel S, Watanabe K . 2014. Pyrosequencing analysis of the microbial diversity of airag, khoormog and tarag, traditional fermented dairy products of Mongolia. Biosci Microbiota Food Health 33 : 53 64[CrossRef].[PubMed]
124. Liu W, Zheng Y, Kwok LY, Sun Z, Zhang J, Guo Z, Hou Q, Menhe B, Zhang H . 2015. High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow's milk in Russia. BMC Microbiol 15 : 45[CrossRef].[PubMed]
125. Bokulich NA, Amiranashvili L, Chitchyan K, Ghazanchyan N, Darbinyan K, Gagelidze N, Sadunishvili T, Goginyan V, Kvesitadze G, Torok T, Mills DA . 2015. Microbial biogeography of the transnational fermented milk matsoni. Food Microbiol 50 : 12 19[CrossRef].[PubMed]
126. Béal C, Helinck S, . 2014. Yogurt and other fermented milks, p 141 187. In Ray RC, Montet D (ed), Microorganisms and Fermentation of Traditional Foods. CRC Press, Boca Raton, FL.
127. Sieuwerts S, de Bok FA, Hugenholtz J, van Hylckama Vlieg JE . 2008. Unraveling microbial interactions in food fermentations: from classical to genomics approaches. Appl Environ Microbiol 74 : 4997 5007[CrossRef].[PubMed]
128. Bisanz JE, Macklaim JM, Gloor GB, Reid G . 2014. Bacterial metatranscriptome analysis of a probiotic yogurt using an RNA-Seq approach. Int Dairy J 39 : 284 292[CrossRef].
129. Sieuwerts S, Molenaar D, van Hijum SA, Beerthuyzen M, Stevens MJA, Janssen PWM, Ingham CJ, de Bok FAM, de Vos WM, van Hylckama Vlieg JE . 2010. Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus. Appl Environ Microbiol 76 : 7775 7784[CrossRef].[PubMed]
130. Hao P, Zheng H, Yu Y, Ding G, Gu W, Chen S, Yu Z, Ren S, Oda M, Konno T, Wang S, Li X, Ji ZS, Zhao G . 2011. Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production. PLoS One 6 : e15964[CrossRef].[PubMed]
131. Settachaimongkon S, Nout MJ, Antunes Fernandes EC, Hettinga KA, Vervoort JM, van Hooijdonk TC, Zwietering MH, Smid EJ, van Valenberg HJ . 2014. Influence of different proteolytic strains of Streptococcus thermophilus in co-culture with Lactobacillus delbrueckii subsp. bulgaricus on the metabolite profile of set-yoghurt. Int J Food Microbiol 177 : 29 36[CrossRef].[PubMed]
132. Akabanda F, Owusu-Kwarteng J, Tano-Debrah K, Glover RL, Nielsen DS, Jespersen L . 2013. Taxonomic and molecular characterization of lactic acid bacteria and yeasts in nunu, a Ghanaian fermented milk product. Food Microbiol 34 : 277 283[CrossRef].[PubMed]
133. Uchida K, Hirata M, Motoshima H, Urashima T, Arai I . 2007. Microbiota of ‘airag’, ‘tarag’ and other kinds of fermented dairy products from nomad in Mongolia. Anim Sci J 78 : 650 658[CrossRef].
134. Sun Z, Liu W, Bao Q, Zhang J, Hou Q, Kwok L, Sun T, Zhang H . 2014. Investigation of bacterial and fungal diversity in tarag using high-throughput sequencing. J Dairy Sci 97 : 6085 6096[CrossRef].[PubMed]
135. Olsen SL, . 2006. Early horse domestication on the Eurasian steppe, p 245 272. In Zeder MA, Bradley DG, Emshwiller E, Smith BD, Bradley D (ed), Documenting Domestication: New Genetic and Archaeological Paradigms. University of California Press, Berkeley, CA.
136. Yao G, Yu J, Hou Q, Hui W, Liu W, Kwok LY, Menghe B, Sun T, Zhang H, Zhang W . 2017. A perspective study of koumiss microbiome by metagenomics analysis based on single-cell amplification technique. Front Microbiol 8 : 165[CrossRef].[PubMed]
137. Vedamuthu ER, . 2013. Other fermented and culture-containing milks, p 393 410. In Chandan RC, Kilara A (ed), Manufacturing Yogurt and Fermented Milks, 2nd ed. John Wiley & Sons, Hoboken, NJ.[CrossRef]
138. Liu WJ, Xi XX, Sudu QG, Kwok LY, Guo Z, Hou QC, Menhe B, Sun TS, Zhang HP . 2015. High-throughput sequencing reveals microbial community diversity of Tibetan naturally fermented yak milk. Ann Microbiol 65 : 1741 1751[CrossRef].
139. Quigley L, O'Sullivan DJ, Daly D, O'Sullivan O, Burdikova Z, Vana R, Beresford TP, Ross RP, Fitzgerald GF, McSweeney PL, Giblin L, Sheehan JJ, Cotter PD . 2016. Thermus and the pink discoloration defect in cheese. mSystems 1 : e00023-16[CrossRef].[PubMed]
140. Guzzon R, Carafa I, Tuohy K, Cervantes G, Vernetti L, Barmaz A, Larcher R, Franciosi E . 2017. Exploring the microbiota of the red-brown defect in smear-ripened cheese by 454-pyrosequencing and its prevention using different cleaning systems. Food Microbiol 62 : 160 168[CrossRef].[PubMed]
141. Brooks BW, Barnum DA . 1984. Characterization of strains of Corynebacterium bovis. Can J Comp Med 48 : 230 232.[PubMed]
142. Taponen S, Liski E, Heikkilä AM, Pyörälä S . 2017. Factors associated with intramammary infection in dairy cows caused by coagulase-negative staphylococci, Staphylococcus aureus, Streptococcus uberis, Streptococcus dysgalactiae, Corynebacterium bovis, or Escherichia coli. J Dairy Sci 100 : 493 503[CrossRef].[PubMed]
143. Weber M, Geißert J, Kruse M, Lipski A . 2014. Comparative analysis of bacterial community composition in bulk tank raw milk by culture-dependent and culture-independent methods using the viability dye propidium monoazide. J Dairy Sci 97 : 6761 6776[CrossRef].[PubMed]
144. Storms V, Devriese LA, Coopman R, Schumann P, Vyncke F, Gillis M . 2003. Arthrobacter gandavensis sp. nov., for strains of veterinary origin. Int J Syst Evol Microbiol 53 : 1881 1884[CrossRef].[PubMed]
145. Styková E, Nemcová R, Gancarčíková S, Valocký I, Lauková A . 2016. Bovine vaginal strain Kocuria kristinae and its characterization. Folia Microbiol (Praha) 61 : 243 248[CrossRef].[PubMed]
146. Feng Z, Huang S, Ai ZW, Zhang M, Zhai S, Chen X . 2016. Evaluation of autochthonous Micrococcus strains as starter cultures for the production of Kedong sufu. J Appl Microbiol 120 : 671 683[CrossRef].[PubMed]
147. Koniarova I . 1993. Some biochemical and physiological characteristics of Propionibacterium acnes strains isolated from the rumen of calves and lambs. Vet Med 38 : 43 52. [In Slovak.][PubMed]
148. Quigley L, McCarthy R, O'Sullivan O, Beresford TP, Fitzgerald GF, Ross RP, Stanton C, Cotter PD . 2013. The microbial content of raw and pasteurized cow milk as determined by molecular approaches. J Dairy Sci 96 : 4928 4937[CrossRef].[PubMed]
149. Wallace RJ, McKain N, Broderick GA, Rode LM, Walker ND, Newbold CJ, Kopecny J . 1997. Peptidases of the rumen bacterium, Prevotella ruminicola. Anaerobe 3 : 35 42[CrossRef].[PubMed]
150. Sánchez-Porro C, Martín S, Mellado E, Ventosa A . 2003. Diversity of moderately halophilic bacteria producing extracellular hydrolytic enzymes. J Appl Microbiol 94 : 295 300[CrossRef].[PubMed]
151. Kopit LM, Kim EB, Siezen RJ, Harris LJ, Marco ML . 2014. Safety of the surrogate microorganism Enterococcus faecium NRRL B-2354 for use in thermal process validation. Appl Environ Microbiol 80 : 1899 1909[CrossRef].[PubMed]
152. Franz CM, Holzapfel WH, Stiles ME . 1999. Enterococci at the crossroads of food safety? Int J Food Microbiol 47 : 1 24[CrossRef].[PubMed]
153. Quigley L, O'Sullivan O, Beresford TP, Paul Ross R, Fitzgerald GF, Cotter PD . 2012. A comparison of methods used to extract bacterial DNA from raw milk and raw milk cheese. J Appl Microbiol 113 : 96 105[CrossRef].[PubMed]
154. Lee J, Jang YS, Han MJ, Kim JY, Lee SY . 2016. Deciphering Clostridium tyrobutyricum metabolism based on the whole-genome sequence and proteome analyses. mBio 7 : e00743-16[CrossRef].[PubMed]
155. Paz HA, Anderson CL, Muller MJ, Kononoff PJ, Fernando SC . 2016. Rumen bacterial community composition in Holstein and Jersey cows is different under same dietary condition and is not affected by sampling method. Front Microbiol 7 : 1206[CrossRef].[PubMed]
156. Munoz MA, Zadoks RN . 2007. Short communication: patterns of fecal shedding of Klebsiella by dairy cows. J Dairy Sci 90 : 1220 1224[CrossRef].[PubMed]
157. Paulin-Curlee GG, Singer RS, Sreevatsan S, Isaacson R, Reneau J, Foster D, Bey R . 2007. Genetic diversity of mastitis-associated Klebsiella pneumoniae in dairy cows. J Dairy Sci 90 : 3681 3689[CrossRef].[PubMed]
158. Mawatari T, Hirano K, Ikeda H, Tsunemitsu H, Suzuki T . 2014. Surveillance of diarrhea-causing pathogens in dairy and beef cows in Yamagata Prefecture, Japan from 2002 to 2011. Microbiol Immunol 58 : 530 535[CrossRef].[PubMed]
159. Korhonen H, Marnila P, Gill HS . 2000. Bovine milk antibodies for health. Br J Nutr 84( Suppl 1) : S135 S146[CrossRef].[PubMed]
160. Rudi K, Moen B, Sekelja M, Frisli T, Lee MRF . 2012. An eight-year investigation of bovine livestock fecal microbiota. Vet Microbiol 160 : 369 377[CrossRef].[PubMed]
161. Kaevska M, Videnska P, Sedlar K, Bartejsova I, Kralova A, Slana I . 2016. Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows. Can J Microbiol 62 : 538 541[CrossRef].[PubMed]
162. Gennari M, Parini M, Volpon D, Serio M . 1992. Isolation and characterization by conventional methods and genetic transformation of Psychrobacter and Acinetobacter from fresh and spoiled meat, milk and cheese. Int J Food Microbiol 15 : 61 75[CrossRef].[PubMed]
163. Andreani NA, Martino ME, Fasolato L, Carraro L, Montemurro F, Mioni R, Bordin P, Cardazzo B . 2014. Tracking the blue: a MLST approach to characterise the Pseudomonas fluorescens group. Food Microbiol 39 : 116 126[CrossRef].[PubMed]
164. Osborne AD, Armstrong K, Catrysse NH, Butler G, Versavel L . 1981. An outbreak of Pseudomonas mastitis in dairy cows. Can Vet J 22 : 215 216.[PubMed]
165. Lusk TS, Ottesen AR, White JR, Allard MW, Brown EW, Kase JA . 2012. Characterization of microflora in Latin-style cheeses by next-generation sequencing technology. BMC Microbiol 12 : 254[CrossRef].[PubMed]
166. De Filippis F, La Storia A, Stellato G, Gatti M, Ercolini D . 2014. A selected core microbiome drives the early stages of three popular italian cheese manufactures. PLoS One 9 : e89680[CrossRef].[PubMed]

Tables

Generic image for table
Table 5.1

The most prevalent bacteria in bovine milk and their likely sources and applications

Citation: Xue Z, Marco M. 2019. Milk and Dairy Products, p 103-123. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch5
Generic image for table
Table 5.2

The most prevalent bacteria in goat milk

Citation: Xue Z, Marco M. 2019. Milk and Dairy Products, p 103-123. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch5
Generic image for table
Table 5.3

High-throughput sequencing studies of cheese and cheese-related environments

Citation: Xue Z, Marco M. 2019. Milk and Dairy Products, p 103-123. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch5
Generic image for table
Table 5.4

Abundant microbes identified in kefir with high-throughput DNA sequencing methods

Citation: Xue Z, Marco M. 2019. Milk and Dairy Products, p 103-123. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch5