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Abstract

Sequencing technologies have deeply changed our approach to the study of food microbial communities. This review describes recent exploitations of high-throughput sequencing applications to improve our knowledge of food microbial consortia. In the past 10 years, target amplicon sequencing has become routinely used in many food microbiology laboratories, providing a detailed picture of food-associated microbiota. Metagenomics and metatranscriptomics approaches are still underexploited in food microbial ecology, despite their potential to uncover the functionality of complex communities. In a near future, sequencing technologies will surely advance our understanding of how to effectively use the invaluable microbial resources to improve food quality and safety.

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2018-03-25
2024-06-17
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Literature Cited

  1. 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 44:136–41 [Google Scholar]
  2. Alessandria V, Ferrocino I, De Filippis F, Fontana M, Rantsiou K. et al. 2016. Microbiota of an Italian Grana like cheese during manufacture and ripening unraveled by 16S rRNA-based approaches. Appl. Environ. Microbiol. 82:133988–95 [Google Scholar]
  3. Allard MW, Luo Y, Strain E, Li C, Keys CE. et al. 2012. High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach. BMC Genom 13:32 [Google Scholar]
  4. Almeida M, Hébert A, Abraham A-L, Rasmussen S, Monnet C. et al. 2014. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC Genom 15:1101 [Google Scholar]
  5. Baillie GJ, Galiano M, Agapow PM, Myers R, Chiam R. et al. 2012. Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis. J. Virol. 86:11–18 [Google Scholar]
  6. Bassi D, Puglisi E, Cocconcelli PS. 2015. Understanding the bacterial communities of hard cheese with blowing defect. Food Microbiol 52:106–18 [Google Scholar]
  7. Benson AK, David JRD, Gilbreth SE, Smith G, Nietfeldt J. et al. 2014. Microbial successions are associated with changes in chemical profiles of a model refrigerated fresh pork sausage during an 80-day shelf-life study. Appl. Environ. Microbiol. 80:175178–94 [Google Scholar]
  8. Bessmeltseva M, Viiard E, Simm J, Paalme T, Sarand I. 2014. Evolution of bacterial consortia in spontaneously started rye sourdoughs during two months of daily propagation. PLOS ONE 9:4e95449 [Google Scholar]
  9. Bokulich NA, Amiranashvili L, Chitchyan K, Ghazanchyan N, Darbinyan K. et al. 2015.a Microbial biogeography of the transnational fermented milk matsoni. Food Microbiol 50:12–19 [Google Scholar]
  10. Bokulich NA, Bamforth CW, Mills DA. 2012.a Brewhouse-resident microbiota are responsible for multi-stage fermentation of American coolship ale. PLOS ONE 7:4e35507 [Google Scholar]
  11. Bokulich NA, Bergsveinson J, Ziola B, Mills DA. 2015.b Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance. eLife 4:e04634 [Google Scholar]
  12. Bokulich NA, Joseph CML, Allen G, Benson AK, Mills DA. 2012.b Next-generation sequencing reveals significant bacterial diversity of botrytized wine. PLOS ONE 7:5e36357 [Google Scholar]
  13. Bokulich NA, Mills DA. 2013.a Facility-specific “house” microbiome drives microbial landscapes of artisan cheesemaking plants. Appl. Environ. Microbiol. 79:5214–23 [Google Scholar]
  14. Bokulich NA, Mills DA. 2013.b Improved selection of internal transcribed spacer-specific primers enables quantitative, ultra-high-throughput profiling of fungal communities. Appl. Environ. Microbiol. 79:82519–26 [Google Scholar]
  15. Bokulich NA, Ohta M, Richardson PM, Mills DA. 2013. Monitoring seasonal changes in winery-resident microbiota. PLOS ONE 8:6e66437 [Google Scholar]
  16. Bokulich NA, Thorngate JH, Richardson PM, Mills DA. 2014. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. PNAS 111:1E139–48 [Google Scholar]
  17. Calasso M, Ercolini D, Mancini L, Stellato G, Minervini F. et al. 2016. Relationships among house, rind and core microbiotas during manufacture of traditional Italian cheeses at the same dairy plant. Food Microbiol 54:115–26 [Google Scholar]
  18. Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP. 2016. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000Research 5:1492 [Google Scholar]
  19. Campanaro S, Treu L, Vendramin V, Bovo B, Giacomini A, Corich V. 2014. Metagenomic analysis of the microbial community in fermented grape marc reveals that Lactobacillus fabifermentans is one of the dominant species: insights into its genome structure. Appl. Microb. Biotechnol. 98:6015–37 [Google Scholar]
  20. Casaburi A, De Filippis F, Villani F, Ercolini D. 2014. Activities of strains of Brochothrix thermosphacta in vitro and in meat. Food Res. Int. 62:366–74 [Google Scholar]
  21. Casaburi A, Nasi A, Ferrocino I, Di Monaco R, Mauriello G. et al. 2011. Spoilage-related activity of Carnobacterium maltaromaticum strains in air-stored and vacuum-packed meat. Appl. Environ. Microbiol. 77:207382–93 [Google Scholar]
  22. Casey A, Fox EM, Schmitz-Esser S, Coffey A, McAuliffe O, Jordan K. 2014. Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility. Front. Microbiol. 5:68 [Google Scholar]
  23. Chaillou S, Chaulot-Talmon A, Caekebeke H, Cardinal M, Christieans S. et al. 2015. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage. ISME J 9:51105–18 [Google Scholar]
  24. Cocolin L, Alessandria V, Dolci P, Gorra R, Rantsiou K. 2013. Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation. Int. J. Food Microbiol. 167:129–43 [Google Scholar]
  25. Cruaud P, Rasplus JY, Rodriguez LJ, Cruaud A. 2017. High-throughput sequencing of multiple amplicons for barcoding and integrative taxonomy. Sci. Rep. 7:41948 [Google Scholar]
  26. De Angelis M, Campanella D, Cosmai L, Summo C, Rizzello CG, Caponio F. 2015. Microbiota and metabolome of un-started and started Greek-type fermentation of Bella di Cerignola table olives. Food Microbiol 52:18–30 [Google Scholar]
  27. De Filippis F, Genovese A, Ferranti P, Gilbert JA, Ercolini D. 2016.a Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Sci. Rep. 6:21871An increase in ripening temperature was shown to modulate the bacterial transcriptome, influencing the volatile compounds typical of cheese flavor. [Google Scholar]
  28. De Filippis F Laiola M, Blaiotta G, Ercolini D. 2017.a Different amplicon targets for sequencing-based studies of fungal diversity. Appl. Environ. Microbiol. 83:e00905–17 [Google Scholar]
  29. De Filippis F, La Storia A, Blaiotta G. 2017.b Monitoring the mycobiota during Greco di Tufo and Aglianico wine fermentation by 18S rRNA gene sequencing. Food Microbiol 63:117–22 [Google Scholar]
  30. 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 9:2e89680 [Google Scholar]
  31. De Filippis F, La Storia A, Villani F, Ercolini D. 2013. Exploring the sources of bacterial spoilers in beefsteaks by culture-independent high-throughput sequencing. PLOS ONE 8:7e70222 [Google Scholar]
  32. De Filippis F, Parente E, Ercolini D. 2017.c Metagenomics insights into food fermentations. Microb. Biotechnol. 10:191–102 [Google Scholar]
  33. De Filippis F, Pellegrini N, Laghi L, Gobbetti M, Ercolini D. 2016.b Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns. Microbiome 4:57 [Google Scholar]
  34. 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. 80:196243–55 [Google Scholar]
  35. De Pasquale I, Di Cagno R, Buchin S, De Angelis M, Gobbetti M. 2016. Spatial distribution of the metabolically active microbiota within Italian PDO ewes’ milk cheeses. PLOS ONE 11:4e0153213 [Google Scholar]
  36. Delcenserie V, Taminiau B, Delhalle L, Nezer C, Doyen P. et al. 2014. Microbiota characterization of a Belgian protected designation of origin cheese, Herve cheese, using metagenomic analysis. J. Dairy Sci. 97:6046–56 [Google Scholar]
  37. 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. 185:127–35 [Google Scholar]
  38. Douillard FP, de Vos WM. 2014. Functional genomics of lactic acid bacteria: from food to health. Microb. Cell Fact. 13:1S8 [Google Scholar]
  39. Dugat-Bony E, Straub C, Teissandier A, Onésime D, Loux V. et al. 2015. Overview of a surface-ripened cheese community functioning by meta-omics analyses. PLOS ONE 10:e0124360 [Google Scholar]
  40. Dzieciol M, Schornsteiner E, Muhterem-Uyar M, Stessl B, Wagner M, Schmitz-Esser S. 2016. Bacterial diversity of floor drain biofilms and drain waters in a Listeria monocytogenes contaminated food processing environment. Int. J. Food Microbiol. 223:33–40 [Google Scholar]
  41. Elizaquível P, Pérez-Cataluña A, Yépez A, Aristimuño C, Jiménez E. et al. 2015. Pyrosequencing vs. culture-dependent approaches to analyze lactic acid bacteria associated to chicha, a traditional maize-based fermented beverage from Northwestern Argentina. Int. J. Food Microbiol. 198:9–18 [Google Scholar]
  42. Ercolini D. 2017. Exciting strain-level resolution studies of the food microbiome. Microb. Biotechnol. 10:154–56 [Google Scholar]
  43. Ercolini D, Casaburi A, Nasi A, Ferrocino I, Di Monaco R. et al. 2010. Different molecular types of Pseudomonas fragi have the same overall behaviour as meat spoilers. Int. J. Food Microbiol. 142:1–2120–31 [Google Scholar]
  44. 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. 78:228142–45 [Google Scholar]
  45. Ercolini D, Ferrocino I, Nasi A, Ndagijimana M, Vernocchi P. et al. 2011. Monitoring of microbial metabolites and bacterial diversity in beef stored under different packaging conditions. Appl. Environ. Microbiol. 77:207372–81 [Google Scholar]
  46. Ercolini D, Pontonio E, De Filippis F Minervini F, La Storia A. et al. 2013. Microbial ecology dynamics during rye and wheat sourdough preparation. Appl. Environ. Microbiol. 79:247827–36 [Google Scholar]
  47. Eren AM, Maignien L, Sul WL, Murphy LG, Grim SL. et al. 2013. Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol. Evol. 4:121111–19 [Google Scholar]
  48. Eren AM, Sogin ML, Morrison HG, Vinei JH, Fisher JC. et al. 2015. A single genus in the gut microbiome reflects host preference and specificity. ISME J 9:90–100 [Google Scholar]
  49. Erkus O, de Jager VC, Spus M, van Alen-Boerrigter IJ, van Rijswijck IM. et al. 2013. Multi-factorial diversity sustains microbial community stability. ISME J 7:2126–36Pangenomics was used for strain monitoring during back-slopping of a cheese natural starter. [Google Scholar]
  50. Fink RC, Black EP, Hou Z, Sugawara M, Sadowsky MJ, Diez-Gonzalez F. 2012. Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves. Appl. Environ. Microbiol. 78:61752–64 [Google Scholar]
  51. Fougy L, Desmonts M-H, Coeuret G, Fassel C, Hamon E. et al. 2016. Salt reduction in raw pork sausages increases spoilage and correlates with reduced bacterial diversity. Appl. Environ. Microbiol. 82:133928–39 [Google Scholar]
  52. 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 [Google Scholar]
  53. Garofalo C, Osimani A, Milanović V, Aquilanti L, De Filippis F. et al. 2015. Bacteria and yeast microbiota in milk kefir grains from different Italian regions. Food Microbiol 49:123–33 [Google Scholar]
  54. Goudeau DM, Parker CT, Zhou Y, Sela S, Kroupitski Y, Brandl MT. 2013. The Salmonella transcriptome in lettuce and cilantro soft rot reveals a niche overlap with the animal host intestine. Appl. Environ. Microbiol. 79:1250–62 [Google Scholar]
  55. Greppi A, Ferrocino I, La Storia A, Rantsiou K, Ercolini D, Cocolin L. 2015. Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches. Int. J. Food Microbiol. 212:67–75 [Google Scholar]
  56. Guidone A, Matera A, Ricciardi A, Zotta T, De Filippis F. et al. 2016. The microbiota of high-moisture Mozzarella cheese produced with different acidification methods. Int. J. Food. Microbiol. 216:9–17 [Google Scholar]
  57. Guzzon R, Carafa I, Tuohy K, Cervantes G, Vernetti L. et al. 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 62:160–68 [Google Scholar]
  58. Hao P, Zheng H, Yu Y, Ding G, Gu W. et al. 2011. Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production. PLOS ONE 6:e15964 [Google Scholar]
  59. Hong X, Chen J, Liu L, Wu H, Tan H. et al. 2016. Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese rice wine. Sci. Rep. 6:26621 [Google Scholar]
  60. Hultman J, Rahkila R, Ali J, Rousu J, Björkroth KJ. 2015. Meat processing plant microbiome and contamination patterns of cold-tolerant bacteria causing food safety and spoilage risks in the manufacture of vacuum-packaged cooked sausages. Appl. Environ. Microbiol. 81:207088–97 [Google Scholar]
  61. Illeghems K, Weckx S, De Vuyst L. 2015. Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample. Food Microbiol 50:54–63 [Google Scholar]
  62. Jeong SH, Lee HJ, Jung JY, Lee SH, Seo HY. et al. 2013. Effects of red pepper powder on microbial communities and metabolites during kimchi fermentation. Int. J. Food Microbiol. 160:3252–59 [Google Scholar]
  63. Jung JY, Lee SH, Jeon CO. 2014. Microbial community dynamics during fermentation of doenjang-meju, traditional Korean fermented soybean. Int. J. Food Microbiol. 185:112–20 [Google Scholar]
  64. Jung JY, Lee SH, Jin HM, Hahn Y, Madsen EL, Jeon CO. 2013. Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation. Int. J. Food Microbiol. 163:2–3171–79 [Google Scholar]
  65. Jung JY, Lee SH, Lee HJ, Seo H-Y, Park W-S, Jeon CO. 2012.a Effects of Leuconostoc mesenteroides starter cultures on microbial communities and metabolites during kimchi fermentation. Int. J. Food Microbiol. 153:378–87 [Google Scholar]
  66. Jung M-J, Nam Y-D, Roh SW, Bae J-W. 2012.b Unexpected convergence of fungal and bacterial communities during fermentation of traditional Korean alcoholic beverages inoculated with various natural starters. Int. J. Food Microbiol. 30:112–23 [Google Scholar]
  67. Justé A, Malfliet S, Waud M, Crauwels S, De Cooman L. et al. 2014. Bacterial community dynamics during industrial malting, with an emphasis on lactic acid bacteria. Food Microbiol 39:39–46 [Google Scholar]
  68. Keisam S, Romi W, Ahmed G, Jeyaram K. 2016. Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods. Sci. Rep. 6:34155 [Google Scholar]
  69. Kembel SW, Wu M, Eisen J, Green JL. 2012. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLOS Comput. Biol. 8:e1002743 [Google Scholar]
  70. Korsak N, Taminiau B, Hupperts C, Delhalle L, Nezer C. et al. 2016. Assessment of bacterial superficial contamination in classical or ritually slaughtered cattle using metagenetics and microbiological analysis. Int. J. Food Microbiol. 247:79–86 [Google Scholar]
  71. Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D. et al. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31:814–21 [Google Scholar]
  72. Lattanzi A, Minervini F, Di Cagno R, Diviccaro A, Antonielli L. et al. 2013. The lactic acid bacteria and yeast microbiota of eighteen sourdoughs used for the manufacture of traditional Italian sweet leavened baked goods. Int. J. Food Microbiol. 163:71–79 [Google Scholar]
  73. Layeghifard M, Hwang DM, Guttman DS. 2016. Disentangling interactions in the microbiome: a network perspective. Trends Microbiol 25:3217–28 [Google Scholar]
  74. Leite AMO, Mayo B, Rachid CTCC, Peixoto RS, Silva JT. et al. 2012. Assessment of the microbial diversity of Brazilian kefir grains by PCR-DGGE and pyrosequencing analysis. Food Microbiol 31:215–21 [Google Scholar]
  75. 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 Genom 15:235 [Google Scholar]
  76. Lhomme E, Lattanzi A, Dousset X, Minervini F, De Angelis M. et al. 2015.a Lactic acid bacterium and yeast microbiotas of sixteen French traditional sourdoughs. Int. J. Food Microbiol. 215:161–70 [Google Scholar]
  77. Lhomme E, Orain S, Courcoux P, Onno B, Dousset X. 2015.b The predominance of Lactobacillus sanfranciscensis in French organic sourdoughs and its impact on related bread characteristics. Int. J. Food Microbiol. 213:40–48 [Google Scholar]
  78. Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M. 2011. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genom 12:S4 [Google Scholar]
  79. Liu W, Zheng Y, Kwok LY, Sun Z, Zhang J. 2015.a 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 [Google Scholar]
  80. Liu X-F, Liu C-J, Zhang H-Y, Gong F-M, Luo Y-Y, Li X-R. 2015.b The bacterial community structure of yond bap, a traditional fermented goat milk product, from distinct Chinese regions. Dairy Sci. Technol. 95:369–80 [Google Scholar]
  81. 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 [Google Scholar]
  82. 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 [Google Scholar]
  83. Marx V. 2016. Microbiology: the road to strain-level identification. Nat. Methods 13:5401–4 [Google Scholar]
  84. Marzano M, Fosso B, Manzari C, Grieco F, Intranuovo M. et al. 2016. Complexity and dynamics of the winemaking bacterial communities in berries, musts, and wines from Apulian grape cultivars through time and space. PLOS ONE 11:6e0157383 [Google Scholar]
  85. Mayo B, Rachid CT, Alegría A, Leite AM, Peixoto RS, Delgado S. 2014. Impact of next generation sequencing techniques in food microbiology. Curr. Genom. 15:4293–309 [Google Scholar]
  86. McMurdie PJ, Holmes S. 2015. Shiny-phyloseq: web application for interactive microbiome analysis with provenance tracking. Bioinformatics 31:2282–83 [Google Scholar]
  87. MetaSUB Int. Consort. 2016. The metagenomics and metadesign of the subways and urban biomes (MetaSUB) International Consortium meeting report. Microbiome 4:124 [Google Scholar]
  88. Minervini F, Lattanzi A, De Angelis M, Celano G, Gobbetti M. 2015. House microbiotas as sources of lactic acid bacteria and yeasts in traditional Italian sourdoughs. Food Microbiol 52:66–76 [Google Scholar]
  89. Monnet C, Dugat-Bony E, Swennen D, Beckerich J-M, Irlinger F. et al. 2016. Investigation of the activity of the microorganisms in a Reblochon-style cheese by metatranscriptomic analysis. Front. Microbiol. 7:536 [Google Scholar]
  90. Møretrø T, Moen B, Heir E, Hansen AA, Langsrud S. 2016. Contamination of salmon fillets and processing plants with spoilage bacteria. Int. J. Food Microbiol. 237:98–108 [Google Scholar]
  91. Nalbantoglu U, Cakar A, Dogan H, Abaci N, Ustek D. et al. 2014. Metagenomic analysis of the microbial community in kefir grains. Food Microbiol 41:42–51 [Google Scholar]
  92. Nam YD, Lee SY, Lim SI. 2012. Microbial community analysis of Korean soybean pastes by next-generation sequencing. Int. J. Food Microbiol. 155:36–42 [Google Scholar]
  93. Nieminen TT, Koskinen K, Laine P, Hultman J, Säde E. et al. 2012. Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics. Int. J. Food. Microbiol. 157:2142–49 [Google Scholar]
  94. Noyes NR, Yang X, Linke LM, Magnuson RJ, Dettenwanger A. et al. 2016. Resistome diversity in cattle and the environment decreases during beef production. eLife 5:e13195 [Google Scholar]
  95. O'Sullivan DJ, Cotter PD, O'Sullivan O, Giblin L, McSweeney PL, Sheehan JJ. 2015. Temporal and spatial differences in microbial composition during the manufacture of a continental-type cheese. Appl. Environ. Microbiol. 81:2525–33 [Google Scholar]
  96. Parente E, Cocolin L, De Filippis F, Zotta T, Ferrocino I. et al. 2016. FoodMicrobionet: a database for the visualization and exploration of food bacterial communities based on network analysis. Int. J. Food. Microbiol. 219:28–37 [Google Scholar]
  97. Park EJ, Chun J, Cha CJ, Park WS, Jeon CO, Bae JW. 2012. Bacterial community analysis during fermentation of ten representative kinds of kimchi with barcoded pyrosequencing. Food Microbiol 30:197–204 [Google Scholar]
  98. Pinto C, Pinho D, Cardoso R, Custodio V, Fernandes J. 2015. Wine fermentation microbiome: a landscape from different Portuguese wine appellations. Front. Microbiol. 6:905 [Google Scholar]
  99. Połka J, Rebecchi A, Pisacane V, Morelli L, Puglisi E. 2015. Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons. Food Microbiol 46:342–56 [Google Scholar]
  100. Porcellato D, Skeie SB. 2016. Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese. Int. Dairy J. 61:182–88 [Google Scholar]
  101. Pothakos V, Stellato G, Ercolini D, Devlieghere F. 2015. Processing environment and ingredients are both sources of Leuconostoc gelidum, which emerges as a major spoiler in ready-to-eat meals. Appl. Environ. Microbiol. 81:103529–41 [Google Scholar]
  102. Quigley L, O'Sullivan O, Beresford TP, Ross PR, Fitzgerald GF, Cotter PD. 2012.a A comparison of methods used to extract bacterial DNA from raw milk and raw milk cheese. J. Appl. Microbiol. 113:96–105 [Google Scholar]
  103. Quigley L, O'Sullivan O, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD. 2012.b High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. Appl. Environ. Microbiol. 78:5717–23 [Google Scholar]
  104. Ranieri ML, Shi C, Moreno Switt AI, den Bakker HC, Wiedmann M. 2013. Comparison of typing methods with a new procedure based on sequence characterization for Salmonella serovar prediction. J. Clin. Microbiol. 51:1786–97 [Google Scholar]
  105. Renouf V, Claisse O, Miot-Sertier C, Lonvaud-Funel A. 2006. Lactic acid bacteria evolution during winemaking: use of rpoB gene as a target for PCR-DGGE analysis. Food Microbiol 23:136–45 [Google Scholar]
  106. Ricciardi A, De Filippis F, Zotta T, Facchiano A, Ercolini D, Parente E. 2016. Polymorphism of the phosphoserine phosphatase gene in Streptococcus thermophilus and its potential use for typing and monitoring of population structure. Int. J. Food Microbiol. 236:138–47 [Google Scholar]
  107. Riquelme C, Câmara S, Dapkevicius Mde L, Vinuesa P, da Silva CC. et al. 2015. Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food). Int. J. Food Microbiol. 192:86–94 [Google Scholar]
  108. Rizzello CG, Cavoski I, Turk J, Ercolini D, Nionelli L. et al. 2015. The organic cultivation of Triticum turgidum spp. durum reflects on the axis flour, sourdough fermentation and bread. Appl. Environ. Microbiol. 81:93192–204 [Google Scholar]
  109. Ronholm J, Nasheri N, Petronella N, Pagotto F. 2016. Navigating microbiological food safety in the era of whole-genome sequencing. Clin. Microbiol. Rev. 29:837–57 [Google Scholar]
  110. Ropars J, Rodriguez de la Vega RC, López-Villavicencio M, Gouzy J, Sallet E. et al. 2015. Adaptive horizontal gene transfers between multiple cheese-associated fungi. Curr. Biol. 25:192562–69 [Google Scholar]
  111. Sakamoto N, Tanaka S, Sonomoto K, Nakayama J. 2011. 16S rRNA pyrosequencing-based investigation of the bacterial community in nukadoko, a pickling bed of fermented rice bran. Int. J. Food Microbiol. 144:352–59 [Google Scholar]
  112. Sattin E, Andreani NA, Carraro L, Fasolato L, Balzan S. et al. 2016. Microbial dynamics during shelf-life of industrial Ricotta cheese and identification of a Bacillus strain as a cause of a pink discolouration. Food Microbiol 57:8–15 [Google Scholar]
  113. Scholz M, Ward DV, Pasolli E, Tolio T, Zolfo M. et al. 2016. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nat. Methods 13:5435–38 [Google Scholar]
  114. Sergeant MJ, Constantinidou C, Cogan T, Penn CW, Pallen MJ. 2012. High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature. PLOS ONE 7:5e38094 [Google Scholar]
  115. Stefanini I, Albanese D, Cavazza A, Franciosi E, De Filippo C. et al. 2016. Dynamic changes in microbiota and mycobiota during spontaneous “Vino Santo Trentino” fermentation. Microb. Biotechnol. 9:195–208 [Google Scholar]
  116. 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. 81:227893–904 [Google Scholar]
  117. Stellato G, La Storia A, De Filippis F, Borriello G, Villani F, Ercolini D. 2016. Overlap of spoilage-associated microbiota between meat and meat processing environment in small-scale and large-scale retail distribution. Appl. Environ. Microbiol. 82:134045–54 [Google Scholar]
  118. Stellato G, Utter DR, Voorhis A, De Angelis M, Eren AM, Ercolini D. 2017. A few Pseudomonas oligotypes dominate in the meat and dairy processing environment. Front. Microbiol. 8:264 [Google Scholar]
  119. Sun Z, Harris HMB, McCann A, Guo C, Argimon S. et al. 2015. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat. Commun. 6:8322 [Google Scholar]
  120. Sun Z, Liu W, Bao Q, Zhang J, Hou Q. et al. 2014. Investigation of bacterial and fungal diversity in tarag using high-throughput sequencing. J. Dairy Sci. 97:6085–96 [Google Scholar]
  121. Tedersoo L, Abarenkov K, Nilsson RH, Schüssler A, Grelet G-A. et al. 2011. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of ITS sequences of mycorrhizal fungi. PLOS ONE 6:9e24940 [Google Scholar]
  122. Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N. 2017. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res 27:4626–38 [Google Scholar]
  123. Turlapati SA, Minocha R, Long S, Ramsdell J, Minocha SC. 2015. Oligotyping reveals stronger relationship of organic soil bacterial community structure with N-amendments and soil chemistry in comparison to that of mineral soil at Harvard Forest, MA, USA. Front. Microbiol. 6:49 [Google Scholar]
  124. Vătrovský T, Baldrian P. 2013. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLOS ONE 8:e57923 [Google Scholar]
  125. Viiard E, Bessmeltseva M, Simm J, Talve T, Aaspõllu A. et al. 2016. Diversity and stability of lactic acid bacteria in rye sourdoughs of four bakeries with different propagation parameters. PLOS ONE 11:2e0148325 [Google Scholar]
  126. Visvalingam J, Hernandez-Doria JD, Holley RA. 2013. Examination of the genome-wide transcriptional response of Escherichia coli O157:H7 to cinnamaldehyde exposure. Appl. Environ. Microbiol. 79:942–50 [Google Scholar]
  127. Walsh AM, Crispie F, Kilcawley K, O'Sullivan O, O'Sullivan MG. et al. 2016. Microbial succession and flavour production in the fermented dairy beverage kefir. mSystems 1:5e00052–16 [Google Scholar]
  128. Wang C, García-Fernández D, Mas A, Esteve-Zarzoso B. 2015. Fungal diversity in grape must and wine fermentation assessed by massive sequencing, quantitative PCR and DGGE. Front. Microbiol. 6:1156 [Google Scholar]
  129. 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 158:422–33The metagenome of surface-ripened cheeses is enriched in genes involved in volatile compound production. [Google Scholar]
  130. Wolfe BE, Dutton RJ. 2015. Fermented foods as experimentally tractable microbial ecosystems. Cell 161:49–55 [Google Scholar]
  131. Yang X, Noyes NR, Doster E, Martin JN, Linke LM. et al. 2016. Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within the microbiome of the beef production chain. Appl. Environ. Microbiol. 82:2433–43 [Google Scholar]
  132. Zheng J, Keys CE, Zhao S, Ahmed R, Meng J, Brown EW. 2011. Simultaneous analysis of multiple enzymes increases accuracy of pulsed-field gel electrophoresis in assigning genetic relationships among homogeneous Salmonella strains. J. Clin. Microbiol. 49:85–94 [Google Scholar]
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