Recent Past, Present, and Future of the Food Microbiome

Annual Review of Food Science and Technology

Volumn 9, Issue , 2018, Pages 589-608

  De Filippis, Francesca ^a   Parente, Eugenio ^b   Ercolini, Danilo ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b UNIVERSITY OF BASILICATA   (Italy)

Author keywords

Amplicon sequencing; Food microbiome; Food microbiota; High throughput sequencing; Metagenomics; Metatranscriptomics; Whole genome sequencing

Indexed keywords

ECOLOGY; FOOD SAFETY; THROUGHPUT;

AMPLICONS; HIGH-THROUGHPUT SEQUENCING; METAGENOMICS; METATRANSCRIPTOMICS; MICROBIOME; MICROBIOTAS; WHOLE GENOME SEQUENCING;

FOOD MICROBIOLOGY;

BIOLOGY; FERMENTATION; FOOD CONTROL; FOOD HANDLING; FOOD SAFETY; GENETICS; HIGH THROUGHPUT SEQUENCING; METAGENOMICS; MICROFLORA; PROCEDURES;

COMPUTATIONAL BIOLOGY; FERMENTATION; FOOD MICROBIOLOGY; FOOD SAFETY; FOOD TECHNOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS; MICROBIOTA;

EID: 85044641220     PISSN: 19411413     EISSN: 19411421     Source Type: Journal    
DOI: 10.1146/annurev-food-030117-012312     Document Type: Review

References (132)

1. Aldrete-Tapia A, Escobar-Ramírez MC, Tamplin ML, Hernández-Iturriaga M. 2014. High-throughput sequencing ofmicrobial communities in Poro cheese, an artisanal Mexican cheese. Food Microbiol. 44:136-41
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(13):3988-95
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
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
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
6. Bassi D, Puglisi E, Cocconcelli PS. 2015. Understanding the bacterial communities of hard cheese with blowing defect. Food Microbiol. 52:106-18
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(17):5178-94
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(4):e95449
9. Bokulich NA, Amiranashvili L, Chitchyan K, Ghazanchyan N, Darbinyan K, et al. 2015a. Microbial biogeography of the transnational fermented milk matsoni. Food Microbiol. 50:12-19
10. Bokulich NA, Bamforth CW, Mills DA. 2012a. Brewhouse-resident microbiota are responsible for multi-stage fermentation of American coolship ale. PLOS ONE 7(4):e35507
11. Bokulich NA, Bergsveinson J, Ziola B, Mills DA. 2015b. Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance. eLife 4:e04634
12. Bokulich NA, Joseph CML, Allen G, Benson AK, Mills DA. 2012b. Next-generation sequencing reveals significant bacterial diversity of botrytized wine. PLOS ONE 7(5):e36357
13. Bokulich NA, Mills DA. 2013a. Facility-specific "house" microbiome drives microbial landscapes of artisan cheesemaking plants. Appl. Environ. Microbiol. 79:5214-23
14. Bokulich NA, Mills DA. 2013b. Improved selection of internal transcribed spacer-specific primers enables quantitative, ultra-high-throughput profiling of fungal communities. Appl. Environ. Microbiol. 79(8):2519-26
15. Bokulich NA, Ohta M, Richardson PM, Mills DA. 2013. Monitoring seasonal changes in winery-resident microbiota. PLOS ONE 8(6):e66437
16. Bokulich NA, Thorngate JH, Richardson PM, Mills DA. 2014. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. PNAS 111(1):E139-48
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
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
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
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
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(20):7382-93
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
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(5):1105-18
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(1):29-43
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
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
27. De Filippis F, Genovese A, Ferranti P, Gilbert JA, Ercolini D. 2016a. Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Sci. Rep. 6:21871
28. De Filippis F Laiola M, Blaiotta G, Ercolini D. 2017a. Different amplicon targets for sequencing-based studies of fungal diversity. Appl. Environ. Microbiol. 83:e00905-17
29. De Filippis F, La Storia A, Blaiotta G. 2017b. Monitoring the mycobiota during Greco di Tufo and Aglianico wine fermentation by 18S rRNA gene sequencing. Food Microbiol. 63:117-22
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(2):e89680
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(7):e70222
32. De Filippis F, Parente E, Ercolini D. 2017c. Metagenomics insights into food fermentations. Microb. Biotechnol. 10(1):91-102
33. De Filippis F, Pellegrini N, Laghi L, Gobbetti M, Ercolini D. 2016b. Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns. Microbiome 4:57
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(19):6243-55
35. DePasquale I, Di Cagno R, Buchin S, DeAngelis M, Gobbetti M. 2016. Spatial distribution of the metabolically active microbiota within Italian PDO ewes' milk cheeses. PLOS ONE 11(4):e0153213
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
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
38. Douillard FP, de Vos WM. 2014. Functional genomics of lactic acid bacteria: from food to health. Microb. Cell Fact. 13(1):S8
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
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
41. Elizaquível P, Pérez-Cataluña A, Yépez A, Aristimuño C, Jiménez E, et al. 2015. Pyrosequencing vs. culturedependent 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
42. Ercolini D. 2017. Exciting strain-level resolution studies of the food microbiome. Microb. Biotechnol. 10(1):54-56
43. Ercolini D, Casaburi A, Nasi A, Ferrocino I, DiMonaco R, et al. 2010. Differentmolecular types of Pseudomonas fragi have the same overall behaviour as meat spoilers. Int. J. Food Microbiol. 142(1-2):120-31
44. Ercolini D, DeFilippis 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(22):8142-45
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(20):7372-81
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(24):7827-36
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(12):1111-19
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
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. 7:2126-36
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(6):1752-64
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(13):3928-39
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
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
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(1):250-62
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
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
57. Guzzon R, Carafa I, Tuohy K, Cervantes G, Vernetti L, et al. 2017. Exploring the microbiota of the redbrown defect in smear-ripened cheese by 454-pyrosequencing and its prevention using different cleaning systems. Food Microbiol. 62:160-68
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
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
60. Hultman J, Rahkila R, Ali J, Rousu J, Björkroth KJ. 2015. Meat processing plantmicrobiome and contamination patterns of cold-tolerant bacteria causing food safety and spoilage risks in the manufacture of vacuumpackaged cooked sausages. Appl. Environ. Microbiol. 81(20):7088-97
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
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(3):252-59
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
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(2-3):171-79
65. Jung JY, Lee SH, Lee HJ, Seo H-Y, Park W-S, Jeon CO. 2012a. Effects of Leuconostoc mesenteroides starter cultures on microbial communities and metabolites during kimchi fermentation. Int. J. Food Microbiol. 153:378-87
66. Jung M-J, Nam Y-D, Roh SW, Bae J-W. 2012b. 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
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
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
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
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
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
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
73. Layeghifard M, Hwang DM, Guttman DS. 2016. Disentangling interactions in the microbiome: a network perspective. Trends Microbiol. 25(3):217-28
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
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
76. Lhomme E, Lattanzi A, Dousset X, Minervini F, De Angelis M, et al. 2015a. Lactic acid bacterium and yeast microbiotas of sixteen French traditional sourdoughs. Int. J. Food Microbiol. 215:161-70
77. Lhomme E, Orain S, Courcoux P, Onno B, Dousset X. 2015b. The predominance of Lactobacillus sanfranciscensis in French organic sourdoughs and its impact on related bread characteristics. Int. J. Food Microbiol. 213:40-48
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
79. Liu W, Zheng Y, Kwok LY, Sun Z, Zhang J, et al. 2015a. High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow's milk in Russia. BMCMicrobiol. 15:45
80. Liu X-F, Liu C-J, Zhang H-Y, Gong F-M, Luo Y-Y, Li X-R. 2015b. The bacterial community structure of yond bap, a traditional fermented goat milk product, from distinct Chinese regions. Dairy Sci. Technol. 95:369-80
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
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
83. Marx V. 2016. Microbiology: the road to strain-level identification. Nat. Methods 13(5):401-4
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(6):e0157383
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(4):293-309
86. McMurdie PJ, Holmes S. 2015. Shiny-phyloseq: web application for interactive microbiome analysis with provenance tracking. Bioinformatics 31(2):282-83
87. Meta SUB Int. Consort. 2016. Themetagenomics andmetadesign of the subways and urban biomes (MetaSUB) International Consortium meeting report. Microbiome 4(1):24
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
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
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
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
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
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(2):142-49
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
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
96. Parente E, Cocolin L, De Filippis F, Zotta T, Ferrocino I, et al. 2016. Food Microbionet: a database for the visualization and exploration of food bacterial communities based on network analysis. Int. J. Food. Microbiol. 219:28-37
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
98. Pinto C, Pinho D, Cardoso R, Custodio V, Fernandes J, et al. 2015. Wine fermentation microbiome: a landscape from different Portuguese wine appellations. Front. Microbiol. 6:905
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
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
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(10):3529-41
102. Quigley L, O'Sullivan O, Beresford TP, Ross PR, Fitzgerald GF, Cotter PD. 2012a. A comparison of methods used to extract bacterial DNA from raw milk and raw milk cheese. J. Appl. Microbiol. 113:96-105
103. Quigley L, O'Sullivan O, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD. 2012b. High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. Appl. Environ. Microbiol. 78:5717-23
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
105. Renouf V, Claisse O, Miot-Sertier C, Lonvaud-Funel A. 2006. Lactic acid bacteria evolution during winemaking: use of rpo B gene as a target for PCR-DGGE analysis. Food Microbiol. 23:136-45
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
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
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(9):3192-204
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
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(19):2562-69
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
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
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(5):435-38
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(5):e38094
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
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(22):7893-904
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(13):4045-54
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
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
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
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(9):e24940
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(4):626-38
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
124. Vǎtrovský T, Baldrian P. 2013. The variability of the 16SrRNAgene in bacterial genomes and its consequences for bacterial community analyses. PLOS ONE 8:e57923
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(2):e0148325
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
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(5):e00052-16
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
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 158:422-33
130. Wolfe BE, Dutton RJ. 2015. Fermented foods as experimentally tractable microbial ecosystems. Cell 161:49-55
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
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