Translating Omics to Food Microbiology

Annual Review of Food Science and Technology

Volumn 8, Issue , 2017, Pages 113-134

  Walsh, Aaron M ^a,b,c   Crispie, Fiona ^a   Claesson, Marcus J ^b,c   Cotter, Paul D ^a,b  

^a TEAGASC FOOD RESEARCH CENTRE   (Ireland)

^b UNIVERSITY COLLEGE CORK   (Ireland)

^c UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

Fermentation; Food microbiology; Foodborne pathogens; Gut microbiota; High throughput sequencing; Probiotics

Indexed keywords

FERMENTATION; FOOD SAFETY; MICROBIOLOGY; MICROORGANISMS; THROUGHPUT;

COMPARATIVE AND FUNCTIONAL GENOMICS; FOOD-BORNE PATHOGENS; GUT MICROBIOTA; HIGH-THROUGHPUT SEQUENCING; HUMAN GUT MICROBIOTA; METATRANSCRIPTOMICS; MICROBIAL COMMUNITIES; PROBIOTICS;

FOOD MICROBIOLOGY;

PROBIOTIC AGENT; TRANSCRIPTOME;

FOOD CONTROL; HIGH THROUGHPUT SEQUENCING; HUMAN; INTESTINE FLORA; METAGENOMICS;

FOOD MICROBIOLOGY; GASTROINTESTINAL MICROBIOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOMICS; PROBIOTICS; TRANSCRIPTOME;

EID: 85014200571     PISSN: 19411413     EISSN: 19411421     Source Type: Journal    
DOI: 10.1146/annurev-food-030216-025729     Document Type: Review

References (153)

1. Aldridge BB, Rhee KY. 2014. Microbial metabolomics: innovation, application, insight. Curr. Opin. Microbiol. 19:90-96
2. Alkema W, Boekhorst J, WelsM, van Hijum SA. 2016. Microbial bioinformatics for food safety and production. Brief. Bioinform. 17:283-92
3. Allard G, Ryan FJ, Jeffery IB, Claesson MJ. 2015. SPINGO: a rapid species-classifier for microbial amplicon sequences. BMC Bioinform. 16:1
4. AllardMW, Strain E, MelkaD, Bunning K, Musser SM, et al. 2016. The PRACTICAL value of food pathogen traceability through BUILDiNG a whole-genome sequencing network and database. J. Clin. Microbiol. 54:1075-83
5. Ashton PM, Nair S, Dallman T, Rubino S, Rabsch W, et al. 2015. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat. Biotechnol. 33:296-300
6. Bachmann H, Pronk JT, Kleerebezem M, Teusink B. 2015. Evolutionary engineering to enhance starter culture performance in food fermentations. Curr. Opin. Biotechnol. 32:1-7
7. Bachmann H, Starrenburg MJ, Molenaar D, Kleerebezem M, van Hylckama Vlieg JE. 2012. Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution. Genome Res. 22:115-24
8. Benitez-Paez A, Portune K, Sanz Y. 2015. Species level resolution of 16S rRNA gene amplicons sequenced throughMinIONTM portable nanopore sequencer. GigaScience 5:4
9. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59
10. Bermudez-BritoM, Plaza-Dáz J, Muñoz-Quezada S, Gómez-Llorente C, Gil A. 2012. Probiotic mechanisms of action. Ann. Nutr. Metab. 61:160-74
11. Betteridge A, Grbin P, Jiranek V. 2015. Improving Oenococcus oeni to overcome challenges of wine malolactic fermentation. Trends Biotechnol. 33:547-53
12. Bienenstock J, Gibson G, Klaenhammer TR, Walker WA, Neish AS. 2013. New insights into probiotic mechanisms: a harvest from functional and metagenomic studies. Gut Microbes 4:94-100
13. Bokulich NA, Bamforth CW, Mills DA. 2012. Brewhouse-resident microbiota are responsible for multi-stage fermentation of American coolship ale. PLOS ONE 7:e35507
14. Bokulich NA, Bergsveinson J, Ziola B, Mills DA. 2015. Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance. eLife 4:e04634
15. Bokulich NA, Lewis ZT, Boundy-Mills K, Mills DA. 2016. A new perspective on microbial landscapes within food production. Curr. Opin. Biotechnol. 37:182-89
16. Bokulich NA, Mills DA. 2013. Facility-specific house microbiome drives microbial landscapes of artisan cheesemaking plants. Appl. Environ. Microbiol. 79:5214-23
17. Borneman AR, Pretorius IS, Chambers PJ. 2013. Comparative genomics: a revolutionary tool for wine yeast strain development. Curr. Opin. Biotechnol. 24:192-99
18. Bourdichon F, Casaregola S, Farrokh C, Frisvad JC, Gerds ML, et al. 2012. Food fermentations: microorganisms with technological beneficial use. Int. J. Food Microbiol. 154:87-97
19. Bourrie BCT, Willing BP, Cotter PD. 2016. The microbiota and health promoting characteristics of the fermented beverage kefir. Front. Microbiol. 7:647
20. Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, et al. 2015. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517:205-8
21. Bull MJ, Jolley KA, Bray JE, AertsM, Vandamme P, et al. 2014. The domestication of the probiotic bacterium Lactobacillus acidophilus. Sci. Rep. 4:7202
22. ÇakarZP, SekerUO, Tamerler C, SondereggerM, Sauer U. 2005. Evolutionary engineering ofmultiple-stress resistant Saccharomyces cerevisiae. FEMS Yeast Res. 5:569-78
23. Çakar ZP, Turanli-Yildiz B, Alk?m C, Yilmaz U. 2012. Evolutionary engineering of Saccharomyces cerevisiae for improved industrially important properties. FEMS Yeast Res. 12:171-82
24. Caplice E, Fitzgerald GF. 1999. Food fermentations: role of microorganisms in food production and preservation. Int. J. Food Microbiol. 50:131-49
25. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, et al. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. PNAS 108:4516-22
26. Chaillou S, Chaulot-Talmon A, Caekebeke H, Cardinal M, Christieans S, et al. 2014. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage. ISME J. 9:1105-18
27. Chakravorty S, Bhattacharya S, Chatzinotas A, Chakraborty W, Bhattacharya D, Gachhui R. 2016. Kombucha tea fermentation: microbial and biochemical dynamics. Int. J. Food Microbiol. 220:63-72
28. Chan BK, Abedon ST, Loc-Carrillo C. 2013. Phage cocktails and the future of phage therapy. Future Microbiol. 8:769-83
29. Chin C-S, AlexanderDH, Marks P, Klammer AA, Drake J, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563-69
30. Cocolin L, Ercolini D. 2015. Zooming into food-associated microbial consortia: a cultural evolution. Curr. Opin. Food Sci. 2:43-50
31. Conesa A, Götz S, Garcá-Gómez JM, Terol J, Talón M, Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674-76
32. Dallman TJ, Byrne L, Ashton PM, Cowley LA, Perry NT, et al. 2015. Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157. Clin. Infect. Dis. 61:305-12
33. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, et al. 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559-63
34. De Filippis F, Genovese A, Ferranti P, Gilbert JA, ErcoliniD. 2016. Metatranscriptomics reveals temperaturedriven functional changes in microbiome impacting cheese maturation rate. Sci. Rep. 6:21871
35. 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:e70222
36. 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. 80:6243-55
37. den Bakker HC, Allard MW, Bopp D, Brown EW, Fontana J, et al. 2014. Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar Enteritidis. Emerg. Infect. Dis. 20:1306
38. Derrien M, van Hylckama Vlieg JE. 2015. Fate, activity, and impact of ingested bacteria within the human gut microbiota. Trends Microbiol. 23:354-66
39. dos Santos FB, de Vos WM, Teusink B. 2013. Towards metagenome-scale models for industrial applications: the case of lactic acid bacteria. Curr. Opin. Biotechnol. 24:200-6
40. Drissi F, Merhej V, Angelakis E, El Kaoutari A, Carrière F, et al. 2014. Comparative genomics analysis of Lactobacillus species associated with weight gain or weight protection. Nutr. Diabetes 4:e109
41. 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
42. Duitama J, Sánchez-Rodríguez A, Goovaerts A, Pulido-Tamayo S, Hubmann G, et al. 2014. Improved linkage analysis of quantitative trait loci using bulk segregants unveils a novel determinant of high ethanol tolerance in yeast. BMC Genom. 15:1
43. Eloe-Fadrosh EA, Brady A, Crabtree J, Drabek EF, Ma B, et al. 2015. Functional dynamics of the gut microbiome in elderly people during probiotic consumption. mBio 6:e00231-15
44. Endersen L, O'Mahony J, Hill C, Ross RP, McAuliffe O, Coffey A. 2014. Phage therapy in the food industry. Annu. Rev. Food Sci. Technol. 5:327-49
45. Ercolini D. 2013. High-throughput sequencing and metagenomics: moving forward in the cultureindependent analysis of food microbial ecology. Appl. Environ. Microbiol. 79:3148-55
46. Escobar-Zepeda A, Sanchez-Flores A, BaruchMQ. 2016. Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota. Food Microbiol. 57:116-27
47. Ferrocino I, Greppi A, La Storia A, Rantsiou K, Ercolini D, Cocolin L. 2016. Impact of nisin-activated packaging on microbiota of beef burgers during storage. Appl. Environ. Microbiol. 82:549-59
48. Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, et al. 2012. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. PNAS 109:21390-95
49. Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, et al. 2015. Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nat. Rev. Microbiol. 13:360-72
50. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, et al. 2008. Microbial community gene expression in ocean surface waters. PNAS 105:3805-10
51. Galimberti A, Bruno A, Mezzasalma V, De Mattia F, Bruni I, Labra M. 2015. Emerging DNA-based technologies to characterize food ecosystems. Food Res. Int. 69:424-33
52. Gibbons JG, Rinker DC. 2015. The genomics of microbial domestication in the fermented food environment. Curr. Opin. Genet. Dev. 35:1-8
53. Hanage WP. 2014. Microbiome science needs a healthy dose of scepticism. Nature 512:247-48
54. Hayes BJ, Lewin HA, Goddard ME. 2013. The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation. Trends Genet. 29:206-14
55. Herrero J, MuffatoM, Beal K, Fitzgerald S, Gordon L, et al. 2016. Ensembl comparative genomics resources. Database 2016:bav096
56. Hettich RL, Sharma R, Chourey K, Giannone RJ. 2012. Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities. Curr. Opin. Microbiol. 15:373-80
57. Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, et al. 2014. Expert consensus document: the International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat. Rev. Gastroenterol. Hepatol. 11:506-14
58. Hong X, Chen J, Liu L, WuH, Tan H, et al. 2016. Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese rice wine. Sci. Rep. 6:26621
59. 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. 81:7088-97
60. Hum. Microbiome Proj. Consort. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-14
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. Ito M, Kim Y-G, Tsuji H, Takahashi T, Kiwaki M, et al. 2014. Transposon mutagenesis of probiotic Lactobacillus casei identifies asnH, an asparagine synthetase gene involved in its immune-activating capacity. PLOS ONE 9:e83876
63. Jääskeläinen E, Hultman J, Parshintsev J, Riekkola M-L, Björkroth J. 2016. Development of spoilage bacterial community and volatile compounds in chilled beef under vacuum or high oxygen atmospheres. Int. J. Food Microbiol. 223:25-32
64. Jeong SH, Jung JY, Lee SH, Jin HM, Jeon CO. 2013. Microbial succession and metabolite changes during fermentation of dongchimi, traditional Korean watery kimchi. Int. J. Food Microbiol. 164:46-53
65. Johnson BR, Klaenhammer TR. 2014. Impact of genomics on the field of probiotic research: historical perspectives to modern paradigms. Antonie van Leeuwenhoek 106:141-56
66. Joyce AR, Palsson BØ. 2006. The model organism as a system: integrating 'omics' data sets. Nat. Rev. Mol. Cell Biol. 7:198-210
67. 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. 163:171-79
68. Jung JY, Lee SH, Kim JM, Park MS, Bae J-W, et al. 2011. Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl. Environ. Microbiol. 77:2264-74
69. Kao RR, Haydon DT, Lycett SJ, Murcia PR. 2014. Supersize me: how whole-genome sequencing and big data are transforming epidemiology. Trends Microbiol. 22:282-91
70. Kelleher P, Murphy J, Mahony J, van Sinderen D. 2015. Next-generation sequencing as an approach to dairy starter selection. Dairy Sci. Technol. 95:545-68
71. Kergourlay G, Taminiau B, Daube G, Champomier Verges MC. 2015. Metagenomic insights into the dynamics of microbial communities in food. Int. J. Food Microbiol. 213:31-39
72. Kim S-W, Suda W, Kim S, Oshima K, Fukuda S, et al. 2013. Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-throughput pyrosequencing. DNA Res. 20:241-53
73. Knight R, Jansson J, Field D, Fierer N, DesaiN, et al. 2012. Unlocking the potential of metagenomics through replicated experimental design. Nat. Biotechnol. 30:513-20
74. Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, et al. 2011. Bayesian community-wide cultureindependent microbial source tracking. Nat. Methods 8:761-63
75. Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER. 2013. The next-generation sequencing revolution and its impact on genomics. Cell 155:27-38
76. Koren S, Phillippy AM. 2015. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr. Opin. Microbiol. 23:110-20
77. Kwong JC, Mercoulia K, Tomita T, Easton M, Li HY, et al. 2015. Prospective whole genome sequencing enhances national surveillance of Listeria monocytogenes. J. Clin. Microbiol. 54:333-42
78. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921
79. Langille MG, 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
80. Larsen N, Vogensen FK, Gøbel R, Michaelsen KF, Al-Soud WA, et al. 2011. Predominant genera of fecal microbiota in children with atopic dermatitis are not altered by intake of probiotic bacteria Lactobacillus acidophilus NCFM and Bifidobacterium animalis subsp. lactis Bi-07. FEMS Microbiol. Ecol. 75:482-96
81. Lee SH, Jung JY, Jeon CO. 2014. Microbial successions and metabolite changes during fermentation of salted shrimp (saeu-jeot) with different salt concentrations. PLOS ONE 9:e90115
82. Lee SH, Jung JY, Jeon CO. 2015. Bacterial community dynamics andmetabolite changes in myeolchi-aekjeot, a Korean traditional fermented fish sauce, during fermentation. Int. J. Food Microbiol. 203:15-22
83. Legras JL, Merdinoglu D, Cornuet J, Karst F. 2007. Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history. Mol. Ecol. 16:2091-102
84. Lei R, Ye K, Gu Z, Sun X. 2015. Diminishing returns in next-generation sequencing (NGS) transcriptome data. Gene 557:82-87
85. Leonard SR, Mammel MK, Lacher DW, Elkins CA. 2015. Application of metagenomic sequencing to food safety: detection of Shiga toxin-producing Escherichia coli on fresh bagged spinach. Appl. Environ. Microbiol. 81:8183-91
86. Lessard M-H, 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
87. Li J, Sung CYJ, Lee N, Ni Y, Pihlajamäki J, et al. 2016. Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice. PNAS 113:E1306-15
88. Li R, Hsieh C-L, Young A, Zhang Z, Ren X, Zhao Z. 2015. Illumina synthetic long read sequencing allows recovery of missing sequences even in the finished C elegans genome. Sci. Rep. 5:10814
89. Licandro-Seraut H, ScornecH, PédronT, Cavin J-F, Sansonetti PJ. 2014. Functional genomics of Lactobacillus casei establishment in the gut. PNAS 111:E3101-9
90. Lindgreen S, Adair KL, Gardner PP. 2016. An evaluation of the accuracy and speed of metagenome analysis tools. Sci. Rep. 6:19233
91. Liu SP, Yu JX, Wei XL, JiZW, Zhou ZL, et al. 2016. Sequencing-based screening of functionalmicroorganism to decrease the formation of biogenic amines in Chinese rice wine. Food Control 64:98-104
92. Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, et al. 2012. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 30:434-39
93. Loman NJ, Pallen MJ. 2015. Twenty years of bacterial genome sequencing. Nat. Rev. Microbiol. 13:787-94
94. Mahony J, McDonnell B, Casey E, van Sinderen D. 2016. Phage-host interactions of cheese-making lactic acid bacteria. Annu. Rev. Food Sci. Technol. 7:267-85
95. Mahony J, van SinderenD. 2015. Novel strategies to prevent or exploit phages in fermentations, insights from phage-host interactions. Curr. Opin. Biotechnol. 32:8-13
96. MarguliesM, EgholmM, AltmanWE, Attiya S, Bader JS, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-80
97. Marsh AJ, Hill C, Ross RP, Cotter PD. 2014. Fermented beverages with health-promoting potential: past and future perspectives. Trends Food Sci. Technol. 38:113-24
98. Mayo B, Rachid CTC, Alegrá A, Leite AM, Peixoto RS, Delgado S. 2014. Impact of next generation sequencing techniques in food microbiology. Curr. Genom. 15:293
99. McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, et al. 2011. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci. Transl. Med. 3:106ra106
100. McPherson JD. 2014. A defining decade in DNA sequencing. Nat. Methods 11:1003-5
101. Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, et al. 2011. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104: H4 outbreak by rapid next generation sequencing technology. PLOS ONE 6:e22751
102. 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
103. 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
104. Moran MA, Satinsky B, Gifford SM, Luo H, Rivers A, et al. 2013. Sizing up metatranscriptomics. ISME J. 7:237-43
105. Mosher JJ, Bowman B, Bernberg EL, Shevchenko O, Kan J, et al. 2014. Improved performance of the PacBio SMRT technology for 16S rDNA sequencing. J. Microbiol. Methods 104:59-60
106. Motherway MOC, Zomer A, Leahy SC, Reunanen J, Bottacini F, et al. 2011. Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. PNAS 108:11217-22
107. Murphy J, Bottacini F, Mahony J, Kelleher P, Neve H, et al. 2016. Comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages. Sci. Rep. 6:21345
108. 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
109. 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
110. O'Sullivan DJ, Giblin L, McSweeney PL, Sheehan JJ, Cotter PD. 2013. Nucleic acid-based approaches to investigate microbial-related cheese quality defects. Front. Microbiol. 4:1
111. Papadimitriou K, Pot B, Tsakalidou E. 2015a. How microbes adapt to a diversity of food niches. Curr. Opin. Food Sci. 2:29-35
112. Papadimitriou K, Zoumpopoulou G, Foligné B, Alexandraki V, KazouM, et al. 2015b. Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches. Front. Microbiol. 6:58
113. Park K-Y, Jeong J-K, Lee Y-E, Daily JW III. 2014. Health benefits of kimchi (Korean fermented vegetables) as a probiotic food. J. Med. Food 17:6-20
114. Po?ka 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
115. 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. 81:3529-41
116. Pothakos V, Taminiau B, Huys G, NezerC, Daube G, Devlieghere F. 2014. Psychrotrophic lactic acid bacteria associated with production batch recalls and sporadic cases of early spoilage in Belgium between 2010 and 2014. Int. J. Food Microbiol. 191:157-63
117. Quick J, Ashton P, Calus S, Chatt C, Gossain S, et al. 2015. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 16:114
118. 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. 78:5717-23
119. Quigley L, O'Sullivan DJ, Daly D, O'Sullivan O, Burdikova Z, et al. 2016. Thermus and the pink discoloration defect in cheese. mSystems 1:00023-16
120. Rebollar EA, Antwis RE, BeckerMH, Belden LK, Bletz MC, et al. 2016. Using omics and integrated multiomics approaches to guide probiotic selection tomitigate chytridiomycosis and other emerging infectious diseases. Front. Microbiol. 7:68
121. Remenant B, Jaffrès E, Dousset X, Pilet M-F, Zagorec M. 2015. Bacterial spoilers of food: behavior, fitness and functional properties. Food Microbiol. 45:45-53
122. Reuter JA, Spacek DV, Snyder MP. 2015. High-throughput sequencing technologies. Mol. Cell 58:586-97
123. Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, et al. 2013. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLOS Med. 10:e1001387
124. Roos S, Dicksved J, Tarasco V, Locatelli E, Ricceri F, et al. 2013. 454 pyrosequencing analysis on faecal samples from a randomized DBPC trial of colicky infants treated with Lactobacillus reuteri DSM 17938. PLOS ONE 8:e56710
125. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, et al. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348-52
126. Salipante SJ, Kawashima T, Rosenthal C, Hoogestraat DR, Cummings LA, et al. 2014. Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling. Appl. Environ. Microbiol. 80:7583-91
127. Samson JE, Moineau S. 2013. Bacteriophages in food fermentations: new frontiers in a continuous arms race. Annu. Rev. Food Sci. Technol. 4:347-68
128. Scallan E, Hoekstra R, Mahon B, Jones T, Griffin P. 2015. An assessment of the human health impact of seven leading foodborne pathogens in the United States using disability adjusted life years. Epidemiol. Infect. 143:2795-804
129. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, et al. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. PNAS 109:6241-46
130. Smid E, Hugenholtz J. 2010. Functional genomics for food fermentation processes. Annu. Rev. Food Sci. Technol. 1:497-519
131. Stasiewicz MJ, den Bakker HC, Wiedmann M. 2015. Genomics tools in microbial food safety. Curr. Opin. Food Sci. 4:105-10
132. Steensels J, Snoek T, Meersman E, NicolinoMP, Voordeckers K, Verstrepen KJ. 2014. Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol. Rev. 38:947-95
133. Steensels J, Verstrepen KJ. 2014. Taming wild yeast: potential of conventional and nonconventional yeasts in industrial fermentations. Annu. Rev. Microbiol. 68:61-80
134. Steyer D, Ambroset C, Brion C, Claudel P, Delobel P, et al. 2012. QTL mapping of the production of wine aroma compounds by yeast. BMC Genom. 13:573
135. Strachan NJ, Rotariu O, Lopes B, MacRae M, Fairley S, et al. 2015. Whole genome sequencing demonstrates that geographic variation of Escherichia coli O157 genotypes dominates host association. Sci. Rep. 5:14145
136. Sun Z, Harris HM, McCann A, Guo C, Argimón S, et al. 2015. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat. Commun. 6:8322
137. Tarazona S, Garcá-Alcalde F, Dopazo J, Ferrer A, Conesa A. 2011. Differential expression in RNA-seq: a matter of depth. Genome Res. 21:2213-23
138. Taylor AJ, Lappi V, Wolfgang WJ, Lapierre P, Palumbo MJ, et al. 2015. Characterization of foodborne outbreaks of Salmonella enterica serovar Enteritidis with whole-genome sequencing single nucleotide polymorphism-based analysis for surveillance and outbreak detection. J. Clin. Microbiol. 53:3334-40
139. Veiga P, Pons N, Agrawal A, Oozeer R, Guyonnet D, et al. 2014. Changes of the human gut microbiome induced by a fermented milk product. Sci. Rep. 4:6328
140. Ventura M, O'Flaherty S, Claesson MJ, Turroni F, Klaenhammer TR, et al. 2009. Genome-scale analyses of health-promoting bacteria: probiogenomics. Nat. Rev. Microbiol. 7:61-71
141. Walsh AM, Crispie F, Kilcawley K, O'Sullivan O, O'Sullivan MG, et al. 2016. Microbial succession and flavor production in the fermented dairy beverage kefir. mSystems. http://dx. doi. org/10. 1128/ mSystems. 00052-16
142. Wang J, Tang H, Zhang C, Zhao Y, Derrien M, et al. 2015. Modulation of gut microbiota during probioticmediated attenuation of metabolic syndrome in high fat diet-fed mice. ISME J. 9:1-15
143. Wang Z-M, Lu Z-M, Shi J-S, Xu Z-H. 2016. Exploring flavour-producing core microbiota in multispecies solid-state fermentation of traditional Chinese vinegar. Sci. Rep. 6:26818
144. Wei Y-X, Zhang Z-Y, Liu C, Malakar PK, Guo X-K. 2012. Safety assessment of Bifidobacterium longum JDM301 based on complete genome sequences. World J. Gastroenterol. 18:479-88
145. Winkler JD, Kao KC. 2014. Recent advances in the evolutionary engineering of industrial biocatalysts. Genomics 104:406-11
146. 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
147. WuQ, Cheung CK, ShahNP. 2015. Towards galactose accumulation in dairy foods fermented by conventional starter cultures: challenges and strategies. Trends Food Sci. Technol. 41:24-36
148. 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
149. Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, et al. 2015. The soil microbiome influences grapevine-associated microbiota. mBio 6:e02527-14
150. ZhangC, Derrien M, Levenez F, BrazeillesR, Ballal SA, et al. 2016. Ecological robustness of the gutmicrobiota in response to ingestion of transient food-borne microbes. ISME J. 10:2235-45
151. Zhang S, Yin Y, Jones MB, Zhang Z, Kaiser BLD, et al. 2015. Salmonella serotype determination utilizing high-throughput genome sequencing data. J. Clin. Microbiol. 53:1685-92
152. Zhao M, ZhangD-L, SuX-Q, Duan S-M, Wan J-Q, et al. 2015. An integrated metagenomics/metaproteomics investigation of the microbial communities and enzymes in solid-state fermentation of Pu-erh tea. Sci. Rep. 5:10117
153. Zheng J, Zhao X, Lin XB, Gänzle M. 2015. Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations. Sci. Rep. 5:18234