Supplemental Table 1. HTS studies of food microbiome. Studies are grouped according to the type of food.

Supplemental Material: Annu. Rev. Food Sci. Technol. 2018. 9:589 608 https://doi.org/10.1146/annurev-food-030117-012312 Recent Past, Present, and Future of the Food Microbiome De Filippis, Parente, and Ercolini Supplemental Table 1. HTS studies of food microbiome. Studies are grouped according to the type of food. Food Category Product Environment sampling 16S V region cereals rice no V6-V8 D cereals sourdough no V1-V3 D cereals chica no V3-V5 D cereals sourdough no V1-V3 D cereals sourdough no V1-V3 D cereals rice beer no V1-V3 ITS2 D Fungi Template Study Aim Microbiota involved in the fermentation of nukadoko, a traditional fermented rice product Microbiota of sourdough used for Italian traditions sweet goods Microbiota diversity in the chica, a maize-based fermented beverage, during the manufacturing steps Monitoring of bacterial populations during organic sourdough fermentation in smallscale and industrial bakeries Characterization of microbiota in 16 French sourdoughs Microbiota in traditional Korean rice beer fermentation produced with different natural starters cereals barley malt no V3-V4 D Microbiota during malting cereals cereals cereals sourdough, sake, beer, yes V1-V3 18S rr cd yes V4 ITS1 D yes V4 D contaminating bakery and involved in sourdough fermentation involved in sake fermentation and contaminating production Bacterial populations during spontaneous fermentation of American coolship ale (beer) Most abundant bacterial species involved in the process Lactobacillus acetotolerans, Lb. namurensis, Lb. acidipiscis, Lb. parabuchneri, Lb. paralimentarius, Acetobacter pasteurianus Lactobacillus sanfranciscensis, Lb. plantarum, Lb. brevis Weissella viridescens, Lactococcus lactis, Lactobacillus plantarum, Lb. rossiae, Enterococcus hirae, Leuconostoc mesenteroides Lactobacillus sanfranciscensis, Lb. hammesii Lactobacillus sanfranciscensis, Lb. hammesii, Lb. plantarum Lactobacillus plantarum, Lb. parabuchneri, Lb. casei, Lb. fermentum, Weissella, Leuconostoc, Pediococcus, Lactococcus Weissella, Leuconostoc pseudomesenteroides, Lactobacillus, Pediococcus pentosaceus Lactobacillus curvatus, Lb. sanfranciscensis, Lb. brevis, Lb. pontis, Weissella cibaria Lactococcus lactis, lactobacillus fermentum, Lb. parabrevis, Lb. plantarum, Lb. acidophilus Pediococcus, Lactobacillus brevis, Lactococcus garviae Most abundant fungal species involved in the process Saccharomyces, Sacharomycopsis, Rhizopus, Pichia Type of process Reference Sakamoto et al., 2011 Lattanzi et al., 2013 Elizaquı vel et al., Lhomme et al., a Lhomme et al., b Jung M-J et al., 2012 Justé et al., 2014 Saccharomyces cerevisiae, Kazachstania exigua Aspergillus flavus, Saccharomyces cerevisiae, Wickerhamomyces anomalus Minervini et al., Bokulich et al., 2014a Bokulich et al., 2012a

cereals sourdough no V1-V2 D cereals sourdough no V2-V3 D cereals sourdough no V1-V3 D a cd cereals sourdough no V1-V3 cd dairy cheese no V3-V4 D dairy cheese no V3-V4 D dairy milk kefir no V1-V2 D Changes in bacterial communities during 56 back-slopping of rye sourdough fermented at different temperatures Bacterial populations during rye sourdough fermentation in 4 different bakeries Bacterial populations during fermentation of rye and wheat sourdoughs propagated for 10 days Effect of agricultural practices on the microbiota involved in sourdough fermentation Effect of whey dilution and temperature during production of a Dutch-type cheese Microbiota diversity in the Mexican Pico cheese produced in different dairy and at different ripening ages Microbial diversity in kefir grains collected in different Brazilian regions Lactobacillus graminis, Lb. paralimentarius, Lb. brevis, Lb. plantarum, Lb. pentosus, Weissella confusa, Leuconostoc citreum Lactobacillus amylovorus, Lb. pontis, Lb. helveticus, Lb. sanfranciscensis Lactobacillus sakei, Leuconostoc, Weissella, Lactobacillus plantarum Lactobacillus plantarum, Leuconostoc citreum, Lactococcus lactis, Lb. brevis, Lb. sanfranciscensis Lactococcus raffinolactis, Lactococcus chungangensis. Leuconostoc mesenteroides, Leuconostoc pseudomesenteroides, Lactobacillus curvatus/sakei, Lactococcus lactis Lactococcus, Streptococcus, Enterococcus, Acinetobacter, Staphylococcus Lactobacillus kefiranofaciens, Lb. kefiri, Leuconostoc mesenteroides, Lactococcus lactis Bessmeltseva et al., 2014 Viiard et al., Ercolini et al., 2013 Rizzello et al., Porcellato et al., Riquelme et al., Leite et al., 2012 dairy kefir no V1-V2 D Microbiota in Turkish kefir grains Lactobacillus kefiranofaciens dairy cheese no V1-V3 D dairy beverage no V4 ITS1 D dairy cheese, yes V1-V3 D Influence of seasonality on the microbiota of the Mexican Poro cheese during manufacturing and ripening Influence of milk type and regionalism on the microbiota of the African fermented milk Matsoni Bacterial populations contaminating dairy and involved in different cheese manufacturing and ripening Streptococcus thermophilus, Lactobacillus delbrueckii, Lactobacillus helveticus, Macrococcus caseolyticus Streptococcus, Lactobacillus, Lactococcus, Enterococcus Streptococcus thermophilus, Lactobacillus helveticus, Lb. delbrueckii, Macrococcus caseolyticus, Lactococcus lactis, Lc. garviae Kluyveromyces marxianus, Saccharomyces cerevisiae, Caida famata Nalbantoglu et al., 2014 Aldrete-Tapia et al., 2014 Bokulich et al., Calasso et al.,

dairy beverage no V1-V3 18S rr D dairy cheese no V4 D dairy cheese, yes V4 ITS1 D dairy cheese no V4 D dairy beverage no V3-V6 D dairy cheese no V1-V3 D dairy kefir no V4-V5 ITS1-2 D dairy cheese no V4-V5 D dairy beverage no V3 ITS1-2 D dairy cheese no V1-V3 D dairy only yes V1-V2 D of traditional fermented milks from Mongolia and Russia Influence of type of milk and ripening time on the microbiota of traditional Irish cheeses and cheese rinds Influence of resident bacterial and fungal populations in dairy on washed rind cheeses microbiota Influence of production time (within the same day) on microbiota composition in a continental-type cheese Microbiota of a traditional Chinese fermented milk (yond baps) produced in different regions Microbiota in Latin-style cheeses produced in different dairies in kefir milk and grains Bacterial populations in Croatian raw ewe s milk cheeses during ripening Bacterial and fungal communities in tarag (fermented milk) from different regions of Mongolia and China Bacterial populations in PDO Herve cheese made with raw or pasteurized cow s milk Bacterial contamination in floor drains of a cheese manufacturing plant Lactobacillus delbrueckii, Lb. helveticus, Lb. kefiranofaciens, Lactococcus, Streptococcus Galactomyces, Pichia, Vanderwaltozyma Lactobacillus, Lactococcus Lactococcus, Brevibacterium, Lactobacillus Debaryomyces hansenii, Penicillium commune, Lachancea thermotholerans Liu W et al., Lactobacillus, Streptococcus, Thermus Lactococcus lactis, Lactobacillus kefiranofaciens, Lactococcus lactis, Vagococcus Exiguobacterium, Lactococcus, Clostridiaceae Lactobacillus, Acetobacter, Lactococcus, Leuconostoc Lactococcus lactis, Streptococcus parauberis, Enterococcus, Leuconostoc mesenteroides Lactobacillus, Streptococcus, Acetobacter, Lactococcus Corynebacterium casei, Psychrobacter, Lactococcus lactis, Staphylococcus equorum, Vagococcus salmoninarum Leuconostoc citreum, Pseudomonas mucidolens, Pseudomonas fragi, Leuconostoc citreum, Acetobacter tropicalis, Lactococcus lactis, Acetobacter tropicalis Quigley et al., 2012 Bokulich et al., 2013a O'Sullivan et al., Liu X-F et al., Lusk et al., 2012 Kazachstania, Kluyveromyces, Naumovozyma Marsh et al., 2013 Fuka et al., 2013 Galactomyces, Saccharomyces, Kluyveromyces Sun et al., 2014 tracking Delcenserie et al., 2014 Dzieciol et al.,

dairy cheese no V3-V4 D dairy ricotta no V3-V4 D dairy cheese no V1-V3 D dairy cheese no V1-V3 cd dairy cheese, yes V1-V3 ITS1-4 D dairy cheese no V1-V3 D dairy cheese, yes V1-V3 26S D dairy milk kefir no V1-V3 26S D dairy cheese no V1-V3 cd dairy cheese no V1-V3 D dairy cheese no V1-V3 D blowing defect of an Italian longripened cheese (Grana Padano) Bacterial populations during shelflife of ricotta cheese Mozzarella cheese manufacturing PDO Fontina cheese ripening and effect of milk from different bovine lactation phases involved in red-brown defect of Fontina cheese and associated ripening shelves curd fermentation of long-ripened and pasta-filata cheeses Environmental microbiota in a dairy and different types of cheeses produced in the same plant in kefir grains from different Italian regions Microbiota involved in fermentation and ripening of Grana-type cheese and influence of raw milk Microbiota involved in spoilage of high-moisture Mozzarella cheese produced with different acidification methods Bacterial populations in natural milk cultures for pasta-filata cheeses production Lactobacillus rhamnosus, Lb. delbrueckii, Lb. buchneri, Lb. casei, Streptococcus, Clostridium tyrobutyricum, Cl. butyricum Bassi et al., Bacillus, Paenibacillus, Clostridium Sattin et al., Streptococcus thermophilus, Lactobacillus delbrueckii, Lb. helveticus, Lactococcus lactis Lactobacillus casei, Lb. delbrueckii, Streptococcus thermophilus, Lactococcus lactis Streptococcus thermophilus, Lactobacillus delbrueckii, Lactococcus lactis, Brevibacterium, Corynebacterium, Leuconostoc Lactobacillus delbrueckii, Lb. helveticus, Streptococcus thermophilus Streptococcus thermophilus, Lactobacillus delbrueckii, Acinetobacter johnsonii, Pseudomonas Lactobacillus kefiranofaciens, Lb. kefiri, Lactococcus lactis Lactobacillus helveticus, Lb. delbrueckii, Lb. casei, Streptococcus thermophilus, Propionibacterium acnes Streptococcus thermophilus, Lactococcus lactis, Lactobacillus helveticus, Lb. delbrueckii, Pseudomonas, Enterobacteriaceae Streptococcus thermophilus, Lactobacillus delbrueckii, Lactococcus lactis Ercolini et al., 2012 Dolci et al., 2014 Debaryomyces, Galactomyces, Candida, Tremellomycetes Kluyveromyces marxianus, Yamadazyma triangularis, Trichosporon faecale, Debaryomyces hansenii Sacharomyces cerevisiae, Kazachstania exigua, Dekkera anomala tracking/ferm entation / Guzzon et al., 2017 De Filippis et al., 2014 Stellato et al., Garofalo et al., Alessandria et al., Guidone et al., Parente et al.,

dairy cheese no V1-V3 cd dairy milk kefir no V3-V4 ITS1-2 D dairy cheese no V1-V3 cd dairy cheese no V1-V3 cd Different refrigerated products ready-to-eat meals, yes V1-V3 D fish surimi no V4 D fish fish salted shrimp salmon no V1-V3 D yes, but not used for HTS V4 D legumes doenjang no V1-V2 D legumes doenjangmeju no V1-V3 D1-D2 region of 28S rr gene D meat pork no V1-V3 D Bacterial populations and metabolome during manufacturing and ripening of PDO Caciocavallo Silano pasta-filata cheese and related metabolome during kefir grains fermentation Bacteria communities and metabolome in ripened Italian ewes milk cheeses Microbiota and metabolome during manufacturing and ripening of an Italian pasta-filata cheese Microbiota involved in spoilage of refrigerated, ready-to-eat meals and contamination of the processing Evolution of microbial populations during surimi fermentation Changes in bacterial populations in fermentation of saeu-jeot (traditional Korean fermented shrimp) fermented with different salt concentrations spoilage of salmon fillets from different processing plants Microbiota during fermentation of a traditional Korean soybean paste involved in the fermentation of doenjang-meju, a traditional Korean product Microbiota and metabolome in spoiled, vacuum-packed pork Lactobacillus casei, Lb. buchneri, Lb. fermentum, Streptococcus thermophilus Lactobacillus kefiranofaciens, Leuconostoc mesenteroides, Acetobacter pasteurianus Lactococcus lactis, Streptococcus thermophilus, Lactobacillus delbrueckii, Lactobacillus buchneri Streptococcus thermophilus, Lactobacillus casei, Lactobacillus paracasei, Lactobacillus buchneri Pseudomonas, Leuconostoc gelidum, Streptococcus, Lactobacillus, Lactococcus Enterobacteriaceae, Bacillaceae, Enterococcus, Stenotrophomonas, Acinetobacter Salimicrobium, Halanaerobium, Halomonas, Salinivibrio Pseudomonas, Photobacterium, Shewanella, Acinetobacter Bacillus licheniformis, Bacillus subtilis, Tetragenococcus halophilus, Enterococcus faecalis, Enterococcus faecium Staphylococcus gallinarum Bacillus, Myroides, Clostridium, Corynebacterium Brochothrix, Photobacterium, Weissella, Lactobacillus Saccharomices, Kazachstania De Filippis et al., Walsh et al., tracking/spoil age De Pasquale et al., De Pasquale et al., 2014 Pothakos et al., Zhao et al., Lee et al., 2014 Moretro et al., 206 Nam et al., 2012 Aspergillus, Mucor, Geotrichum, Scopulariopsis Jung et al., 2014 Nieminem et al.,

meat beef no V1-V3 D meat salami no V3-V4 D meat meat meat white pudding cattle carcasses pig carcasses no V1-V3 D no V1-V3 D no V1-V2 D meat minced meat no V4-V5 D meat beef no V1-V3 D meat sausages, yes V1-V3 D meat sausages no V1-V3 D meat ham no V4 D microbiota and metabolite production in beef stored under-vacuum or in highoxygen atmosphere Microbiota during fermentation of traditional Italian salami produced in 6 local factories spoilage of Belgian white pudding (meat + oatmeal) Differences in superficial contamination of cattle carcasses according to the slaughtering practice (classical or Halal) Bacterial contamination of pig carcasses spoilage of minced meat stored under modified atmosphere with the addition of different preservatives spoilage of beefsteaks stored under modified atmosphere spoilage of vacuum-packaged sausages and contamination in related processing Effect of packaging (vacuum or modified atmosphere) and salt content on bacterial populations involved in pork sausages spoilage and related metabolites vacuum-packed, cooked ham spoilage and effect on sensorial properties Lactobacillus, Leuconostoc, Photobacterium, Lactococcus Staphylococcus saprophyticus, Staph. xylosus, Staph. equorum, Lactobacillus sakei Carnobacterium maltaromaticum, Lactococcus lactis, Lactobacillus fuchuensis, Lb. graminis, Serratia Staphylococcus, Prevotella, Macrococcus, Corynebacterium Serratia proteamaculans, Pseudomonas syringae, Aeromonas allosaccharophila, Brochothrix thermosphacta, Acidiphilium cryptum, Escherichia coli Lactobacillus algidus, Leuconostoc, Pseudomonas, Propionibacterium acnes, Photobacterium Brochothrix, Carnobacterium, Leuconostoc, Lactococcus Leuconostoc, Lactobacillus, Yersinia, Brochothrix, Streptococcus Lactobacillus sakei, Lactococcus piscium, Carnobacterium divergens, Carnobacterium maltaromaticum, Serratia proteamaculans, Brochothrix thermosphacta Brochothrix thermosphacta, Lactobacillus, Micrococcus, Pseudomonas, Vagococcus Jääskeläinen et al., Polka et al., tracking tracking Cauchie et al., Korsak et al., Mann et al., Stoops et al., Sade et al., 2017 tracking/spoil age Hultman et al., Fougy et al., Piotrowska- Cyplik et al.,

meat meat meat beefsteaks, cattle carcasses, beef, pork, sausages yes V1-V3 D yes V1-V3 D yes, but not used for HTS V1-V3 cd meat beef no V1-V3 cd meat beef no V1-V3 D meat sausages no V1-V2 D meat meat/fish sausage casings beef, bacon, poultry sausages, shrimps, salmon, cod no V3-V4 D no V1-V3 D other salt no V3-V5 D aerobic spoilage of beefsteaks and contamination from butcher's shop Environmental microbiota in small- and large-scale meat retails and related beef/pork meat Bacterial populations during Italian salami fermentation and ripening Microbial populations involved in spoilage of beef burgers packaged under-vacuum or in nisinactivated packaging Changes in spoilage-associated microbiota a metabolome accordingly to storage conditions (air, vacuum, active packaging, MAP) Effect of different concentrations of lactate and di-acetate in fresh pork sausages spoilage Microbial populations in natural casings for sausages production Identification of core and foodspecific bacterial populations involved in spoilage of seafood and meta products and their ecological origin Archaea diversity in food-grade salt Brochothrix thermosphacta, Pseudomonas, Psychrobacter, Acinetobacter Pseudomonas, Brochothrix, Streptococcus, Psychrobacter Lactobacillus sakei, Leuconostoc carnosum, Staphylococcus succinus, Lb. curvatus Photobacterium phosphoreum, Lactococcus piscium, Lactobacillus sakei, Leuconostoc carnosum Pseudomonas, Brochothrix, Carnobacterium divergens, Lactococcus, Streptococcus, Lactobacillus, Ralstonia Leuconostoc citreum, Pseudomonas lini, Carnobacterium divergens, Lactobacillus graminis, Lb. gasseri, Serratia Vagococcus, Clostridium, Pediococcus, Lactobacillus, Acinetobacter, Staphylococcus Staphylococcus, Pseudomonas, Brochothrix, Leuconostoc, Flavobacterium, Chryseobacterium, Photobacterium, Corynebacterium, Propionibacterium, Lactobacillus, Enterococcus, Clostridium Haloarcula, Halonotius, Halorubrum tracking/spoil age tracking/spoil age tracking tracking/spoil age tracking De Filippis et al., 2013 Stellato et al., Greppi et al., Ferrocino et al., Ercolini et al., 2011 Benson et al., 2014 Rebecchi et al., Chaillou et al., Henriet et al., 2014

other Different refrigerated products (cheese, ready-to-eat meals, turkey slices, boiled eggs) no V1-V3 D tea kombucha no V4-V5 ITS1-2 D vegetables kimchi no V1-V3 D vegetables vinegar no V1-V3 D vegetables grape no V3-V6 D vegetables vegetables grape (vineyard) grape (must a grape bunches) no V6 ITS2 a D2 domai n of LSU rr gene D no V5-V6 D vegetables olives no ITS1-2 D vegetables kimchi no V1-V3 D Microbial populations involved in spoilage of different refrigerated products during kombucha (a fermented tea) fermentation Effect of red pepper powder on kimchi microbiota and metabolome Batch effect in microbiota composition and metabolome of fermented aromatic vinegar Microbial populations during grape marc fermentation Monitoring of fungal and bacterial populations during the year in a vineyard (leaves) Monitoring of bacterial populations during fermentation of three wine variety Monitoring fungal populations during table olive fermentation in three industries Effect of addition of Leuconostoc mesenteroides as starter in microbiota and metabolome during kimchi fermentation Leuconostoc gelidum, Leuconostoc carnosum, Lactobacillus sakei Pothakos et al., 2014 Gluconacetobacter Zygosaccharomyces, Pichia Marsh et al., 2014 Lactobacillus, Leuconostoc, Weissella Jeong et al., 2013 Lactobacillus, Acetobacter, Leuconostoc Wang et al., Gluconobacter, Gluconacetobacter, Tatumella, Lactobacillus fabifermentans, Oenococcus Enterococcus, Leuconostoc, Weissella, Streptococcus, Lactococcus Gluconobacter, Oenococcus, Shewanella, Halomonas Rhizopus, Mucor, Aureobasidium, Sporormiella, Alternaria Pichia, Saccharomyces, Candida Campanaro et al., 2014 Pinto et al., 2014 Lactobacillus, Leuconostoc, Weissella Marzano et al., Arroyo-Lopez et al., Jung JY et al., 2012

vegetables kimchi no V1-V3 D vegetables olives no V1-V3 vegetables grape no V6 vegetables grape no vegetables grape no vegetables grape no vegetables grapes (winery ) V4 and V5 ITS2 a D2 domai n of LSUof rr gene D1-D2 region of 28S rr gene 18S rr D and cd D D D D yes V4 ITS1-2 D vegetables grape no V4 ITS1-2 D Microbiota in different types of kimchi Influence of starter addition on the microbiota of table olives during fermentation in Portuguese wine from different regions Fungal populations during Spanish wine fermentation Fungal populations during organic, conventional and ecophyto Chardonnay grape must fermentation Bacterial populations during fermentation of wine with and without Saccharomyces inoculum. The comparison of results obtained with different 16S V regions was carried out. in winery Associations of fungal and bacterial populations of different vineyards with climate and geographical origin and influence on must microbiota Weissella, Leuconostoc, Lactobacillus Park et al., 2012 Lactobacillus plantarum, Lb. coryniformis, Lb. pentosus, Lb. brevis, Enterobacteriaceae, Halomonadaceae Acetobacter, Gluconobacter, Gluconacetobacter Pseudomonas, Flavobacterium, Bacillus, Brevundimonas Gluconobacter, Acetobacter, Pseudomonas Aureobasidium, Rhodotorula, Hanseniaspora, Saccharomyces, Lachancea Hanseniaspora uvarum, Starmerella bacillaris, Saccharomyces cerevisiae, Aureobasidium pullulans Hanseniaspora, Candida, Cladosporium Saccharomyces cerevisiae, Cryptococcus, Hanseniaspora uvarum Cladosporium, Penicillium, Aureobasidium pullulans, Botrytis cinerea, Saccharomyces cerevisiae, Hanseniaspora huvarum De Angelis et al., Pinto et al., Wang et al., David et al., 2014 Bokulich et al., 2012b Bokulich et al., 2013b Bokulich et al., 2014b

vegetables grape no V1-V3 ITS1-2 D vegetables ready-to-eat leaf vegetables vegetables tomatoes no V2 no V6-V8 D 18S rr D vegetables spinach no V4 D vegetables olives no V1-V3 D and cd vegetables grape no 18S D during fermentation of Vin Santo in 3 different winery Bacterial contamination of readyto-eat leafy vegetables grown organically or conventionally associated to tomatoes associated to fresh and packages spinach during storage Monitoring of bacterial populations involved in olive fermentation for 90 days and effect of NaOH treatment Fungal populations during fermentation of two Italian wines Oenococcus Acinetobacter, Erwinia, Flavobacterium, Pseudomonas, Pantoea, Serratia Xanthomonas, Sphingomonas, Rhizobium, Pseudomonas, Pantoea Massilia, Oxalobacteraceae, Comamonadaceae, Naxibacter, Pseudomonas, Brevuimonas Enterobacter, Lactobacillus plantarum, Halomonas Aureobasidium pullulans, Candida zemplinina, Saccharomyces cerevisiae, Hanseniaspora osmophila Aureobasidium, Fusarium Saccharomyces cerevisiae, Candida zeylanoides, Hanseniaspora uvarum, Zygosaccharomyces rouxii tracking Stefanini et al., Jackson et al., 2013 Ottesen et al., 2013 Lopez-Velasco et al., 2011 Cocolin et al., 2013 De Filippis et al., 2017

Supplemental Literature Cited Aldrete-Tapia A, Escobar-Ramírez MC, Tamplin ML, Hernández-Iturriaga M. 2014. Highthroughput sequencing of microbial communities in Poro cheese, an artisanal Mexican cheese. Food Microbiol. 44:136--41 Alessandria V, Ferrocino I, De Filippis F, Fontana M, Rantsiou K, et al.. Microbiota of an Italian Grana like cheese during manufacture and ripening unraveled by 16S rr-based approaches. Appl. Environ. Microbiol. 82(13):3988 95 Arroyo-López FN, Medina E, Ruiz-Bellido MÁ, Romero-Gil V, Montes-Borrego M, Landa BB.. Enhancement of the knowledge on fungal communities in directly brined Aloreña de Málaga green olive fermentations by metabarcoding analysis. PLOS ONE 11(9):e0163135 Bassi D, Puglisi E, Cocconcelli PS.. Understanding the bacterial communities of hard cheese with blowing defect. Food Microbiol. 52:106 18 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 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 Bokulich, Ohta M, Lee M, Mills DA. 2014a. Indigenous bacteria and fungi drive traditional kimoto sake fermentations. Appl. Environ. Microbiol. 80(17):5522 29 Bokulich, Bamforth CW, Mills DA. 2012a. Brewhouse-resident microbiota are responsible for multi-stage fermentation of American coolship ale. PLOS ONE 7(4):e35507 Bokulich, Amiranashvili L, Chitchyan K, Ghazanchyan N, Darbinyan K, et al.. Microbial biogeography of the transnational fermented milk matsoni. Food Microbiol. 50:12 19 Bokulich, Mills DA. 2013a. Facility-specific house microbiome drives microbial landscapes of artisan cheesemaking plants. Appl. Environ. Microbiol. 79:5214--23 Bokulich, Joseph CML, Allen G, Benson AK, Mills DA. 2012b. Next-generation sequencing reveals significant bacterial diversity of botrytized wine. PLOS ONE 7(5):e36357 Bokulich, Ohta M, Richardson PM, Mills DA. 2013b. Monitoring seasonal changes in winery-resident microbiota. PLOS ONE 8(6):e66437 Bokulich, Thorngate JH, Richardson PM, Mills DA. 2014b. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. PS 111(1):E139 48 Calasso M, Ercolini D, Mancini L, Stellato G, Minervini F, et al.. Relationships among house, rind and core microbiotas during manufacture of traditional Italian cheeses at the same dairy plant. Food Microbiol. 54:115 26 Campanaro S, Treu L, Vendramin V, Bovo B, Giacomini A, Corich V. 2014. Metagenomic analysis of the microbial community in fermented grape marc revelas that Lactobacillus fabifermentans is one of the dominant species: insights into its genome structure. Appl. Microb. Biotechnol. 98:6015--37 Cauchie E, Gand M, Kergourlay G, Taminiau B, Delhalle L, et al.. The use of 16S rr gene metagenetic monitoring of refrigerated food products for understanding the kinetics of microbial subpopulations at different storage temperatures: the example of white pudding. Int. J. Food Microbiol. 247:70 78 Chaillou S, Chaulot-Talmon A, Caekebeke H, Cardinal M, Christieans S, et al.. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage. ISME J. 9(5):1105--18 Cocolin L, Alessandria V, Botta C, Gorra R, De Filippis F, et al. 2013. NaOH-debittering induces changes in bacterial ecology during table olives fermentation. PLOS ONE 8(7):e69074

David V, Terrat S, Herzine K, Claisse O, Rousseaux S, et al. 2014. High throughput sequencing of amplicons for monitoring yeast biodiversity in must and during alcoholic fermentation. J. Ind. Microbiol. Biotechnol. 41:811 21 De Angelis M, Campanella D, Cosmai L, Summo C, Rizzello CG, Caponio F.. Microbiota and metabolome of un-started and started Greek-type fermentation of Bella di Cerignola table olives. Food Microbiol. 52:18 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 De Filippis F, Genovese A, Ferranti P, Gilbert JA, Ercolini D.. Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Sci. Rep. 6:21871 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 De Filippis F, La Storia A, Blaiotta G. 2017. Monitoring the mycobiota during Greco di Tufo and Aglianico wine fermentation by 18S rr gene sequencing. Food Microbiol. 63:117--22 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 De Pasquale I, Di Cagno R, Buchin S, De Angelis M, Gobbetti M.. Spatial distribution of the metabolically active microbiota within Italian PDO ewes milk cheeses. PLOS ONE 11(4):e0153213 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 Dolci P, De Filippis F, La Storia A, Ercolini D, Cocolin L. 2014. rr-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 Dzieciol M, Schornsteiner E, Muhterem-Uyar M, Stessl B, Wagner M, Schmitz-Esser S.. Bacterial diversity of floor drain biofilms and drain waters in a Listeria monocytogenes contaminated food processing. Int. J. Food Microbiol. 223:33 40 Elizaquı vel P, Pérez-Cataluña A, Yépez A, Aristimuño C, Jiménez E, et al.. 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 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 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(22):8142 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 Ferrocino I, Greppi A, La Storia A, Rantsiou K, Ercolini D, Cocolin L.. Impact of nisinactivated packaging on microbiota of beef burgers during storage. Appl. Environ. Microbiol. 82(2):549--59 Fougy L, Desmonts M-H, Coeuret G, Fassel C, Hamon E, et al.. Salt reduction in raw pork sausages increases spoilage and correlates with reduced bacterial diversity. Appl. Environ. Microbiol. 82(13):3928--39

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 Garofalo C, Osimani A, Milanović V, Aquilanti L, De Filippis F, et al.. Bacteria and yeast microbiota in milk kefir grains from different Italian regions. Food Microbiol. 49:123--33 Guidone A, Matera A, Ricciardi A, Zotta T, De Filippis F, et al.. The microbiota of highmoisture Mozzarella cheese produced with different acidification methods. Int. J. Food. Microbiol. 216:9 17 Greppi A, Ferrocino I, La Storia A, Rantsiou K, Ercolini D, Cocolin L.. Monitoring of the microbiota of fermented sausages by culture independent rr-based approaches. Int. J. Food Microbiol. 212:67 75 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 Henriet O, Fourmentin J, Delincé B, Mahillon J. 2014. Exploring the diversity of extremely halophilic archaea in food-grade salts. Int. J. Food Microbiol. 191:36 44 Hultman J, Rahkila R, Ali J, Rousu J, Björkroth KJ.. 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(20):7088--97 Ja a skela inen E, Hultman J, Parshintsev J, Riekkola M-L, Björkroth J.. Development of spoilage bacterial community and volatile compounds in chilled beef under vacuum or high oxygen atmospheres. Int. J. Food Microbiol. 223:25 32 Jackson CR, Randolph KC, Osborn SL, Tyler HL. 2013. Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables. BMC Microbiol. 13:274 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 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 Jung JY, Lee SH, Lee HJ, Seo H-Y, Park W-S, Jeon CO. 2012. Effects of Leuconostoc mesenteroides starter cultures on microbial communities and metabolites during kimchi fermentation. Int. J. Food Microbiol. 153:378--87 Jung M-J, Nam Y-D, Roh SW, Bae J-W. 2012. 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 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 Korsak N, Taminiau B, Hupperts C, Delhalle L, Nezer C, et al.. Assessment of bacterial superficial contamination in classical or ritually slaughtered cattle using metagenetics and microbiological analysis. Int. J. Food Microbiol. 247:79--86 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 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(2):e90115 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

Lhomme E, Orain S, Courcoux P, Onno B, Dousset X. a. The predominance of Lactobacillus sanfranciscensis in French organic sourdoughs and its impact on related bread characteristics. Int. J. Food Microbiol. 213:40 48 Lhomme E, Lattanzi A, Dousset X, Minervini F, De Angelis M, et al. b. Lactic acid bacterium and yeast microbiotas of sixteen French traditional sourdoughs. Int. J. Food Microbiol. 215:161--70 Liu W, Zheng Y, Kwok LY, Sun Z, Zhang J, et al.. 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 Liu X-F, Liu C-J, Zhang H-Y, Gong F-M, Luo Y-Y, Li X-R.. The bacterial community structure of yond bap, a traditional fermented goat milk product, from distinct Chinese regions. Dairy Sci. Technol. 95:369 80 Lopez-Velasco G, Welbaum GE, Boyer RR, Mane SP, Ponder MA. 2011. Changes in spinach phylloepiphytic bacteria communities following minimal processing and refrigerated storage described using pyrosequencing of 16S rr amplicons. J. Appl. Microbiol. 110:1203 14 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 Mann E, Wetzels SU, Pinior B, Metzler-Zebeli BU, Wagner M, Schmitz-Esser S.. Psychrophile spoilers dominate the bacterial microbiome in musculature samples of slaughter pigs. Meat Sci. 117:36 40 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 Marsh AJ, O Sullivan O, Hill C, Ross RP, Cotter PD. 2014. Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples. Food Microbiol. 38:171 78 Marx V.. Microbiology: the road to strain-level identification. Nat. Methods 13(5):401- -4 Marzano M, Fosso B, Manzari C, Grieco F, Intranuovo M, et al.. 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 May A, Abeln S, Crielaard W, Heringa J, Brandt BW. 2014. Unraveling the outcome of 16S rd-based taxonomy analysis through mock data and simulations. Bioinformatics 30(11):1530 38 Minervini F, Lattanzi A, De Angelis M, Celano G, Gobbetti M.. House microbiotas as sources of lactic acid bacteria and yeasts in traditional Italian sourdoughs. Food Microbiol. 52:66 76 Møretrø T, Moen B, Heir E, Hansen AA, Langsrud S.. of salmon fillets and processing plants with spoilage bacteria. Int. J. Food Microbiol. 237:98--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 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 Nieminen TT, Dalgaard P, Björkroth J.. Volatile organic compounds and Photobacterium phosphoreum associated with spoilage of modified-atmosphere-packaged raw pork. Int. J. Food Microbiol. 218:86 95 O Sullivan DJ, Cotter PD, O Sullivan O, Giblin L, McSweeney PL, Sheehan JJ.. Temporal and spatial differences in microbial composition during the manufacture of a continentaltype cheese. Appl. Environ. Microbiol. 81:2525--33

Ottesen AR, Peña AG, White JR, Pettengill JB, Li C, et al. 2013. Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiol. 13(1):114 Parente E, Guidone A, Matera A, De Filippis F, Mauriello G, Ricciardi A.. Microbial community dynamics in thermophilic undefined milk starter cultures. Int. J. Food. Microbiol. 217:59 67 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 Pinto C, Pinho D, Sousa S, Pinheiro M, Conceição E, et al. 2014. Unravelling the diversity of grapevine microbiome. PLOS ONE 9(1):e85622 Pinto C, Pinho D, Cardoso R, Custodio V, Fernandes J, et al.. Wine fermentation microbiome: a landscape from different Portuguese wine appellations. Front. Microbiol. 6:905 Piotrowska-Cyplik A, Myszka K, Czarny J, Ratajczak K, Kowalski R, et al. 2017. Characterization of specific spoilage organisms (SSOs) in vacuum-packed ham by culture-plating techniques and MiSeq next-generation sequencing technologies. J. Sci. Food Agric. 97(2):659 68 Połka J, Rebecchi A, Pisacane V, Morelli L, Puglisi E.. Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rr amplicons. Food Microbiol. 46:342--56 Porcellato D, Skeie SB.. Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese. Int. Dairy J. 61:182 88 Pothakos V, Stellato G, Ercolini D, Devlieghere F.. Processing and ingredients are both sources of Leuconostoc gelidum, which emerges as a major spoiler in ready-toeat meals. Appl. Environ. Microbiol. 81(10):3529--41 Pothakos V, Taminiau B, Huys G, Nezer C, 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 Quigley L, O Sullivan O, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD. 2012. Highthroughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. Appl Environ. Microbiol. 78:5717--23 Rebecchi A, Pisacane V, Miragoli F, Polka J, Falasconi I, et al.. High-throughput assessment of bacterial ecology in hog, cow and ovine casings used in sausages production. Int. J. Food Microbiol. 212:49--59 Riquelme C, Câmara S, Enes Dapkevicius MLN, Vinuesa P, da Silva CC, et al.. Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food). Int. J. Food Microbiol. 192:86 94 Rizzello CG, Cavoski I, Turk J, Ercolini D, Nionelli L, et al.. The organic cultivation of Triticum turgidum subsp. durum is reflected in the flour-sourdough fermentation-bread axis. Appl. Environ. Microbiol. 81(9):3192--204 Säde E, Penttinen K, Björkroth J, Hultman J. 2017. Exploring lot-to-lot variation in spoilage bacterial communities on commercial modified atmosphere packaged beef. Food Microbiol. 62:147- -52 Sakamoto N, Tanaka S, Sonomoto K, Nakayama J. 2011. 16S rr pyrosequencing-based investigation of the bacterial community in nukadoko, a pickling bed of fermented rice bran. Int. J. Food Microbiol. 144:352--59 Sattin E, Andreani, Carraro L, Fasolato L, Balzan S, et al.. 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 Stefanini I, Albanese D, Cavazza A, Franciosi E, De Filippo C, et al.. Dynamic changes in microbiota and mycobiota during spontaneous Vino Santo Trentino fermentation. Microb. Biotechnol. 9:195 208

Stellato G, De Filippis F, La Storia A, Ercolini D.. Coexistence of lactic acid bacteria and potential spoilage microbiota in a dairy-processing. Appl. Environ. Microbiol. 81(22):7893 904 Stellato G, La Storia A, De Filippis F, Borriello G, Villani F, Ercolini D.. Overlap of spoilage-associated microbiota between meat and meat processing in small-scale and large-scale retail distribution. Appl. Environ. Microbiol. 82(13):4045--54 Stoops J, Ruyters S, Busschaert P, Spaepen R, Verreth C, et al.. Bacterial community dynamics during cold storage of minced meat packaged under modified atmosphere and supplemented with different preservatives. Food Microbiol. 48:192--99 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 Viiard E, Bessmeltseva M, Simm J, Talve T, Aaspõllu A, et al.. Diversity and stability of lactic acid bacteria in rye sourdoughs of four bakeries with different propagation parameters. PLOS ONE 11(2):e0148325 Walsh AM, Crispie F, Kilcawley K, O Sullivan O, O Sullivan MG, et al.. Microbial succession and flavour production in the fermented dairy beverage kefir. msystems 1(5):e00052-16 Wang C, García-Fernández D, Mas A, Esteve-Zarzoso B.. Fungal diversity in grape must and wine fermentation assessed by massive sequencing, quantitative PCR and DGGE. Front. Microbiol. 6:1156 Zhao D, Lu F, Qiu M, Ding Y, Zhou X.. Dynamics and diversity of microbial community succession of surimi during fermentation with next-generation sequencing. J. Food Safety 36(3):308- -16