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

Transcription

1 Supplemental Material: Annu. Rev. Food Sci. Technol : 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

2 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.,

3 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.,

4 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.,

5 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.,

6 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.,

7 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

8 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

9 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

10 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

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