FoodMicrobionet 2.0.2 Project table (June 2016).

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Study FMBN version Target Region Platform Read length (bp) 2 Sequencing center Data analysis software OTU picking method Assign taxonomy method Database Sequence accession number Samples Short description Reference Commercial high-moisture De novo, QIIME produced Guidone et al., 1 0.6.2 16S DNA V1-V3 GSJ 504 DA-UNINA uclust RDP Greengenes SRP052240 29

1.8.0 with different acidification 2016 pipeline methods (A02QJ) De novo, Undefined strain starters (milk QIIME Parente et al., 2 0.6.2 16S DNA V1-V3 GSJ 498 DA-UNINA uclust RDP Greengenes SRP057506 24 cultures) for high-moisture

1.8.0 2016 pipeline Mozzarella cheese (A048Y) Undefined strain starters (whey cultures, A048Y) and cheese De novo, QIIME curds for water-buffalo De Filippis et 3 0.6.2 16S DNA V1-V3 GSJ 465 DA-UNINA uclust RDP Greengenes SRP033419 50

1.6.0 Mozzarella (A02QJ), al., 2014 pipeline Padano (A02ZQ) and Parmigiano Reggiano cheese (A02ZS) Raw milk (A02MD), whey culture (A048Y), curd before and De novo, QIIME after fermentation and water- Ercolini et al., 4 0.6.2 16S DNA V1-V3 GSJ 492 DA-UNINA uclust RDP Greengenes SRP014821 10

1.5.0 cheese 2012 pipeline (A02QJ) from two different manufactures De novo, QIIME Kefir grain and kefir milk from Marsh et al., 5 0.6.2 16S DNA V4-V5 GSFLX 346 TFRC uclust BLASTN SILVA v100 ERP002650 46

1.6.0 different sources (A02NV) 2013 pipeline De novo, Milk (A02MC), curd and ewe's 16S RNA QIIME De Pasquale et 6 0.6.2 V1-V3 GSJ 485 DA-UNINA uclust RDP Greengenes SRP038100 11 milk cheese during

(cDNA) 1.6.0 al., 2014a pipeline ripening (A02YH). BLASTN+ De novo, Milk (A02LY), curd and 16S RNA QIIME distribute De Pasquale et 7 0.6.2 V1-V3 GSFLX 515 RTL usearch Greengenes Not deposited 11 cheese during

(cDNA) 1.6.0 d .NET al., 2014b pipeline ripening (A02ZL). algorithm Milk (from different lactation De novo, 16S RNA QIIME stages, A02LY), curd and Dolci et al., 8 0.6.2 V1-V3 GSJ 490 DA-UNINA uclust RDP Greengenes SRP040575 27

(cDNA) 1.7.0 cheese (A02TY) from three 2014 pipeline different dairies Piedmont hard cheese made De novo, 16S RNA QIIME from raw milk: milk (A02LV), Alessandria et 9 0.6.2 V1-V3 GSJ 469 DA-UNINA uclust RDP Greengenes SRP044294 39

(cDNA) 1.8.0 curd and cheese throughout al., 2016 pipeline ripening (A02ZQ) Caciocavallo Silano cheese 16S DNA De novo, manufacture: starter culture and 16S QIIME De Filippis et 10 1.0.3 V1-V3 GSJ 601 DA-UNINA uclust RDP Greengenes SRP061555 68 (A048Y), milk (A02LY), curd and

RNA 1.8.0 al., 2016 pipeline cheere throughout ripening (cDNA) (A02ZL). Swabs from bovine De novo, carcass/butchery environment 1.0.3, QIIME De Filippis et 11 16S DNA V1-V3 GSJ 457 DA-UNINA uclust RDP Greengenes SRP021108 94 and samples of fresh (t0) and

1.1 1.6.0 al., 2013 pipeline spoiled (t6) beefsteaks (A01QX). Environmental samples De novo, 16S RNA QIIME Piedmontese fermented meat Greppi et al., 12 1.0.3 V1-V3 GSJ 469 DA-UNINA uclust RDP Greengenes PRJNA264135 30

(cDNA) 1.8.0 during ripening (A024V) 2015 pipeline Hamburgers (controls or with De novo, 16S RNA QIIME added preservatives, Ferrocino et 13 1.0.3 V1-V3 GSJ 472 DA-UNINA uclust RDP Greengenes SRP052241 52

(cDNA) 1.8.0 nisin+EDTA) during storage in al., 2016 pipeline vacuum packaging (A049S) 16S DNA Olive surfaces (A01BP) and brine De novo, and 16S QIIME during fermentation. Samples Cocolin et al., 14 1.0.3 V1-V3 GSFLX 432 RTL usearch BLASTn Greengenes SRP019475 20

RNA 1.6.0 were treated or untreated with 2013 pipeline (cDNA) NaOH 1% v/w De novo, Ercolini et al., QIIME Sourdoughs for croissant 15 1.0.3 16S DNA V1-V3 GSJ 496 DA-UNINA uclust RDP Greengenes NA 16 unpublished 1.9.0 production (A008K) pipeline data Durum wheat flour (cultivar De novo, Senatore Cappelli) grown under 16S RNA QIIME Rizzello et al., 16 1.0.3 V1-V3 GSJ 486 DA-UNINA uclust RDP Greengenes SRP044788 8 organic and conventional

(cDNA) 1.6.0 2015 pipeline farming and related sourdoughs (A008K) De novo, 16S RNA QIIME Rye and wheat sourdough Ercolini et al., 17 1.0.3 V1-V3 GSJ 477 DA-UNINA uclust RDP Greengenes SRP019996 15

(cDNA) 1.6.0 A008K) 2013 pipeline Environmental swabs from an Italian dairy plant and different De novo, kind of (Mozzarella QIIME Stellato et al., 18 1.1 16S DNA V1-V3 GSJ 454 DA-UNINA uclust RDP Greengenes SRP058584 45 A02QJ; , A02QL;

1.9.0 2015 pipeline A02XL; Caciocavallo A02ZL; Grancacio A02ZL) produced in the same plant Environmenal swabs, De novo, intermediate of production and QIIME Pothakos et 19 1.1 16S DNA V1-V3 GSJ 462 DA-UNINA uclust RDP Greengenes SRP049628 46 end products from a plant

1.9.0 al., 2015 pipeline producing ready-to-eat meals (A03VB) in Belgium De novo, QIIME Environmental swabs in a Stellato et al., 20 1.1 16S DNA V1-V3 GSJ 441 DA-UNINA uclust RDP Greengenes Not deposited 81

1.9.0 hospital cooking center 2015 pipeline

Environmental swabs in De novo, different butcher shops and beef QIIME 18 Stellato et al., 21 1.1 16S DNA V1-V3 GSJ 462 DA-UNINA uclust RDP Greengenes SRP072347 (A01QX) and pork (A01RG)

1.9.0 4 2016 pipeline slices collected in the same shops

Environmental swabs from an Italian dairy plant and different De novo, QIIME kind of cheeses (Caciotta A02SV; Calasso et al., 22 1.1 16S DNA V1-V3 GSJ 465 DA-UNINA uclust RDP Greengenes Not deposited 48

1.9.0 Caciocavallo Pugliese A02XE) 2016 pipeline and cow milk produced in the same plant cheese (A02ZQ) Mothur samples with blowing defect, Mothur Illumina Mothur dist.seqs from different factories, at Bassi et al., 23 1.1 16S DNA V3-V4 398 Fasteris classify.ot Greengenes PRJNA277133 37

MiSeq 1.35.0 and different ripening times, 2015 u cluster produced with and without lysozime Mothur Mothur Illumina Mothur dist.seqs Hog, cow and ovine casings used Rebecchi et al., 24 1.1 16S DNA V3-V4 398 Fasteris classify.ot Greengenes PRJNA322751 21

MiSeq 1.35.0 and in the production of sausages 2015 u cluster Continental (Swiss type cheese De novo, A02YM) produced early and late QIIME O'Sullivan et 25 1.1 16S DNA V4-V5 GSFLX 232 TFRC uclust BLASTN SILVA v1.06 PRJEB8181 31 in the day, core and rind samples

1.4.0 al., 2015 pipeline included, different ripening times 16S DNA De novo, and 16S QIIME NCBI 16S Started and unstarted Bella di De Angelis et 26 2 V1-V3 GSFLX NA RTL usearch BLASTn Not deposited 25

RNA 1.4.0 Microbial Cerignola (A01BP) table olives al., 2015 pipeline (cDNA) De novo, Flour, doughs and food 16S RNA Illumina NCBI 16S Minervini et 27 2 V1-V3 NA RTL QIIME usearch BLASTn PRJNA268304 6 environments for traditional

(cDNA) MiSeq Microbial al., 2015 pipeline Italian sourdouhgs (A008K) Beckman Coulter De novo, QIIME Epiphytic bacterial community Ceuppens et 28 2 16S DNA V1-V4 GSFLX 413 Genomics USA uclust RDP Greengenes PRJNA288639 19

1.9.0 on basil leaves (A00VV) al., 2015 (Danvers, MA, pipeline USA) Food samples during processing Institute of (intermediate AO1RG, A024G, De novo, Biotechnology QIIME finished, spoiled) and Hultman et al., 29 2 16S DNA V1-V3 GSFLX 430 uclust RDP Greengenes PRJNA293141 91

, University of 1.9.0 environmental sample for a 2015 pipeline Helsinki cooked sausage (A025J) processing plant Fresh produce (lettuce, A00KX; mushrooms, A00TQ; pepper, Engencore A00JA; spinach, A00MJ; alfaalfa De novo, facility at the QIIME 20 sprouts, A00SH;mung bean Leff and 30 2 16S DNA V5 GSFLX 200 uclust RDP Greengenes ERP002018

University of 1.9.0 8 sprouts, A00SR; tomato A00HQ ) Frierer, 2013 pipeline South Carolina and fruits (apple, A01DH; grapes, A01DX; peach, A01GL; strawberry, A01EA) Meat (bacon dice, A022X; ground beef and veal, A01QX; poultry sausage, ) and seafood (cod Eurofins, De novo, QIIME 16 fillets, A02BT; cooked shrimps Chaillou et al., 31 2 16S DNA V1-V3 GSFLX 506 Ebersberg, uclust RDP Greengenes PRJEB4975

1.9.0 0 A02GH; salmon fillets A028P, 2014 Germany) pipeline Smoked salmon, A02KF) at the beginning and end of refrigerated storage Artisanal soft (A02RH), semi- QIIME De novo, hard (A02ST) and hard cheeses Quigley et al., 32 2 16S DNA V4 GSFLX 500 TFRC 1.6.0+MOT uclust BLASTN SILVA v100 Not deposited 62 (A02YE) from raw or

2012 HUR pipeline pasteurized cow, goat, or Investigating the role of the microbiota in Pink Cheese. De novo, QIIME Cheddar (A02YD), Emmental Quigley et al., 33 2 16S DNA V4 GSFLX 500 TFRC uclust blast SILVA PRJEB6952 59 1.9.0 (A02YM) and cheese coloured 2016 pipeline with Annatto (A02YM), either unspoiled or spoiled.