Table 2.

Summary of NGS projects analyzing food-associated microbiotas, including working conditions and major findings.

Food sample/source	Sequencing project	Amplicon length (bp)	Sequencing platform	Taxonomic resolution	Database useda	Major findings	Reference
Material of plant origin
Table olives fermentation	V1-V3 16S rDNA and cDNA	>250	454FLX	Genus/ species	NCIB nr	Agreement for the DNA and RNA data; high level of halophilic bacteria at the beginning of fermentation; Lactobacillus spp. at the end	[40]
Wine made from botrytized grapes	Separate V4 and V5 16S rDNA	>150	Illumina	Family/ genus	RDP	Similar community structure with V4 and V5 amplicons; Acetobacteriaceae and Proteobacteria dominant organisms	[48]
Ray and wheat sourdough fermentation	V1-V3 16S rDNA and cDNA	>300	454FLX	Genus/ species	RDP	Grain-associated bacteria do not progress in dough, except for E. coli; Weissella, Lactobacillus and Leuconostoc dominate the fermentation	[51]
Fermentation of African pearl millets	V3 16S rDNA	>180	454 FLX	Genus	RDP	Weissella, Pediococcus and Lactobacillus were the only genera after 24 h of fermentation; high intersample variability	[89]
“Cheonggukjang” fermentation	V1-V2 16S rDNA	>300	454 FLX	Genus	SILVA	Bacillus spp. dominates the fermentation, but the actual majority species was different in different samples	[91]
Korean soybean pastes	V1-V2 16S rDNA	>300	454 FLX	Genus	SILVA	High diversity in different brands; Bacillus spp. dominant in a majority of products; LAB species occasionally dominant	[92]
“Kochujang” fermentation	V1-V2 16S rDNA	>300	454 FLX	Genus	SILVA	Bacillus spp. dominates the fermentation, but the actual majority species was different in different samples	[93]
Ten kinds of “kimchi”	V1-V3 16S rDNA	>300	454 FLX	Genus/ species	ExTaxon database	Bacteria diversity and richness varied highly and depended on the type of “kimchi”	[94]
Fermented shrimp, kimchi and sauerkraut	V1-V3 16S rDNA, total DNA	>300 na	454 FLX	Genus	RDP	Viral and hosts communities; discrepancy on phage hosts via homology comparison and rDAN sequencing	[94]
Fermentation of “kimchi”	Total DNA	na	454 FLX	Species	RDP and MG-RAST	Leuconostoc, Lactobacillus and Weissella dominant organisms; Leuc. mesenteroides and Lb. sakei genomes highly represented; phage-related sequences	[95]
Winery-associated microbiota before, during and after harvest	V4 16S and ITS1 from rDNA of bacteria and fungi	>150	Illumina	Family/ genus	Greengenes and UNITE	Saccharomyces colonized winery surfaces; microbial communities were dependent on the production context at each site, shaped by technological practices, processing stage and season	[106]
Cocoa bean fermentation	Total DNA	na	454 FLX	Species	RDP and NCBI nr	Complex fermentation including bacteria (Acetobacter pasteurianus and Lb. fermentum) and yeasts Hansenulla uvarum, Hansenulla opuntiae and Saccharomyces cerevisieae)	[111]
Fermented sushi (“narezushi”)	V1-V2 16S rDNA	>300	454 FLX	Genus	RDP	Species of Lactobacillus and Pediococcus always present; occasional presence of genera of LAB and other bacterial groups	[113]
Fermented rice brand mash (“nukadoko”)	V6-V8 16S rDNA	>400	454 FLX	Genus/ species	RDP	Rice-associated bacteria are replace by Lb. namurensis, Lb. acetotolerans, and some other Lactobacillus during fermentation	[114]
American coolship ale beer fermentation	V4 16S rDNA	>150	Illumina	Family/ genus	Greengenes	Initial Enterobacteriaceae are overgrowth by LAB species though fermentation; Pediococcus spp. becomes dominant after few weeks	[115]
Korean rice beer fermentation	V1-V3 16S rDNA and ITS1 from bacteria and fungi	>350	454 FLX	Genus/ species	Genus	Proteobacteria are replaced by LAB species through fermentation; amylolytic yeasts drive saccharification; alcohol-producing S. cerevisiae) dominate at the end of the fermentation	[116]
Fermentation of medieval sushi (“kaburazushi”)	V1-V2 16S rDNA	>300	454 FLX	Genus	NCIB nr	Bacillus and Staphylococcus are replaced by Lactobacillus through fermentation; Lb. sakei constitutes 80% of the microbiota.	[117]
Milk and dairy products
Raw milk cheeses	V3-V4 16S rDNA and cDNA	nr	454 FLX	Genus	RDP	Fate of starters and inoculated pathogens in cheese. Listeria innocua and Stap. aureus do not progress in cheese but E. coli does	[39]
Brazilian kefir grains	V3 16S rDNA	>300	454 FLX	Genus/ species	RDP	Dominant species Lb. kefiranofaciens, Lb. kefiri, Lb. parakefiri; Acetobacter spp. in only one sample	[49]
Pasteurized, cultured raw milk	V3 16S rDNA	>300	454 FLX	Genus/ species	RDP	S. thermophilus dominant organism; Lb. delbrueckii, Lb. helveticus, and Enterococcus spp. subdominant components	[50]
Healthy and culture-negative mastitic milk	V1-V2 16S rDNA	>200	454 FLX	Genus	SILVA RDP	Pseudomonas, Ralstonia, Psychrobacter reads higher in milk from healthy udders; uncultured bacteria as causative agents in some mastitis	[71]
Healthy and mastitic milk	V1-V2 16S rDNA	250-500	454 FLX	Genus	RDP	DNA sequences from recognized pathogens, from pathogens not associated with mastitis and from bacteria not known to be pathogens	[96]
Irish kefir grain and associated kefir beverage	V4 16S rDNA	nr	454 FLX	Genus/ species	RPD	Lactobacillus spp., as majority organisms including Lb. kefiranofaciens, Lb. kefiri, Lb. parabuchneri, and Lb. helveticus.	[97]
Danish raw milk cheeses made with starter cultures	V3-V4 16S rDNA	>200 na	454 FLX	Genus	RDP	Streptococcus, Lactococcus and Lactobacillus constitute the largest groups; minor discrepancies between pyrosequencing and DGGE	[98]
Oscypeck traditional PDO Polish cheese	V5-V6 16S rDNA	>150	454 FLX	Genus	SILVA	Lactococcus spp. as dominant organism; presence of Bifidobacterium spp. and Enhydrobacter spp. Reads	[99]
Milk, whey starters and Mozzarella cheese	V1-V3 16S rDNA	>200	454 FLX	Genus/ species	RDP	Acinetobacter spp. and Pseudomonas spp. dominant in milk; S. thermophilus, Lb. delbrueckii and Lb. helveticus in cheese.	[102]
Latin-style cheeses	V1-V3 16S rDNA	>200	454 FLX	Genus/ species	RDP	High bacterial diversity in different brands; presence of high numbers of Exiguobacteirum in one of the brands	[101]
Artisanal Irish cheeses and associated cheese rinds	V4 16S rDNA	>150	454 FLX	Genus	NCBI nr	Detection for the first time in cheese of Arthrobacter, Brachybacterium, Faecalibacterium, Helcococcus and Prevotella	[100]
Artisan American cheeses	V4 16S and ITS1 from rDNA and cDNA of bacteria and fungi	>150	Illumina	Family/ genus	Greengenes and UNITE	Debaryomyces and Lactococcus as dominant fungi and bacteria, respectively; similar microbial communities occupy the same type surfaces; facility-specific microorganisms	[103]
Subclinical mastitic milk	Total DNA	na	454 FLX	Species	SEED	Presence of E. coli, Pseudomonas mendocina, Staphylococcus aureus and Klebsiella pneumoniae and their phages	[107]
Industrial starter for Gouda cheese	Genomes, total DNA	na	454 FLX, Illumina	Strain	NCBI nr	Metabolic complementation of starter components, Lc. Lactis and Leuc. mesenteroides; starter stability by “kill-the-winner”-phage dynamics	[109]
Meat and fish products
“Jeotgal” (fermented fish and seafood products)	V3 16S rRNA, archaea, bacteria	>100	454 FLX	Family	Greengenes	High microbial diversity, Halorobum, Alalkalicoccus, dominant archaeal genera; Weissella and Lactobacillus major LAB genera	[47]
Packaging of beef meat	V1-V3 16S rDNA	500	454 FLX	Genus/ species	RDP	Inhibition of Enterobacteriaceae by modified atmospheres; nisin-active vacuum packaging inhibited Brochrotys thermosphacta	[105]
Marinated and unmarinated broiler meat	V1-V3 16S rDNA, total DNA	>250 na	454 FLX	Family/ genus	SILVA NCBI nr	Carnobacteriaceae, Clostridiaceae, Entorococcaceae, Enterobacteriaceae, and Vibrionaceae more common in unmarinated meat samples	[110]

^aRDP, Ribosomal Database Project; NCIB nr, National Center for Biotechnology Information non-redundant nucleotide database; MG-RAST, Meta Genome Rapid Annotation server based on Subsystem Technology; SILVA (quality-controlled database of aligned ribosomal RNA gene sequences); Greengenes (a chimera-checked 16S rRNA gene database); EzTaxon (a web-based tool for identification of prokaryotes based on 16S rDNA sequences).

nr, not reported.

na, not applicable.