Table 2 Overview of the major whole genome sequencing projects generated using NGS technologies for some food microorganisms
From: Next-generation sequencing and its potential impact on food microbial genomics
Species (strain) | Origin | GenBank accession no. | Size (Mb) | Sequencing platform | Biological role | Reference |
|---|---|---|---|---|---|---|
LAB | ||||||
 Lactobacillus casei (BD-II) | Homemade Koumiss, China | CP002618 CP002619 | 3.1 | Roche 454 and Solexa (Illumina) | Probiotics | Ai et al. 2011 |
 Lactobacillus delbrueckii subsp. bulgaricus (ND02) | Fermented Yak milk, China. | CP002341 CP002342 | 2.1 | Roche 454 and Solexa (Illumina) | Dairy starter for yoghurt production | Sun et al. 2011 |
 Lactobacillus plantarum (ST-III) | Kimichi | CP002222 | 3.3 | Roche 454 and Solexa (Illumina) | Probiotic supplement for dairy and food products | Wang et al. 2011 |
 Lactobacillus casei (LC2W) | Traditional dairy product, Mongolia | CP002616 | 3.0 | Roche 454 and Solexa (Illumina) | Probiotics | Chen et al. 2011 |
CP002617 | ||||||
 Lactobacillus buchneri (NRRL B-30929) | Ethanol plant | CP002653 | 2.5 | Whole-genome shotgun strategy using Roche 454 Titanium pyrosequencing | Prevention of silage spoilage by yeast and molds and anti-bacterial property | Lui et al. 2011 |
CP002654 | ||||||
CP002655 | ||||||
 Lactobacillus ruminis (ATCC 27782) | Bovine and human intestine | XXYYZZ123a | 2.1 | Roche 454 and Solexa (Illumina) | Probiotics | Forde et al. 2011 |
 Lactobacillus farciminis (KCTC 3681) | Kimichi, Korea | AEOT00000000 | 2.5 | Whole-genome shotgun strategy using Roche 454 Titanium pyrosequencing | Kimichi fermentation | Nam et al. 2011a |
AEOT01000000 | ||||||
 Lactobacillus coryniformis subsp. coryniformis (KCTC 3167) | Kimichi, Korea | AELK00000000 | 3.0 | Whole-genome shotgun strategy using Roche 454 Titanium pyrosequencing | Kimichi fermentation | Nam et al. 2011b |
AELK01000000 | ||||||
 Weissella koreensis (KACC 15510) | Kimichi, Korea | CP002899 | 1.4 | Roche 454 GS FLX Titanium pyrosequencing | Kimichi fermentation | Lee et al. 2011 |
Other bacteria | ||||||
 Salmonella enterica serovar typhi (CT18 and Ty2) | Contaminated food and water | AL513382 | __b | Roche 454 and Solexa (Illumina) | Food spoilage | Holt et al. 2008 |
AE014613 | ||||||
AE006468 | ||||||
CP000026 | ||||||
Yeasts | ||||||
Saccharomyces cerevisiae: S288C and RMII-Ia | __ | __ | 4.4/5.2 | Solexa (Illumina) | Bakery and beverages | Qi et al. 2009 |
 Lalvin QA23 | Lallemand Inc. | ADVV00000000 | 11.6 | Roche 454 GS FLX Titanium | Wine | Borneman et al. 2011 |
 AWRI796 | Maurivin | ADVS00000000 | 11.6 | Roche 454 GS FLX Titanium | Wine | |
 Vin13 | Anchor Bio-Technologies | ADXC00000000 | 11.5 | Roche 454 GS FLX Titanium | Wine | |
 FostersO | Fosters Group Ltd. | AEEZ00000000 | 11.4 | Roche 454 GS FLX Titanium | Brewing | |
 FostersB | Fosters Group Ltd. | AEHH00000000 | 11.5 | Roche 454 GS FLX Titanium | Brewing | |
 VL3 | Laffort | AEJS00000000 | 11.4 | Roche 454 GS FLX Titanium | Wine | |
 13 strains involved in fermentation and 3 in baking | __ | __ | __ | ABI 3730 and Solexa (Illumina) | Bakery and beverages | Liti et al. 2009 |
 Saccharomyces paradoxus 35 strains from different geographical regions | __ | __ | __ | ABI 3730 and Solexa (Illumina) | Bakery and beverages | Liti et al. 2009 |