Table 3.
Application of DNA microarray assay for detection and evaluation of food materials.
| Food Source or Material | Material Detected or Subject Examined | Type of Microarray Used (Source a/Dye) | Reference |
|---|---|---|---|
| Allergy/Poisoning/Toxicity | |||
| Bovine milk/Pork | Staphylococcal food poisoning | Genotyping (Clondiag/TMB) | Johler et al., 2011 [141] |
| Cheese | Staphylococcus aureus poisoning | Genotyping (Alere/TMB) | Johler et al., 2015 [142] |
| Cheese/Fish/Meat, etc. | Staphylococcus aureus poisoning | Genotyping (Clondiag/TMB) | Baumgartner et al., 2014 [143] |
| Citrinin | Mycotoxin toxicity | Gene expression (Custom/Cy3, Cy5) | Iwahashi et al., 2007 [144] |
| Food | Bacillus cereus poisoning | Genotyping (Custom, E) | Liu et al., 2007 [145] |
| Food | Coagulase-negative staphylococci | Genotyping (Custom/Cy5) | Seitter et al., 2011 [146] |
| Food | 69 Salmonella virulence genes | Genotyping (Custom/Cy3) | Zou et al., 2011 [147] |
| Food | Salmonella serogroups | Genotyping (Custom, C/SG) | Braun et al., 2012 [148] |
| Food | Clostridium perfringens poisoning | Genotyping (Custom/Cy3, Cy5) | Lahti et al., 2012 [149] |
| Food | Allergen-specific response | Gene expression (Affymetrix/PE) | Martino et al., 2012 [150] |
| Food | Staphylococcal food poisoning | Genotyping (Clondiag/TMB) | Wattinger et al., 2012 [151] |
| Food | Silver-nanoparticle-induced genotoxicity | Gene expression (Agilent/Cy3, Cy5) | Xu et al., 2012 [152] |
| Food | 46 Salmonella O serogroups | Genotyping (Custom/Cy3) | Guo et al., 2013 [153] |
| Food | Campylobacter pathotypes | Genotyping (Custom/Cy3) | Marotta et al., 2013 [154] |
| Food | Botulinum neurotoxin poisoning | Genotyping (Custom/PE) | Vanhomwegen et al., 2013 [155] |
| Food | 117 antibiotic resistance genes | Genotyping (Custom, C/True Blue) | Strauss et al., 2015 [156] |
| Food additive | Toxicity in liver | Gene expression (Custom/Cy3, Cy5) | Stierum et al., 2008 [157] |
| Horseradish | Quorum sensing inhibitors | Gene expression (Custom/PE) | Jakobsen et al., 2012 [158] |
| Meat | Shiga toxin-producing Escherichia coli | Genotyping (GeneSystems/6-FAM) | Miko et al., 2014 [159] |
| Meat | Cephalosporin-resistant Escherichia coli | Genotyping (Alere/TMB) | Vogt et al., 2014 [160] |
| Meat/Milk | Coagulase-negative staphylococci | Genotyping (Custom/Cy3, Cy5) | Even et al., 2010 [161] |
| Pancake with chicken | Staphylococcus aureus poisoning | Genotyping (Clondiag/TMB) | Johler et al., 2013 [162] |
| Pork | Salmonella enterica pathogenicity genes | Genotyping (Custom/Alexa Fluor 555/647) | Hauser et al., 2011 [163] |
| Pufferfish | Tetrodotoxin accumulation | Gene expression (Custom/Cy3) | Feroudj et al., 2014 [164] |
| Rice | Cadmium toxicity | Gene expression (Custom, C/CSPD) | Zhang et al., 2012 [165] |
| Vegetable | Latex and/or vegetable food allergy | Gene expression (Affymetrix/PE) | Saulnier et al., 2014 [166] |
| Contamination | |||
| Alfalfa/Cilantro/Mung bean, etc. | Detection of Yersinia enterocolitica | Genotyping (Custom/Cy3, Cy5) | Siddique et al., 2009 [167] |
| Beef | Pathogenic Escherichia coli O157 | Gene expression (Custom/Cy3, Cy5) | Fratamico et al., 2011 [168] |
| Beer | Beer spoilage bacterial contamination | Beer spoilage bacterial contamination | Weber et al., 2008 [169] |
| Beef/Egg/Fish/Milk | 26 probes for pathogenic bacteria | Genotyping (Custom/Cy3) | Wang et al., 2007 [170] |
| Bread (Whole-grain/Fiber-rich) | Intestinal microbiota composition | Genotyping (Agilent/Cy3, Cy5) | Lappi et al., 2013 [171] |
| Cantaloupe | 24 probes for Listeria monocytogenes | Genotyping (Affymetrix/PE) | Laksanalamai et al., 2012 [172] |
| Chicken | Rapid analysis of pathogenic bacteria | Genotyping (Custom/Cy3, Cy5) | Quiñones et al., 2007 [173] |
| Chicken/Pork | Salmonella enterica probes | Genotyping (Custom/Alexa Fluor 555/647) | Hauser et al., 2012 [174] |
| Compost/Digestate/Waste | Microbial community | Genotyping (Custom/Cy3, Cy5) | Franke-Whittle et al., 2014 [175] |
| Egg/Meat/Milk, etc. | Listeria spp. contamination | Genotyping (Custom/Cy5) | Hmaïed et al., 2014 [176] |
| Egg/Meat/Milk/Rice, etc. | 16S rRNA probes for pathogens | Genotyping (Custom/Alexa Fluor 647) | Hwang et al., 2012 [177] |
| Food | 250 probes for pathogenic bacteria | Genotyping (Custom/Cy3) | Kim et al., 2008 [178] |
| Food | Rapid analysis of pathogenic bacteria | Genotyping (Custom/Cy3) | Kim et al., 2010 [179] |
| Food | Rapid analysis of pathogenic bacteria | Genotyping (Custom, C/Luminol) | Donhauser et al., 2011 [180] |
| Food | Yersinia pestis/Bacillus anthracis | Genotyping (Custom/Alexa Fluor 555/647) | Goji et al., 2012 [181] |
| Food | 50 probes for pathogenic bacteria | Genotyping (Custom/Cy3) | Lee et al., 2011 [182] |
| Food | Diversity of Arcobacter butzleri | Genotyping (Custom/Cy3, Cy5) | Merga et al., 2013 [183] |
| Food | Pathogenic Escherichia coli/Salmonella | Genotyping (Alere/TMB) | Fischer et al., 2014 [184] |
| Food/Water | 63 probes for pathogenic bacteria | Genotyping (Custom/TAMRA) | Kostić et al., 2010 [185] |
| Juice | Alicyclobacillus spp. contamination | Genotyping (Custom/Cy3, Cy5) | Jang et al., 2011 [186] |
| Maize | 96 probes for mycotoxigenic fungi | Genotyping (Custom/Cy3, Cy5) | Lezar & Barros, 2010 [187] |
| Meat | Rapid analysis of pathogenic bacteria | Genotyping (Custom/Cy3) | Suo et al., 2010 [188] |
| Meat (Ready-to-eat) | Listeria monocytogenes contamination | Gene expression (PFRGC/Cy3, Cy5) | Bae et al., 2011 [189] |
| Potato | DNA/RNA pathogens | Genotyping (Custom, C/SG) | Dobnik et al., 2014 [190] |
| Poultry meat | 102 pathogenicity genes | Genotyping (Custom/Alexa Fluor 555/647) | Toboldt et al., 2014 [191] |
| Sausage (Thai Nham) | 164 probes for lactobacilli | Genotyping (Custom/Cy3, Cy5) | Rungrassamee et al., 2012 [192] |
| Water | 26 probes for pathogenic bacteria | Genotyping (Custom/Cy3) | Zhou et al., 2011 [193] |
| Water | Pathogenic Legionella spp. | Genotyping (Custom/Cy3) | Cao et al., 2014 [194] |
| Efficacy/Mechanism | |||
| Beverage/Dairy/Food | Interaction between yeast and bacteria | Gene expression (Affymetrix/PE) | Mendes et al., 2013 [195] |
| Cassava | Drought stress response | Gene expression (Custom/Cy3) | Utsumi et al., 2012 [196] |
| Chitooligosaccharide | Immune responses in adipocytes | Gene expression (Illumina/NS) | Choi et al., 2012 [197] |
| Food | Metabolic change in white blood cells | Gene expression (Affymetrix/PE) | Kawakami et al., 2013 [198] |
| Food (High-cholesterol diet) | Osteoporosis risk | Gene expression (Affymetrix/PE) | You et al., 2011 [199] |
| Food (High-fat diet) | Inflammation-associated genes | Gene expression (Illumina/NS) | Ding et al., 2014 [200] |
| Herb (Hochuekkito) | Mucosal IgA antibody response | Gene expression (Custom/Cy3) | Matsumoto et al., 2010 [201] |
| Herb (Licorice) | Estrogen-like effect | Gene expression (Custom/ Cy3, Cy5) | Dong et al., 2007 [202] |
| Imbibed soybean | New protein food item | Gene expression (Custom/Cy3) | Tamura et al., 2014 [203] |
| Phenolic preservative | Oxidative stress/DNA damage | Gene expression (Custom/Cy3, Cy5) | Martín et al., 2014 [204] |
| Pineapple (Ananas comosus) | Absorption of phenolic acid | Gene expression (Custom/Cy3, Cy5) | Dang & Zhu, 2015 [205] |
| Polyunsaturated fatty acid, etc. | Growth and metabolic status of rats | Gene expression (Illumina/Cy3) | Castañeda-Gutiérrez et al., 2014 [206] |
| Psyllium | Lipid consumption in skeletal muscle | Gene expression (Mitsubishi/Cy5) | Togawa et al., 2013 [207] |
| Quercetin | Improvement of diabetic symptoms | Gene expression (Affymetrix/PE) | Kobori et al., 2009 [208] |
| Skim milk | Survival of L. monocytogenes | Gene expression (Custom/Alexa Fluor 555/647) | Liu & Ream, 2008 [209] |
| Sweet corn | Effect of suppressing cancer | Gene expression (GE Healthcare/Cy5) | Tokuji et al., 2009 [210] |
| Tea (Eucommia ulmoides) | Plasma triglyceride-lowering effect | Gene expression (Agilent/Cy3) | Kobayashi et al., 2012 [211] |
| Xanthan gum | Xanthomonas arboricola metabolism | Genotyping (Custom/Cy3, Cy5) | Mayer et al., 2011 [212] |
| Quality Control/Safety | |||
| Canola | Genetically modified organism | Genotyping (Custom/Cy3) | Schmidt et al., 2008 [213] |
| Canola/Cotton/Maize/Soybean | Genetically modified organism | Genotyping (Custom/Cy5) | Kim et al., 2010 [214] |
| Cereal (Barley/Oat/Rice/Wheat) | Authenticity of plant | Genotyping (Custom/Fluorescein) | Rønning et al., 2005 [215] |
| Crop | Authenticity of food | Genotyping (Custom/Cy3) | Voorhuijzen et al., 2012 [216] |
| Ginseng | Food adulteration | Genotyping (Custom/Cy3) | Niu et al., 2011 [217] |
| Kothala himbutu (Medicinal plant) | Food safety assessment | Genotyping (Affymetrix/PE) | Im et al., 2008 [218] |
| Maize/Potato | Food safety assessment | Gene expression | van Dijk et al., 2010 (review) [219] |
| Maize/Soybean, etc. | Genetically modified organism | Genotyping (Custom, C/Silverquant) | Leimanis et al., 2006 [220] |
| Olive | Authenticity of plant | Genotyping (Custom/Cy3, Cy5) | Consolandi et al., 2007 [221] |
| Potato | Food safety assessment | Gene expression (Custom/Cy3, Cy5) | van Dijk et al., 2009 [222] |
| Royal jelly | Food safety assessment | Gene expression (Amersham/Cy5) | Kamakura et al., 2005 [223] |
a The sources of DNA microarrays are either custom arrays (Custom) or microarrays supplied by companies as follows: Agilent: Agilent Technologies, USA; Alere: Alere Technologies, Germany; Amersham/GE Healthcare: GE Healthcare, USA; Clondiag: Clondiag Chip Technologies (renamed as Alere Technologies), Germany; GeneSystems: GeneSystems, France; Mitsubishi: Mitsubishi Rayon, Japan; and PFRGC: Pathogen Functional Genomic Research Center, USA. The type of microarrays used includes fluorescent assays with indicated fluorescent dyes, and non-fluorescent assays (C: colorimetric/chemiluminescent assays; or E: assays with electric arrays) with indicated chromogenic dyes/chemiluminescent substrates. CSPD: chloro-5-substituted adamantyl-1,2-dioxetane phosphate; 6-FAM: 6-carboxyfluorescein; NS: not specified; PE: phycoerythrin; SG: Seramun Green; TAMRA: carboxytetramethylrhodamine; and TMB: 3,3′,5,5′-tetramethylbenzidine.