{"id":159637,"date":"2025-03-03T11:22:32","date_gmt":"2025-03-03T11:22:32","guid":{"rendered":"https:\/\/test.merieuxnutrisciences.com\/spoilage-investigation-with-metabarcoding\/"},"modified":"2025-08-13T15:02:20","modified_gmt":"2025-08-13T14:02:20","slug":"spoilage-investigation-with-metabarcoding","status":"publish","type":"page","link":"https:\/\/www.merieuxnutrisciences.com\/za\/spoilage-investigation-with-metabarcoding\/","title":{"rendered":"Spoilage Investigation with Metabarcoding"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\" id=\"in-addition-to-sequencing-the-genomes-of-individual-food-related-microorganisms-next-generation-sequencing-ngs-can-be-used-to-study-mixed-microbial-communities-in-foods\"><strong>In addition to sequencing the genomes of individual food-related microorganisms,&nbsp;Next Generation Sequencing (NGS) can be used to study mixed microbial communities in foods.<\/strong><\/h2>\n\n\n\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p class=\"wp-block-paragraph\">Recent advances in DNA sequencing and analytical technology and bioinformatics have allowed scientists and researchers to effectively use these meta-omics tools to study microbiomes in various microbial ecosystems.&nbsp;Microbial diversity analysis using NGS can be applied in a wide variety of food, environmental food process samples and environmental factory samples.&nbsp;<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"spoilage-investigation-in-a-nutshell\">Spoilage Investigation in a Nutshell<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Human and raw materials are reservoirs of spoilage microorganisms, which are able to grow and survive in a processing environment. Process flow (materials, air, and human), cleaning, temperature, and humidity are mainly used to control microbial communities. The origins of pathogen and spoilage microorganisms found in these processing plants are mostly unknown. This growing field of food environmental microbiology has been enabled by DNA sequencing and big data technologies.&nbsp;<strong>High-Throughput DNA Sequencing (HTS) gives a perspective of the global population dynamics in food facilities as microbial ecosystems.<\/strong>&nbsp;The potential applications for this technique are limited only by the microorganism populations that can be found, making it perfect for spoilage investigations, shelf life analyses, and environmental monitoring. It will also provide more information to food manufacturers familiar with a simple classical count technique.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\" id=\"our-spoilage-and-microorganisms-investigation-services\"><strong>Our Spoilage and Microorganisms Investigation Services<\/strong><\/h3>\n\n\n        <div class=\"wp-block-accordion\">\n            \n                                    <div class=\"nq-c-Dropdown\" data-nqis=\"Dropdown\">\n                        <div data-nqdisplay=\"small\"><\/div>\n                        <div data-nqdisplay=\"large\"><\/div>\n    \n                        <div class=\"nq-c-Dropdown-toggler nq-c-Heading nq-u-blue\" data-lvl=\"3\" aria-expanded=\"false\">\n                            <span class=\"nq-c-Dropdown-toggler-txt\">Metabarcoding<\/span>\n                            <span class=\"nq-c-Dropdown-toggler-icon\">\n                                \n                                <span class=\"icon-minus-accordion\"><?xml version=\"1.0\" standalone=\"no\"?>\n<!DOCTYPE svg PUBLIC \"-\/\/W3C\/\/DTD SVG 20010904\/\/EN\"\n \"http:\/\/www.w3.org\/TR\/2001\/REC-SVG-20010904\/DTD\/svg10.dtd\">\n<svg version=\"1.0\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"\n width=\"20.000000pt\" height=\"20pt\" viewBox=\"0 0 512.000000 512.000000\"\n preserveAspectRatio=\"xMidYMid meet\">\n\n<g transform=\"translate(0.000000,512.000000) scale(0.100000,-0.100000)\"\nfill=\"#000000\" stroke=\"none\">\n<path d=\"M936 2697 c-109 -61 -106 -221 5 -277 38 -20 66 -20 1619 -20 1553 0\n1581 0 1619 20 113 57 113 223 0 280 -38 20 -66 20 -1621 20 l-1583 0 -39 -23z\"\/>\n<\/g>\n<\/svg>\n<\/span>\n                                <span class=\"icon-plus-accordion\"><?xml version=\"1.0\" standalone=\"no\"?>\n<!DOCTYPE svg PUBLIC \"-\/\/W3C\/\/DTD SVG 20010904\/\/EN\"\n \"http:\/\/www.w3.org\/TR\/2001\/REC-SVG-20010904\/DTD\/svg10.dtd\">\n<svg version=\"1.0\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"\n width=\"20pt\" height=\"20pt\" viewBox=\"0 0 512.000000 512.000000\"\n preserveAspectRatio=\"xMidYMid meet\">\n\n<g transform=\"translate(0.000000,512.000000) scale(0.100000,-0.100000)\"\nfill=\"#000000\" stroke=\"none\">\n<path d=\"M2480 4288 c-18 -13 -43 -36 -54 -51 -21 -28 -21 -35 -24 -773 l-2\n-744 -744 -2 c-738 -3 -745 -3 -773 -24 -98 -73 -98 -195 0 -268 28 -21 35\n-21 773 -24 l744 -2 2 -744 c3 -738 3 -745 24 -773 73 -98 195 -98 268 0 21\n28 21 35 24 773 l2 744 744 2 c738 3 745 3 773 24 98 73 98 195 0 268 -28 21\n-35 21 -773 24 l-744 2 -2 744 c-3 738 -3 745 -24 773 -35 48 -82 73 -134 73\n-32 0 -57 -7 -80 -22z\"\/>\n<\/g>\n<\/svg>\n<\/span>\n                                \n                            <\/span>\n                        <\/div>\n                        <div class=\"nq-c-Dropdown-menu\" hidden>\n                                                            <p><strong>Metabarcoding<\/strong>, via a sequencing food factory approach, enables new insight into the<strong>\u00a0global ecology and microorganism behavior in the food chain.<\/strong>\u00a0DNA metabarcoding is the targeted metasequencing of taxonomically informative genetic markers, which allows biodiversity to be measured rapidly, cheaply, comprehensively, repeatedly, and verifiably.<\/p>\n<p><strong>Advantages of microbial diversity analysis (also referred to as microbial profiling, 16S profiling, metabarcoding\u00a0 or 16S metagenomics) studies based on NGS compared to classical methods include:<\/strong><\/p>\n<ul>\n<li>Identification of thousands of microorganisms in one analysis<\/li>\n<li>Identification of non-cultivable microorganisms<\/li>\n<li>Determination of the relative abundance of microorganisms<\/li>\n<li>Extremely fast screening of complex ecosystems<\/li>\n<li>Improved understanding and control of the microbial flora<\/li>\n<li>Minimization of spoilage by improving hygiene practices in food production facilities<\/li>\n<\/ul>\n    \n                                                                                    <\/div>\n                    <\/div>\n                            \n                                    <div class=\"nq-c-Dropdown\" data-nqis=\"Dropdown\">\n                        <div data-nqdisplay=\"small\"><\/div>\n                        <div data-nqdisplay=\"large\"><\/div>\n    \n                        <div class=\"nq-c-Dropdown-toggler nq-c-Heading nq-u-blue\" data-lvl=\"3\" aria-expanded=\"false\">\n                            <span class=\"nq-c-Dropdown-toggler-txt\">Metasequencing<\/span>\n                            <span class=\"nq-c-Dropdown-toggler-icon\">\n                                \n                                <span class=\"icon-minus-accordion\"><?xml version=\"1.0\" standalone=\"no\"?>\n<!DOCTYPE svg PUBLIC \"-\/\/W3C\/\/DTD SVG 20010904\/\/EN\"\n \"http:\/\/www.w3.org\/TR\/2001\/REC-SVG-20010904\/DTD\/svg10.dtd\">\n<svg version=\"1.0\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"\n width=\"20.000000pt\" height=\"20pt\" viewBox=\"0 0 512.000000 512.000000\"\n preserveAspectRatio=\"xMidYMid meet\">\n\n<g transform=\"translate(0.000000,512.000000) scale(0.100000,-0.100000)\"\nfill=\"#000000\" stroke=\"none\">\n<path d=\"M936 2697 c-109 -61 -106 -221 5 -277 38 -20 66 -20 1619 -20 1553 0\n1581 0 1619 20 113 57 113 223 0 280 -38 20 -66 20 -1621 20 l-1583 0 -39 -23z\"\/>\n<\/g>\n<\/svg>\n<\/span>\n                                <span class=\"icon-plus-accordion\"><?xml version=\"1.0\" standalone=\"no\"?>\n<!DOCTYPE svg PUBLIC \"-\/\/W3C\/\/DTD SVG 20010904\/\/EN\"\n \"http:\/\/www.w3.org\/TR\/2001\/REC-SVG-20010904\/DTD\/svg10.dtd\">\n<svg version=\"1.0\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"\n width=\"20pt\" height=\"20pt\" viewBox=\"0 0 512.000000 512.000000\"\n preserveAspectRatio=\"xMidYMid meet\">\n\n<g transform=\"translate(0.000000,512.000000) scale(0.100000,-0.100000)\"\nfill=\"#000000\" stroke=\"none\">\n<path d=\"M2480 4288 c-18 -13 -43 -36 -54 -51 -21 -28 -21 -35 -24 -773 l-2\n-744 -744 -2 c-738 -3 -745 -3 -773 -24 -98 -73 -98 -195 0 -268 28 -21 35\n-21 773 -24 l744 -2 2 -744 c3 -738 3 -745 24 -773 73 -98 195 -98 268 0 21\n28 21 35 24 773 l2 744 744 2 c738 3 745 3 773 24 98 73 98 195 0 268 -28 21\n-35 21 -773 24 l-744 2 -2 744 c-3 738 -3 745 -24 773 -35 48 -82 73 -134 73\n-32 0 -57 -7 -80 -22z\"\/>\n<\/g>\n<\/svg>\n<\/span>\n                                \n                            <\/span>\n                        <\/div>\n                        <div class=\"nq-c-Dropdown-menu\" hidden>\n                                                            <p>Metasequencing can be used to\u00a0<strong>highlight stages in the production chain or areas in the production facility where improvements in hygiene practices are necessary.\u00a0<\/strong>In addition, 16S targeted metasequencing can be used to assess the\u00a0<strong>impact of food preservation measures on the growth of spoilage bacteria.<\/strong>\u00a0Metabarcoding can assist the selection of optimal food-preservation measures.<\/p>\n<p>Metagenomic methods are<strong>\u00a0useful to evaluate bacterial community diversity and its dynamic all over a processing factory.<\/strong>\u00a0The food factory can be seen as a smart microbial ecosystem (Smart Microbial Ecosystem of Food Factory: SMEFF) where microbial communities or contamination hotspots can be identified and continuously monitored. This allows targeted interventions on equipments, workflow designs, and hygienic practices. In this new SMEFF concept, the quality and shelf life of final products would be enhanced. Environmentally harmful cleaning inputs would be reduced,\u00a0<strong>leading to reductions in production costs.\u00a0<\/strong>In food processing factories, the routine monitoring of microbiota leads to\u00a0<strong>safer, more efficient, and sustainable production practices.<\/strong><\/p>\n    \n                                                                                    <\/div>\n                    <\/div>\n                            \n                                    <div class=\"nq-c-Dropdown\" data-nqis=\"Dropdown\">\n                        <div data-nqdisplay=\"small\"><\/div>\n                        <div data-nqdisplay=\"large\"><\/div>\n    \n                        <div class=\"nq-c-Dropdown-toggler nq-c-Heading nq-u-blue\" data-lvl=\"3\" aria-expanded=\"false\">\n                            <span class=\"nq-c-Dropdown-toggler-txt\">Nucleic Acid extraction <\/span>\n                            <span class=\"nq-c-Dropdown-toggler-icon\">\n                                \n                                <span class=\"icon-minus-accordion\"><?xml version=\"1.0\" standalone=\"no\"?>\n<!DOCTYPE svg PUBLIC \"-\/\/W3C\/\/DTD SVG 20010904\/\/EN\"\n \"http:\/\/www.w3.org\/TR\/2001\/REC-SVG-20010904\/DTD\/svg10.dtd\">\n<svg version=\"1.0\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"\n width=\"20.000000pt\" height=\"20pt\" viewBox=\"0 0 512.000000 512.000000\"\n preserveAspectRatio=\"xMidYMid meet\">\n\n<g transform=\"translate(0.000000,512.000000) scale(0.100000,-0.100000)\"\nfill=\"#000000\" stroke=\"none\">\n<path d=\"M936 2697 c-109 -61 -106 -221 5 -277 38 -20 66 -20 1619 -20 1553 0\n1581 0 1619 20 113 57 113 223 0 280 -38 20 -66 20 -1621 20 l-1583 0 -39 -23z\"\/>\n<\/g>\n<\/svg>\n<\/span>\n                                <span class=\"icon-plus-accordion\"><?xml version=\"1.0\" standalone=\"no\"?>\n<!DOCTYPE svg PUBLIC \"-\/\/W3C\/\/DTD SVG 20010904\/\/EN\"\n \"http:\/\/www.w3.org\/TR\/2001\/REC-SVG-20010904\/DTD\/svg10.dtd\">\n<svg version=\"1.0\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"\n width=\"20pt\" height=\"20pt\" viewBox=\"0 0 512.000000 512.000000\"\n preserveAspectRatio=\"xMidYMid meet\">\n\n<g transform=\"translate(0.000000,512.000000) scale(0.100000,-0.100000)\"\nfill=\"#000000\" stroke=\"none\">\n<path d=\"M2480 4288 c-18 -13 -43 -36 -54 -51 -21 -28 -21 -35 -24 -773 l-2\n-744 -744 -2 c-738 -3 -745 -3 -773 -24 -98 -73 -98 -195 0 -268 28 -21 35\n-21 773 -24 l744 -2 2 -744 c3 -738 3 -745 24 -773 73 -98 195 -98 268 0 21\n28 21 35 24 773 l2 744 744 2 c738 3 745 3 773 24 98 73 98 195 0 268 -28 21\n-35 21 -773 24 l-744 2 -2 744 c-3 738 -3 745 -24 773 -35 48 -82 73 -134 73\n-32 0 -57 -7 -80 -22z\"\/>\n<\/g>\n<\/svg>\n<\/span>\n                                \n                            <\/span>\n                        <\/div>\n                        <div class=\"nq-c-Dropdown-menu\" hidden>\n                                                            <p><strong>Nucleic Acid extraction is routinely performed at our laboratories facilities, providing support to our customers directly from raw material.<\/strong><\/p>\n<ul>\n<li>DNA extraction from samples (different DNA extraction protocols are adapted, depending on the starting biological material)<\/li>\n<li>Metabarcoding library construction for the target taxonomic groups<\/li>\n<li>Sequencing on Illumina\u00ae MiSeq\u00ae system<\/li>\n<li>Bioinformatics analysis of the sequencing data (bioinformatics pipeline includes de-multiplexing and quality filtering, read clustering in OTUs and taxon assignment and classification at several taxonomic levels: kingdom, phylum, class, order, family, and genus, etc.).<\/li>\n<li>A detailed scientific report including tables and graphs that summarize information on the different samples and complete method summary<\/li>\n<\/ul>\n    \n                                                                                    <\/div>\n                    <\/div>\n                                    <\/div>\n    \n\n\n<p class=\"wp-block-paragraph\">Quality standards applied to the sequencing services are&nbsp;<strong>fully in line with ISO 9001 standards and expert professional recommendations.<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Our network, from expert Food Science Center laboratories (Food scientists, biomolecular experts, bioinformaticians) supports your projects and tests from the study design to the final report.<\/strong>&nbsp;<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Everything is adapted to fit your needs, from specific biomolecular techniques to bioinformatics pipelines and data storage. M\u00e9rieux NutriSciences offers expert analysis and recommendations to add value to complex sequencing results for practical application and enhanced food safety and quality.<\/p>\n\n\n\n<div class=\"wp-block-buttons is-layout-flex wp-block-buttons-is-layout-flex\">\n<div class=\"wp-block-button\"><a class=\"wp-block-button__link wp-element-button\" href=\"https:\/\/www.merieuxnutrisciences.com\/za\/contact\/\" target=\"_blank\" rel=\"noreferrer noopener\">Contact us<\/a><\/div>\n<\/div>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>In addition to sequencing the genomes of individual food-related microorganisms,&nbsp;Next Generation Sequencing (NGS) can be used to study mixed microbial communities in foods. Recent advances in DNA sequencing and analytical technology and bioinformatics have allowed scientists and researchers to effectively use these meta-omics tools to study microbiomes in various microbial ecosystems.&nbsp;Microbial diversity analysis using NGS&#8230;<\/p>\n","protected":false},"author":53,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"open","ping_status":"open","template":"","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_kad_post_transparent":"","_kad_post_title":"","_kad_post_layout":"","_kad_post_sidebar_id":"","_kad_post_content_style":"","_kad_post_vertical_padding":"","_kad_post_feature":"","_kad_post_feature_position":"","_kad_post_header":false,"_kad_post_footer":false,"_kad_post_classname":"","footnotes":""},"folder":[],"class_list":["post-159637","page","type-page","status-publish","hentry"],"acf":[],"taxonomy_info":[],"featured_image_src_large":false,"author_info":{"display_name":"darko","author_link":"https:\/\/www.merieuxnutrisciences.com\/za\/author\/darko-tapollostudio-fr\/"},"comment_info":0,"_links":{"self":[{"href":"https:\/\/www.merieuxnutrisciences.com\/za\/wp-json\/wp\/v2\/pages\/159637","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.merieuxnutrisciences.com\/za\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.merieuxnutrisciences.com\/za\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.merieuxnutrisciences.com\/za\/wp-json\/wp\/v2\/users\/53"}],"replies":[{"embeddable":true,"href":"https:\/\/www.merieuxnutrisciences.com\/za\/wp-json\/wp\/v2\/comments?post=159637"}],"version-history":[{"count":4,"href":"https:\/\/www.merieuxnutrisciences.com\/za\/wp-json\/wp\/v2\/pages\/159637\/revisions"}],"predecessor-version":[{"id":203958,"href":"https:\/\/www.merieuxnutrisciences.com\/za\/wp-json\/wp\/v2\/pages\/159637\/revisions\/203958"}],"wp:attachment":[{"href":"https:\/\/www.merieuxnutrisciences.com\/za\/wp-json\/wp\/v2\/media?parent=159637"}],"wp:term":[{"taxonomy":"folder","embeddable":true,"href":"https:\/\/www.merieuxnutrisciences.com\/za\/wp-json\/wp\/v2\/folder?post=159637"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}