IBM and Mars Are Applying Metagenomics to Food Safety

A comprehensive new gene cataloging project could help food processors and others in the supply chain prevent contamination on a massive scale.

By Jennifer Weeks and the Institute of Food Technologists

An ambitious new project, led by an IBM computational biologist, could help food processors prevent contamination on a massive scale.

The Consortium for Sequencing the Food Supply Chain, announced in early 2015 by joint sponsors IBM and Mars, will attempt to catalog all the active genes that typically exist in different food environments, from farms through transport, processing and distribution, under normal conditions and when contamination occurs. If suppliers and manufacturers can detect changes in the life forms present in all foods that could lead to contamination, they should be better able to prevent the contamination from happening.

The resulting wealth of new data, says IBM's James Kaufman, could revolutionize the safety of our food supply. Today food safety is about detecting pathogens — ideally during production, but all too often in foods that have already gone to market and infected people. Kaufman and his colleagues want to reduce foodborne illness by making the system more predictive.

Instead of just isolating known pathogens such as salmonella and listeria, the initiative will use metagenomics — analyzing microbial genetic material collected from environmental samples, such as swabs from storage bins or processing vats in a food manufacturing or distribution facility.

IBM and Mars Connect

IBM and Mars also teamed up in 2008 with USDA and academic researchers to sequence the genome of cacao (cocoa), a major agricultural commodity and the basic ingredient in chocolate. Mars was interested in identifying genes associated with flavorful and hardy cacao cultivars.

The first phase of work has already started at a Mars pet food factory near Reno, Nev. Researchers will sample and sequence a half-dozen major ingredients, such as chicken meal and cornmeal, when they arrive at the plant and as they move through it, analyzing how the microbial communities within the foods vary seasonally and as they are processed. Periodically, samples will be spiked with heavy metals or other contaminants to see how the foods’ microbiomes respond.

The analysis will take place at IBM Almaden and in microbiology laboratories at collaborating universities. Kaufman estimates about two years will be needed to produce metagenomic sequences for the target ingredients at the Reno factory. Results will be published in peer-reviewed journals and later made publicly available for free.

If the consortium grows as planned, Kaufman expects that within five years it will have produced a large body of data on genes that should be present in foods and on other genes that signal spoilage.

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