Consortium for Sequencing the Food Supply Chain - Transforming Food Safety with Big Data

Minimizing contaminated food outbreaks is a big public health issue. In the U.S. alone, one in ten people are affected by foodborne diseases each year. That results in 128,000 hospitalizations, 3,000 deaths, and $9 billion in medical costs. Add to that another $75 billion annually in contaminated food that has to be recalled and thrown away. As the food supply chain becomes more global and complex, food safety issues will continue to increase until there are new scientific methods to mitigate the safety hazards within the system.

In a world, where sequencing technologies have become ubiquitous, we continue to discover new genomes at an impressive pace. The Consortium has assembled more genomes in 2018 than the rest of the world has produced in about 20 years, improving the gold standard database by 50x. In the last three years, the team has generated insights from 500 terabytes of complex genomic and microbiome data, the equivalent of analyzing 100,000 high definition movies, or 17 years of non-stop watching time for one individual. All of this data is necessary to build the scientific foundations and demonstrate that safe ingredients have a distinct and potentially fairly standard microbial ecology (the microbiome). Any shift in the microbiome could be indicative of a food safety issue— helping us better understand the presence of an unknown hazard or whether an ingredient doesn’t meet its required specification. For instance, is the chicken on your plate truly chicken and could you be at risk of getting sick due to something not appropriately identified?”

new genome sequence data in 2017

Using DNA and RNA sequencing, we profile microbiomes (communities of microorganisms) in the supply chain where food production and delivery occur. Food ingredient microbiome analysis is used to detect anomalies and understand the upstream supply chain. Sampling of factory locations is used to measure the biome response to protective measures. A robust informatics infrastructure is necessary to move quickly from data to decisions.


In a consortium study, comparative analysis of food ingredients of a similar type revealed that there are components of the microbiome that are stably maintained sample to sample as well as minor abundant microbes which vary in their abundance. In the view below, each microbiome is shown as a vertical bar with the component microbes and their quantities shown. The variable segments of the microbiomes indicate perturbations in the supply chain. Our results from this sample collection indicated deviations associated with a contamination in the supply chain and were confirmed by quantitative differences in the microbiome and in the food ingredient composition itself.

baseline sample microbiomes

The view above is one example of how members can explore their food microbiome data. All identified microbial components are shown and samples are juxtaposed for comparisons within a collection of samples. This view allows highlighting hazardous microbes, qualitative and quantitative filtering, overlaying metadata as well as full search capability by organism name or taxonomic id.