In January 2015, IBM Research and global food manufacturer Mars launched the Consortium for Sequencing the Food Supply Chain, and a year later were joined by Bio-Rad Laboratories. This initiative, financed by the three companies, aims to “provide data to redefine food safety rules and establish new standards,” according to Gerard Dubois, PhD, senior manager, IBM Research—Almaden, and director of the Consortium.

Instead of analyzing food samples for food safety threats that are known, the Consortium is using metagenomics and metabolites analysis to test for threats that are not known yet.

Food safety has been historically approached from a reactionary perspective. Numerous protocols have been developed around the world to deal with contamination and adulteration in foods, but were always aimed at detecting and identifying the target after the damage had been done. Instead of analyzing food samples for food safety threats that are known, the Consortium is using metagenomics and metabolites analysis to test for threats that are not yet known.

As Dr. Dubois explained, “We started two years ago with two questions: 1) Is there a microbiome baseline? [and] 2) Can we use the microbiome to detect a non-hazard? To both questions, we can answer yes, and we are preparing a paper that hopefully will be out this year.” The microbiome baseline represents the “normal” microbiome community in a sample. This data is then compared to the microbiome community in the sample under different conditions to detect anomalies.

During the first two years, the Consortium worked with samples taken from Mars’ pet food facility in Reno, Nevada, analyzing chicken meal and other raw ingredients. The samples were shipped to a University of California, Davis microbiology laboratory, where they were either prepared for NGS for research on nucleic acids composition or analyzed by MS for metabolites detection. NGS was performed by a third party using two different Illumina systems, with the data analyzed by IBM’s Almaden Research Laboratory in San Jose, California. In the future, sequencing may be performed at Mars’ global food safety facility in Huairou, China.

The Consortium is currently only testing for the presence of micro-organisms and how they change in response to the environment. However, David Crean, vice president of Corporate R&D for Mars, expressed to IBO that, “The ecology may indicate other hazards that could be present, such as heavy metals or pesticides . . .  potentially the microbiome could be an indicator of other non-microbial hazards.”

The current approach of a scientist in a laboratory doing analysis with open source tools on a single computer is not a long-term solution.

For this project’s success, informatics is just as important as biological data, explained James Kaufman, PhD, manager, Public Health Research, at IBM Research—Almaden, and the Consortium’s chief scientist. “Gigantic databases relating gene to proteins to pathways to metabolites already exist,” he noted. “What is new here is cloud computing: it is possible to access vast number of machines to do a computation very quickly when you need it; ‘return’ those machines [for other uses] when you don’t need it; store large amounts of data; [and] associate the data with the references. So you can go back and do the same calculations three years later and get the same answer.” The current approach of a scientist in a laboratory doing analysis with open source tools on a single computer is not a long-term solution, he said. However, Dr. Kaufman said that the Consortium’s aim is that “informatics can become ubiquitous, routine and affordable.”

Analyzing the metagenomics of a food supply chain can be tedious, daunting and challenging, explained Dr. Crean. Therefore, in order to achieve success, the right contributors have to be involved. “The first challenge is that nobody has done this before, so it is brand new,” said Dr. Crean. “For these kind of challenges, people that normally wouldn’t work together take a very creative approach. This partnership, we think, is unusual.” To the Consortium, Mars brings its competence in understanding food supply, manufacturing and food safety. IBM brings its ability to develop informatics solutions and analyze data, as well as its expertise in biological applications. Bio-Rad’s testing expertise will result in deeper insights from the findings, which can potentially be utilized for the development or improvement of food safety analysis systems and consumables.

This novel partnership was started in the US, but is not expected to end there. As Drs. Doboic and Crean told IBO, they hope to expand the membership of the Consortium to include academics, regulators and other businesses on a global level, so more stakeholders can understand how to use the insights to establish new standards.

The innovative approach of the Consortium includes a variety of challenges. Two of the biggest are to bring together the multiple aspects of the project and to think outside the box. “It is important to highlight the interdependency between bioinformatics, microbiology, advancing the science, and even all the work around data and databases, because we need to be successful in all of these parameters to help this project be a success,” explained Dr. Dubois. “This is not only interesting but challenging at the same time.”

“What is being learned from the molecular data can be translated to new, relatively inexpensive high-speed tests.”

Current food safety testing techniques will not be replaced; rather they will be complemented by the Consortium’s findings, according to Dr. Crean. “We are getting a much better understanding of what testing tells us and what we should be looking for,” he noted. “In the future, I don’t think we will be reducing the number of ELISAs or PCRs or other test methods.” The project outcomes will contribute to getting more information from current testing methods. As an example, Dr. Kaufman said, “What is being learned from the molecular data can be translated to new, relatively inexpensive high-speed tests.”

The Consortium represents an opportunity not only for the partners involved, but for the whole food ecosystem to rethink how to tackle an old problem. Now more than ever, this type of fluid collaboration between informatics experts and a variety of industries is essential to solving health, economic and biological issues, such as food safety.