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Mapping the microbiome will protect us from bad bacteria.


The prediction

Within five years, food safety inspectors around the world will gain a new superpower: the ability to understand how millions of microbes coexist within the food supply chain. These microbes—some healthy for human consumption, others not—are everywhere –in foods at farms, factories, and grocery stores. The ability to constantly and cheaply monitor the behaviors of microbes at every stage of the supply chain represents a huge leap in food safety. In this microbial world, IBM Research has decided to study the dynamics of microbial communities for application in food safety.

What's happening today

Millions of microbes coexist within the food supply chain – some are healthy for human consumption and other are not. Those that cause food-borne illnesses account for $9 billion in medical costs and another $75 billion in recalls and destroyed food annually. What’s more, food-borne illnesses cause 128,000 hospitalizations and 3,000 deaths every year in the U.S. alone. Traditional culture test could take days to perform and may only indicate the existence of one target problematic bacteria. This inability to proactively sound an alarm bell about a potential anomaly in a microbiome costs governments and companies billions of dollars.


Solutions for the future

Using DNA and RNA sequencing, researchers may soon be able to profile microbiomes everywhere that food production or food delivery occurs. These analyses can be used to detect anomalies in the microbiome¬—for example, a sudden and unanticipated uptick of a pathogenic bacteria within a pork sausage sample, or a shift in the overall microbiome composition. A traditional culture test of the sausage would take days to perform and may only indicate the existence of one targeted problematic bacteria. Advanced big data analytics of NGS results of this food, however, could be performed in a fraction of the time and map out all of the microbes present in the food. These findings could reveal early signals that this microbiome is favorable for the growth of pathogenic bacteria, broadening researchers’ understanding of the entire microbial universe.

By developing a world-class database of microbes and harnessing advances in NGS big data analytics in each stage of the food supply chain, those harrowing numbers could move faster to zero. And food safety becomes predictive instead of reactive.

Developments at IBM Research

Consortium  for Sequencing the Food Supply Chain

By sequencing the genomes of the microbiome, or community of microbes, present in the food we eat, IBM researchers as well as partnering organizations like Mars, Inc., Bio-Rad, and Cornell University are turning the corner to a new and more predictive kind of food testing. This new regimen may allow inspectors to identify dangerous pathogens inhabiting food with better sensitivity well before they make anyone sick. This rapidly evolving field at the intersection of big data and microbiology is built upon the technology of next generation sequencing (NGS), which researchers are using to amass an unprecedented reference database of genomes through an IBM-led partnership called the Consortium for Sequencing the Food Supply Chain.

In 2018, the consortium assembled a database of all of the bacterial genomes that have been sequenced by researchers over the past two decades. With the insight gained from 500 terabytes of complex experimental data, the team was able to ascertain the differences between the microbiomes of safe ingredients (which researchers believe have a distinct and standard composition) and potentially dangerous ones (which could be detected as deviations from the standard composition, indicating contamination by pathogens or other ingredients.)