Fits the Profile

UGA food scientists track the culprits of foodborne illness by pioneering research in bioinformatics

Like most researchers, University of Georgia food scientists Xiangyu Deng and Henk den Bakker have traditional white coats and labs filled with beakers, flasks and Bunsen burners. As pioneers in the field of food safety bioinformatics, however, they spend most of their time at their computers. This UGA College of Agricultural and Environmental Sciences research team fights foodborne pathogens by developing computer software.

The software creates graphs that are used to find genomic differences between strains of foodborne bacteria.

“By studying graphs of complete populations of a pathogen, we can look for genetic variation in genomes that help us to fingerprint bacterial strains,” den Bakker said. “Basically, this makes it easier to find bacteria with a similar genomic fingerprint, for instance, bacteria involved in a disease outbreak.”

This work means that scientists can detect the source of a foodborne illness outbreak faster. The sooner the source is found, the sooner the outbreak can be stopped.

Together with Lee Katz, a bioinformatician at the Centers for Disease Control and Prevention, den Bakker and Deng, who was awarded a Creative Research Medal from the UGA Research Foundation for his work, formed the UGA Food Safety Informatics Group.

“We are able to analyze really large chunks of data in a matter of hours using the data Dr. Deng has collected through SeqSero and the software program I created,” said den Bakker, who joined the Center for Food Safety faculty on UGA’s Griffin campus last spring. “We recently analyzed 390 salmonella genomes in about four hours. This normally takes scientists days to do. And we can now add new genomes to the data set and rerun the data in just 20 minutes.”

The publicly accessible National Center for Biotechnology Information Sequence Read Archive currently includes genomic information for more than 70,000 genomes, what den Bakker calls a “ginormous chunk of data.” The cloud-based SeqSero software tool quickly classifies strains of salmonella and identifies serotypes, or individual, distinct strains, using whole-genome sequencing.

Developed by CAES food science researcher Shaokang Zhang under Deng’s direction, SeqSero is used by public health officials and scientists across the globe. After researchers upload sequence files, the system sends an analysis in minutes, 24 hours a day, seven days a week, at no charge.

Deng compared the system to a detective investigating a crime.

“For investigation and surveillance purposes, you need to be able to profile your suspects at different levels, from general demographics to fingerprints. If your suspect is salmonella, serotype determination, or serotyping, is the first step of your profiling,” he said. “It’s now possible to do all the profiling with whole-genome sequencing, and it saves a lot of time and (steps in) workflow.”

The research team sees its data collection and next-generation analysis algorithms being used to help food companies test raw products for pathogens before allowing them into their plants, den Bakker said.

Learn more about the food safety center at

By Sharon Dowdy Cruse

UGA food scientists Xiangyu Deng (left) and Henk den Bakker developed software that uses bioinformatics to mitigate foodborne pathogens.

Foodborne Bacteria At Large artwork