Webinar: Mapping the Microbiome to Manage Risk During Production



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Have you ever wondered what microorganisms are found in a facility and where they reside? In what combinations and proportions do they appear? How do they grow, move, and survive? How does the production environment affect them, and how the microorganisms affect the environment? Is it possible to use this information to predict and prevent spoilage or even outbreaks and reduce food safety risks? 

The SAFE project, a three-year initiative, brought together the industry, government, and academia in Ireland and, with the use of High Throughput/Next Generation Sequencing (HTS/NGS), mapped the microbiome of food manufacturing facilities across the region. The results from that project provide insight for developing models to predict the likelihood of the occurrence of a pathogen or a spoiler within a production environment before it actually occurs. This enables a preventive approach to food safety, thereby reducing or eliminating the potential for holding a shipment, wasting product, or the brand damage associated with a product recall. 

This webinar is a prelude to initiate a similar collaborative project here in the United States between the Institute for Food Safety and Health, Creme Global, and food companies interested in participating in the project.


Institute for Food Safety and Health

The Institute for Food Safety and Health (IFSH) is a world-class consortium of Illinois Institute of Technology, the U.S. Food and Drug Administration (FDA), and the food Industry. It builds on and expands the vital work of the National Center for Food Safety and Technology (NCFST—established 1988), producing knowledge-based outcomes in the areas of food safety, food defense, and nutrition for stakeholders in government, industry, and academia.

IFSH High-Throughput Sequencing Initiative

The IFSH High-Throughput Sequencing Initiative (IHI) provides the latest technology for IFSH researchers, especially in the food industry. The IHI offers HTS laboratory and analytical services to all, particularly our colleagues in the food companies.

Creme Global

Creme Global is a scientific modeling, data analytics, and computing company that delivers predictive analytics and modeling to help industries make better decisions. The company’s experts in mathematical modeling, statistics, software development, food science, and nutrition develop and deploy the software models for consumer intake modeling, product safety assessment, regulatory affairs, and innovation projects.


Behzad Imanian

Institute for Food Safety and Health, Illinois Tech

Since March 2016 Imanian has been leading the High-Throughput Sequencing (HTS) Initiative at IFSH. The IFSH HTS laboratory he helped to establish is equipped with advanced HTS sequencers, and it offers a variety of services that include Whole Genome Sequencing (WGS), metagenomics (16s rDNA and shotgun sequencing) for environmental monitoring, transcriptomics (RNA-seq), and other HTS applications. In addition to directing the HTS laboratory, Imanian has established the bioinformatics facility in IFSH. This facility currently houses three high-performance computers (HPC), and it will be expanding in the future. The IFSH bioinformatics center is capable of providing analytical services from quality control, genome, and transcriptome assembly to annotation, SNP, phylogenetic analyses, and much more to all researchers at IFSH, Illinois Tech, and within the food industry, as well as outside collaborators. The center also provides direct access to the IFSH HPCs for all our collaborators who desire to conduct the analytical work on their data themselves.

Professor Seamus Fanning

University College Dublin

In 2002 Fanning was appointed to the chair of Food Safety and Zoonoses at University College Dublin. Currently, his research themes include the application of molecular methods to food safety as applied for the control of zoonotic disease agents of public health importance. The activities of this group have focused on extending our understanding of the molecular mechanisms of antimicrobial and biocide resistance in zoonotic bacteria and how they relate to external environmental stresses. Fanning was appointed to the National Zoonoses Committee in 2012, and is a lead microbiologist with the China National Center for Food Safety and Risk Assessment in Beijing. He currently serves as an editor of Research in Microbiology and FEMS Microbiology Letters, and is a member of the editorial boards of Applied and Environmental Microbiology; Foodborne Pathogens and Disease; and the Journal of Food Protection and Microbial Drug Resistance

Scott Nguyen

Creme Global & University College Dublin

Nguyen received a Ph.D. in microbiology and immunology at the University of Oklahoma Health Sciences Center (2013), with studies on the human pathogen Streptococcus pyogenes and streptococcal bacteriophages. Subsequently, he was a postdoctoral microbiologist at the United States Department of Agriculture U.S. Meat Animal Research Center (2015–2017) in Clay Center, Nebraska. He studied Enterobacteriaceae in cattle and humans there, with a primary focus on Salmonella and next-generation sequencing. He joined the University College Dublin Centre for Food Safety (2018–present) as a molecular microbiologist/bioinformatician under Profesor Seamus Fanning, with a focus on foodborne pathogens (primarily Salmonella, Yersinia, and Escherichia).

Noel Rogers

Creme Global

Rogers works as a data scientist at Creme Global, specializing in mathematical modeling and statistics. He has a background in physics and math, with an M.Sc. in mathematics from Maynooth University and an M.Sc. in data analytics from Dublin Institute of Technology. He has extensive experience in data analytics and mathematical modeling across a number of domains including financial risk, fraud, chemical exposure, and food safety.

Brendan Ring

Creme Global

Ring is the commercial director at Creme Global, and has worked with a wide range of companies in the food, medical, and ICT space over the last two decades. He is experienced in engaging with C-level management and technical teams to scope complex requirements and deliver scientific solutions. He completed an engineering degree at Dublin City University and an M.B.A. in the University of Cambridge.


10:30–10:40 a.m.

Introduction: HTS, bioinformatics, and collaborative projects in IFSH

Behzad Imanian

10:40–10:50 a.m.

The field of predictive microbiology: An overview

Professor Seamus Fanning

10:50–11:00 a.m.

Microbiological analysis from the SAFE project

Scott Nguyen

11:00–11:10 a.m.

Developing predictive models: Our approach

Noel Rogers

11:10–11:20 a.m. 

The Service Implementation

Brendan Ring

11:20–11:45 a.m.

Questions and Answers

Please note: You can forward your questions ahead of time to Behzad Imanian at bimanian@iit.edu. You will also be able to pose your questions through text during the webinar.

Register for the Webinar

Getting to Campus