USING GENOME-SCALE METABOLIC MODELS OF BACTERIA TO MAKE FOOD SAFER AND PREVENT HUMAN DISEASE: A SYSTEMS BIOLOGY APPROACH AT FOOD SAFETY

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: TERMINATED
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1006996
• Project No.: MIN-18-110
• Project Start Date: Oct 1, 2015
• Project End Date: Sep 30, 2020

Project Director
Baumler, DA.

Recipient Organization
UNIV OF MINNESOTA
(N/A)
ST PAUL,MN 55108

Performing Department
Food Science & Nutrition

Non Technical Summary
Systems biology is an approach to connect all of the information known about an organism together using computational approaches to guide experimental design and lead to new understandings about biological organisms such as humans, bacteria, and viruses. These approaches lead to the development of new treatment methods for human disease and ways to make foods safer. This research combines computational modeling with experimental approaches to study foodborne pathogens to address human disease and food safety.

Animal Health Component

0%

Research Effort Categories

Basic

50%

Applied

50%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
712	4099	1100	100%

Knowledge Area
712 - Protect Food from Contamination by Pathogenic Microorganisms, Parasites, and Naturally Occurring Toxins;

Subject Of Investigation
4099 - Microorganisms, general/other;

Field Of Science
1100 - Bacteriology;

Keywords

systems

biology

approach

for

food

safety

Goals / Objectives
The long term goal of this project is to use new systems biology methods to generate computational metabolic models of numerous foodborne pathogens such as Listeria, Salmonella, and E. coli. These computational models will be used to make growth predictions, identify new control targets, and to shed new understanding about the evolutionary diversity of these groups of foodborne pathogens. We plan to conduct computational and "wet-lab" experiments with these pathogenic strains to validate computational predictions and to lead to new discovery. The specific goals of this proposal are: #1) Examination of the evolutionary diversity of Listeria spp. through genome-scale metabolic modeling#2) Evaluation of growth and metabolic variations of Salmonella spp. strains related to host-specificity using computational metabolic models#3) Determination of the metabolic capabilities and new control targets for the European foodborne outbreak strain of E. coli O104:H4

Project Methods
Computational modeling of bacterial metabolism offers a promising approach to predict strain-to-strain variation in metabolic capabilities and microbial strategies used in different environments, including host tissues. The number of available genome-scale metabolic models (GEMs) has grown in the last ten years to over 100 GEMs, and they capture the metabolic capabilities of numerous microbial taxa important to human health, biotechnology and bioengineering. Systems biology combines computational and experimental approaches to study the complexity of biological networks at a systems level, where the cellular components and their interactions lead to complex cellular behaviors. Genome-scale biological networks have proven useful for interpreting high-throughput data and generating computational models. Mathematical models are constructed from network reconstructions, and they include variables, parameters, and equations to describe the potential behavior of these networks. Currently this approach has been used to examine the evolutionary diversity of metabolic networks for E. coli and Shigella strains [1-3], and we propose to initially construct a set of 5 genome-scale metabolic models representing a single member from each L. monocytogenes lineage (I, II, III, and IV) and also for Listeria innocua.To accomplish this, draft genome scale metabolic models will be generated using ModelSeed[4], and these models will be manually compared to experimental data to resolve inconsistencies due to missing reactions in the metabolic network using a gap filling approach. Using this approach with Yersinia metabolic models found that ModelSeed generated models that could accurately predict nutrient capabilities to over 80% accuracy from over 600 substrates for utilization of carbon, nitrogen, phosphorous, sulfur, and iron compounds. Therefore, we will conduct this analysis both in silico and experimentally using phenotypic nutrient array assays. Once our computational models are validated for nutrient utilization capabilities, we will conduct analysis of an array of 40 nutrients found in host environment niches where Listeria associate with human cells. Using in silico methods, we will then predict the reactions and genes that are essential for the ability of growth during host-interactions.In addition to examining numerous strains of Listeria spp. through the construction of genome-scale metabolic models, we also propose to construct a model representing the ancestral core of this genus of bacteria. Dr. Baumler has started a new area of research called "Paleo Systems Biology", in which the conserved genome content from modern-day strains can be identified and this evolutionarily shared content can be used to build a metabolic model of a strain that may have existed ~10 millions of years ago (mya). This paleo systems biology research approach will help us to better understand the evolution of the modern-day strains and to lend new insight into bacterial evolution. For this project, we will also be examining constructed genome-scale metabolic models of numerous strains of Listeria monocytogenes and also a relative strain Listeria innocua. We will be using computational methods to better understand the nutrient capabilities and genomic properties that all modern-day Listeria strains share in common, and also those that differentiate them during host-interactions in niches these microorganisms occupy in vertebrate hosts such as humans.#2) Numerous genomes of Salmonella strains have been completed and have led to a preliminary analysis of gene content differences among these strains isolated from humans, bovine, or avian hosts. One new method to gain further understanding of the metabolic capabilities of microbial strains is through the construction of genome-scale metabolic models[8]. A genome is all the genetic information possessed by any organism i.e. the human genome, the cow genome, the yeast genome. We can utilize genome-scale metabolic models (GEMs) to connect all of the information contained in a genome into a computational format that allows investigation into the nature of the organism, and to conduct simulations mimicking the real world conditions found in humans or animals[9].Currently the construction of metabolic networks for bacteria relies primarily on information derived from analysis of the genome, databases of biological information, and published scientific literature. By combining all of the information collected from these resources, the function of all of the cellular machinery can be identified and included in a computational model to predict what nutrients can be used by the bacteria in environments such as foods or humans. By comparing GEMs for good and bad strains of related bacteria, metabolic differences can be identified that may lead to the development of new control strategies for associated human diseases.Therefore we propose to use ModelSeed to construct GEMs of three Salmonella strains that are found in human, avian, or bovine hosts. We plan to use computational modeling to determine what metabolic capabilities differ between these strains that may offer them a competitive advantage to grow and persist in these hosts. We also plan to identify essential reactions, defined as reactions that are absolutely necessary to live and grow in each of these host environments, and also in poultry and beef food products. Ultimately this project will provide a new understanding of the evolution of Salmonella strains, and lead to new control strategies to make foods safer, and to prevent associated human disease.#3) In accordance with the goal of training scientists who can device interventional strategies to limit microbial growth in food, prevent contamination of food, reduce food waste through spoilage and enhance detection of contamination or degradation of food, we shall use ModelSeed to construct a genome-scale metabolic model (GEM) of the German E. coli O104:H4 to better understand its global metabolic capacity, compared to the existing E. coli O157:H7 GEMs. We shall conduct a thorough examination to identify known and putative virulence genes (both unique and shared ones). In addition, we shall determine new targets to control and/or treat human infections from similar strains. GEMs capture the metabolic capabilities of microbial taxa important to biotechnology, bioengineering, and human health. These GEMs have been used to conduct simulations investigating metabolic processes during host-microbe interactions and to identify differentiating metabolic properties between commensal and pathogenic E. coli strains[2, 3]. Therefore this research project using a GEM of this outbreak strain would lead to new information about this pathogen beyond the analysis of the genomic sequence alone.This disastrous pathogen was suspected to be from Egypt and is one of the only pathogenic E. coli strains with a sequenced genome from Africa. Considering that most countries in Africa are classified as third world both in food safety and medicine, an outbreak such as the one in Germany would be catastrophic. By understanding the metabolic capacity of E. coli O104:H4, we shall be better placed to tackle the outbreak, should it re-occur. In addition, computer models allow us as microbiologists to study the organism as a whole before going into the lab, reducing the amount of time and resources needed during experiments. Also, a GEM for O104:H4 is a good stepping stone towards understanding related pathogens, such as Salmonella.

Progress 10/01/15 to 09/30/20

Outputs
Target Audience:Several audiences are the potential recipients of this project's outcomes: first the undergraduate and graduate students who take my Introductory Microbiology or Food Microbiology courses at the University of Minnesota, second, food safety scientists and members of the Minnesota Food Protection Association, third, regulators that could use the information for policy framework, and consumers who may be better able to understand the risks associated with these products. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?It has afforded training and professional development opportunities for the graduate student researchers working on the projects. How have the results been disseminated to communities of interest?Through numerous posters and oral presentations at three major scientific conferences and through peer reviewed publications. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Specific goal #1: "Examination of the evolutionary diversity of Listeria spp. through genome-scale metabolic modeling": was accomplished and resulted in a publication in a peer-reviewed journal and a Masters thesis. Specific goal #2: "Evaluation of growth and metabolic variations of Salmonella spp. strains related to host-specificity using computational metabolic models": resulted in a Masters thesis. Specific goal #3: "Determination of the metabolic capabilities and new control targets for the European foodborne outbreak strain of E. coli O104:H4": this project was terminated, since the researcher move onto another project in a different lab and they had completed little to no progress for this goal.

Publications

• Type: Journal Articles Status: Published Year Published: 2020 Citation: Chen, D., Wiertzema, J.R., Peng, P., Cheng, Y., Wang, Y., Liu, J., Ma, Y., Min, M., Chen, P., Baumler, D.J., Chen, C., Lee, L., Vickers, Z., Feirtag, J., Ruan, R. 2020. Catalytic intensive pulse light inactivation of Cronobacter sakazakii and other pathogens in non-fat dry milk and wheat flour. Food Chemistry Journal 332, 127420.

Progress 10/01/18 to 09/30/19

Outputs
Target Audience:Several audiences are the potential recipients of this project's outcomes: first the undergraduate and graduate students who take my Introductory Microbiology or Food Microbiology courses at the University of Minnesota, second, food safety scientists and members of the Minnesota Food Protection Association, third, regulators that could use the information for policy framework, and consumers who may be better able to understand the risks associated with these products. Changes/Problems:Specific goal #3: "Determination of the metabolic capabilities and new control targets for the European foodborne outbreak strain of E. coli O104:H4": this project was terminated, since the graduate student quit and revealed they had completed little to no progress for this goal. What opportunities for training and professional development has the project provided?It has afforded training and professional development opportunities for the graduate student researchers working on the projects How have the results been disseminated to communities of interest?Through numerous posters and oral presentations at three major scientific conferences What do you plan to do during the next reporting period to accomplish the goals?Continue to work on the projects as stated to see them through completion

Impacts
What was accomplished under these goals? Specific goal #1: "Examination of the evolutionary diversity of Listeria spp. through genome-scale metabolic modeling": was accomplished and resulted in a publication in a peer-reviewed journal. Specific goal #2: "Evaluation of growth and metabolic variations of Salmonella spp. strains related to host-specificity using computational metabolic models": is currently in preparation for submission of a scientific research manuscripts Specific goal #3: "Determination of the metabolic capabilities and new control targets for the European foodborne outbreak strain of E. coli O104:H4": this project was terminated, since the graduate student quit and revealed they had completed little to no progress for this goal.

Publications

• Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Wiertzema, J.R., Borchardt, C., Beckstrom, A.K., Dev, K., Chen, P., Chen, C., Vickers, Z., Feirtag, J., Lee, L., Ruan, R., Baumler, D.J. 2019. Evaluation of Methods for Inoculating Dry Powder Food Ingredients with Salmonella enterica serovar Typhimurium LT2, Enterococcus faecium or Cronobacter sakazakii. Journal of Food Protection 82(6), 1082-1088.

Progress 10/01/17 to 09/30/18

Outputs
Target Audience:Several audiences are the potential recipients of this project's outcomes: first the undergraduate and graduate students who take my Introductory Microbiology or Food Microbiology courses at the University of Minnesota, second, food safety scientists and members of the Minnesota Food Protection Association, third, regulators that could use the information for policy framework, and consumers who may be better able to understand the risks associated with these products. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?It has afforded training and professional development opportunities for the graduate student researchers working on the projects. How have the results been disseminated to communities of interest?Through numerous posters and oral presentations at three major scientific conferences What do you plan to do during the next reporting period to accomplish the goals?Continue to work on the projects as stated to see them through completion.

Impacts
What was accomplished under these goals? Specific goal #1: "Examination of the evolutionary diversity of Listeria spp. through genome-scale metabolic modeling": was accomplished and resulted in a publication in a peer-reviewed journal. Specific goal #2: "Evaluation of growth and metabolic variations of Salmonella spp. strains related to host-specificity using computational metabolic models": is currently underway collecting experimental and in silico data, and will result in multiple future submissions or scientific research manuscripts Specific goal #3: "Determination of the metabolic capabilities and new control targets for the European foodborne outbreak strain of E. coli O104:H4": this project is in the development stage as the genome scale metabolic models have been constructed and in silico analysis has been started.

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: Metz, Z.P., Ding, T., Baumler, D.J. 2018. Using genome-scale metabolic models to compare serovars of the foodborne pathogen Listeria monocytogenes. PLoS One. Jun 7;13(6):e0198584. doi: 10.1371/journal.pone.0198584. eCollection 2018. (Original Research) PMID: 29879172

Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Several audiences are the potential recipients of this project's outcomes: first the undergraduate and graduate students who take my Introductory Microbiology or Food Microbiology courses at the University of Minnesota, second, food safety scientists and members of the Minnesota Food Protection Association, third, regulators that could use the information for policy framework, and consumers who may be better able to understand the risks associated with these products. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?It has afforded training and professional development opportunities for the graduate student researchers working on the projects. How have the results been disseminated to communities of interest?Through numerous posters and oral presentations at three major scientific conferences What do you plan to do during the next reporting period to accomplish the goals?Continue to work on the projects as stated to see them through completion.

Impacts
What was accomplished under these goals? Specific goal #1: "Examination of the evolutionary diversity of Listeria spp. through genome-scale metabolic modeling": was accomplished and have resulted in a manuscript currently under review in a peer-reviewed journal. Specific goal #2: "Evaluation of growth and metabolic variations of Salmonella spp. strains related to host-specificity using computational metabolic models": is currently underway collecting experimental and in silico data, and will result in multiple future submissions or scientific research manuscripts Specific goal #3: "Determination of the metabolic capabilities and new control targets for the European foodborne outbreak strain of E. coli O104:H4": this project is in the development stage as the genome scale metabolic models have been constructed and in silico analysis has been started.

Publications

Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Several audiences are the potential recipients of this project's outcomes: first the undergraduate and graduate students who take my Introductory Microbiology or Food Microbiology courses at the University of Minnesota, second, food safety scientists and members of the Minnesota Food Protection Association, third, regulators that could use the information for policy framework, and consumers who may be better able to understand the risks associated with these products. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?It has afforded training and professional development opportunities for the graduate student researchers working on the projects. How have the results been disseminated to communities of interest?Through numerous posters and oral presentations at three major scientific conferences. What do you plan to do during the next reporting period to accomplish the goals?Continue to work on the projects as stated to see them through completion.

Impacts
What was accomplished under these goals? Specific goal #1: "Examination of the evolutionary diversity of Listeria spp. through genome-scale metabolic modeling": was accomplished and have resulted in a publication currently under review in a peer-reviewed journal. Specific goal #2: "Evaluation of growth and metabolic variations of Salmonella spp. strains related to host-specificity using computational metabolic models": is currently underway collecting experimental and in silico data, and will result in multiple future submissions or scientific research manuscripts Specific goal #3: "Determination of the metabolic capabilities and new control targets for the European foodborne outbreak strain of E. coli O104:H4": this project is in the development stage as the genome scale metabolic models have been constructed and in silico analysis has been started.

Publications

• Type: Journal Articles Status: Published Year Published: 2016 Citation: Ding, T., Case, K.A., Omolo, M.A., Reiland, H.A., Metz, Z.P, Diao, X., and D.J. Baumler. 2016. Predicting essential metabolic genome content of niche-specific enterobacterial human pathogens during simulation of host environments. PLOS One. Feb 17;11(2):e0149423.
• Type: Journal Articles Status: Under Review Year Published: 2016 Citation: Metz, Z.P. and D.J. Baumler. Using Genome-Scale Metabolic Models to Compare Serovars of the Foodborne Pathogen Listeria monocytogenes. Submitted to BMC Systems Biology
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Zachary P. Metz and David J. Baumler, Using Genome-Scale Metabolic Modeling to Compare Strains of the Foodborne Pathogen Listeria monocytogenes, International Association for Food Protection's annual meeting in St. Louis, MO on August 1st, 2016 Zachary P. Metz and David J. Baumler, Using Genome-Scale Metabolic Modeling to Compare Strains of the Foodborne Pathogen Listeria monocytogenes, Institute of Food Technologists annual meeting in Chicago, IL on July 18th, 2016 David J. Baumler, Using Genome-scale Metabolic Models of Foodborne Pathogens to Address Human Disease and Food Safety, International Association for Food Protection's 12th European Symposium on Food Safety in Athens, Greece on May 13th, 2016