Source: PENNSYLVANIA STATE UNIVERSITY submitted to NRP
TRAINING FOOD MICROBIOLOGISTS TOWARD DATA SCIENCE FLUENCY AND CODE COMPETENCY
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1025223
Grant No.
2021-38420-34066
Cumulative Award Amt.
$164,000.00
Proposal No.
2020-08176
Multistate No.
(N/A)
Project Start Date
Jan 15, 2021
Project End Date
Sep 16, 2025
Grant Year
2021
Program Code
[KK]- National Needs Graduate Fellowships Program
Recipient Organization
PENNSYLVANIA STATE UNIVERSITY
408 Old Main
UNIVERSITY PARK,PA 16802-1505
Performing Department
Food Science
Non Technical Summary
Scientific fields including food microbiology and food safety increasingly need a workforce that is comfortable working with large datasets. Examples include the critical analysis of thousands of genomes from foodborne bacteria or viruses to understand the source of an outbreak, or evaluation of datasets that provide insights into how the large number of microorganisms that exist in human intestinal tracts impact health and well-being. We propose a training program for M.S. students in Food Science, that includes both traditional training as well as that to develop leaders with expertise in big data analyses. These Fellows will gain leadership skills through organizing seminars in collaboration with experts in the professional workforce, and through training their peers in large-scale data analyses. The effectiveness of this training program will be evaluated through several internal and external assessments.
Animal Health Component
25%
Research Effort Categories
Basic
50%
Applied
25%
Developmental
25%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
7124010110050%
7124020110225%
7014010101025%
Knowledge Area
712 - Protect Food from Contamination by Pathogenic Microorganisms, Parasites, and Naturally Occurring Toxins; 701 - Nutrient Composition of Food;

Subject Of Investigation
4010 - Bacteria; 4020 - Fungi;

Field Of Science
1100 - Bacteriology; 1102 - Mycology; 1010 - Nutrition and metabolism;
Goals / Objectives
Advances in DNA sequencing and data analysis have transformed the field of food microbiology and agricultural sciences. The increasing need for a workforce with competencies in microbiology and data science highlight a shortage of leaders who have both a solid microbiology background and the ability to work with large datasets while being able to communicate the impacts of such work. To address this need and transform food microbiology education at the graduate level, we propose a graduate student fellowship program that will initiate this long-term effort by training four M.S. students under TESA "Food Science, Human Sciences, and Human Nutrition" and "Data Science", in the Relevant Discipline "Food Science/Technology/Manufacturing/Safety". Fellow recruitment will leverage the strong relationship between our Food Science Department and underrepresented minority-serving institutions, along with other programs in the Department and College of Agricultural Sciences that have a proven track record of recruiting underrepresented students. Recruited fellows will pursue degrees in Food Science advised or co-advised by faculty specialized in food microbiology and sequencing data analyses. Training will follow our "Data-Development-Decisions" (3D) framework.
Project Methods
Fellows will receive rigorous academic and leadership training through: 1. Coursework that includes both Food Science and Data Science disciplines; 2) Research integrating microbiology with focus on next generation sequencing; 3. Specialized training through participation in Penn State's Bioinformatics Workshop, hosted by the Microbiome Center; 4. Becoming trainers and future leaders of the Bioinformatics Workshop; 5. Peer-to-peer training through Penn State's Data Analyses Working Group (DAWG); 5. Organizing science communications and policy-making projects and outreach in collaboration with professions in these fields; 6. Visits to government labs that use big data for making policy in food microbiology.We will assess the success of this approach using formative/summative assessment, Kirkpatrick model for training evaluation, internal and external program evaluations, in addition to the regular evaluations in place for all graduate students in Penn State's Food Science Department. Fellows will be tracked for at least 5 years post-graduation.

Progress 01/15/21 to 09/16/25

Outputs
Target Audience:Individuals from academia, industry, and government who are using, or interested in how to use, large sequence-based datasets for regulatory policy, and how to train groups of individuals in such technologies. This project was also directed at graduate students intereested in learning these skills, and how to apply findings to public policy. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Preparation for the seminar mentioned above included meeting monthly with different scientists, all of whom use their skills in some type of policy development. Thus, they gained insights into how scientific data is used to drive public policy and regulation. The research projects pursued as part of the M.S. programs prepared each of the students for professional careers, as evident by their employment in respective agencies. How have the results been disseminated to communities of interest?Students have given public seminars, and presented their work in poster form at scientific meetings. Peer-reviewed publications are included in this report. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Four M.S. students successfully matriculated through this program. The students became employed as follows: 1.Research Technologist II Penn State University Plant Pathology (University Park, PA) 2. Lab analyst with Eurofins (Homewood, IL) 3. Sales Account Executive, Jogue, Inc (Plymouth, MI) 4. R&D Scientist, Kraft Heinz (Pittsburgh, PA) The students completed the required Department seminar presentation in collaboration with external mentors they identified, and all tasks described in this proposal.

Publications

  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Pseudomonadaceae increased the tolerance of Listeria monocytogenes to sanitizers in multi-species biofilms. Voloshchuk O, Rolon ML, Bartlett KV, Mendez Acevedo M, LaBorde LF, Kovac J. Food Microbiol. 2025 Jun;128:104687. doi: 10.1016/j.fm.2024.104687. Epub 2024 Nov 29. PMID: 39952739 Mendez Acevedo, Marysabel; Rolon, M. Laura; B. Johnson, Beth; Burns, Logan; Stacy, Joshua; Aurand-Cravens, Ashley; et al. (2025). Data from: Sanitizer Resistance and Persistence of Listeria monocytogenes Isolates in Tree Fruit Packing Facilities. Ag Data Commons. Dataset. https://doi.org/10.15482/USDA.ADC/28740530
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Impact of Improved Sanitation Standard Operating Procedures on Microbial Populations at Three Tree Fruit Packing Facilities. Rolon ML, Mendez Acevedo M, Sinclair P, Macarisin D, LaBorde LF, Kovac J. J Food Prot. 2025 Jan 2;88(1):100436. doi: 10.1016/j.jfp.2024.100436. Epub 2024 Dec 17. PMID: 39701447 Free article. https://submit.nal.usda.gov/node/6087
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Sanitizer Resistance and Persistence of Listeria monocytogenes Isolates in Tree Fruit Packing Facilities. M�ndez Acevedo M, Rolon ML, Johnson BB, Burns LH, Stacy J, Aurand-Cravens A, LaBorde L, Kovac J. J Food Prot. 2024 Oct;87(10):100354. doi: 10.1016/j.jfp.2024.100354. Epub 2024 Aug 30. PMID: 39218076 Free article. https://submit.nal.usda.gov/node/6088.


Progress 01/15/24 to 01/14/25

Outputs
Target Audience:Academic, government, and industry scientists interested in promoting the next generation of food microbiology professionals. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest?We are currently writing the final publications and will be uploading links to PubAg and associated data to the data commons. What do you plan to do during the next reporting period to accomplish the goals?Write the final report, and upload required information to PubAg and the data commons.

Impacts
What was accomplished under these goals? All students funded by this project graduated in Summer 2023. We are in the process of writing the final report for this project.

Publications


    Progress 01/15/23 to 01/14/24

    Outputs
    Target Audience:Academic, government, and industry scientists interested in promoting the next generation of food microbiology professionals. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Preparation for the seminar mentioned above included meeting monthly with different scientists, all of whom use their skills in some type of policy development. Thus, they gained insights into how scientific data is used to drive public policy and regulation. How have the results been disseminated to communities of interest?Students have given public seminars, and presented their work in poster form at scientific meetings. Peer-reviewed publications are in preparation. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

    Impacts
    What was accomplished under these goals? The four graduate students who began Fall 2021 all graduated Spring 2023. In the previous year, they met with several scientific and policy mentors over Zoom, and constructed a presentation on the promise and challenges of wastewater surveillance for advancing public health. The presentation included ethical challenges of implementing such surveillance nationwide. This was delivered at the weekly Thursday Food Science Seminar Series that is held within the Department. Three of the four students are known to be employed, as a Research and Development Scientist for Kraft Heinz (Pittsburgh, PA), a laboratory technician in the Department of Plant Pathology and Environmental Microbiolology at Penn State, and a Sales Associate at Jorge (Plymouth, Michigan).

    Publications

    • Type: Conference Papers and Presentations Status: Accepted Year Published: 2023 Citation: Pickens T., Carney H., DeMartino P, Paff A, Cockburn DW. 2023. Presenting Whole Holes: The Development of a Synbiotic Breakfast or Snack Food Product. IFT First, Chicago, IL.
    • Type: Conference Papers and Presentations Status: Accepted Year Published: 2023 Citation: Mendez Acevedo, M., Kovac, J. (April 14, 2023). Intruder alert! Detection of resistant and persistent strains of L. monocytogenes in packinghouses, Controlling Listeria in produce packinghouses workshop, Fruit Research and Extension center, Biglerville, PA. Local.
    • Type: Conference Papers and Presentations Status: Accepted Year Published: 2023 Citation: Tin, L. K., & Wee, J. (Author). (2023). "Using Non-Saccharomyces Yeast to Lower Ethanol Levels in Wines," 2023 Pennsylvania Wine and Grape Industry Conference, Pennsylvania Wine Marketing and Research Program Board, State College, PA, USA, 80 in attendance, Invited. Regional.
    • Type: Websites Status: Accepted Year Published: 2023 Citation: "Pa. winemakers uncork new possibilities with help of Penn State researchers," Internet, Penn State News. (2023).


    Progress 01/15/22 to 01/14/23

    Outputs
    Target Audience:Individuals from academia, industry, and government who are using, or interested in how to use, large sequence-based datasets for regulatory policy, and how to train groups of individuals in such technologies. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The students have met with several individuals in industry and government who are directly involved in translating science to public policy, with a focus on food safety. They will be delivering a seminar Spring 2023 to the entire Food Science Department about their findings and lessons learned. This activity expanded their view of career possibilities outside of academia. All students have finished their required coursework, and served as a TA for one course. How have the results been disseminated to communities of interest?Presentations at scientific meetings and peer-reviewed research publications. What do you plan to do during the next reporting period to accomplish the goals?We anticipate all students will have graduated and be gainfully employed by Summer 2023.

    Impacts
    What was accomplished under these goals? The four students all pursued independent research this year including: 1. Studying the effect of different cleaning and sanitizing protocols applied in apple packing facilities on the total arerobic mesophilic microbial load, L. monocytogenes, and microbiota composition. 2. Characterization of strains generated by high throughput screening collaboration with GALT industries. This unfortunately did not produce any novel resistant starch degrading organisms as we speculated it would. This student has since pivoted to two alternative, complementary approaches, using samples for which we have 16S and shotgun metagenomics data. In the first approach she is attempting to culture resistant starch degrading organisms from samples that are lacking the two known primary degraders Ruminococcus bromii and Bifidobacterium adolescentis. In the second approach she is assembling genomes from samples that contain different strains of Ruminococcus bromii that have exhibited different properties in our human clinical trial feeding resistant starch, one associated with an anti-inflammatory response, the other associated with a pro-inflammatory response and looking for key genomic differences. 3. Genomics and bioinformatics to identify and characterize non-Saccharomyces yeasts for their ability to decrease ethanol and acetic acid during wine fermentation. This student determined that increases in global temperatures have resulted in wine grapes with higher glucose and fructose levels. Genomics and bioinformatics identified and characterized ten different non-Saccharomyces yeasts including three commercial strains for their ability to reduce ethanol during fermentation. Outcomes from this work can help develop new yeast strains for fermentation as a solution to control ethanol levels in fermented beverages. 4. Screening of wastewaters from two treatment plants in central PA for the presence of SARS-CoV-2 and potential pathogenic Escherichia coli. This student identified that low levels of virus were found in the treatment facilities during Jan-June 2022, and that variants identified tracked with those causing human disease. She also isolated and whole genome sequenced 50 E. coli isolated during the same time period, finding about 10% were from a sequence type designated ST131, which is a highly concerning, pandemic, antimicrobial resistant group. Many of these strains were resistant to the antibiotic fluoroquinolone.

    Publications

    • Type: Conference Papers and Presentations Status: Accepted Year Published: 2022 Citation: Tin, L, Feng, CT, Wee, J. Combined genomics and bioinformatics analysis provide insights into selection of non-Saccharomyces yeasts for ethanol and acetic acid production in Chambourcin wine fermentation. American Society of Enology and Viticulture 2022, San Diego, CA.
    • Type: Conference Papers and Presentations Status: Accepted Year Published: 2022 Citation: Carney H and Cockburn, DW. Characterization of carbohydrate degrading ability of human gut isolates. American Society for Microbiology Microbe 2022, Washington DC.
    • Type: Conference Papers and Presentations Status: Accepted Year Published: 2022 Citation: M Mendez Acevedo, ML Rolon, P Sinclair, D Macarisin, L LaBorde, J Kovac. The effect of different sanitation treatments on the frequency of Listeria monocytogenes detected on non-food contact surfaces in apple packinghouses. IAFP 2022, Pittsburgh, PA.
    • Type: Conference Papers and Presentations Status: Accepted Year Published: 2022 Citation: Tin, L. K., & Wee, J. (Author). (2022). "Comparing the Fermentation Potential of Non-Saccharomyces Yeast, Hanseniaspora uvarum with Saccharomyces cerevisiae: A Preliminary Study," The International Fermentation Conference Fermentation 2022, The Fermentation Association, Chicago, Illinois, United States.
    • Type: Conference Papers and Presentations Status: Accepted Year Published: 2022 Citation: Mendez-Acevedo, M., Rolon, M. L., Sinclair, P., Macarisin, D., LaBorde, L. F., &Kovac, J.(October 26, 2022). "The effect of different sanitation treatments on the frequency ofListeria monocytogenesdetected on non-food contact surfaces in apple packinghouses," 2022 National Diversity in STEM meeting, The Society for Advancement of Chicanos/Hispanics and Native Americans in Science, San Juan, Puerto Rico.


    Progress 01/15/21 to 01/14/22

    Outputs
    Target Audience:During the reporting period, four graduate students pursuing M.S. degrees in Food Science were recruited. The target audience also includes individuals who are using, or interested in how to use, large sequence-based datasets for regulatory policy. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?In the coming summer, the students will participate in the Penn State Microbiome Center Kick-Start Workshop. The students were participants in summer 2021, and this summer will be expected to take on the role of co-instructors. This is part of "The Development" portion of our training program, where the students are expected to build planning and leadership skills to ensure a successful program for the summer 2022 participants. How have the results been disseminated to communities of interest?By presentations at scientific meetings. What do you plan to do during the next reporting period to accomplish the goals?By the next reporting period, all four graduate fellows should be completing their research projects and in the writing stage of their M.S. theses. They will also design and deliver a seminar to the Food Science Department on how high throughput sequencing and analysis is being used to support regulatory policies.

    Impacts
    What was accomplished under these goals? We recruited 4 students for the M.S. program in Food Science, all who started Fall 2021. All four are women, with two from underrepresented backgrounds who are first-generation graduate students. The students all have research projects designed around training in sequence analysis, including: 1) Screening rural wastewater treatment facilities for SARS-CoV-2, including targeted sequencing to identify current and emerging variants; 2) genomics and bioinformatics to identify and characterize non-Saccharomyces yeasts for their ability to decrease ethanol and acetic acid during wine fermentation; 3) using fecal cultures enriched with resistant starch to isolate resistant starch degrading organisms, followed by genomic and phenotypic characterization; and 4) studying the effect of different cleaning and sanitizing protocols applied in apple packing facilities on the total arerobic mesophilic microbial load, L. monocytogenes, and microbiota composition. All students are in their second semester, and we anticipate will be done with the majority of formal coursework in order to focus on other goals of the program during their second year.

    Publications

    • Type: Conference Papers and Presentations Status: Accepted Year Published: 2021 Citation: Carney H, Aston, L, Miranda-Perez A, Cockburn, DW. Characterization of carbohydrate degrading ability of human gut isolates. ABASM 2021, Virtual.