Location: Food and Feed Safety Research
2025 Annual Report
Objectives
Objective 1: Determine factors affecting colonization, maintenance, and dissemination of foodborne pathogens and antimicrobial resistant bacteria in the bovine and swine gastrointestinal tract, lymphatic system and their production and processing environments.
Sub-objective 1.A: Identify and characterize factors affecting the infection, colonization, carriage and dissemination of foodborne pathogens and antimicrobial resistant bacteria within the production environment and the resident and transient populations of arthropods in farm and processing environments.
Sub-objective 1.B: Identify and characterize factors affecting colonization and maintenance of Salmonella in the swine proximal alimentary, distal gastrointestinal tract, and associated lymphatics system.
Sub-objective 1.C: Evaluate factors influencing intestinal mucosal integrity of the distal intestinal tract of feedlot cattle and correlation to Salmonella carriage in peripheral lymph nodes.
Objective 2: Identify, develop, and test interventions, including possible synergies of multiple interventions and GRAS (generally regarded as safe) alternatives, to yield effective technologies to control foodborne pathogens or mitigate their virulence and resistance.
Sub-objective 2.A: Determine best-user practices to achieve effective pathogen control for commercially relevant organic acid mixtures and biocides under the varied applications protocols currently used by industry.
Sub-objective 2.B: Overcome the lipophilic limitations of essential oils by chitosan-encapsulation, use of natural or synthetic higher molecular weight carbohydrate-glycosidic conjugates or co-administration with appropriate emulsifiers.
Sub-objective 2.C: Characterize effects of short chain nitrocompounds on hydrogen ecology, redox homeostasis, pathogen competitiveness and gene expression by zoonotic pathogens and resolve uncertainties pertaining to their safe use in animal agriculture.
Approach
The long-term goal of our project is to develop practical, cost-effective, and environmentally compatible strategies to reduce the prevalence and concentration of foodborne pathogens associated with food-producing animals, thus reducing the risk of transmission of foodborne disease and antimicrobial resistance to the American consumer. To accomplish these goals, we need to better understand ecological and biological factors affecting the ability of foodborne pathogens to colonize particular habitats present in animal agriculture and how we can interrupt their ability to survive and persist in these environments. The overall goals of Objective 1 of this project are to determine factors affecting colonization, maintenance, and dissemination of foodborne pathogens and antimicrobial resistant bacteria in the bovine and swine gastrointestinal tract, lymphatic system, and their production and processing environments. The goals of Objective 2 seek to identify, develop, and test interventions, including possible synergies of multiple interventions and GRAS (generally regarded as safe) alternatives, to yield effective technologies to control foodborne pathogens or mitigate their virulence and resistance and apply this knowledge, as well as existing knowledge, to develop interventions to reduce the colonization, carriage, and ultimately the shedding of pathogenic and antimicrobial resistant bacteria in food-producing animals. Ultimately, results obtained from this research will facilitate the development of sound, science-based microflora management strategies to improve gut health and function by reducing the risk of transmission of foodborne disease and antimicrobial resistance in food-producing animals and their production environment.
Progress Report
Work conducted by this project during FY 2025 made substantial progress in achieving the goals of Objective 1, particularly in identifying factors affecting colonization, maintenance, and dissemination of foodborne pathogens and antimicrobial-resistant bacteria in the bovine and porcine gastrointestinal tract, lymphatic system, and production environments. The work advanced considerably, and data are undergoing thorough analysis. Studies examined specific food processing and animal waste management practices, along with prospective monitoring technologies, to generate new insights into key contributors to the contamination and dissemination of pathogenic and antimicrobial-resistant bacteria in animal-produced foods and their environments. Under Objective 2, research progressed significantly on the identification, development, and testing of intervention strategies. The focus of this effort is on synergistic combinations of approaches that enhance effectiveness and includes interventions using natural or generally recognized as safe (GRAS) alternatives to conventional antibiotic or pathogen control methods. The aim is to develop innovative technologies and protocols that effectively manage foodborne pathogens or mitigate their virulence and resistance. These interventions will boost the efficiency and profitability of animal production, with industry partners actively collaborating to support the integration of these technologies into commercial production systems. Success in this work will empower U.S. farmers and ranchers to deliver safer and higher-quality meat and dairy products to the consumer, and at lower cost.
Accomplishments
1. Practical spray technology to safeguard silage and improve food safety. Ensiling preserves forage by creating an oxygen-free fermentation process that supports beneficial lactic acid-producing bacteria and ensures high-quality silage. However, exposure to oxygen during the feeding phase can allow spoilage organisms and harmful pathogens to grow, compromising both the safety and economic value of silage. ARS researchers at College Station, Texas, collaborated with industry and university partners to develop practical, sprayable formulations made from naturally occurring plant compounds including chlorophylls, dimethyl sulfone, tannins, medium-chain fatty acids, and hop extracts. These formulations successfully prevented mold proliferation and reduced foodborne pathogens and antimicrobial-resistant bacteria, preventing spoilage and even rescuing spoiled silages. This technology provides farmers with a cost-effective solution to enhance feed quality, safeguard animal health, and improve food safety. Practical application of this mitigation strategy will provide a real-world approach to reducing silage spoilage and contamination. It will also enhance the safety of livestock feedstuffs to the animals and also of meat and dairy products reaching the consumer.
2. Characterizing protist diversity in dairy microbiomes: Ecological and food safety implications. Dairy farming is a vital U.S. industry that supports both the economy and national nutritional health. Maintaining a healthy environment in dairy facilities is challenging; the nature and composition of microbial communities associated with dairy ecosystems is poorly understood and can impact dairy health and safety. Protists are a diverse group of microorganisms that are not plants, animals, or fungi; they can significantly impact microbial dynamics in certain environments including those associated with dairies. Understanding the occurrence, actions, and impacts of protists in dairy systems, including manure, lagoons, and troughs, is essential for assessing their risks and benefits. ARS researchers at College Station, Texas, analyzed protist diversity across different dairy environments and management styles, focusing on protist interactions with two fly species that serve as microbial vectors. The work identified substantial differences in protist composition, with troughs and lagoons harboring both beneficial microbes and potential pathogens. This accomplishment provides foundational information for development of improved dairy management and sanitation strategies that will assure animal health and safety and also helps assure that food products leaving the dairy will be microbiologically safe.
Review Publications
Jackson, S.J., Andrews, K., Droleskey, R.E., Banz, W.J., Apgar, G.A., Rivenbark, K.J., Wang, M., Anderson, R.C., Harvey, R.B., Phillips, T.D. 2025. NutriClayZn binds aflatoxin B1 and suppresses pathogenic, antimicrobial resistant bacteria across the food supply chain. Journal of Food Science. 88(5). Article 100486. https://doi.org/10.1016/j.jfp.2025.100486.
Wottlin, L.R., Harvey, R.B., Norman, K.N., Droleskey, R.E., Andrews, K., Jackson, S.J., Anderson, R.C., Poole, T.L. 2024. Prevalence and characterization of Salmonella during pork sausage manufacturing. Microorganisms. 12(8). Article 1599. https://doi.org/10.3390/microorganisms12081599.
Salinas-Chavira, J., Arzolar-Alvarez, C., Hume, M.E., Fonseca, M., Ruiz-Barrera, O., Castillo-Castillo, Y., Ontiveros-Magadan, M., Jones, B., Crippen, T.L., Poole, T.L., Zúñiga-Serrano, A., Anderson, R.C. 2024. Influence of medium chain fatty acids on selected microbes and on in vitro ruminal fermentation of air-exposed corn silage. Frontiers in Veterinary Science. 11. Article 1416695. https://doi.org/10.3389/fvets.2024.1416695.
Feye, K., Rasmussen, M.A., Anderson, R.C., Crippen, T.L., Harvey, R.B., Poole, T.L., Ricke, S.C., Yeater, K.M. 2024. Chlorophyllin supplementation of medicated or unmedicated swine diets impact on fecal Escherichia coli and enterococci. Animals. 14(13). Article 1955. https://doi.org/10.3390/ani14131955.
Maynez-Perez, A., Jahuey-Martinez, F., Martinez-Quintana, J.A., Hume, M., Anderson, R.C., Corral-Luna, A., Rodriguez-Almeida, F., Castillo-Castillo, Y., Felix-Portillo, M. 2024. The rumen microbiome composition from Raramuri Criollo and European cattle in an extensive system. Microorganisms. 12(11). Article 2203. https://doi.org/10.3390/microorganisms12112203.
Assumpcao, A., Jesudhasan, P., Arsi, K., Alharbi, K.S., Asnayanti, A., Trieu, A.D., Read, Q.D., Perera, R., Shwani, A., Hasan, A., Pillai, S.D., Anderson, R.C., Donoghue, A.M., Rhoads, D., Alrubaye, A. 2024. Electron beam-killed Staphylococcus vaccine reduced lameness in broiler chickens. Vaccine. https://doi.org/10.3390/vaccines12111203.