Location: Warmwater Aquaculture Research Unit
2025 Annual Report
Objectives
Research will address methods to determine the presence of pathogens in catfish/catfish products and to maximize elimination methods. Detection techniques will be developed to aid in processing and packaging operations, which should further enhance product safety. Specifically the new objectives are:
1. Optimize safety of aquaculture products through innovative processes for reducing microbiological, physical and chemical hazards in seafood/aquaculture products.
2. Determine the mechanisms influencing microbial survival of selected pathogens in seafood/aquaculture products.
3. Optimize the market value of seafood/aquaculture products through enhanced food safety and quality.
Approach
Catfish: Determine optimum rates of microbial reduction through innovative processing in catfish products including evaluation of consumer acceptance. Determine viable methods of hazard reduction (smoking, acidulants, antimicrobials, etc) in catfish products during processing and storage. Determine the methods by which these methods reduce hazards within the products evaluated. Enhance the physical safety of catfish fillets with innovative analysis technology.
Seafood/Produce: Determine the efficacy of IQF freezing, irradiation, and high pressure processing and other technologies on the safety and quality of oysters, shrimp and produce.
Objective 2. Catfish/ Seafood/Produce: Determine the mechanistic approach by which the certain pathogenic bacteria may be reduced in aquatic species. Utilize PCR analysis and other assays to determine the sensitivity and specificity of various isolates in response to innovative treatments.
Objective 3. Catfish: Enhance product value through innovative smoking and further processing of catfish fillets. Value-added analysis will compared products to commodity value for product enhancement addition. Evaluate value-added products to address potential food safety issues.
Seafood/Produce: Evaluate consumer acceptance of products enhanced through various processing methods. Preparation techniques, ingredient inclusion, packaging and storage methods will be evaluated at various time frames and inclusion rates to determine specie specific parameters limitations. Analyze economics of various market potentials.
Catfish: Determine optimum rates of microbial reduction through innovative processing in catfish products including evaluation of consumer acceptance. Determine viable methods of hazard reduction (smoking, acidulants, antimicrobials, etc) in catfish products during processing and storage. Determine the methods by which these methods reduce hazards within the products evaluated. Enhance the physical safety of catfish fillets with innovative analysis technology.
Seafood/Produce: Determine the efficacy of IQF freezing, irradiation, and high pressure processing and other technologies on the safety and quality of oysters, shrimp and produce.
Objective 2. Catfish/Seafood/Produce: Determine the mechanistic approach by which the certain pathogenic bacteria may be reduced in aquatic species. Utilize PCR analysis and other assays to determine the sensitivity and specificity of various isolates in response to innovative treatments.
Objective 3. Catfish: Enhance product value through innovative smoking and further processing of catfish fillets. Value-added analysis will compared products to commodity value for product enhancement addition. Evaluate value-added products to address potential food safety issues.
Seafood/Produce: Evaluate consumer acceptance of products enhanced through various processing methods. Preparation techniques, ingredient inclusion, packaging and storage methods will be evaluated at various time frames and inclusion rates to determine specie specific parameters limitations. Analyze economics of various market potentials.
Progress Report
Progress has been achieved across all project objectives, with particular emphasis placed on advancing efforts that align with (1) the food safety of catfish, seafood and produce, and are under the National Program 108-Food Safety, Component I: Food Borne Contaminants, and (2) food quality improvement under the National Program 306- Quality and Utilization of Agricultural Products, Component I: Foods.
The production, handling, and distribution systems for fish, seafood, and produce are highly complex and varied, making them susceptible to contamination from environmental, biological, and logistical sources. Notable advancements were made toward enhancing aquaculture product safety through novel approaches aimed at minimizing microbiological, physical, and chemical hazards. These advancements are supported by multiple ongoing projects, which have already led to several peer-reviewed journal articles and numerous conference presentations, with additional manuscripts currently in development.
A key milestone was the ceremonial groundbreaking for the Northern Gulf Aquatic Food Research Center (NGAFRC) on March 10, 2025. This marks the start of construction on an $8 million federally and state-funded initiative located on an 8-acre site in Ocean Springs, Mississippi. As the first phase of a planned three-phase effort, the facility is slated for completion by Summer 2026 and is expected to significantly boost research infrastructure while attracting nationally and internationally recognized scientists.
The continued, effective collaboration with the USDA-Agricultural Research Service (ARS) and the catfish aquaculture industry has led to major improvements in both fillet and by-product safety and quality. Our recent work includes improved detection and identification of harmful pathogens in catfish and other aquatic food products, development of effective methods to reduce off-flavors in freshwater aquaculture species, creation of a targeted assay for Vibrio parahaemolyticus, and further development of a singulation system to enhance fillet handling and processing. Findings from this work have been published in peer-reviewed scientific journals.
In support of program expansion and research diversification, an internal Mississippi State University request for proposals was issued through the Mississippi Center for Enhancing Utilization and Safety of Catfish and Other Aquatic Foods. This RFP encouraged proposals addressing one of two key aims: 1) to detect, characterize, and eliminate harmful contaminants in catfish and related products as influenced by environmental and processing factors; and 2) to apply innovative science and engineering to improve processing efficiency, meat and protein recovery, shelf life, and value-added utilization of byproducts and bycatch.
In 2023, five seed grant projects were launched under this program, each beginning July 1 for a one-year period. These awards support novel research directions with the goal of increasing publication output and securing future competitive external funding. The initial results, now published, are included in this annual report.
In the following year, seven additional projects were funded starting July 1, 2024, each also supported for 12 months. Early outcomes from these projects have already led to conference presentations and journal submissions, many of which are detailed in this report and others to follow as peer-review processes are completed. The seven funded projects are: 1) “Understanding the accumulation and transmission of microbial-derived toxins in catfish and associated risk factors”; 2) “Assessing Consumer Awareness and Preferences for Food Safety Enhanced Catfish Products”; 3) “Automated Preparation Technology for Skewering Operations”; 4) “Optimizing ingredient formulations and processing variables associated with the marination of catfish”; 5) “Assessment of chemical residues in store-bought catfish from Mississippi groceries”; 6) “Evaluating the silage technology to add value to catfish processing plants' by-products (year 2 funding)”; and 7) “A Comprehensive Culturomics Approach to Recover and Characterize Catfish Spoilage Bacteria”; Collectively, these projects are strengthening the scientific foundation of this research program and deepening our collaboration with USDA-ARS. These supported projects have already resulted in published outputs, with additional manuscripts in review or preparation.
Accomplishments
1. Development of sustainable technologies to recycle catfish processing waste into feed ingredients and advanced materials. Two studies explored novel uses for catfish byproducts to support sustainability and reduce waste. One study developed fermented silage from viscera, heads, frames, and whole byproducts by optimizing bacterial and carbohydrate additions. The resulting silage showed good emulsification and protein solubility, with viscera-based silage offering the highest soluble protein. Another project recycled catfish bone into fish bone powder (FBP), which was used in 3D-printed silicone composites. These composites, produced via direct ink writing (DIW), exhibited tunable mechanical properties and dimensional stability. The research demonstrated that both silage and bone waste can be transformed into high-value inputs for aquaculture feed and biomanufacturing, creating new markets while reducing waste.
2. Enhanced diagnostic tools and microbial resistance studies to safeguard catfish and other aquatic foods from pathogenic threats. Three projects focused on improving food safety in catfish and other aquatic foods production. Two addressed Vibrio parahaemolyticus detection: one enhanced the FDA's PCR assay for clearer, more reliable detection of tlh, trh, and tdh genes, while the other developed a field-friendly MIRA-LFD assay capable of detecting tdh and trh genes rapidly and accurately without lab equipment. A third study examined the survival and regrowth of Listeria monocytogenes in the presence of quaternary ammonium compounds like benzalkonium chloride (BAC). It revealed that sublethal BAC concentrations in food processing environments could support Listeria persistence and generate resistant colony variants. These efforts support improved diagnostics, surveillance, and disinfection strategies in the aquatic foods sector.
3. Identified consumer willingness to pay for sustainably and domestically produced freshwater fish products. A consumer study evaluated national preferences for catfish based on sustainability certification and domestic origin. Using a choice experiment, researchers found that consumers are willing to pay more for catfish that is both sustainably raised and produced in the U.S. The interaction between these attributes was especially significant for environmentally conscious and locally oriented individuals. These insights provide valuable guidance to industry stakeholders and policymakers, suggesting marketing strategies that highlight sustainability and local sourcing can boost market value and consumer trust in U.S.-farmed catfish.
4. Investigated how ammonia stress affects catfish growth, fillet quality, and intestinal microbiota. Two complementary studies examined the impact of ammonia stress—common in pond aquaculture—on catfish performance. One study showed that high ammonia levels reduced growth in both channel and hybrid catfish, with hybrids more adversely affected. Although some sensory qualities of fillets changed, overall flavor and texture were not significantly altered. A second study used Nanopore 16S sequencing to evaluate gut microbiomes under ammonia stress. Hybrid catfish had higher microbial richness but were dominated by Lactococcus lactis, while channel catfish had a more balanced microbial profile. Differences in microbial communities were attributed more to fish species than to ammonia exposure. These findings suggest host species plays a larger role than environment in shaping gut microbiota, but growth performance still suffers under ammonia stress.
5. Developed tools and insights for microbial spoilage tracking and contaminant monitoring in catfish products. Two studies tackled spoilage and contamination in catfish. One used a combined culturomics and Nanopore sequencing approach to profile spoilage microbes during refrigerated storage. The study found spoilage was driven by specific taxa such as Aeromonas sobria, Pseudomonas fragi, and Shewanella baltica, and that antibiotic-enriched media recovered resistant or niche organisms missed by traditional methods. A second study tested for legacy and emerging contaminants—such as pesticides and trace metals—in catfish fillets from stores and ponds. Diuron metabolites and trace metals like lead and cadmium were detected, including a thiamethoxam residue above the regulatory threshold. These efforts improve our understanding of microbial spoilage and highlight the need for continued monitoring of chemical contaminants to ensure safe, high-quality catfish products.
Review Publications
Jing, L., Lyu, J., Liu, W., Yao, T., Cao, Y., Lu, Y., Zhang, X. 2024. Automated Handling and Feeding Techniques for Skewering Operations. Proceedings of the American Society of Agricultural and Biological Engineers International (ASABE). 67(5)1181-1190. https://doi.org/10.13031/ja.15940.
Park, S.B. 2025. Dual Detection of Pathogenic tdh and trh Genes of Vibrio parahaemolyticus in Oysters Using Multienzyme Isothermal Rapid Amplification (MIRA) Combined with Lateral-Flow Dipstick (LFD) Assay. Microbiology Research. 16(5)87. https://doi.org/10.3390/microbiolres16050087.
Park, S.B., Zhang, Y. 2024. Innovative Multiplex PCR Assay for Detection of tlh, trh, and tdh Genes in Vibrio parahaemolyticus with Reference to the U.S. FDA’s Bacteriological Analytical Manual (BAM). Pathogens. 13(9). https://doi.org/10.3390/pathogens13090774.