Catfish is one of the leading finfish species produced in the U.S., with 94.6 % of total food-size fish sold after processing. The control of microbial contamination during processing is a key factor for ensuring the microbial safety, quality, and shelf life of fish products. Unfortunately, how microorganisms present in the processing environment (e.g., equipment and line workers) and fish harvesting and processing seasons shape the microbial compositions of fish and fish products remains largely uninvestigated. To address this need, this research team applied the amplicon sequencing approach to characterize microorganisms present on the intact fish skin, in fish intestine, on fish fillets, and in environmental samples collected from catfish processing plants to categorize factors determining the microbial compositions of fish and fish products based on their significance.
Three catfish processing facilities in Southeast U.S participated in this study and two visits were conducted for each plant representing the the Spring and Fall harvesting and processing seasons.
A total of 70 environmental swab samples were collected representing the microbial populations present on the blade of de-heading machines, conveyor belts, worker gloves, floors of the sorting, processing, and packaging areas and the exterior of bins used for holding and transferring of final fish products. In addition, swabs (n= 46 for fish and n= 46 for fillet) were used to collect microbes present in the intestine, on the skin of intact fish and on the fish fillets. DNA was extracted from swab samples using QIAGEN DNeasy PowerSoil Pro Kits, followed by library preparation and sequencing.
Figure 1A shows that fillet samples, although grouped separately from other sample types, are closer to the centroid of environmental samples than fish samples, indicting that the processing environment has a larger impact on the microbial composition of final fillet products. Both season and facility have an influence on shaping the bacterial communities of environmental samples (Figures 1B-C). Samples collected from Facility 3 formed a distinct cluster compared with other two facilities (F1 and F2).