Effects of thermal versus non-thermal microbial decontamination treatments on quality and bacterial community in prepared deboned chicken feet: a PacBio SMRT sequencing-assisted comparison

We compared the effects of thermal and non-thermal treatments on the microbial safety and quality of prepared deboned chicken feet (PDCF). Samples were subjected to high-temperature short-time pasteurization (HTST, 75°C, 30 s), low-temperature long-time pasteurization (LTLT, 62°C, 30 min), microwave (MW, 800 W, 25°C, 40 s), electron beam irradiation (EBI, 6 kGy, 25°C), ultrasonication(US, 560 W, 25°C, 30 min) and high-pressure processing(HPP, 450 MPa, 25°C, 10 min). Treated samples were evaluated for total viable count (TVC), texture profile (shear force), myofibrillar fragmentation index (MFI), microstructure, sensory score, and bacterial community. The results showed that HPP achieved effective microbial reduction (TVC 0.39 ± 0.08 log CFU/g) while preserving the product’s textural quality (shear force 0.77 ± 0.01 N and MFI 25.30 ± 0.35). Microstructural analysis showed moderately densified tissue, and sensory evaluation yielded the highest total score (8.77 ± 0.11). Pacific Biosciences (PacBio) Single-Molecule Real-Time (SMRT) sequencing revealed that HPP effectively inhibited the initial dominant spoilage bacteria (e.g. Enterobacter), with Lactococcus (24.07%) identified as the primary biomarker. In contrast, other treatments showed notable drawbacks. EBI received a lower sensory score (7.31 ± 0.20), and its bacterial community was dominated by Staphylococcus (99.43%), posing a potential risk. Thermal treatments (HTST, LTLT, MW) and US caused texture softening, reduced sensory acceptance, and promoted spoilage and pathogenic bacteria. Overall, HPP best balanced microbial inactivation efficiency, quality retention, and microbial safety, making it the preferred choice for PDCF. This study provides important evidence for selecting decontamination methods for PDCF and similar high-collagen meat products.