Viability differentiation enhances microbial community profiling in commercial ready-to-eat meat manufacturing

Aims The objective of this study was to evaluate 16S rRNA gene sequencing with viability differentiation as a diagnostic tool to assess microbial contamination during ready-to-eat (RTE) meat manufacturing. Methods and Results Product samples were collected from a commercial RTE meat manufacturing facility raw (n = 45), after cooking, chilling, holding, staging, slicing, and packaging (n = 27, N = 207). After homogenization, samples were split and either not treatment (Control) or treated with propidium monoazide (PMA). DNA was subsequently extracted, sequenced, and bioinformatically analyzed. Statistical significance of α- and β-diversity metrics were determined using ANOVA and ADONIS, respectively, and differentially abundant taxonomic groups were identified using ANCOM (P ≤ 0.05, Q ≤ 0.05). PMA treated samples exhibited a less rich microbial community, but the impact of PMA treatment varied by location. Thermal processing had a similar effect on the microbial community of both treatment groups; however, in PMA treated samples a second shift was observed after slicing along with an increase in the relative abundance of Lactobacillus. The presence of this microorganisms was further confirmed through the culture-based identification of Latilactobacillus sakei. Conclusions PMA treatment improved the resolution of 16S rRNA gene sequencing, allowing for better identification of viable spoilage contaminants during RTE meat manufacturing.