RNA-based Surveillance of Meat Processing Environments Revealed Selective Pressures of Gaseous Ozone on Abattoir Microbiota

Microbial contamination of beef cuts mainly occurs during the deboning and cutting phases, where meat contact surfaces of the processing rooms can concurrently act as reservoirs and donors of psycrotrophic spoilage bacteria. Cleaning and sanitization of these environments is a challenging task for meat industries that are constantly seeking for new, eco-friendly and economic disinfection processes, such as the gaseous ozone. This oxidative gas has proven to be an efficient disinfectant towards several bacterial species. However, its effect over abattoir resident microbiota still needs to be investigated in situ. Herein, the RNA-based amplicon target sequencing of 16S gene was applied, in parallel with targeted microbial counts, to monitor the effects of gaseous ozone on the potentially active microbiota of meat processing environments. A total of 278 environmental swabs were collected from two abattoirs before cleaning (BC), after cleaning/sanitization (ACS) and after three overnight ozone treatments (AOT) at 4, 20 and 40 ppm. The results showed a shift in the microbiota composition in parallel to the reduction of total microbial counts after the cleaning step, with a significant increase of α-diversity and a decrease of Firmicutes, which constituted the transient, animal-derived microbiota of the abattoirs. Afterwards, the 4 ppm ozonisation did not significantly diminish the ACS counts whereas, between the two effective treatments, the ozonisation at 40 ppm mainly affected Proteobacteria and determined a significant variation of β-diversity between the ACS and AOT communities. The amplicon sequencing data highlighted inactivation of Pseudomonaceae and Brochothrix by the highest ozone concentrations, while Staphylococcaceae showed a remarkable survival capability. Our outcomes suggest a synergistic activity between gaseous ozone and the routine cleaning procedures, since the high-concentrated ozonisations acted preferentially on abattoir microbiota originating from water/soil and towards some of the major meat spoilage organism