Ecological Dynamics of Microbiomes in Food Processing Facilities: Pathways to Improved Sanitation

Abstract

Food processing environments serve as complex niches for bacterial colonization, adaption, persistence and dispersal, which subsequently shapes the microbial composition and diversity. This Ph.D. dissertation investigated the impact of biofilm formation, bacterial communication and cooperation on microbial community assembly, providing insights into the novel and specific intervention strategy. The presence of microbes in food products depends on contamination from the raw materials or microbial communities in food processing facilities. By re-analysing data from 39 published studies, we found that while each food commodity possesses its own accessory microbiome, a core surface-associated microbiome exists across all commodities. Nutrient levels on food environment surfaces significantly impact biofilm community composition more than environmental processing surfaces. The longitudinal study in a pork processing facility revealed a high diversity of microbes, with addition of 74 novel species. Repeated isolation of the same meat-spoilage-associated strain across different sites and times displayed their transmission patterns and persistence over six months, pinpointing processing environments as the primary sources of microbes and identified specific sites for further interventions. The presence of transmissible locus of stress tolerance (tLST) among gamma-proteobacteria enhances their microbial resistance to sanitation chemicals in planktonic state cells. Biofilms, the natural state of cells in food processing facilities, further reduce sanitation efficacy and facilitate microbial dispersal and persistence. Our investigations on the link of tLST to biofilm formation and disinfectant resistance showed that the presence of tLST in E. coli yielded higher biofilm biomass and enhanced their resistance to chlorine, hydrogen peroxide, and peroxyacetic acid in biofilm-embedded cells. The phenotypic switch from floating biofilms (pellicle) to surface-iii associated biofilms is regulated more by bacterial communication and cooperation (quorum sensing) than unique gene presence/absence. The application of ozone nanobubble on meat products in situ and in vitro showed that it displayed comparable bactericidal effect to peracetic acid and altered microbial composition, particularly eliminating the more undesirable microbes. Taking together, these findings contribute to a better understanding of the microbial ecology of food processing environments, facilitate the implementation of novel and site-specific interventions and potentially reduce food waste and outbreaks, promoting the development of a more sustainable food systems.