High-Resolution Exploration of Microbial Consortia in Food Processing Environments

Microorganisms inhabiting food-processing environments play an important role in defining the initial contamination pattern of food and, therefore, influence the shelf-life and quality of the final product. Monitoring the presence of spoilage microorganisms in the food-processing environment and mapping the possible contamination routes is necessary to prevent microbial spread along the processing chain and, consequently, the transition to the finished product. However, facility-resident microbiota is sometimes addressed as a source of microbes that may be beneficially involved in the manufacturing process.

Different food processing and manufacturing environments, including beef, dairy, and ready-to-eat meals processing plants, were analysed by culture-independent, high-throughput sequencing. Swabs were collected from plant surfaces, tools, and operators’ hands. Moreover, food products from the same manufacturers were evaluated.

The presence of a resident microbiota was highlighted, consisting of a few taxa that were well adapted to the considered environment, where food residues and exudates can act as substrates. This resident microbiota can be the source of food contamination and proliferate during storage to unacceptable levels, compromising food quality and safety. Nevertheless, depending on the type of manufacturing considered, food processing microbiota may sometimes play a positive role. Indeed, cheese manufacturing plants often harbour lactic acid bacteria, which are beneficially involved in the fermentative and ripening processes. Therefore, depending on the nature of the microorganisms and on the type of food manufacturing process, the environmental microbiota can exert positive functional activities or be a hazard for product quality and safety. Food-environment relationships deserve to be further explored, since they have the potential to affect the food processing dynamics and the quality of final products.