Strain-level diversity analysis of Pseudomonas fragi after in situ pangenome reconstruction shows distinctive spoilage-associated metabolic traits clearly selected by different storage conditions

Microbial spoilage of raw meat causes huge economic losses every year. Understanding the microbial ecology associated to the spoilage and its dynamics during refrigerated storage of meat can help in preventing and delaying the spoilage-related activities. Raw meat microbiota is usually complex but only few members will develop during storage and cause spoilage, upon the pressure of several external factors, such as temperature and oxygen availability. We characterized the metagenome of beef packed aerobically or under-vacuum during refrigerated storage to explore how different packaging conditions may influence microbial composition and potential spoilage-associated activities. Different population dynamics and spoilage-associated genomic repertoires occurred in beef stored in air or vacuum-packaging. Moreover, pangenomics of Pseudomonas fragi strains extracted from metagenomes was carried out. We demonstrated the presence of specific, storage-driven strain-level profiles of Pseudomonas fragi, characterized by a different gene repertoire, thus potentially able to act differently during meat spoilage. The results provide new knowledge on strain-level microbial ecology associated to meat spoilage and can be of value for future strategies of spoilage prevention and food waste reduction.IMPORTANCE This work provides insights on the mechanisms involved in raw beef spoilage during refrigerated storage and on the selective pressure exerted by the packaging conditions. We highlighted the presence of different microbial metagenomes during spoilage of beef packaged aerobically or under-vacuum. The packaging condition was able to select specific Pseudomonas fragi strains, with a distinctive genomic repertoire. This study may help in deciphering the behaviour of different biomes directly in-situ in food and in understanding the specific contribution of different strains to food spoilage.