Dairy Spoilage Bacteria and Their Lipases: Prevalence Patterns and Molecular Traits

Dairy product spoilage is primarily caused by microbial contamination and lipase activity. Systematically assessing contamination risks and elucidating the structural and functional characteristics of key lipases form a crucial foundation for achieving precise prevention and control. This article integrated 79 studies (2003–2025) to preliminarily explore the geographical distribution characteristics of spoilage bacterial contamination. The combined contamination rates were relatively high in South America (89.5%), North America (88.3%) and Asia (87.3%), followed by Europe (86.0%) and Oceania (82.2%), while Africa showed a lower rate (57.6%) based on limited data. Product-level risk differences were also identified. Considering data robustness, in addition to raw milk (92.6%), milk powder also showed a high contamination rate (86.8%). The spoilage bacterial community was highly concentrated, with Bacillus (40.7%) and Pseudomonas (20.3%) as the dominant genera, and Pseudomonas fluorescens (21.1%) and Bacillus licheniformis (20.1%) as the core spoilage species. Furthermore, structural analysis of 37 key lipases demonstrated that these enzymes universally possess a hydrophobic surface, high lipid affinity, and a conserved α/β hydrolase folding conformation. Based on these predictions, we propose a structural hypothesis: these characteristics may be related to their retained activity after thermal processing. Unlike traditional meta-analyses that merely report pollution rates, and unlike independent bioinformatics studies that analyze lipases from arbitrary strains, this study ensures that the lipases analyzed have epidemiological relevance. This work provides scientific grounds for monitoring, early warning, and risk assessment of dairy spoilage. It also lays a theoretical foundation for developing novel inhibitors targeting thermostable lipases.