Beyond Taxonomy in Dairy Microbiology: Microbiome–Resistome–Mobilome–Phageome Interactions Shaping Quality and Safety

Dairy microbial ecosystems cannot be adequately described by total microbial counts, pathogen detection, or taxonomic profiling alone. Milk and dairy products contain interconnected microbial and genetic layers—the microbiome, resistome, mobilome, and phageome—shaped by animal-associated reservoirs, farm and processing environments, starter cultures, technological operations, and storage. This structured critical narrative review integrates these four components within a common microbial–genetic framework and examines how dairy processing reconfigures their interactions. Particular attention is given to cooling, heat treatment, fermentation, ripening, packaging, and storage and to the distinction between molecular detection and biological relevance. Across the reviewed evidence, the significance of microorganisms, antimicrobial resistance genes, mobile genetic elements, and phage-associated sequences depends on viability, functional activity, host assignment, genomic context, transfer potential, persistence, and exposure. Shotgun and long-read metagenomics, metatranscriptomics, metaproteomics, metaviromics, and viability-resolved methods provide increasingly detailed information, but interpretation remains constrained by methodological heterogeneity and limited experimental validation. Future progress requires standardized workflows, longitudinal sampling, stronger ARG–MGE–host resolution, validated phage–host interactions, and studies linking microbial identity and genetic mobility with technological outcomes and dairy safety.