Milk is considered an essential source of nutrients for humans that provides high quality protein, various vitamins and minerals, along with bioactive compounds such as microorganism and miRNAs. The presence of the latter in bovine milk confers functionality beyond nutrient supply. In this context, the composition of bovine milk is influenced by several factors related to the environment or to the animal. The aim of this study was to determine the influence of dairy production systems on the levels of minerals, fatty acids, miRNAs and microbiota in raw bulk tank milk. For this purpose, samples were collected from intensive (INT), intensive with robotic milking (ROB), pasture-based (GRA), and organic (ORG) herds. Results indicate a tendency towards higher sodium concentrations in ORG and GRA milk, although significant differences were only observed between ORG and ROB systems. But mean iodine content is approximately half in ORG and GRA milk compared to conventional systems. A more favourable lipid profile was observed in milk from outdoor-reared cattle, more abundant in trans-C18:1 isomers and lower n-6/n-3 ratios (1.9–2.3 in ORG and GRA vs. 2.9–5.3 in INT and ROB systems). Extracellular vesicles miRNAs varied significantly among the four systems, with reductions of miR-148a-3p and miR-29 b-3p in GRA milk, whereas ORG presented lower miR-200c-3p and higher let-7f-5p and miR-30a-5p levels. As for milk microbiota, no significant differences were detected in alpha or beta diversity, with Firmicutes (35–47 %), Actinobacteria (23–32 %), and Proteobacteria (21–34 %) dominating across all systems, while reads taxonomically assigned to S. agalactiae were detected exclusively in INT farms. These differences are compatible with a greater dependence on pasture and forage-based feeding strategies in GRA and ORG systems, although the effects of production system and feeding regime cannot be separated in the present study design.
