ETD

• bovino
• caprino
• cow
• estrazione del DNA
• goat
• latte
• microbiota
• microbiota; DNA extraction
• milk
• ovino
• sheep

Sheep’s milk is a complex and strategic matrix for the Mediterranean dairy sector, but its high fat and protein content makes the application of molecular methods challenging. Next-generation sequencing (NGS) techniques offer innovative perspectives for microbiota characterization, with impacts on food safety, traceability, and product valorization. However, the lack of standardized DNA extraction protocols limits the reproducibility and comparability of studies. A literature review (2015–2025) was therefore conducted to identify extraction protocols from ruminant milk. Among them, the Milk Bacterial DNA Isolation Kit was selected and applied to sheep’s milk samples from Sarda breed flocks in 10 farms located in the provinces of Grosseto and Viterbo. DNA yield and purity were assessed by spectrophotometry and agarose gel electrophoresis; in parallel, culture-based microbiological analyses were carried out for comparison, while data processing was performed using descriptive statistical tools. The kit provided optimal yields, including those for PCR. The analyses also revealed differences among farms in the two provinces, suggesting that environmental, management, and sanitary factors may influence the composition of the milk microbiota. The validated protocol proved effective and reproducible, laying the groundwork for future metagenomic studies and the application of NGS to support the sheep dairy supply chain.