Unveiling the unique microbiome and nutritional profile of milk from the caprine Nera di Verzasca local breed

The Nera di Verzasca (NV) goat, native to Lombardy, is essential for sustainable farming and high quality dairy production, often raised alongside commercial breeds. This study analyzes the nutritional profile and microbiome of NV milk, comparing it with Camosciata delle Alpi and Saanen. Individual milk samples (n. 266) were collected from 4 mixed-breed farms: n. 50 from Camosciata delle Alpi, n. 104 from NV and n.112 from Saanen (each of them present in three farms). Analyses covered composition, somatic cell count, minerals, milk fat globules, coagulation properties, modeled curd-firming over time parameters, cheese-making traits and microbiome. Milk composition was determined via infrared spectroscopy (Mastersizer 3000). Milk cream was used for lipid extraction and fatty acid (FA) transesterification with FA methyl esters (FAME) analyzed in hexane using an Agilent 7890 GC system (CP-Sil88 column, 100 m × 0.25 mm × 25 μm) with pure methyl ester standards peak identification. Microbiological analyses included total aerobic counts and lactic acid bacteria enumeration using standard methods. Bacterial DNA was extracted and sequenced via 16S rRNA-metabarcode sequencing on NextSeq 2000 (Illumina), with data processed through a pipeline involving quality filtering, clustering into zero-radius Operational Taxonomic Units (zOTUs), and taxonomic classification against the SILVA 138 database. NV milk exhibited excellent cheese-making efficiency due to low somatic cell counts, large fat globules, ideal mineral profile, and good curd firming traits. Polyunsaturated fatty acids, including α-linolenic and c9 t11 conjugated linoleic acid, varied by farm, reflecting differences in diet and management. Total bacterial counts ranged from 2.00 to 3.23 Log10 cfu/mL with minimal variability across breeds, producers, and grazing periods, while lactic acid bacteria remained below 2.00 Log10 cfu/mL. Microbiota analysis revealed a strong influence from the producer and, to a lesser extent, the breed on biodiversity and composition. Grazing periods significantly reshaped microbiota due to dietary and environmental changes. These findings emphasize NV dairy products’ quality and role in traditional farming. Differences among producers and grazing effects on microbiota highlight the product's role in preserving biodiversity. Integrating local and commercial breeds supports genetic diversity and traditional practices in modern livestock, offering economic and conservation benefits. Research supported by the BIO4VERBA Project, PSR 2014/2020 – Operation 10.2.01 “Conservation of animal and plant biodiversity”, financed by Lombardy region in the framework of FEASR funds.