The Effects of Milking and Cleaning Procedures on the Quality and Microbiome of Raw Goat Milk

The rising popularity of raw goat milk has heightened concerns about its safety. This study examined how differences in milking and cleaning practices influence the quality and microbiota of goat milk from small-scale Oregon farms during July and August. Milk quality was assessed through somatic cell counts (SCCs) and components, while microbiota was evaluated using viable counts and 16S rRNA sequencing. Sequencing revealed a diverse microbial community, dominated by genera such as <i>Staphylococcus</i>, <i>Escherichia-Shigella</i>, and <i>Pseudomonas</i>, with pathogenic taxa like <i>Salmonella</i> and <i>Campylobacter</i> largely absent or detected at negligible levels. Alpha diversity varied significantly among sample types but not across farms, and beta diversity indicated considerable dissimilarity in microbial composition. Importantly, regression models identified significant associations between hygiene practices and bacterial abundance: the absence of glove use and hand sanitation was linked to increased levels of <i>Escherichia-Shigella</i>, <i>Kocuria</i>, <i>Enterococcus</i>, and <i>Corynebacterium</i>, while the use of bleach-chlorhexidine sanitizer was associated with higher <i>Deinococcus</i>. These findings highlight the role of rigorous hygiene protocols in shaping the microbiota of raw goat milk and emphasize the need for targeted practices to minimize contamination risks.