International Journal of Pathogen Research

Milk is a nutritionally complete food pivotal to food security and rural livelihood in Nigeria. Goat milk is valued for its digestibility and nutrient dense, while cow milk remains widely consumed due to production volume. Despite these benefits, traditional handling practice which involve manual milking, use of non-sterile utensils, untreated water, and open-air exposure create significant risks of microbial contamination. This study provides a microbiological assessment of contamination route of cow and goat milk handling in four Local Government Areas (LGAs) of Oyo State: Akinyele, Ido, Ibarapa East and Ibadan North while simultaneously evaluating their nutritional profiles. Samples were collected from milking utensils, water sources and air using WHO recommendation protocols. Protein fractions were determined by Kjeldahl method, fatty acids by soxhlet extraction and gas chromatography and microbial loads by standard plate counts. Statistical analysis employed ANOVA within Duncan post hoc tests at p<0.05. Results revealed that protein analysis of goat milk constantly contained higher crude protein (4.70-5.15%) compared to cow milk (3.91-3.96%), with more casein, whey, and bioactive peptide fractions. Fatty acid analysis revealed goat milk had higher total fat (up to 4.80%), saturated fatty acids (3.36%) and favorable monounsaturated and polyunsaturated profiles, indicating its better digestibility and nutritional value. Therefore, it has a nutritionally advantageous alternative especially for vulnerable populations such as malnourished children, the elderly, and individuals with cow milk intolerance. However, microbial contaminations was widespread. Water sources recorded the highest total bacteria counts (up to 4.60 × 10⁵ CFU/mL), followed by utensils and air. Coliforms were detected in all water samples, exceeding WHO’s recommended limit of 0 CFU/100 mL, indicating fecal contamination. Regional disparities were evident: Akinyele LGA exhibited the highest contamination, while Ido LGA showed the lowest, reflecting differences in hygienic practices. The findings highlight the dual reality of cow and goat milk in Nigeria: nutritionally indispensable yet microbiologically hazardous under traditional handlings. This have public health implications with risks of foodborne illnesses. Addressing this challenge requires hygienic training for farmers, provision of clean water and utensils and community-based behavioral change initiatives. Ultimately, safeguarding milk nutritional integrity while reducing microbial contamination is essential for improving dietary quality and protecting consumer’s health in Nigeria’s informal dairy sector.