Microbial Contamination and Molecular Identification of Predominant Bacteria in Fermented Milk Products in Mbarara, Uganda

Background: Fermented milk products are widely consumed in Uganda for their nutritional and cultural value. However, informal production practices and limited quality control raise concerns regarding microbial safety. This study evaluated the microbiological safety of commonly consumed fermented dairy products in Mbarara City, Uganda. Methods: A total of 192 samples, including yogurt, cheese, homemade butter, and eshabwe (a traditional butter sauce), were analysed. Culture-based testing was performed on 175 samples to detect Escherichia coli, Staphylococcus aureus, and Salmonella spp. Partial 16S rRNA gene sequencing (Sanger method) was conducted on 17 representative samples to identify predominant bacterial taxa. Results: Overall, 12.0% of cultured samples were positive for at least one pathogen. Cheese had the highest contamination rate (42.9%), followed by eshabwe (8.6%) and yogurt (4.3%), while homemade butter showed no detectable pathogens. Molecular analysis confirmed the presence of fermentation-associated lactic acid bacteria and identified potential opportunistic and pathogenic taxa, including Klebsiella spp and Enterobacter spp. Conclusions: Fermented dairy products in Mbarara City contain beneficial fermentative bacteria but also demonstrate measurable pathogen contamination, particularly in products under informal conditions. Targeted hygiene improvements, safe starter use, and routine microbial monitoring are needed to enhance food safety while preserving traditional production practices across Uganda