The interest in milk originating from donkeys is growing worldwide due to its claimed functional and nutritional properties, especially for sensitive population groups, such as infants with cow milk protein allergy. The current study aimed to assess the microbiological quality of donkey milk produced in a donkey farm in Cyprus using cultured-based and high-throughput sequencing (HTS) techniques. The culture-based microbiological analysis showed very low microbial counts, while important food-borne pathogens were not detected in any sample. In addition, HTS was applied to characterize the bacterial communities of donkey milk samples. Donkey milk was mostly comprised of: Gram-negative Proteobacteria, including Sphingomonas, Pseudomonas Mesorhizobium and Acinetobacter; lactic acid bacteria, including Lactobacillus and Streptococcus; the endospores forming Clostridium; and the environmental genera Flavobacterium and Ralstonia, detected in lower relative abundances. The results of the study support existing findings that donkey milk contains mostly Gram-negative bacteria. Moreover, it raises questions regarding the contribution: a) of antimicrobial agents (i.e. lysozyme, peptides) in shaping the microbial communities and b) of the bacterial microbiota to the functional value of donkey milk.
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