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The presence of probiotic microbes and other health promoting nutritional characteristics of kefir increasing the consumer’s interest. The microbial as well as volatile profile of kefir are the two chief factors that determine the basis of quality kefir drink. In this study, we characterized the three milk kefir drinks prepared by sheep, goat and cow milk on the bases of amplicon-based sequencing for microbial diversity and volatile profile along with physio-chemical and colorimetric features. The bacterial and mycobiota analysis showed that the bacteria Acetobacter syzygii, Lactobacillus lactic and Lactobacillus plantarum and yeasts Kluyveromyces marxianus, Saccharomyces cerevisiae, Peronospora manshurica, and Pichia fermentans were predominantly found in sheep kefir which exhibited optimum physio-chemical colorimetric profile and maintained volatile compounds that play important role regarding antimicrobial and pleasant sensory profile of milk kefir. It is concluded that sheep milk significantly supported the probiotic and health promoting features of kefir.