The aim of this research was to determine the microbiota of commercial kefir, koumiss and homemade kefir samples using metagenomic analysis and compare some probiotic properties of lactic acid bacteria isolated from these beverages and Lactobacillus casei, used in yakult production. One koumiss, 5 commercially available kefir beverages with different brands, and 1 homemade kefir were used as samples. Microbial diversity of kefir and koumiss samples were determined by metagenomic analysis, targeting V1-V2 region of 16S rRNA gene. Streptococcus thermophilus and Lactococcus lactis were detected as dominant in direct DNA isolation from commercially available kefir beverages. Lc. lactis and Leuconostoc mesenteroides were dominant in MRS agars, and Lc. lactis were dominant in M17 agars. In kefir beverages produced by kefir grains, Lb. kefiranofaciens was determined as the dominant bacteria. Lb. kefiri and Enterococcus durans were found dominant in MRS and M17 agars respectively. Lb. kefiranofaciens, Lb. kefiri, and Str. thermophilus were the dominant bacterias of koumiss beverages. Microorganisms isolated from kefir and koumiss beverages were found to exhibit basic probiotic properties, similar to the lactic acid bacteria isolated from yakult. This research presented bacterial microflora and probiotic properties of lactic acid bacteria isolated from kefir and koumiss beverages consumed in Turkey.