Kombucha has recently become popular in the Brazilian beverage market as a healthy alternative to soft drinks. However, little is known about the microbial composition and physicochemical characteristics of products available on the market. To investigate the microbial profile of kombuchas, high-throughput sequencing of the 16S rRNA and ITS genes, in samples belonging to six brands was utilized. In addition, the drinks were characterized based on the physicochemical parameters of pH, total acidity and alcohol content. Through the metagenetic analysis, the most abundant prokaryotic species identified were Liquorilactobacillus nagelii, Oenococcus oeni, Komagataeibacter rhaeticus, Liquorilactobacillus ghanensis, Gluconobacter oxydans, Komagataeibacter saccharivorans, Acetobacter peroxydans and Pantoea stewartii, while the mainly eukaryotic species were Dekkera bruxellensis, Dekkera anomala, Saccharomyces cerevisiae and Lanchancea fermentati. Interestingly, we identified six different oligotypes of D. bruxellensis, showing a wide diversity of strains belonging to this species. The results obtained for the physicochemical analyses, within the shelf life of the products, presented a range between 2.88 ± 0.06 and 3.43 ± 0.04 of pH, values between 1.80 ± 0.59 and 4.86 ± 0.72 for the total titratable acidity and 1.03 ± 0.24 to 2.54 ± 0.39 referring to alcohol content, demonstrating significant differences between brand. In addition, all samples had alcohol content above 0.5%, resulting in the classification of alcoholic beverages, which need proper labelling. The data generated in this work helped to understand the composition of the kombuchas available in the Brazilian market, as well as in the development of the identity and quality standard of the drink
