Bioinformatic analysis of the microbial composition in Kombucha (tea fungus)

Kombucha, a fermented tea composed of symbiotic culture of yeasts and bacteria, has gained popularity worldwide in recent years due to its potential beneficial effects on human health. Thus, many studies have been made on its biochemical properties and microbial composition. To date, culture-dependent methods and amplicon based sequencing have been used to study Kombucha microbiome. However, these methods have limited resolution for taxonomic analysis and do not allow functional profiling of microbial communities. Here, we applied whole metagenome and amplicon (16S rRNA and Internal Transcribed Spacers 1 (ITS1)) sequencing to investigate both bacterial and fungal community of Kombucha. We determined taxonomic and functional profiles at three time points of fermentation and investigated differences between biofilm and liquid phase. Taxonomic analysis indicated that Komagataeibacter becomes the baskın bacterial genus (>90%) in all samples while yeast community is dominated by Zygosaccharomyces (>95%) genus. Three genomes belonging to Komagataeibacter genus and one Zygosaccharomyces bailii genome were recovered by metagenome assembly analysis. Functional analysis of these dominant genomes revealed genomic level determinants of the characteristics of Kombucha such as vitamin production, metal biosorption, cellulose synthesis and antimicrobial production. Furthermore, the study revealed the metabolic interactions between dominant bacterial and yeast thus improved understanding of fermentation dynamics of Kombucha. Our results provide a comprehensive picture of functional and taxonomic characteristics of Kombucha microbiome throughout fermentation process.