Kombucha is a fermented tea beverage whose microbial composition critically influences its quality, safety, and functional properties. This study used whole metagenome shotgun (WMS) sequencing to characterise the taxonomic and functional makeup of kombucha microbiomes, employing both locally generated Oxford Nanopore Technologies (ONT) reads and publicly available Illumina datasets. The analysis was carried out entirely within the Galaxy web-based bioinformatics platform.Taxonomic profiling with Kraken2 and KronaTools showed a community mainly consisting of Komagataeibacter xylinus, K. rhaeticus, other acetic acid bacteria (AAB), and Saccharomyces cerevisiae, fermentative yeasts. Functional annotation using Prokka and eggNOG-mapper identified pathways for cellulose biosynthesis, ethanol oxidation, gluconic acid production, and B-vitamin synthesis. The presence of both bacterial and yeast species highlighted the cross-kingdom metabolic cooperation essential to kombucha fermentation, including ethanol-acetic acid cross-feeding and biofilm matrix production. Comparison between ONT and Illumina datasets revealed a consistently present core microbiome in kombucha across both platforms, while functional profiling confirmed taxa-specific roles in metabolite production and the structural stability of the SCOBY. The study also emphasised microbial traits of industrial relevance, such as high-purity bacterial cellulose production and natural vitamin enrichment. The Galaxy platform effectively replicated results similar to those from traditional pipelines while providing an intuitive, reproducible, and transparent analytical environment. Its accessibility is especially important for education, low-resource settings, and rapid applied research in food biotechnology. This research offers a methodological and ecological framework for future kombucha microbiome studies, demonstrating how open web-based bioinformatics tools can promote inclusive, high- impact microbiome science.