MPK
DNA Extraction and Sequencing: Total genomic DNA from the kombucha samples was processed using Manta, a semi-automated magnetic-bead extractor (Cambrian Bioworks, India), following the manufacturers protocol. Briefly, samples were lysed in Manta Lysis Buffer to release nucleic acids, insoluble material was pelleted by centrifugation, and the clarified supernatant underwent bead-based purification (binding to Cambrian magnetic beads, sequential washes, and elution of DNA). Eluates were collected into 1.5-ml DNA low-bind tubes. DNA quantity and purity were assessed using the Qubit 2.0 DNA HS Assay (Thermo Fisher Scientific).Sequencing (ONT long-read WMS): Whole-metagenome libraries were prepared and run on PromethION flow cells using a PromethION P2-Integrated (P2i) instrument. Basecalling and demultiplexing of sequence reads were performed using the latest Guppy version with assistance from the MinKNOW GUI. Raw sequencing reads were stored in FastQ format for further computational analysis.