This training session introduces Bioconductor tools for hologenome and multiomics data science through a practical case study. It focuses on a framework built around TreeSummarizedExperiment and MultiAssayExperiment data containers, designed for improved efficiency, scalability, and integrated analysis of multiple omics layers. Participants will gain hands-on experience with common analysis and visualization methods using the mia package family and other multiomics-compatible tools from the Bioconductor ecosystem. After the session, participants can continue learning through the freely available Orchestrating Microbiome Analysis (OMA) online book.