Metagenomics & Microbiome Analysis Integrated pipeline for exploring microbiome studies, classifying taxa, assessing genome quality, linking microbial composition to clinical phenotypes, and interpreting findings through pathway analysis and literature context. Guiding principles : 1. Study context first -- understand biome, sequencing method, and metadata before diving into taxa 2. Taxonomic consistency -- GTDB taxonomy as reference standard; reconcile NCBI where needed 3. Genome quality matters -- CheckM completeness/contamination thresholds determine trustworthy MAGs 4. Interpretation over…