Strain-level functional inversion in the gut microbiome drives Type 2 diabetes pathophysiology and metformin response

Complete reproducible pipeline and supplementary data for the manuscript "Strain-level functional inversion in the gut microbiome drives Type 2 diabetes pathophysiology and metformin response." This dataset includes 245 processed metagenomes from the Latvian (PRJEB39500) and Danish MetaHIT (PRJEB4336) cohorts. The pipeline performs: (1) QC & host removal, (2) Taxonomic & Functional profiling, (3) Pangenome analysis and Strain phylogeny, (4) Ecological networks (SparCC) & Enterotypes (DMM), (5) Differential abundance (MaAsLin2), and (6) Machine learning cross-cohort classification