Schematic of multiomics genotype-microbiome association testing methodology. Host genome-microbiome association testing involves potentially thousands or millions of genetic polymorphisms and hundreds or thousands of bacterial taxa and genes. Full feature-by-feature association testing is likely to be underpowered in all but the largest cohorts or meta-analyses; therefore, our methodology includes careful feature selection from both data types. Raw genetic polymorphisms were derived from Immunochip data and filtered by known IBD associations from a large-cohort GWAS study . Microbiome sequences were binned by lineage at all taxonomic levels. After data normalization and filtering (see Methods), a simple linear test was performed for association between minor allele count and bacterial taxon relative abundance while controlling for clinical covariates. QTL, quantitative trait loci.