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The gut microbiota is associated with human health and disease. Here we conducted a genome-wide association study of host genetic factors influencing gut microbiota composition in 12,652 individuals from the Trøndelag Health Study (HUNT), with replication in Nordic cohorts (n = 16,017–21,976). We identified 12 reproducible SNP–species associations across six genomic loci, including known (LCT, ABO
