The gut microbiota has been typically viewed as an environmental factor for human health. Twins are well suited for investigating the concordance of their gut microbiomes and decomposing genetic and environmental influences. However, existing twin studies utilizing metagenomic shotgun sequencing have included only a few samples. Here, we sequenced fecal samples from 250 adult twins in the TwinsUK registry and constructed a comprehensive gut microbial reference gene catalog. We demonstrate heritability of many microbial taxa and functional modules in the gut microbiome, including those associated with diseases. Moreover, we identified 8 million SNPs in the gut microbiome and observe a high similarity in microbiome SNPs between twins that slowly decreases after decades of living apart. The results shed new light on the genetic and environmental influences on the composition and function of the gut microbiome that could relate to risk of complex diseases. Display omitted •Metagenomic data from the UK confirm saturation of the gut microbiome gene content•Sharing of household and geographic region influences the similarity of gut microbiome•Much of gut microbial composition and functions is heritable•Microbial SNPs are often shared between twins and slowly diverge after living apart Xie et al. present the first large cohort of shotgun sequenced dataset for the gut microbiome in twins, including 250 adult twins in the TwinsUK registry, leading to an updated reference gene catalog of 11.4 million genes. Heritability was identified in microbial taxa and potential functions, and sharing of microbial SNPs between twins was demonstrated, all underscoring the value of twins for the understanding of the genetic and environmental underpinnings of the gut microbiome.