1 More than a decade of gut microbiome studies have a common goal for human 2 health. As most of the disease studies sample the elderly or the middle-aged, a 3 reference cohort for young individuals has been lacking. It is also not clear what 4 other omics data need to be measured to better understand the gut microbiome.5 Here we present high-depth metagenomic shotgun sequencing data for the fecal 6 microbiome together with other omics data in a cohort of 2,183 adults, and observe 7 a number of vitamins, hormones, amino acids and trace elements to correlate with 8 the gut microbiome and cluster with T cell receptors. Associations with physical 9 fitness, sleeping habits and dairy consumption are identified in this large multi-omic 1 0 cohort. Many of the associations are validated in an additional cohort of 1,404 1 1 individuals. Our comprehensive data are poised to advise future study designs to 1 2 better understand and manage our gut microbiome both in population and in 1 3 mechanistic investigations.