The core gut microbiome consists of stable pathways present despite variation in microbial abundances. Profiles of 118 stool samples from healthy individuals, showing the relative abundances of microbial organisms (red), inferred microbial pathways  (green), and microbial pathways after randomization (blue, all data from ). All relative abundances are shown as median and interquartile range across all samples (y-axis) ranked by median (x-axis) and square-root (sqrt) scaled for visualization. As illustrated by several studies (for example, [1, 89]), a stable distribution of habitat-adapted microbial pathways is maintained on a functional level (green) rather than on a phylogenetic level (red). Random assignment of microbes to samples followed by re-inference of functional potential (blue) results in a metagenome that is more variable, more skewed, and of distinct composition from that in the observed 'core' of gut microbiome functions.