Correlation of microbial gene families estimated from 16S gene pyrosequencing and whole-genome shotgun sequencing data. Ancestral state reconstruction was used to infer metagenomes using 16S gene pyrosequencing of samples from multiple body sites from the Human Microbiome Project (see Materials and methods). The relative abundance of KOs inferred from 16S sequencing and measured from paired whole-community genome sequencing samples were correlated (Spearman rank correlation) and plotted per body site. Each box plot shows the distribution of the correlation of relative KO abundance from 16S and whole-genome sequencing; specific sample-pair correlations are plotted as dots. Median correlation for Human Microbiome Project stool samples is 0.75 for an average n = 75 per body site. As each correlation is calculated over approximately 5,400 KOs, correlation values above 0.59 are significant at a Bonferroni-corrected P < 0.05.