Comparison of saliva microbiome frequencies from full genome and exome-capture sequencing. Estimates of the relative abundance of saliva microbiota obtained via exome capture (x-axis) strongly correlate with those obtained from shotgun metagenomes produced from the same sample (y-axis). The above dot plots illustrate this result for two KhoeSan individuals involved in our study: A) SA1000 and B) SA1025. Each dot represents a genome. A linear model representing the relationship between exome-capture and non-capture estimates of relative abundance is shown in blue; the variance in the predictions from the model are shaded in grey. A Spearman correlation test indicates that this relationship is very strong (rho > 0.65; p < 2.2e-16).