Fig. 5

Microbiome community analysis. a Sample clustering using Bray-Curtis dissimilarity. Different sample types are marked by the colors, healthy versus SCID are shown by the shapes. b Comparison of stool samples for each patient queried to healthy controls. Samples were clustered using Bray-Curtis dissimilarity. Each panel compares one SCID subject samples (indicated at the top) to healthy control samples (shown in gray). Elapsed time is shown using the color code (bottom). c The longitudinal species richness of each patient’s oral, nasal, and stool samples is shown in separate panels. The 95% CI of the healthy child richness for that sample type is shown in tan. d Representation of selected antibiotic resistance genes in the stool samples studied. Each column indicates a metagenomic data set from the subject listed at the top. Each row summarizes the abundance of an antibiotic resistance gene class. The tiles are colored by reads per kilobase of target per million sequence reads (RPKM); the color code is to the right of the panel