Microbiome samples were collected from up to 18 body sites at one or two time points from 242 individuals clinically screened for absence of disease2 . Samples were subjected to 16S rRNA gene pyrosequencing (454 Life Sciences), and a subset were shotgun sequenced for metagenomics using the Illumina GAIIx platform1 . 16S data processing and diversity estimates were performed using QIIME27 (link), and metagenomic data were taxonomically profiled using MetaPhlAn13 , metabolically profiled by HUMAnN26 , and assembled for gene annotation and clustering into a unique catalog1 . Potential pathogens were identified using the PATRIC database14 (link), isolate reference genome annotations drawn from KEGG28 (link), and reference genome mapping performed by BWA29 (link) to a reduced set of genomes to which short reads could be matched30 (link). Microbial associations were assessed by similarity measures accounting for compositionality23 , and phenotypic association testing was performed in R. All data and additional protocol details are available at http://hmpdacc.org. Full methods accompany this paper.