Sequencing and Taxonomy
Following sample processing, sequencing, and quality control, a total of 1,740 16S rRNA amplicon sequence libraries were generated, with an average read depth of 65,595 reads per library (standard devion [SD]. +/- 47,441 reads). A total of 1,606 libraries were retained for analyses following rarefaction (Supplemental Table S1). All subsequent results were derived from rarefied data. Taxonomic composition across all body sites was dominated by Proteobacteria and Firmicutes, although relative abundance of these and other phyla differed between body sites (Fig. 2, Supplemental Table S2).