Figure 1: Personalization, niche association, and reference genome coverage in strain-level metagenomic profiles.
From: Strains, functions and dynamics in the expanded Human Microbiome Project
a, Mean phylogenetic divergences17 between strains of species with sufficient coverage at each targeted body site (minimum 2 strain pairs). b, Individuals tended to retain personalized strains, as visualized by a principal coordinates analysis (PCoA) plot for Actinomyces sp. oral taxon 448, in which lines connect samples from the same individual. c, Quantification of niche association (Methods; only species with sufficient coverage in at least five samples at two or more body sites). Higher values indicate greater phylogenetic separation between body sites. d, PCoA showing niche association of Haemophilus parainfluenzae, showing subspecies specialization to three different body sites. e, PCoA for Eubacterium siraeum. f, Coverage of human-associated strains by the current 16,903 reference genome set (Methods). Top 25 species by mean relative abundance when present (>0.1% relative abundance) are shown (minimum prevalence of 50 samples). Sample counts in Supplementary Table 2, and distance matrices are available from Extended Data Table 1b.
