Extended Data Figure 3: Core and distinguishing functions of human body site microbiomes.

This figure extends Fig. 3, with additional details and examples. a, 28 metabolic pathways were core (>75% prevalent) at all major body sites. We refer to these as ‘supercore’ pathways. b, Pathways core to greater numbers of body sites tended to have broader taxonomic ranges, with supercore pathways among the most broadly distributed (Tukey boxplots). c, 19 pathways (including two supercore pathways, starred in a) were core in multiple body areas and specifically enriched among taxa inhabiting the human microbiome (annotated to <10% of non-human-associated genera). Human-microbiome-enriched pathways include specific MetaCyc-defined variants of more broadly defined or distributed processes, for example, peptidoglycan biosynthesis (PWY-6471). d, ‘Site-enriched’ pathways are considerably more abundant at one body site than at sites from all other body areas. Black dots indicate the site where each site-enriched pathway achieved its peak abundance. Heat map values reflect the first quartile of relative abundance in a particular body site (coordinated with the percentile cutoff for a core pathway). e–g, Additional examples of the three pathway classes enumerated in a, c, and d, respectively. In each example, total (community) abundance is log-scaled, and the contributions of the top seven genera are proportionally scaled within the community total. ‘Other’ encompasses pathway contributions from genera outside of the top seven, and ‘unclassified’ encompasses pathway contributions from unidentified members of the community.