Fig. 2: Niche-specific signatures of core active species and transcribed functions.
a, Bar plots showing median relative abundances (total sum scaled) of reads assigned to various skin commensals across different skin sites presented in log2 scale. Abundances for metagenomes and metatranscriptomes are shown. b, Bubble plot showing core, common and variable components of skin metagenomes (DNA) and metatranscriptomes (RNA) across different body sites. A species was called present in a metagenome if it had ≥0.1% relative abundance. A species was called present in a metatranscriptome if it had ≥0.1% relative abundance and was also detected in the metagenome. Core species in metagenomes and metatranscriptomes were defined as those present across more than 75% of samples at a given skin site. Common species for a skin site were defined as those present in between 50% and 75% of samples. Variable species for a given skin site refer to other species that do not fall into the previous two categories but that are present in three or more individuals. For RNA, bubbles are also shaded according to median transcriptional activity, defined as the ratio of normalized RNA counts of a species to that of their DNA. For visual clarity, only species that were core in at least one skin site are represented here. c, Scatter plot of mean beta diversity (Bray–Curtis dissimilarity) against mean alpha diversity (Simpson index) of core microbial pathways. Core microbial pathway expression was computed using HUMAnN3. Core microbial pathways were defined as those that were present (non-zero expression) at a skin site in more than 75% of individuals and with less than 25% unclassified reads at species level. d, Stacked bar plots for species-level pathway contributions at the RNA level, estimated with HUMAnN3 for staphyloferrin A biosynthesis and with Kraken 2 for community-level relative abundances at the RNA level. For all subfigures, Sc, Ch, Ac, Vf and Tw indicate the skin sites scalp, cheek, antecubital fossa, volar forearm and toe web, respectively. Alpha or beta diversity scores >0.5 and ≤0.5 were considered ‘high’ and ‘low’ diversity, respectively.
