Figure 4: Comparison of intra-individual to inter-individual and inter-familial distances between microbial profiles at the different omic levels.

a, Comparisons of Jensen–Shannon divergences or Soerensen dissimilarities between all possible combinations of individuals, in terms of taxonomic profiles based on metagenomic (red) and metatranscriptomic (blue) data, functional profiles based on metagenomic (red), metatranscriptomic (blue) and metaproteomic (olive green) functional profiles, as well as the human proteins (light green). b, Multiple co-inertia analysis of per-individual medians of inferred metagenomic and metatranscriptomic abundances of mOTUs, metagenomic, metatranscriptomic and metaproteomic abundances of functional categories and human protein abundances. The colour/symbol scheme denoting the individuals is identical to that used in the other figures as defined in Fig. 1a. c, Comparison of the dissimilarities of functional potential of closely related population-level genomes reconstructed from different samples of the same individual and genomes of related organisms reconstructed from samples of different individuals. Over the whole set of taxa, intra- and inter-individual dissimilarity indices were significantly different (P < 0.05, Wilcoxon signed rank test). d, Comparison of correlations between expression profiles of closely related population-level genomes reconstructed from different samples of the same individual and expression profiles of genomes of the same organisms reconstructed from samples of different individuals. Spearman's correlation coefficients of the functional annotations present in all analysed genomes are displayed. Over the whole set of taxa, intra- and inter-individual correlations were significantly different (P < 0.05, Wilcoxon signed rank test). In c and d, only genomes with >67% essential unique genes were evaluated. The mOTUs with reconstructed genomes allowing intra- versus inter-individual comparison of at least three individuals are displayed; upper Clostridiales mOTU: mOTU linkage group 126, Bacteroidales: mOTU linkage group 135, lower Clostridiales mOTU: mOTU linkage group 310. Numbers of compared genomes (n) are shown as pink and blue numbers. In a, c and d, asterisks indicate statistically significant direct comparisons (P < 0.05, Wilcoxon rank sum test). Boxes span the first to third quartiles, the central thick bars represent the medians, whiskers extend to 1.5 times the interquartile ranges, and data points outside these ranges are indicated as outlier points.