Extended Data Fig. 5. Nestedness of community composition based on microbially-related metabolites.

a, Presence-absence of superclasses across samples, with superclasses (rows) sorted by prevalence and samples (columns, n = 618) sorted by richness. With increasing sample richness, superclasses tended to be gained but not lost (SES = 108.61, p-value < 0.0001 vs. a null model from a two-tailed test; nestedness measure based on overlap and decreasing fills [NODF] statistic = 0.87). Samples are colored by EMPO 2. b, As in a but with samples colored by EMPO 3. c, As in a but with samples colored by EMPO 4. d, Nestedness as a function of annotation level, from superclass to molecular formula, across all samples and within environments based on EMPO 2. Also shown are median null model NODF scores (± s.d.) for all samples, as well as samples at each level of EMPO 2. NODF measures the average fraction of metabolites from less diverse communities that occur in more diverse communities. All environments at all annotation levels examined were more nested than expected randomly, with nestedness higher at higher annotation levels (p-value < 0.0001 for all comparisons, from two-tailed tests). e, As in c but with each environment at EMPO 2 shown separately, with samples colored by EMPO 4.