Extended Data Fig. 9: Metabolic indices estimated between gut microbiome species and Enterobacteriaceae.

a, Metabolic competition and complementary indices estimated with PhyloMint between co-excluders or co-colonizers and all Enterobacteriaceae species detected at >1% prevalence. b, Distribution of metabolic distance scores between co-colonizers (n = 4292 comparisons) and co-excluders (n = 4773 comparisons) in relation to Enterobacteriaceae. c, Comparison of metabolic distances within and between co-excluders and co-colonizers. Co-excluders vs. co-excluders: n = 8256 comparisons; co-colonizers vs. co-colonizers: n = 6670 comparisons; co-colonizers vs. co-excluders: n = 14,964 comparisons. d, Reproducibility of metabolic distance scores of co-colonizers (n = 4292 comparisons) and co-excluders (n = 4773 comparisons) compared to Enterobacteriaceae after simulating models with defined gut media (M1) supplemented with diets from the Virtual Metabolic Human database, or with the M3 rich growth media. All comparisons were statistically significant (P < 0.0001). Box lengths represent the IQR of the data, the central line represents the median value, and the whiskers depict the lowest and highest values within 1.5 times the IQR of the first and third quartiles, respectively. P values were derived from a two-sided Wilcoxon rank-sum test.