Extended Data Fig. 6: Relationships between phylogeny, taxonomy and metabolome.
From: A metabolomics pipeline for the mechanistic interrogation of the gut microbiome
a, Metabolomic profiles of 158 bacterial strains grown in mega medium. Individual taxonomies are clustered by metabolomic profile distances (fold change, log2-transformed) across all metabolites. Individual metabolites are hierarchically clustered (Ward’s method) using Euclidean distance between the fold-change (log2-transformed) values across all taxonomies. Metabolites shown are detected in at least 50% of the 158 taxonomies to enable Ward clustering. b, Metabolic similarities between two phylogenetically distant species grown in mega medium. Taxonomies are clustered by metabolomic profile distances (fold change, log2-transformed) across all metabolites. Data are mean ± s.e.m. of one experiment with n = 3 biological replicates. c, Scatter plot of pairwise metabolomic profile comparison between two phylogenetically distant species. Each dot represents an averaged fold-change value (log2-transformed) of one experiment with n = 3 biological replicates. Pearson correlation of pairwise metabolomic profile comparison between these two species, performed on standardized and scaled fold-change data, r = 0.7090. d, Venn diagram of unique and overlapping compounds (by PubChem CID) identified in the culture supernatant of 158 mega-medium grown strains and caecal contents of conventional mice.
