Fig. 4

Phenylalanine pathway enzymes encoded by Roseburia are prevalent and abundant. A A subtree of the phylogenetic relationships among detected MSPs, containing the majority of MSPs mapped to the Roseburia genus (PhyloPhlAn 3.0). B Total abundance of each genus in the cohort. C Assembled genes encoding 20 of the 77 enzymes in the phenylalanine metabolism pathway (KEGG ortholog ko00360) across samples, sorted by MSPs in each genus. Heatmap shows samples where a gene is detected. D Total abundance of individual genes in the phenylalanine metabolism pathway. For each KEGG ortholog group, statistics of all assembled homologs were aggregated. Each enzyme encoded by Roseburia was tested for increased abundance (read per million mapped reads, RPKM) compared to the other four genera in the panel. The minimal P-value from up to four comparisons is shown for the cases where Roseburia has the highest abundance. Black points show the median, and the error bars mark the 25th and 75th percentiles. E Spearman correlations of MSPs in the panel with 16 detected metabolite features (mass-to-charge, m/z, peaks in mass spectra) mapping to the phenylalanine metabolism pathway. Only the top matching compound name is shown, while ambiguous matches are shown on the right. For each genus, the strongest effect associated with any relevant MSP was chosen and marked as significant subject to P < 0.05. The effects associated with MSP 112 (Roseburia) are highlighted in the black box