Fig. 4: Comparison of mutational spectra between lung and environmental niches.
From: Mutational spectra are associated with bacterial niche
A Upper panel - principal component analysis on mutation proportions in the SBS spectra across Mycobacteria and Burkholderia. Axes labels include the inferred proportion of variance each principal component describes. Points are coloured by niche; clades with a previously unknown niche are labelled. Environmental includes B. pseudomallei and known environmental clades of Mycobacteria. Lower panel - comparison of the proportion of T > C and proportion of C > A mutations in Mycobacteria and Burkholderia SBS spectra. B Decomposition of mutational spectra into their underlying components. Only mutations elevated within the respective clade compared to a closely related clade in a different niche were included. Known environmental clades were decomposed into the set of previously extracted environmental mutagen signatures5 while known lung clades and clades with unknown niche were decomposed into the set of previously extracted lung signatures from human data. B. cenocepacia ECs: B. cenocepacia epidemic clones. Nitro-PAH: nitro-polycyclic aromatic hydrocarbons; PAH: polycyclic aromatic hydrocarbons; ROS: reactive oxygen species. C Composition of signature Bacteria_Lung1 extracted from NMF decomposition of Mycobacteria and Burkholderia SBS spectra. D The proportion of mutations within each Mycobacteria and Burkholderia SBS spectrum assigned to signature Bacteria_Lung1. Boxplot centre lines show median value; upper and lower bounds show the 25th and 75th quantile, respectively; upper and lower whiskers show the largest and smallest values within 1.5 times the interquartile range above the 75th percentile and below the 25th percentile, respectively. All clade values are shown as points (number of clades included: Human lung = 9, Unknown = 2, Animal lung = 3, Environmental = 11). E Dendrogram shows phylogenetic relationships between Mycobacteria and Burkholderia. The left hand heatmap shows niche of each clade; lung clades have arisen on multiple independent occasions across the tree. The right hand heatmap shows the proportion of mutations assigned to signature Bacteria_Lung1 in a decomposition analysis of the Mycobacteria and Burkholderia spectra. More mutations are consistently assigned to Bacteria_Lung1 in lung clades than environmental clades and lung clades exhibit a higher assignment to Bacteria_Lung1 than closely related environmental clades. Source data are provided as a Source Data file.
