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Statistical analyses

FJ Frances Patricia Jones
IC Ian M. Clark
RK Robert King
LS Liz J. Shaw
MW Martin J. Woodward
PH Penny R. Hirsch
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The Biolog data was analysed using principal components analysis (PCA) using the inbuilt function, prcomp, in R (version 3.2.2). For visualisation of the PCA, biplots were drawn using PC1 and PC2 and the loadings matrix was extracted (see Supplementary Information S3). This identified specific substrates which were associated with the isolates and also substrates making the greatest contribution to the principal component. These pathways were then examined in the genomes. The substrates were grouped into carbohydrates, carboxylic acids, amines and amides, amino acids, polymers and miscellaneous according to categories identified in previously published work58.

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