PCA
PCA was performed on VST-transformed DNA or transcript counts for the 837 MAGs passing the filter described in the ‘Defining the relationship between MAG abundances and WLZ’ section above. The PCA performed on transcript abundances encompassed 27,518 genes expressed by these MAGs at thresholds for levels and prevalence that are described in the ‘Microbial RNA-seq analysis of MAG gene expression’ section above. PCA was performed in R using the ‘prcomp’ function, with each data type centred but not scaled as the dataset was already VST-normalized. The functions ‘get_eigenvalues,’ ‘get_pca_ind’ and ‘get_pca_var’ from the factoextra