Calculation of MAG Relative Abundances.

To calculate the relative abundance, reads from each metagenomic dataset were mapped to the dereplicated MAGs using CoverM v0.3.1 with the “contig” command and a cutoff of 95% minimum identity and minimum aligned read length of 75% of each read. Coverage of each contig was calculated with the CoverM “trimmed_mean” option and the coverage for each MAG was calculated as the average of all contig coverages, weighted by their length. The relative abundance of MAGs in each metagenomic dataset was calculated as its coverage divided by the total coverage of all genomes in the dereplicated MAG dataset.