Diversity estimates
Alpha and beta diversity estimates were calculated from rarefied abundance matrices created by the random sampling of reads without replacement. Within each data type (e.g., gene, MGS), all samples were represented by the same number of informative sequencing reads: rarefaction of MGS abundance was performed by sampling only from reads mapped to the MGS signature genes, and rarefaction of Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology (KO) abundance was performed by sampling only from reads mapped to a gene with an assigned KO. However, rarefaction of gene abundance was performed by sampling the reads mapped to the entire gene catalog. Alpha diversity was calculated as the number of entities detected (richness) or as the Shannon index based on a natural logarithm. Both measures were calculated from the downsized MGS abundance estimates. Beta diversity was calculated using Bray – Curtis dissimilarity and Jaccard index.