Fig. 5

NMDS ordination of resistome composition at the class level, for a the entire resistome (i.e., all gene accessions identified) and b the low-abundance resistome (i.e., the additional gene accessions identified via enrichment). Each mark is one sample, mark color indicates sample type (blue beef, orange poultry, red swine, gray WWTP), and mark shape indicates library prep assay (circle Resistome-UMI, diamond Resistome, asterisk Metagenome-UMI, triangle, Metagenome). In both a and b, ordination by sample type was significant with a large effect size (R = 0.73 and P < 0.001 for both), while ordination by library preparation assay was significant but with a small effect size in a (R = 0.13 and P < 0.001) and insignificant in b (R = 0.54, P = 0.12). Three dimensions were used for ordination