“… 17 Functional metagenomics directly screens genes for resistance phenotypes and therefore this approach can identify novel ARGs with high specificity, and can be used for the development and augmentation of custom ARG databases. 18 , 19 Through sequence homology to known ARGs, the widespread use of shotgun metagenomics has further enabled detailed analysis of mammalian-associated resistomes across body sites, 20–22 demonstrating that the resistome displays inter-individual variation and correlates with a number of factors further discussed below, including diet, 23 , 24 travel, 25 antibiotic usage, 2 , 22 , 26 , 27 hospital environments, 28 and breastfeeding. 15 , 27 , 29 Yet, determining the clinical relevance of a given ARG presence within the gut microbiome depends not just on its abundance, but also on the relative risks posed by different ARG classes and the frequencies by which they may transmit to pathogens or pathobionts.…”