Taxonomical profiling was performed with Kraken2 2.0.8 and Bracken 2.5 using the Genome taxonomy database for improved performance (GTDB) . ARG relevant to the antibiotics chosen to select for antibiotic resistant bacteria in this study were identified using the Comprehensive Antibiotic Resistance Database (CARD) and Resistance Gene Identifier (RGI; 5.1.1). An inhouse R script was used to process the metagenomic data. Low abundance taxa were filtered using a pre-processing step by removing Operational Taxonomic Units (OTUs) that had non-zero values in ≤ 10% of samples.