Shotgun analysis of dairy livestock agroecosystem

Quality Control of sequenced samples was performed by FASTQC software, and trimming by TrimGalore. Trimmed reads were the input for SqueezeMeta pipeline in sequential mode with a minimum identity of 60 percent using 16 threads and an amount of RAM of 64 Gb. Resistome risk score determination, defined as potential for ARGs to be associated with MGE-genes and mobilize to pathogens was calculated. Resistome risk was performed from the assembled contigs using MetaCompare pipeline. Before being used as input for Metacompare, sequences were preprocessed using MEGAHIT for the contig assembly step and Prodigal for gene prediction. The predicted ARGs were analyzed with BLASTX (E-value < 1E-10, Identity > 60% and Minimum alignment length > amino acids) against CARD and MGE-genes against ACLAME. We obtained three types of contigs that contain ARGs, ARG and MGE-like sequences and ARG, MGE and human pathogen-like sequences based on the co-occurrence of ARGs n MGE-like n pathogen-like sequences.