The identification of antibiotic resistance genes (ARGs) in microbial communities is one of the most challenging tasks in biology. The evolution and improvement of genome sequencing techniques, combined with the improvement of computational analysis techniques, have allowed us to acquire increasingly detailed information on the complex and varied microbial community that coexists and coevolves in the most heterogeneous environment. This chapter describes how to identify and quantify ARGs, using specific tools (Bowtie2, Bedtools for coverage, G/C content, and the estimated number of reads mapping each open reading frame; RGI tool, with the support of CARD database, to inspect the distribution of antibiotic resistance genes). Once this information is obtained, scientists would be able to highlight the relative abundance of ARGs in the metagenome analyzed and be able to understand how antibiotic resistance mechanisms evolve in microbial communities.
Keywords: Antibiotic resistance genes (ARGs); Bioinformatics; Metagenomic; Sequencing coverage.