“…Shotgun whole-metagenome sequencing (WMS) is a reliable tool that can provide a comprehensive and high-resolution analysis of the microbiome and resistome ( Schmieder and Edwards, 2011 ; Nesme et al, 2014 ; Ghanbari et al, 2019 ; Ma et al, 2021 ), and it has been applied to quantify the abundance of many resistance genes in parallel in poultry ( Wang et al, 2017 ; Kumar et al, 2020 ), cattle ( Thomas et al, 2017 ), pig ( Ghanbari et al, 2019 ; MencĂa-Ares et al, 2020 ) and the human gut ( Feng et al, 2018 ). Other metagenomic studies have found multiple ARGs in chicken gut as well ( Tong et al, 2017 ; Xiong et al, 2018 ; Eckstrom and Barlow, 2019 ; Wang Y. et al, 2021 ; De Cesare et al, 2022 ). However, WMS provides only limited information regarding ARG activity or the overall functional profile of the active microbial community.…”