Resistflow_MAGs

Between March and April 2016, a total of 47 microbial biomass samples were taken from the primarily clarified influent, the denitrifying bioreactors, the nitrifying bioreactors and the secondarily clarified effluent of 12 urban WWTPs across Switzerland. Total DNA and RNA extractions, processing of the mRNA internal standards , data pretreatment, and metagenome assembly were performed as previously described in Ju et al. (https://doi.org/10.1038/s41396-018-0277-8) . The metagenomes and metatranscriptomes generated by our preliminary study have been used to gain a comprehensive overview on the fate and expression patterns of known antibiotic, biocide and metal resistance genes throughout the varying compartments of the WWTPs. However, the identity, multi-resistance, pathogenicity, distribution, activity and other functional traits of ARG-hosts remained unknown, due to the fragmented nature of metagenome assemblies obtained. In this study, we filled this knowledge gap by re-analysis of the datasets using a genome-centric metatranscriptomic strategy.