DNA was extracted from environmental samples using the ZymoBiomics DNA Miniprep Kit (Zymo Research, USA) following the manufacturer's instructions. Briefly, effluent and raw sewer samples were centrifuged at 5000 rpm for 1 hour to pellet the material. To capture the prokaryotic cells from drinking water samples, they were filtered through 0.45 m membrane filters (Sigma-Aldrich, St. Louis, MO) at approximately 2 bar using a vacuum pump system (SM 1753, Sartorius). The membrane filters were subsequently cut into smaller pieces and placed in bead-beating columns according to the ZymoBiomics DNA Miniprep Kit protocol. Additionally, 250 mg of soil samples and the pelleted effluent and raw sewer samples were respectively measured and transferred into bead-beating tubes. Subsequently, metagenomic DNA was extracted from all sample types using the ZymoBiomics DNA Miniprep Kit, adhering to the protocol provided by the manufacturer. Extracted DNA were stored at -800C freezer for further analysis. Subsequently, the extracted DNA was shipped in triple packaging and in compliance to IATA regulations to the Genomic Competence Centre, Robert Koch Institute in Germany for sequencing. Before sequencing, the DNA concentrations were analyzed using Qubit Flex Fluorometers (Thermo Fisher Scientific Inc. Waltham, MA, USA). Paired-end libraries were prepared following the Nextera XT prep kit (Illumina, Inc., San Diego, CA, USA) and sequenced on an Illumina NextSeq 2000 system using a P3 cartridge.