Time-series drinking water metagenomes: Assemblies & MAGs

Samples (n = 12) were collected over a period of 6 months from a tap in a commercial building located in Boston, MA (United States). Prior to sample collection, the system was flushed for at least 30 min at a flow rate ranging between 3.0 and 3.3 l.min-1 and then approximately 1,500 ml of tap water was collected for microbial community analysis in a sterile (by autoclaving) 2 L DURAN® GLS 80® wide mouth borosilicated glass bottle (DURAN®, Cat. No.: 1112715). The samples were filtered immediately through Sterivex-GP Pressure Filter Units (EMD Millipore, Cat. No.: SVGP01050) containing a 0.22μm polyethersulfone (PES) filter membrane, using the Geotech Geopump™ Series II peristaltic pump (Geotech Environmental Equipment, Inc., Cat. No.: 91350113) and sterile SZ 15 Geotech silicone tubing (Geotech Environmental Equipment, Inc., Cat. No.: 77050000) and stored at -80°C until further analysis. DNA extractions were performed using a modified version of the DNeasy PowerWater Kit® (QIAGEN, Cat. No.: 14900-50-NF or 14900-100-NF) protocol that utilizes enzymatic, chemical, and mechanical lysis strategies to enhance recovery of DNA from drinking water samples. Sequencing libraries were prepared using the Ovation® Ultralow DNA-Seq Library Preparation Kit (NuGEN, Cat. No.: 0344NB). Metagenomic sequencing was performed on one SP lane of the NovaSeq 6000 sequencing system (Illumina) at the Roy J. Carver Biotechnology Centre at the University of Illinois Urbana-Champaign (UIUC) Sequencing Core (Champaign, IL, United States). For MAG reconstruction, a combination of assembly (metaSPAdes v.3.13.1 and MEGAHIT v.1.2.9), binning (CONCOCT v.1.1.1, MetaBAT v.2.12, MaxBin v.2.2.4) and bin aggregating software (DAS Tool v.1.1.0) were evaluated using four assembly strategies, including individual assembly and three co-assembly approaches, i.e., co-assembly with all samples, MASH distance-based assembly, and time-discrete assembly.