Metagenome of Site 4
The samples were processed and analyzed with the ZymoBIOMICS Shotgun Metagenomic Sequencing Service for Microbiome Analysis (Zymo Research, Irvine, CA). DNA extraction was performed using ZymoBIOMICSTM DNA/RNA  Miniprep Kit (Cat  No: R2002). Genomic DNA samples were profiled with shotgun metagenomic sequencing. Illumina DNA Library Prep Kit (Illumina, San Diego, CA) with up to 500 ng DNA input following the manufacturers protocol using unique dual-index 10 bp barcodes with Nextera adapters (Illumina, San Diego, CA). All libraries were pooled in equal abundance and the final pool was quantified using qPCR and TapeStation (Agilent Technologies, Santa Clara, CA). The final library was sequenced on NovaSeq (Illumina, San Diego, CA). The ZymoBIOMICS Microbial Community DNA Standard (Zymo Research, Irvine, CA) was used as a positive control for each library preparation. Negative controls (i.e. blank extraction control, blank library preparation control) were included to assess the level of bioburden carried by the wet-lab process.