Samples were categorized based on DNA yield and qPCR Cq values. For samples with low DNA concentration and high Cq, a two-step PCR was performed using universal and barcoded fusion primers 515F and 802R targeting the hypervariable V4 region of the 16S rRNA gene of both Bacteria and Archea. Samples with sufficient DNA were amplified using a single PCR step with barcoded primers. A high-fidelity polymerase was used to minimize amplification bias. Amplicons were purified using the Agencourt AMPure XP system with a 1:1 bead-to-sample ratio, and concentrations were quantified via Qubit 2.0. Equal concentrations of barcode-tagged amplicons were pooled and sequenced using the Genexus Ion Torrent System with the ION GX5 Chips.