16S rRNA amplicon sequencing of synthetic community in-vitro experiment
A two-step PCR was used to amplify the V3-V4 regions of the 16S rRNA gene as well as the GI gene (hamPCR), followed by a magnetic bead cleanup. Indexed primers used a dual-indexing scheme. PCR products were pooled based on fluorescence. The final library was sequenced on a MiSeq with 10% PhiX genomic DNA for 2x150bp cycles.