DNA from samples (0.25 g) was extracted using the PowerSoil DNA Isolation kit (MoBio Laboratories Inc., Carlsbad, California), according to the manufacturer’s protocol. We amplified and sequenced a fragment of the 16S rRNA gene covering the V4 region with a dual-index sequencing strategy as described by Kozich et al. (2013).   Kozich, J.J., Westcott, S.L., Baxter, N.T., Highlander, S.K., Schloss, P.D., 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology, 79, 5112-5120.
MiSeq