title: corn silage
design: Equimolar concentrations of PCR amplicons were pooled prior to  paired-end sequencing (2  300) on an Illumina MiSeq platform (Illumina, San  Diego, CA, USA). The raw data were quality-filtered using Trimmomatic and  merged with FLASH (Mago and Salzberg, 2011) based upon the criteria that  follow: (i) all sequences were truncated at any ste that had a < 20  average quality score over a sliding 50 bp window; (ii) any reads were  removed if they contained ambiguous bases or were exact matches to primer  sequences with up to a two nucleotide mismatch; and (iii) any sequences that  had > 10 bp of overlap were merged together. UPARSE (version 7.1) was used  for operational taxonomic unit (OTU) clustering based upon a 97% similarity  threshold, with UCHIME (Edgar, 2013) used for chimeric sequence  identification and removal. To analyze the taxonomy, the Silva (SSU123) 16S  rRNA database was used for alignment of 16S rRNA sequences based upon the RDP  classifier algorithm (version 2.2) (Wang et al., 2007) with a 70% confidence  threshold. Alpha diversity indices (Shannon index, Chao richness estimator,  and Goods coverage estimator) and beta diversity indices were determined  using QIIME (v1.7.0). R (v2.15.29) was used for principle component analysis  (PCA).