Impact of different sequencing and analysis methods for 16S rRNA gene-based bacterial community analysis in dairy products

We studied the impact of sequencing and analysis methods on observed bacterial diversities and OTU assignments using synthetic bacterial mock communities consist of bacterial species commonly found in dairy environment. We constructed both 16S amplicon and bacterial gDNA standards for comparison of two popular benchtop sequencer, Illumina Miseq and Ion Torrent PGM as well the upstream bioinformatics assembly of sequence reads (join paired-end sequences).