Microbial Profiling of Fermented Quinoa Flour

Cells harvested from 10 g of fermented quinoa flour were resuspended in sterile saline and treated with 2.5 mM propidium monoazide (PMA) stock solution (1.3 mg/mL PMA in 20% DMSO; Biotium, Inc., Hayword, CA, USA) to eliminate dead bacterial and extracellular DNA as described by (Pan and Breidt, 2007). PMA-treated samples were stored as cell pellets at −20 °C until DNA extraction was performed. Total genomic DNA was extracted using a MasterPure^TM DNA Purification Kit (Epicentre, Madison, WI, USA). The 16S rDNA gene regions V3 to V4 were amplified by PCR using the Bakt_341F/Bakt_805R primers [37 (link)]. Primers were barcoded as described by the manufacturer for the Illumina MiSeq sequencing technology. For the fungi analysis, primers ITS1F/ITS2 were used. Sequencing services were obtained from the Carver Biotech Laboratory at the WM Keck Center for Comparative and Functional Genomics (Chicago, IL, USA). Twenty-two samples corresponding to 3 quinoa flour-type fermentations including real, red and black collected at different time points (day 1, 6 and 8) were subjected to DNA extractions and sequencing data processing.