title: Illumina sequencing of whole grain long fermentation dough after 0 h fermentation
design: The V3-V4 region of the bacterial 16S rRNA gene and the V9 region of the eukaryotic 18S rRNA gene were amplified from each sample at external facilities (www.starseq.com). Briefly, triplicate end-point PCR reactions for V3-V4 and V9 regions were performed using previously described primers (V3V4, 341f806r [Klinworh et al 2013]; V9, Illumina_Euk_1391fIllumina_EukBr_1510r [Amaral-Zettler et al 2009]) and equimolarly pooled to reduce bias. Pooled libraries were gel purified and spiked with 8.510% PhiX prior to sequencing. Paired-end (2 x 300 base pair) high-throughput DNA sequencing was carried out using the MiSeq platform (Illuimna). Obtained reads were processed with the DADA2 pipeline and phyloseq R package (Callahan et al 2016, McMurdie et al 2013). Subsequently, a sequence table was constructed, taxonomy was assigned, and abundance was calculated at all possible taxonomic levels. Alpha- and Beta-diversity indices were computed using distinct R packages.