RNA-seq of dry digestate enrichment
Next Generation Sequencing Ilumina MiSeq v3 run (2 x 300 bp) of the V3-4 region of the 16S rDNA was performed by MicroSynth (Switzerland) on previously isolated DNA. The company is ISO certified according to 9001:2008 and ISO / IEC 17025. Library preparation included sample quality control and Nextera two step PCR amplification using primer set 341f_ill/802r_ill, PCR product purification, quantification and equimolar pooling. Bioinformatic analysis included demultiplexing, merging of forward and reverse reads, quality filtering, trimming, chimera removal, OTU clustering (97 % identity threshold) and subsampling for even sample size (rarefaction to the lower number of reads per sample). Taxonomy assignment was based on the SILVA 16S database v.123 (> 60 % confidence).