Amplicon sequencing:SP2
Genomic DNA extraction from the different fermented food sources was conducted using the DNeasy PowerSoil Pro kit (Qiagen, Germany) according to the manufacturer`s instructions. DNA quality and quantity were measured using a NanoDrop UV-Vis spectrophotometer and a Qubit fluorometer 2.0 (Thermo Fisher Scientific, USA). Illumina Miseq sequencing platform (Illumina, San Diego, CA, USA) with single-end 250 bp reads was used for the generation of an NGS library based on the amplification of the V4 hypervariable region (~ 428 bp) of the bacterial small subunit ribosomal RNA (16S rRNA) gene using V4F (5-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GTG NCA GCM GCC GCG GTR A-3) and V4R (5-GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC GAC TAC NVG GGT WTC TAA TC-3) primers. The bacterial amplicon was amplified with 25 cycles of polymerase chain reaction (PCR) with EmeraldAmp PCR master mix (Takara Bio Inc., Japan) and the set of primers V4F/V4R containing P5 and P7 Nextera adapters, respectively