“…The challenges of using NGS to characterize viral content are numerous, including the absence of universal marker genes ( Eric Wommack et al, 2012 ), the low concentration of viral DNA for preparation of genomic libraries ( Garmaeva et al, 2019 ), the contamination of the sample with bacterial and fungal DNA ( Kim and Bae, 2011 ), and the scarcity of databases for virus sequences as they remain largely unknown ( Bikel et al, 2015 ; Garmaeva et al, 2019 ). Nevertheless, some food microbiome studies have detected, but not classified viruses in fermented food systems ( Liu et al, 2020 ; Lyu et al, 2013 ). To a lesser extent, some studies have achieved a classification, even though it was focused on bacterial and fungal communities ( Agyirifo et al, 2019 ; Illeghems et al, 2012 ; Kumar et al, 2019 ).…”