Viruses in fermented foods: are they good or bad? Two sides of the same coin

Abstract

The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.

Two Faces of Fermented Foods—The Benefits and Threats of Its Consumption

“…The low number of these microorganisms in food products and the greater difficulty of detecting them may also be a reason. Foodborne viruses include hepatitis A and E virus, noroviruses, and rotaviruses ( Maske et al, 2021 ). In 2016, two cases of tick-borne encephalitis were reported in Germany after consumption of unpasteurized goat cheese ( Brockmann et al, 2018 ).…”

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

“…Metagenomics has shed light on the viromes present in fermented foods whereas culture-based methods allow the study of only singular phages causing fermentation flaws or singular foodborne viruses at a time [ 163 ]. Virome studies are scarce in fermented foods but should not be neglected.…”

“…However, the sequencing of viruses in fermented foods can be problematic due to their low abundance and smaller genome size compared to bacterial and fungal populations present in the food. This is especially true for foodborne viruses that do not multiply in food substrates [ 163 ]. Virus genomes can be DNA or RNA-encoded and only small percentages of viromes have been taxonomically assigned [ 210 , 211 ].…”

“…The direct sequencing of RNA, without first converting to cDNA, is a developing field with a few platforms, such as ONT and TERA-Seq, introducing native RNA sequencing [ 212 , 213 ]. However, library preparation involving RNA to cDNA conversion coupled with targeted amplification can improve representation of low abundance viral RNA [ 163 ].…”

Metagenomics of Virus Diversities in Solid-State Brewing Process of Traditional Chinese Vinegar

“…However, the diversity of viruses varied in diverse fermented foods due to the different environments. It has been observed that some viruses can positively influence the fermentation process of fermented foods [ 5 ]. Reports showed that, in some fermented food such as cocoa beans and milk cheese, viruses can regulate bacterial community succession during fermentation, and might have beneficial effects on the quality and sensory characteristics of fermented products [ 6 , 7 ].…”