Metagenomic Analysis of the Viral Communities in Fermented Foods

Abstract

Viruses are recognized as the most abundant biological components on Earth, and they regulate the structure of microbial communities in many environments. In soil and marine environments, microorganisminfecting phages are the most common type of virus. Although several types of bacteriophage have been isolated from fermented foods, little is known about the overall viral assemblages (viromes) of these environments. In this study, metagenomic analyses were performed on the uncultivated viral communities from three fermented foods, fermented shrimp, kimchi, and sauerkraut. Using a high-throughput pyrosequencing technique, a total of 81,831, 70,591 and 69,464 viral sequences were obtained from fermented shrimp, kimchi and sauerkraut, respectively. Moreover, 37 to 50% of these sequences showed no significant hit against sequences in public databases. There were some discrepancies between the prediction of bacteriophages hosts via homology comparison and bacterial distribution, as determined from 16S rRNA gene sequencing. These discrepancies likely reflect the fact that the viral genomes of fermented foods are poorly represented in public databases. Double-stranded DNA viral communities were amplified from fermented foods by using a linker-amplified shotgun library. These communities were dominated by bacteriophages belonging to the viral order Caudovirales (i.e., Myoviridae, Podoviridae, and Siphoviridae). This study indicates that fermented foods contain less complex viral communities than many other environmental habitats, such as seawater, human feces, marine sediment, and soil.

Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

“…A high percentage of unknown sequences has been reported in other viral metagenomic studies (40 to 90% unknown sequences) (3,40), and the current study also found that greater than 50% of the sequences of the three land use types and rainwater were uncharacterized. Taxonomy-independent analysis of the four viromes using a cross-BLAST search showed that the RD virome was more different from the FR virome than the IC virome, which differed from the comparison of viral taxonomy profiles, suggesting that a large number of novel viruses may be present in the atmosphere.…”

“…Repeated density gradient purification using ultracentrifugation was conducted before morphological analysis of airborne viruses using protocols described previously (40). In brief, air samples were passed sequentially through 3-m-, 0.45-m-, and 0.2-mpore-size filters (Advantec).…”

Next-generation approaches to the microbial ecology of food fermentations

“…It has been remarkably well-utilized for studying Korean fermented foods, including bacteria and archaea of fermented seafood (68), bacterial and fungal communities of Makgeolli (rice beer) (69), meju (70) and doenjang (soybean pastes) (71), kochujang (fermented red pepper condiment) (72), and kimchi (73). It has also been used to study the viral communities inhabiting a range of Korean fermented food products (74). The greater sequence coverage and lower cost of Illumina sequencing has prompted its growing application in the study of microbial ecology in favor of pyrosequencing, and food microbiology is no exception.…”

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

“…Finally, since little is known about the ecological role of bacteriophages in fermented foods, shotgun sequencing of viral DNA can also be used to define the viral communities in foods, as recently shown in fermented shrimp, kimchi, and sauerkraut (28).…”