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, microorganism-infecting 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.

FIG. 1.

Overview of relative abundance and distribution of viral taxonomic groups based on MEGAN analysis of viral genotypes from the three fermented food viral metagenomes. Colors: blue, fermented shrimp; red, kimchi; green, sauerkraut.

FIG. 2.

Comparison of host diversity of phage and prophages to bacterial diversity in each of the three fermented foods. Phage host and prophage host diversity were identified comparing to the GenBank and ACLAME databases, and bacterial community was determined based on 16S rRNA gene sequences. (A) Fermented shrimp; (B) kimchi; (C) sauerkraut. Colors: red, 16S rRNA gene-based bacterial community; yellow, phage host distribution; blue, prophage host distribution.

FIG. 3.

Comparison of viral communities represented as viral families in fermented foods, potable water, human feces, seawater, coral, paddy soil, and an Antarctic lake. The percent representations of divisions in each virome are shown. The activated sludge viral metagenome sequences (n = 109) (33), the potable water viral metagenome sequences (n = 231,715) (40), the human feces data obtained and combined from two independent studies (n = 95) (7, 8), the coral metagenome sequences (n = 1,580) (30), the seawater data set (n = 131) (11), the paddy soil data (n = 785) (21), and the Antarctic lake virome (n = 3,360) (25) were obtained from each of the studies, and the fermented-food virome was obtained from the present study.