Plant RNA Virus Sequences Identified in Kimchi by Microbial Metatranscriptome Analysis

Abstract

Plant pathogenic RNA viruses are present in a variety of plant-based foods. When ingested by humans, these viruses can survive the passage through the digestive tract, and are frequently detected in human feces. Kimchi is a traditional fermented Korean food made from cabbage or vegetables, with a variety of other plant-based ingredients, including ground red pepper and garlic paste. We analyzed microbial metatranscriptome data from kimchi at five fermentation stages to identify plant RNA virus-derived sequences. We successfully identified a substantial amount of plant RNA virus sequences, especially during the early stages of fermentation: 23.47% and 16.45% of total clean reads on days 7 and 13, respectively. The most abundant plant RNA virus sequences were from pepper mild mottle virus, a major pathogen of red peppers; this constituted 95% of the total RNA virus sequences identified throughout the fermentation period. We observed distinct sequencing read-depth distributions for plant RNA virus genomes, possibly implying intrinsic and/or technical biases during the metatranscriptome generation procedure. We also identified RNA virus sequences in publicly available microbial metatranscriptome data sets. We propose that metatranscriptome data may serve as a valuable resource for RNA virus detection, and a systematic screening of the ingredients may help prevent the use of virus-infected low-quality materials for food production.

Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi

“…However, PMMoV belonging to Tobamovirus was highly dominant in the USM and NM. In a study by Kim et al (2014) , it was found that most of the plant RNA viruses of kimchi were PMMoV, which is consistent with our results. Moreover, the reason for the high ratio of PMMoV as the major pathogenic virus of plants in the genus Capsicum ( Jarret et al, 2008 ) in the USM and NM was presumed to be due to the chili powder used in kimchi.…”

Identification of a novel plant amalgavirus (Amalgavirus, Amalgaviridae) genome sequence in Cistus incanus

“…Transcriptome or metatranscriptome data generated from total RNA isolated from organism or environmental samples often contain sequence reads derived from viral genomic RNAs, which can be identified by comprehensive bioinformatics analysis (Kim et al, 2014;Liu et al, 2012;Nibert et al, 2016). As a result, many plant RNA virus genome sequences were discovered by analyzing transcriptome datasets Kim et al, 2018;Park et al, 2018;Park and Hahn, 2017a,b).…”

Identification of Two Novel Amalgaviruses in the Common Eelgrass (Zostera marina) and in Silico Analysis of the Amalgavirus +1 Programmed Ribosomal Frameshifting Sites

“…When total RNA from plant samples was extracted for transcriptomic analysis, viral genome RNAs were isolated together with the host RNAs. As a result, many plant RNA-seq datasets contain associated RNA virus sequences, which can be identified by comprehensive bioinformatic analysis ( Kim et al, 2014 ; Liu et al, 2012 ; Park and Hahn, 2017a , 2017b ). In this study, two novel amalgaviruses were identified in a transcriptome dataset obtained for the common eelgrass ( Kong et al, 2014 ).…”