Plant RNA virus sequences identified in kimchi by microbial metatranscriptome analysis.
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.
Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea.
Dong Seon
DS
Kim
Ji Young
JY
Jung
Yao
Y
Wang
Hye Ji
HJ
Oh
Dongjin
D
Choi
Che Ok
CO
Jeon
Yoonsoo
Y
Hahn
D001937:Brassica / Q000821:virology*; D005285:Fermentation; D020869:Gene Expression Profiling / Q000379:methods*; D056186:Metagenomics / Q000379:methods*; D012328:RNA Viruses / Q000145:classification / Q000235:genetics*; D012367:RNA, Viral / Q000032:analysis / Q000235:genetics / Q000302:isolation & purification; D017423:Sequence Analysis, RNA / Q000379:methods
D012367:RNA, Viral