Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut

Ji-Woo Park, Yeo-Eun Yun, Jin Ah Cho, Su-In Yoon, Su-A In, Eun-Jin Park () and Min-Soo Kim ()
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Ji-Woo Park: Chungnam National University
Yeo-Eun Yun: Chungnam National University
Jin Ah Cho: Chungnam National University
Su-In Yoon: Chungnam National University
Su-A In: Chungnam National University
Eun-Jin Park: Jeju National University
Min-Soo Kim: Chungnam National University

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Fresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigate the diversity and ecology of phyllosphere viromes of six leafy green vegetables using virus-like particle (VLP) enrichment and shotgun metagenome sequencing. On average, 9.2 × 107 viruses are present per gram of leaf tissue. The majority (93.1 ± 6.2%) of these viruses are taxonomically unclassified. Virome compositions are distinct among vegetable types and exhibit temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) are more dominant than temperate phages with host fitness-benefiting AMGs. Analysis of 1498 human fecal VLP metagenomes reveals that approximately 10% of vegetable viruses are present in the human gut virome, including viruses commonly observed in multiple studies. These gut-associated vegetable viruses are enriched with short-term vegetable intake, and depleted in individuals with metabolic and immunologic disorders. Overall, this study elucidates the ecological contribution of the fresh vegetable virome to human gut virome diversity.

Date: 2025
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DOI: 10.1038/s41467-025-58856-6

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