ArticleMicrobiology spectrum2026
SS-VIME: a single-source virome-microbiome extraction protocol toward comprehensive soil community analysis.
Article in Microbiology spectrum, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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3 authors.
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Abstract
Integrated analysis of soil microbiomes and their associated viromes is critical for understanding ecosystem function, yet is hampered by the profound spatial heterogeneity of soil, which introduces significant bias when using separate extraction workflows and/or subsampling strategies to capture fungal, bacterial, and viral communities. Here, we present single-source extraction for unified soil virome-microbiome profiling (SS-VIME), a protocol that overcomes this limitation. Based on extended cellulose column chromatography, this method sequentially elutes distinct DNA and double-stranded RNA (dsRNA) fractions from a single soil lysate. We validated the protocol using sterilized soil co-spiked with a ZymoBIOMICS microbial community standard and a synthetic viral dsRNA fragment. Sequencing confirmed that the DNA fraction accurately recovered the theoretical bacterial (16S rRNA gene) and fungal (ITS) community profiles, while the dsRNA fraction demonstrated highly specific recovery of the target viral signature. The protocol was then successfully applied to characterize the complex native communities in environmental soil samples. The SS-VIME protocol provides a streamlined approach for isolating high-quality nucleic acids suitable for downstream applications. By using dsRNA as a proxy for viral activity and eliminating subsample bias, this method provides a robust, accessible, and unified platform to investigate virus-host dynamics
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