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We explored gut mucosal virome alterations in UC1 and appreciate the insightful comments from the authors who highlighted some of the important limitations of human gut virome studies.2 Unlike the bacteria microbiome, the gut virome remains largely underexplored. There is currently no gold standard on the optimal pipelines or methods for virome analysis. In addition, the lack of consensus in both methodology and virus taxonomy classification underscores significant limitations and challenges in virome metagenomics analysis.3 4
Most metagenomic studies of the human gut virome have adopted practical methods based on filtration with subsequent precipitation or ultrafiltration of virus-like particles (VLPs).3 Such protocols including that of ours can introduce considerable amounts of residual DNA into the samples, such as …
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