Comparison of experimental methodologies based bulk-metagenome and virus-like particle enrichment

Retrospective study to characterize the fecal virome for comparison of viral metagenomics approaches. Stool samples from 10 healthy adults, carriers of Lynch syndrome mutations were collected, and the virome was extracted following three protocols: Protocol 1, based on based on bulk metagenomics, and 2 and 3, based on virus-like particle (VLP) enrichment, with two replicas per protocol. Negative controls of extraction, retrotranscription and amplification were run in parallel to samples Libraries were sequenced on the Illumina NextSeq 500 producing 1x150 bp single-end reads. The resulting single-end reads were filtered for quality and taxa were assigned using Kaiju. Alpha diversity was analyzed by Shannon index and beta diversity by Bray-Curtis dissimilarity.