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Bio Protoc. 2017 Mar 5;7(5). pii: e2159. doi: 10.21769/BioProtoc.2159.

Next-generation Sequencing of the DNA Virome from Fecal Samples.

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Department of Medicine, Washington University School of Medicine, St. Louis, USA.
Ragon Institute of MGH, MIT, and Harvard, Cambridge, USA.
Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, USA.


Herein we describe a detailed protocol for DNA virome analysis of low input human stool samples (Monaco et al., 2016). This protocol is divided into four main steps: 1) stool samples are pulverized to evenly distribute microbial matter; 2) stool is enriched for virus-like particles and DNA is extracted by phenol-chloroform; 3) purified DNA is multiple-strand displacement amplified (MDA) and fragmented; and 4) libraries are constructed and sequenced using Illumina Miseq. Subsequent sequence analysis for viral sequence identification should be sensitive but stringent.


Illumina Miseq; MDA; Viral microbiome; Virome; Virus-like particles

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