title: Comparison of tissue sample processing methods for harvesting the viral metagenome and a snapshot of the RNA viral community in a turkey gut.
abstract: RNA viruses have been associated with enteritis in poultry and have been isolated from diseased birds. The same viral agents have also been detected in healthy flocks bringing into question their role in health and disease. In order to understand better eukaryotic viruses in the gut, this project focused on evaluating alternative methods to purify and concentrate viral particles, which do not involve the use of density gradients, for generating viral metagenome data. In this study, the sequence outcomes of three tissue processing methods have been evaluated and a data analysis pipeline has been established for RNA viruses from the gastrointestinal tract. In addition, with the use of the best method and increased sequencing depth, a glimpse of the RNA viral community in the gastrointestinal tract of a clinically normal 5-week old turkey is presented. The viruses from the Reoviridae and Astroviridae families together accounted for 76.3% of total viruses identified. The rarefaction curve at the species level further indicated that majority of the species diversity was included with the increased sequencing depth, implying that viruses from other viral families were present in very low abundance.
authors.affiliation: Veterinary and Biomedical Sciences, University of Minnesota, MN, USA.
authors.forename: Jigna D
authors.initials: JD
authors.lastname: Shah
authors.affiliation: Minnesota Supercomputing Institute, University of Minnesota, MN, USA.
authors.forename: Joshua
authors.initials: J
authors.lastname: Baller
authors.affiliation: Minnesota Supercomputing Institute, University of Minnesota, MN, USA.
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Minnesota Supercomputing Institute, University of Minnesota, MN, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Silverstein
authors.affiliation: Veterinary and Biomedical Sciences, University of Minnesota, MN, USA.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Xing
authors.affiliation: Veterinary and Biomedical Sciences, University of Minnesota, MN, USA. Electronic address: ccardona@umn.edu.
authors.forename: Carol J
authors.initials: CJ
authors.lastname: Cardona
mesh_terms: D000818:Animals; D058448:Biota; D041981:Gastrointestinal Tract / Q000821:virology*; D056186:Metagenomics / Q000379:methods*; D012328:RNA Viruses / Q000235:genetics / Q000302:isolation & purification*; D012367:RNA, Viral / Q000235:genetics / Q000302:isolation & purification*; D013048:Specimen Handling / Q000379:methods*; D014422:Turkeys
chemical_list: D012367:RNA, Viral
keywords: Gastrointestinal virome; RNA viral metagenomics; Turkey