Literature DB >> 28713847

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

Cynthia L Monaco1, Douglas S Kwon2,3.   

Abstract

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.

Entities:  

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

Year:  2017        PMID： 28713847      PMCID： PMC5510652          DOI： 10.21769/BioProtoc.2159

Source DB:  PubMed          Journal:  Bio Protoc        ISSN： 2331-8325


  9 in total

1.  Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome.

Authors:  Scott A Handley; Larissa B Thackray; Guoyan Zhao; Rachel Presti; Andrew D Miller; Lindsay Droit; Peter Abbink; Lori F Maxfield; Amal Kambal; Erning Duan; Kelly Stanley; Joshua Kramer; Sheila C Macri; Sallie R Permar; Joern E Schmitz; Keith Mansfield; Jason M Brenchley; Ronald S Veazey; Thaddeus S Stappenbeck; David Wang; Dan H Barouch; Herbert W Virgin
Journal:  Cell       Date:  2012-10-12       Impact factor: 41.582

Review 2.  The virome in mammalian physiology and disease.

Authors:  Herbert W Virgin
Journal:  Cell       Date:  2014-03-27       Impact factor: 41.582

3.  Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut.

Authors:  Alejandro Reyes; Meng Wu; Nathan P McNulty; Forest L Rohwer; Jeffrey I Gordon
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-20       Impact factor: 11.205

4.  Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome.

Authors:  Cynthia L Monaco; David B Gootenberg; Guoyan Zhao; Scott A Handley; Musie S Ghebremichael; Efrem S Lim; Alex Lankowski; Megan T Baldridge; Craig B Wilen; Meaghan Flagg; Jason M Norman; Brian C Keller; Jesús Mario Luévano; David Wang; Yap Boum; Jeffrey N Martin; Peter W Hunt; David R Bangsberg; Mark J Siedner; Douglas S Kwon; Herbert W Virgin
Journal:  Cell Host Microbe       Date:  2016-03-09       Impact factor: 21.023

5.  VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.

Authors:  Guoyan Zhao; Guang Wu; Efrem S Lim; Lindsay Droit; Siddharth Krishnamurthy; Dan H Barouch; Herbert W Virgin; David Wang
Journal:  Virology       Date:  2017-01-18       Impact factor: 3.616

6.  Disease-specific alterations in the enteric virome in inflammatory bowel disease.

Authors:  Jason M Norman; Scott A Handley; Megan T Baldridge; Lindsay Droit; Catherine Y Liu; Brian C Keller; Amal Kambal; Cynthia L Monaco; Guoyan Zhao; Phillip Fleshner; Thaddeus S Stappenbeck; Dermot P B McGovern; Ali Keshavarzian; Ece A Mutlu; Jenny Sauk; Dirk Gevers; Ramnik J Xavier; David Wang; Miles Parkes; Herbert W Virgin
Journal:  Cell       Date:  2015-01-22       Impact factor: 41.582

7.  Identification of novel viruses using VirusHunter--an automated data analysis pipeline.

Authors:  Guoyan Zhao; Siddharth Krishnamurthy; Zhengqiu Cai; Vsevolod L Popov; Amelia P Travassos da Rosa; Hilda Guzman; Song Cao; Herbert W Virgin; Robert B Tesh; David Wang
Journal:  PLoS One       Date:  2013-10-22       Impact factor: 3.240

Review 8.  Metagenomics and future perspectives in virus discovery.

Authors:  John L Mokili; Forest Rohwer; Bas E Dutilh
Journal:  Curr Opin Virol       Date:  2012-01-20       Impact factor: 7.090

9.  Resident viruses and their interactions with the immune system.

Authors:  Breck A Duerkop; Lora V Hooper
Journal:  Nat Immunol       Date:  2013-07       Impact factor: 25.606
  9 in total
  4 in total

1.  Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX.

Authors:  Christian Milani; Eoghan Casey; Gabriele Andrea Lugli; Rebecca Moore; Joanna Kaczorowska; Conor Feehily; Marta Mangifesta; Leonardo Mancabelli; Sabrina Duranti; Francesca Turroni; Francesca Bottacini; Jennifer Mahony; Paul D Cotter; Fionnuala M McAuliffe; Douwe van Sinderen; Marco Ventura
Journal:  Microbiome       Date:  2018-08-20       Impact factor: 14.650

2.  Transkingdom Analysis of the Female Reproductive Tract Reveals Bacteriophages form Communities.

Authors:  Ferralita S Madere; Michael Sohn; Angelina K Winbush; Breóna Barr; Alex Grier; Cal Palumbo; James Java; Tracy Meiring; Anna-Lise Williamson; Linda-Gail Bekker; David H Adler; Cynthia L Monaco
Journal:  Viruses       Date:  2022-02-19       Impact factor: 5.818

Review 3.  Bacteriophages: Underestimated vehicles of antibiotic resistance genes in the soil.

Authors:  Yue Zhang; Yajie Guo; Tianlei Qiu; Min Gao; Xuming Wang
Journal:  Front Microbiol       Date:  2022-08-04       Impact factor: 6.064

4.  The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut.

Authors:  Ann C Gregory; Olivier Zablocki; Ahmed A Zayed; Allison Howell; Benjamin Bolduc; Matthew B Sullivan
Journal:  Cell Host Microbe       Date:  2020-08-24       Impact factor: 21.023
  4 in total

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