Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery

Worldwide, approximately 1.8 million children die from diarrhea annually, and millions more suffer multiple episodes of nonfatal diarrhea. On average, in up to 40% of cases, no etiologic agent can be identified. The advent of metagenomic sequencing has enabled systematic and unbiased characterizatio...

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Main Authors:	Finkbeiner, Stacy R., Allred, Adam F., Tarr, Phillip I., Klein, Eileen J., Kirkwood, Carl D., Wang, David
Format:	Online
Language:	English
Published:	Public Library of Science 2008
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2290972/

id	pubmed-2290972
recordtype	oai_dc
spelling	pubmed-22909722008-04-09 Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery Finkbeiner, Stacy R. Allred, Adam F. Tarr, Phillip I. Klein, Eileen J. Kirkwood, Carl D. Wang, David Research Article Worldwide, approximately 1.8 million children die from diarrhea annually, and millions more suffer multiple episodes of nonfatal diarrhea. On average, in up to 40% of cases, no etiologic agent can be identified. The advent of metagenomic sequencing has enabled systematic and unbiased characterization of microbial populations; thus, metagenomic approaches have the potential to define the spectrum of viruses, including novel viruses, present in stool during episodes of acute diarrhea. The detection of novel or unexpected viruses would then enable investigations to assess whether these agents play a causal role in human diarrhea. In this study, we characterized the eukaryotic viral communities present in diarrhea specimens from 12 children by employing a strategy of “micro-mass sequencing” that entails minimal starting sample quantity (<100 mg stool), minimal sample purification, and limited sequencing (384 reads per sample). Using this methodology we detected known enteric viruses as well as multiple sequences from putatively novel viruses with only limited sequence similarity to viruses in GenBank. Public Library of Science 2008-02-29 /pmc/articles/PMC2290972/ /pubmed/18398449 http://dx.doi.org/10.1371/journal.ppat.1000011 Text en Finkbeiner et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Finkbeiner, Stacy R. Allred, Adam F. Tarr, Phillip I. Klein, Eileen J. Kirkwood, Carl D. Wang, David
spellingShingle	Finkbeiner, Stacy R. Allred, Adam F. Tarr, Phillip I. Klein, Eileen J. Kirkwood, Carl D. Wang, David Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery
author_facet	Finkbeiner, Stacy R. Allred, Adam F. Tarr, Phillip I. Klein, Eileen J. Kirkwood, Carl D. Wang, David
author_sort	Finkbeiner, Stacy R.
title	Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery
title_short	Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery
title_full	Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery
title_fullStr	Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery
title_full_unstemmed	Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery
title_sort	metagenomic analysis of human diarrhea: viral detection and discovery
description	Worldwide, approximately 1.8 million children die from diarrhea annually, and millions more suffer multiple episodes of nonfatal diarrhea. On average, in up to 40% of cases, no etiologic agent can be identified. The advent of metagenomic sequencing has enabled systematic and unbiased characterization of microbial populations; thus, metagenomic approaches have the potential to define the spectrum of viruses, including novel viruses, present in stool during episodes of acute diarrhea. The detection of novel or unexpected viruses would then enable investigations to assess whether these agents play a causal role in human diarrhea. In this study, we characterized the eukaryotic viral communities present in diarrhea specimens from 12 children by employing a strategy of “micro-mass sequencing” that entails minimal starting sample quantity (<100 mg stool), minimal sample purification, and limited sequencing (384 reads per sample). Using this methodology we detected known enteric viruses as well as multiple sequences from putatively novel viruses with only limited sequence similarity to viruses in GenBank.
publisher	Public Library of Science
publishDate	2008
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2290972/
_version_	1611440397737787392

Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery

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