Abstract
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.
Highlights
While traditional sequencing approaches are designed to characterize genomes of a single species of interest, metagenomic approaches, such as mass sequencing, transcend species boundaries allowing one to explore the makeup of microbial communities
We used an experimental strategy termed ‘‘micro-mass sequencing’’ to systematically identify viruses present in stool from a number of patients suffering from diarrhea
One implication of this study is that there are likely to be many more unknown viruses that can be identified in this fashion. By studying these viruses, we will come to a more complete understanding of the role viruses play in diarrhea
Summary
While traditional sequencing approaches are designed to characterize genomes of a single species of interest, metagenomic approaches, such as mass sequencing, transcend species boundaries allowing one to explore the makeup of microbial communities Such methods provide a holistic look at microbial diversity within a given sample, completely bypassing the need for culturing [1,2,3,4,5]. Mass sequencing affords an opportunity to explore the viral diversity (including both known and novel viruses) present in stool during acute episodes of diarrhea in a systematic and unbiased fashion, thereby laying the foundation for future studies aimed at assessing whether any novel or unexpected viruses detected play a causal role in human diarrhea
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