Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes Public Deposited

http://ir.library.oregonstate.edu/concern/articles/vd66w205d

This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Public Library of Science. The published article can be found at:  http://journals.plos.org/ploscompbiol/

Supporting information is available online at:  http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004573#sec023

Data Availability Statement: The Gilbert et al. L4 metagenomes and metatranscriptomes are available from the MG-RAST database (project number 109,  http://metagenomics.anl.gov/metagenomics.cgi? page=MetagenomeProject&project=109), the Qin et al. MetaHIT inflammatory bowel disease metagenomes are available in the EBI (accession ERA000116), and the Nielsen et al. MGS inflammatory bowel disease metagenomes are available in the EBI (accession ERP002061).

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  • Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn’s disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease
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  • Nayfach, S., Bradley, P. H., Wyman, S. K., Laurent, T. J., Williams, A., Eisen, J. A., ... & Sharpton, T. J. (2015). Automated and accurate estimation of gene family abundance from shotgun metagenomes. PLoS Computational Biology, 11(11), e1004573. doi:10.1371/journal.pcbi.1004573
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  • description.provenance : Made available in DSpace on 2016-01-13T16:26:33Z (GMT). No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) SharptonThomasMicrobiologyAutomatedAccurateEstimation.pdf: 1578460 bytes, checksum: 0eb8d93aa2a620308c36ee7a1f735ac5 (MD5) Previous issue date: 2015-11
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