Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.

Metagenomics has transformed our understanding of the microbial world, allowing researchers to bypass the need to isolate and culture individual taxa and to directly characterize both the taxonomic and gene compositions of environmental samples. However, associating the genes found in a metagenomic...

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Autores principales:	Rogan Carr, Shai S Shen-Orr, Elhanan Borenstein
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/bdb8f86c68644a5b8d9c29dd9e97a4bb
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spelling	oai:doaj.org-article:bdb8f86c68644a5b8d9c29dd9e97a4bb2021-11-18T05:53:30ZReconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.1553-734X1553-735810.1371/journal.pcbi.1003292https://doaj.org/article/bdb8f86c68644a5b8d9c29dd9e97a4bb2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24146609/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Metagenomics has transformed our understanding of the microbial world, allowing researchers to bypass the need to isolate and culture individual taxa and to directly characterize both the taxonomic and gene compositions of environmental samples. However, associating the genes found in a metagenomic sample with the specific taxa of origin remains a critical challenge. Existing binning methods, based on nucleotide composition or alignment to reference genomes allow only a coarse-grained classification and rely heavily on the availability of sequenced genomes from closely related taxa. Here, we introduce a novel computational framework, integrating variation in gene abundances across multiple samples with taxonomic abundance data to deconvolve metagenomic samples into taxa-specific gene profiles and to reconstruct the genomic content of community members. This assembly-free method is not bounded by various factors limiting previously described methods of metagenomic binning or metagenomic assembly and represents a fundamentally different approach to metagenomic-based genome reconstruction. An implementation of this framework is available at http://elbo.gs.washington.edu/software.html. We first describe the mathematical foundations of our framework and discuss considerations for implementing its various components. We demonstrate the ability of this framework to accurately deconvolve a set of metagenomic samples and to recover the gene content of individual taxa using synthetic metagenomic samples. We specifically characterize determinants of prediction accuracy and examine the impact of annotation errors on the reconstructed genomes. We finally apply metagenomic deconvolution to samples from the Human Microbiome Project, successfully reconstructing genus-level genomic content of various microbial genera, based solely on variation in gene count. These reconstructed genera are shown to correctly capture genus-specific properties. With the accumulation of metagenomic data, this deconvolution framework provides an essential tool for characterizing microbial taxa never before seen, laying the foundation for addressing fundamental questions concerning the taxa comprising diverse microbial communities.Rogan CarrShai S Shen-OrrElhanan BorensteinPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 10, p e1003292 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Rogan Carr Shai S Shen-Orr Elhanan Borenstein Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.
description	Metagenomics has transformed our understanding of the microbial world, allowing researchers to bypass the need to isolate and culture individual taxa and to directly characterize both the taxonomic and gene compositions of environmental samples. However, associating the genes found in a metagenomic sample with the specific taxa of origin remains a critical challenge. Existing binning methods, based on nucleotide composition or alignment to reference genomes allow only a coarse-grained classification and rely heavily on the availability of sequenced genomes from closely related taxa. Here, we introduce a novel computational framework, integrating variation in gene abundances across multiple samples with taxonomic abundance data to deconvolve metagenomic samples into taxa-specific gene profiles and to reconstruct the genomic content of community members. This assembly-free method is not bounded by various factors limiting previously described methods of metagenomic binning or metagenomic assembly and represents a fundamentally different approach to metagenomic-based genome reconstruction. An implementation of this framework is available at http://elbo.gs.washington.edu/software.html. We first describe the mathematical foundations of our framework and discuss considerations for implementing its various components. We demonstrate the ability of this framework to accurately deconvolve a set of metagenomic samples and to recover the gene content of individual taxa using synthetic metagenomic samples. We specifically characterize determinants of prediction accuracy and examine the impact of annotation errors on the reconstructed genomes. We finally apply metagenomic deconvolution to samples from the Human Microbiome Project, successfully reconstructing genus-level genomic content of various microbial genera, based solely on variation in gene count. These reconstructed genera are shown to correctly capture genus-specific properties. With the accumulation of metagenomic data, this deconvolution framework provides an essential tool for characterizing microbial taxa never before seen, laying the foundation for addressing fundamental questions concerning the taxa comprising diverse microbial communities.
format	article
author	Rogan Carr Shai S Shen-Orr Elhanan Borenstein
author_facet	Rogan Carr Shai S Shen-Orr Elhanan Borenstein
author_sort	Rogan Carr
title	Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.
title_short	Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.
title_full	Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.
title_fullStr	Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.
title_full_unstemmed	Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.
title_sort	reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/bdb8f86c68644a5b8d9c29dd9e97a4bb
work_keys_str_mv	AT rogancarr reconstructingthegenomiccontentofmicrobiometaxathroughshotgunmetagenomicdeconvolution AT shaisshenorr reconstructingthegenomiccontentofmicrobiometaxathroughshotgunmetagenomicdeconvolution AT elhananborenstein reconstructingthegenomiccontentofmicrobiometaxathroughshotgunmetagenomicdeconvolution
_version_	1718424690334105600

Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.

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