U.S. Department of EnergyOffice of Scientific and Technical Information
Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes
Abstract
Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set ofmore »
- Authors:
-
- San Diego State Univ., San Diego, CA (United States); Cairo Univ., Cairo (Egypt); Argonne National Lab., Argonne, IL (United States)
- Univ. of South Florida St. Petersburg, St. Petersburg, FL (United States)
- San Diego State Univ., San Diego, CA (United States)
- San Diego State Univ., San Diego, CA (United States); Argonne National Lab., Argonne, IL (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1221992
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 6; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; virus, bacteriophage; genomics; metagenomics; ecology
Citation Formats
Aziz, Ramy K., Dwivedi, Bhakti, Akhter, Sajia, Breitbart, Mya, and Edwards, Robert A. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes. United States: N. p., 2015.
Web. doi:10.3389/fmicb.2015.00381.
Aziz, Ramy K., Dwivedi, Bhakti, Akhter, Sajia, Breitbart, Mya, & Edwards, Robert A. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes. United States. https://doi.org/10.3389/fmicb.2015.00381
Aziz, Ramy K., Dwivedi, Bhakti, Akhter, Sajia, Breitbart, Mya, and Edwards, Robert A. 2015.
"Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes". United States. https://doi.org/10.3389/fmicb.2015.00381. https://www.osti.gov/servlets/purl/1221992.
@article{osti_1221992,
title = {Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes},
author = {Aziz, Ramy K. and Dwivedi, Bhakti and Akhter, Sajia and Breitbart, Mya and Edwards, Robert A.},
abstractNote = {Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.},
doi = {10.3389/fmicb.2015.00381},
url = {https://www.osti.gov/biblio/1221992},
journal = {Frontiers in Microbiology},
issn = {1664-302X},
number = ,
volume = 6,
place = {United States},
year = {Fri May 08 00:00:00 EDT 2015},
month = {Fri May 08 00:00:00 EDT 2015}
}
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Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition
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Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets
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- Schmieder, Robert; Edwards, Robert
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Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing
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