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Aziz RK, Dwivedi B, Akhter S, et al. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes. Front Microbiol. 2015;6:381doi: 10.3389/fmicb.2015.00381.
Aziz, R. K., Dwivedi, B., Akhter, S., Breitbart, M., & Edwards, R. A. (2015). Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes. Frontiers in microbiology, 6381. https://doi.org/10.3389/fmicb.2015.00381
Aziz, Ramy K, et al. "Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes." Frontiers in microbiology vol. 6 (2015): 381. doi: https://doi.org/10.3389/fmicb.2015.00381
Aziz RK, Dwivedi B, Akhter S, Breitbart M, Edwards RA. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes. Front Microbiol. 2015 May 08;6:381. doi: 10.3389/fmicb.2015.00381. eCollection 2015. PMID: 26005436; PMCID: PMC4424905.
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Front Microbiol. 2015 May 08;6:381. doi: 10.3389/fmicb.2015.00381. eCollection 2015.

Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes.

Frontiers in microbiology

Ramy K Aziz, Bhakti Dwivedi, Sajia Akhter, Mya Breitbart, Robert A Edwards

Affiliations

  1. Department of Computer Science, San Diego State University San Diego, CA, USA ; Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University Cairo, Egypt ; Computing, Environment, and Life Sciences, Argonne National Laboratory Argonne, IL, USA.
  2. College of Marine Science, University of South Florida St. Petersburg St. Petersburg, FL, USA.
  3. Department of Computer Science, San Diego State University San Diego, CA, USA.
  4. Department of Computer Science, San Diego State University San Diego, CA, USA ; Computing, Environment, and Life Sciences, Argonne National Laboratory Argonne, IL, USA.

PMID: 26005436 PMCID: PMC4424905 DOI: 10.3389/fmicb.2015.00381

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. We propose adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.

Keywords: bacteriophage; ecology; genomics; metagenomics; virus

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