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

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

Research output: Contribution to journalArticle

15 Citations (Scopus)

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.

Original languageEnglish
Article number381
Number of pages13
JournalFrontiers in Microbiology
Volume6
Issue numberMay 2015
DOIs
Publication statusPublished - 8 May 2015
Externally publishedYes

Bibliographical note

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted,provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice.No use, distribution or reproduction is permitted which does not comply with these terms.

Keywords

  • Bacteriophage
  • Ecology
  • Genomics
  • Metagenomics
  • Virus

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