Resolution of habit-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking

Lesley Ogilvie, Jonathan Nzakizwanayo, Fergus Guppy, Cinzia Dedi, David Diston, Huw Taylor, James Ebdon, Brian Jones

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Just as the expansion in genome sequencing has revealed and permitted the exploitation of phylogenetic signals embedded in bacterial genomes, the application of metagenomics has begun to provide similar insights at the ecosystem-level for microbial communities. However, little is known regarding this aspect of bacteriophage associated with microbial ecosystems, and if phage encode discernible habitat-associated signals diagnostic of underlying microbiomes. Here we demonstrate that individual phage can encode clear habitat-related “ecogenomic signatures”, based on relative representation of phage encoded gene homologues in metagenomic datasets. Furthermore, we show the ecogenomic signature encoded by the gut-associated ɸB124-14 can be used to segregate metagenomes according to environmental origin, and distinguish “contaminated” environmental metagenomes (subject to simulated in silico human faecal pollution) from uncontaminated datasets. This indicates phage encoded ecological signals likely possess sufficient discriminatory power for use in biotechnological applications, such as development of microbial source tracking tools for monitoring water quality.
Original languageEnglish
Pages (from-to)942-958
Number of pages17
JournalISME Journal
Volume12
DOIs
Publication statusPublished - 19 Dec 2017

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bacteriophage
genome
ecosystem
habitat
microbial community
phylogenetics
water quality
pollution
gene
monitoring

Bibliographical note

This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Keywords

  • Human gut microbiome
  • metagenomics
  • faecal pollution
  • phage ecology

Cite this

Ogilvie, Lesley ; Nzakizwanayo, Jonathan ; Guppy, Fergus ; Dedi, Cinzia ; Diston, David ; Taylor, Huw ; Ebdon, James ; Jones, Brian. / Resolution of habit-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking. In: ISME Journal. 2017 ; Vol. 12. pp. 942-958.
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Resolution of habit-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking. / Ogilvie, Lesley; Nzakizwanayo, Jonathan; Guppy, Fergus; Dedi, Cinzia; Diston, David; Taylor, Huw; Ebdon, James; Jones, Brian.

In: ISME Journal, Vol. 12, 19.12.2017, p. 942-958.

Research output: Contribution to journalArticleResearchpeer-review

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