Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14

Lesley A Ogilvie, Jonathan Caplin, Cinzia Dedi, David Diston, Elizabeth Cheek, Lucas Bowler, Huw Taylor, James Ebdon, Brian V Jones

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

Bacteriophage associated with the human gut microbiome are likely to have an important impact on community structure and function, and provide a wealth of biotechnological opportunities. Despite this, knowledge of the ecology and composition of bacteriophage in the gut bacterial community remains poor, with few well characterized gut-associated phage genomes currently available. Here we describe the identification and in-depth (meta)genomic, proteomic, and ecological analysis of a human gut-specific bacteriophage (designated φB124-14). In doing so we illuminate a fraction of the biological dark matter extant in this ecosystem and its surrounding eco-genomic landscape, identifying a novel and uncharted bacteriophage gene-space in this community. φB124-14 infects only a subset of closely related gut-associated Bacteroides fragilis strains, and the circular genome encodes functions previously found to be rare in viral genomes and human gut viral metagenome sequences, including those which potentially confer advantages upon phage and/or host bacteria. Comparative genomic analyses revealed φB124-14 is most closely related to φB40-8, the only other publically available Bacteroides sp. phage genome, whilst comparative metagenomic analysis of both phage failed to identify any homologous sequences in 136 non-human gut metagenomic datasets searched, supporting the human gut-specific nature of this phage. Moreover, a potential geographic variation in the carriage of these and related phage was revealed by analysis of their distribution and prevalence within 151 human gut microbiomes and viromes from Europe, America and Japan. Finally, ecological profiling of φB124-14 and φB40-8, using both gene-centric alignment-driven phylogenetic analyses, as well as alignment-free gene-independent approaches was undertaken. This not only verified the human gut-specific nature of both phage, but also indicated that these phage populate a distinct and unexplored ecological landscape within the human gut microbiome.

Original languageEnglish
Article numbere35053
JournalPLoS ONE
Volume7
Issue number4
DOIs
Publication statusPublished - 25 Apr 2012

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Bacteriophages
bacteriophages
Meta-Analysis
digestive system
Genes
Microbiota
Metagenomics
genome
Genome
Bacteroides fragilis
Metagenome
genomics
Bacteroides
genes
Viral Genome
Ecology
Sequence Homology
sequence homology
geographical variation
bacterial communities

Keywords

  • Amino Acid Sequence
  • Bacteroides fragilis/virology
  • Base Sequence
  • Cluster Analysis
  • Computational Biology
  • Demography
  • Europe
  • Gastrointestinal Tract/microbiology
  • Genome Components
  • Genome, Viral/genetics
  • Humans
  • Japan
  • Metagenome/genetics
  • Microscopy, Electron, Transmission
  • Molecular Sequence Data
  • Phylogeny
  • Proteomics
  • Sequence Analysis, DNA
  • Sequence Homology
  • Siphoviridae/genetics
  • United States

Cite this

Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14. / Ogilvie, Lesley A; Caplin, Jonathan; Dedi, Cinzia; Diston, David; Cheek, Elizabeth; Bowler, Lucas; Taylor, Huw; Ebdon, James; Jones, Brian V.

In: PLoS ONE, Vol. 7, No. 4, e35053, 25.04.2012.

Research output: Contribution to journalArticle

Ogilvie, LA, Caplin, J, Dedi, C, Diston, D, Cheek, E, Bowler, L, Taylor, H, Ebdon, J & Jones, BV 2012, 'Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14', PLoS ONE, vol. 7, no. 4, e35053. https://doi.org/10.1371/journal.pone.0035053
Ogilvie, Lesley A ; Caplin, Jonathan ; Dedi, Cinzia ; Diston, David ; Cheek, Elizabeth ; Bowler, Lucas ; Taylor, Huw ; Ebdon, James ; Jones, Brian V. / Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14. In: PLoS ONE. 2012 ; Vol. 7, No. 4.
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