Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2011 Feb 24;6(2):e16900.
doi: 10.1371/journal.pone.0016900.

Host-associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition

Affiliations
Free PMC article
Comparative Study

Host-associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition

J Gregory Caporaso et al. PLoS One. .
Free PMC article

Abstract

Phylogenetic profiling has been widely used for comparing bacterial communities, but has so far been impossible to apply to viruses because of the lack of a single marker gene analogous to 16S rRNA. Here we developed a reference tree approach for matching viral sequences and applied it to the largest viral datasets available. The resulting technique, Shotgun UniFrac, was used to compare host-associated and non-host-associated phage communities (130 total metagenomes), and revealed a profound split similar to that found with bacterial communities. This new informatics approach complements analysis of bacterial communities and promises to provide new insights into viral community dynamics, such as top-down versus bottom-up control of bacterial communities by viruses in a range of systems.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Schematic of the Shotgun UniFrac analysis pipeline.
Figure 2
Figure 2. Principal Coordinates plot of weighted Shotgun UniFrac distances between viral communities where each point represents a metagenome colored by (a) host type and (b) data source.
Figure 3
Figure 3. (a) UPGMA clustering of individuals by weighted Shotgun UniFrac distances between metagenomes.
Cases where metagenomes from a single individual cluster monophyletically are highlighted in red. Cases where only a single metagenome for an individual was included are highlighted in blue. 1000 jackknife iterations were performed at a depth of 200 sequences per metagenome, and jackknife support values are provided for each node. The Reyes et al. analysis from which these samples were derived studied gut microbial communities from human twins and their mothers. The labels for each sample indicate the individual where: Fn corresponds to family number n; M corresponds to mother; and T1 and T2 refer to twin 1 and twin 2, respectively. (b) Histograms of within individual (grey) and between individual (pink) Shotgun UniFrac distances.

Similar articles

See all similar articles

Cited by 13 articles

See all "Cited by" articles

References

    1. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol. 2008;6:776–788. - PMC - PubMed
    1. Allen B, Willner D, Oechel WC, Lipson D. Top-down control of microbial activity and biomass in an Arctic soil ecosystem. Environ Microbiol. 2009;12:642–648. - PubMed
    1. Sandaa RA, Gomez-Consarnau L, Pinhassi J, Riemann L, Malits A, et al. Viral control of bacterial biodiversity–evidence from a nutrient-enriched marine mesocosm experiment. Environ Microbiol. 2009;11:2585–2597. - PubMed
    1. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, et al. Functional metagenomic profiling of nine biomes. Nature. 2008;452:629–632. - PubMed
    1. Rohwer F, Edwards R. The Phage Proteomic Tree: a genome-based taxonomy for phage. J Bacteriol. 2002;184:4529–4535. - PMC - PubMed

Publication types

Feedback