The phylogenetic diversity of metagenomes

Steven W. Kembel, Jonathan A Eisen, Katherine S. Pollard, Jessica L. Green

Research output: Contribution to journalArticle

61 Citations (Scopus)

Abstract

Phylogenetic diversity-patterns of phylogenetic relatedness among organisms in ecological communities-provides important insights into the mechanisms underlying community assembly. Studies that measure phylogenetic diversity in microbial communities have primarily been limited to a single marker gene approach, using the small subunit of the rRNA gene (SSU-rRNA) to quantify phylogenetic relationships among microbial taxa. In this study, we present an approach for inferring phylogenetic relationships among microorganisms based on the random metagenomic sequencing of DNA fragments. To overcome challenges caused by the fragmentary nature of metagenomic data, we leveraged fully sequenced bacterial genomes as a scaffold to enable inference of phylogenetic relationships among metagenomic sequences from multiple phylogenetic marker gene families. The resulting metagenomic phylogeny can be used to quantify the phylogenetic diversity of microbial communities based on metagenomic data sets. We applied this method to understand patterns of microbial phylogenetic diversity and community assembly along an oceanic depth gradient, and compared our findings to previous studies of this gradient using SSU-rRNA gene and metagenomic analyses. Bacterial phylogenetic diversity was highest at intermediate depths beneath the ocean surface, whereas taxonomic diversity (diversity measured by binning sequences into taxonomically similar groups) showed no relationship with depth. Phylogenetic diversity estimates based on the SSU-rRNA gene and the multi-gene metagenomic phylogeny were broadly concordant, suggesting that our approach will be applicable to other metagenomic data sets for which corresponding SSU-rRNA gene sequences are unavailable. Our approach opens up the possibility of using metagenomic data to study microbial diversity in a phylogenetic context.

Original languageEnglish (US)
Article numbere23214
JournalPLoS One
Volume6
Issue number8
DOIs
StatePublished - 2011

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Metagenome
Metagenomics
Genes
phylogeny
rRNA Genes
Phylogeny
ribosomal RNA
genes
Bacterial Genomes
Biota
microbial communities
DNA Sequence Analysis
Oceans and Seas
Scaffolds
Microorganisms
genetic markers
Ecosystems

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Kembel, S. W., Eisen, J. A., Pollard, K. S., & Green, J. L. (2011). The phylogenetic diversity of metagenomes. PLoS One, 6(8), [e23214]. https://doi.org/10.1371/journal.pone.0023214

The phylogenetic diversity of metagenomes. / Kembel, Steven W.; Eisen, Jonathan A; Pollard, Katherine S.; Green, Jessica L.

In: PLoS One, Vol. 6, No. 8, e23214, 2011.

Research output: Contribution to journalArticle

Kembel, SW, Eisen, JA, Pollard, KS & Green, JL 2011, 'The phylogenetic diversity of metagenomes', PLoS One, vol. 6, no. 8, e23214. https://doi.org/10.1371/journal.pone.0023214
Kembel, Steven W. ; Eisen, Jonathan A ; Pollard, Katherine S. ; Green, Jessica L. / The phylogenetic diversity of metagenomes. In: PLoS One. 2011 ; Vol. 6, No. 8.
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