Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome

PLoS One. 2014 Feb 4;9(2):e87924. doi: 10.1371/journal.pone.0087924. eCollection 2014.

Abstract

Metagenomic approaches are widespread in microbiological research, but so far, the knowledge on extrachromosomal DNA diversity and composition has largely remained dependant on cultivating host organisms. Even with the emergence of metagenomics, complete circular sequences are rarely identified, and have required manual curation. We propose a robust in silico procedure for identifying complete small plasmids in metagenomic datasets from whole genome shotgun sequencing. From one very pure and exhaustively sequenced metamobilome from rat cecum, we identified a total of 616 circular sequences, 160 of which were carrying a gene with plasmid replication domain. Further homology analyses indicated that the majority of these plasmid sequences are novel. We confirmed the circularity of the complete plasmid candidates using an inverse-type PCR approach on a subset of sequences with 95% success, confirming the existence and length of discrete sequences. The implication of these findings is a broadened understanding of the traits of circular elements in nature and the possibility of massive data mining in existing metagenomic datasets to discover novel pools of complete plasmids thus vastly expanding the current plasmid database.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cecum / metabolism*
  • Computational Biology / methods
  • DNA, Circular*
  • High-Throughput Nucleotide Sequencing
  • Metagenomics*
  • Phylogeny
  • Plasmids*
  • Rats
  • Replicon
  • Reproducibility of Results

Substances

  • DNA, Circular

Grant support

The work was partly funded by a grant from the Lundbeck Foundation (www.lundbeckfoundation.com) project DK nr R44-A4384, the European Union's 7th Framework Programme for Research and Technological Development (grant agreement no. 222625 METAEXPLORE, EU FP7 Theme KBBE-2007-3-3-05) and the Networks for Initial Training project “TRAINBIODIVERSE ITN” (FP7-PEOPLE-2011-ITN, Project reference: 289949) through the European Seventh Framework Program (FP7) and the Community Research and Development Information Service (CORDIS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.