Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome

Brian V Jones, Julian R Marchesi

Research output: Contribution to journalArticlepeer-review

83 Citations (SciVal)

Abstract

The bacterial community of the human gut is a complex ecosystem composed of >1,000 species, the majority of which are Gram positive and uncultured. To study plasmids resident within this community, we developed a culture-independent transposon aided capture method (TRACA), which does not rely on any plasmid-encoded traits. TRACA facilitated acquisition of plasmids from metagenomic DNA extracts, and subsequent maintenance and selection in an Escherichia coli host. We confirmed the presence of the transposon in captured plasmids and demonstrate that these plasmids are mainly of a Gram-positive origin. Sequencing of plasmids designated pTRACA10 (7 kb) and pTRACA17 (2.7 kb) revealed genes involved in plasmid mobilization and replication. From the homologies of these genes we conclude that pTRACA17 originates from a Gram-positive host belonging to the Firmicute division. pTRACA10 had two additional open reading frames with similarity to a conserved hypothetical protein and phosphoesterase or phosphohydrolase enzymes (Clusters of Orthologous Groups number 4186). Both plasmids lacked any conventional selectable markers.

Original languageEnglish
Pages (from-to)55-61
Number of pages7
JournalMethods
Volume4
Issue number1
Early online date26 Nov 2006
DOIs
Publication statusPublished - Jan 2007

Keywords

  • DNA Transposable Elements/genetics
  • DNA, Bacterial/genetics
  • Escherichia coli/genetics
  • Gastrointestinal Tract/microbiology
  • Gene Transfer Techniques
  • Genome, Bacterial
  • Humans
  • Molecular Sequence Data
  • Plasmids/genetics
  • Sequence Analysis, DNA

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