Assessment of helminth biodiversity in wild rats using 18S rDNA based metagenomics

PLoS One. 2014 Oct 23;9(10):e110769. doi: 10.1371/journal.pone.0110769. eCollection 2014.

Abstract

Parasite diversity has important implications in several research fields including ecology, evolutionary biology and epidemiology. Wide-ranging analysis has been restricted because of the difficult, highly specialised and time-consuming processes involved in parasite identification. In this study, we assessed parasite diversity in wild rats using 18S rDNA-based metagenomics. 18S rDNA PCR products were sequenced using an Illumina MiSeq sequencer and the analysis of the sequences using the QIIME software successfully classified them into several parasite groups. The comparison of the results with those obtained using standard methods including microscopic observation of helminth parasites in the rat intestines and PCR amplification/sequencing of 18S rDNA from isolated single worms suggests that this new technique is reliable and useful to investigate parasite diversity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Animals, Wild / parasitology*
  • Biodiversity*
  • Databases, Genetic
  • Helminths / genetics*
  • Helminths / isolation & purification
  • Intestines / parasitology
  • Metagenomics*
  • Parasites / genetics
  • Parasites / isolation & purification
  • Phylogeny
  • RNA, Ribosomal, 18S / genetics*
  • Rats
  • Sequence Analysis, DNA
  • Software
  • Species Specificity

Substances

  • RNA, Ribosomal, 18S

Grants and funding

This work was supported in part by JSPS KAKENHI (grants numbers 24780044, 24659190, 26460510 and 26292178), the Project of Establishing Medical Research Base Networks against Infectious Diseases in Okinawa (grants number CBB13001), and the Integrated Research Project for Human and Veterinary Medicine of the University of Miyazaki. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.