title: Assessment of helminth biodiversity in wild rats using 18S rDNA based metagenomics.
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.
authors.affiliation: Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Ryusei
authors.initials: R
authors.lastname: Tanaka
authors.affiliation: Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Akina
authors.initials: A
authors.lastname: Hino
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Isheng J
authors.initials: IJ
authors.lastname: Tsai
authors.affiliation: Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Juan Emilio
authors.initials: JE
authors.lastname: Palomares-Rius
authors.affiliation: Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Ayako
authors.initials: A
authors.lastname: Yoshida
authors.affiliation: Division of Microbial Genomics, Department of Genomics and Bioenviromental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan.
authors.forename: Yoshitoshi
authors.initials: Y
authors.lastname: Ogura
authors.affiliation: Division of Microbial Genomics, Department of Genomics and Bioenviromental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Hayashi
authors.affiliation: Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Haruhiko
authors.initials: H
authors.lastname: Maruyama
authors.affiliation: Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Taisei
authors.initials: T
authors.lastname: Kikuchi
mesh_terms: D000818:Animals; D000835:Animals, Wild / Q000469:parasitology*; D044822:Biodiversity; D030541:Databases, Genetic; D006376:Helminths / Q000235:genetics* / Q000302:isolation & purification; D007422:Intestines / Q000469:parasitology; D056186:Metagenomics; D010271:Parasites / Q000235:genetics / Q000302:isolation & purification; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics*; D051381:Rats; D017422:Sequence Analysis, DNA; D012984:Software; D013045:Species Specificity
chemical_list: D012337:RNA, Ribosomal, 18S