2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2019

Amaiur Esnaola, Aitor Arrizabalaga-Escudero, Jorge Gonzalez-Esteban, Arturo Elosegi, Joxerra Aihartza. Determining diet from faeces: Selection of metabarcoding primers for the insectivore Pyrenean desman (Galemys pyrenaicus). PLoS One, 13(12):e0208986. 2018.

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Download from publisher: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294389 PubMed

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Molecular techniques allow non-invasive dietary studies from faeces, providing an
invaluable tool to unveil ecological requirements of endangered or elusive
species. They contribute to progress on important issues such as genomics,
population genetics, dietary studies or reproductive analyses, essential
knowledge for conservation biology. Nevertheless, these techniques require
general methods to be tailored to the specific research objectives, as well as to
substrate- and species-specific constraints. In this pilot study we test a range 
of available primers to optimise diet analysis from metabarcoding of faeces of a 
generalist aquatic insectivore, the endangered Pyrenean desman (Galemys
pyrenaicus, E. Geoffroy Saint-Hilaire, 1811, Talpidae), as a step to improve the 
knowledge of the conservation biology of this species. Twenty-four faeces were
collected in the field, DNA was extracted from them, and fragments of the
standard barcode region (COI) were PCR amplified by using five primer sets
(Brandon-Mong, Gillet, Leray, Meusnier and Zeale). PCR outputs were sequenced on 
the Illumina MiSeq platform, sequences were processed, clustered into OTUs
(Operational Taxonomic Units) using UPARSE algorithm and BLASTed against the NCBI
database. Although all primer sets successfully amplified their target fragments,
they differed considerably in the amounts of sequence reads, rough OTUs, and
taxonomically assigned OTUs. Primer sets consistently identified a few abundant
prey taxa, probably representing the staple food of the Pyrenean desman. However,
they differed in the less common prey groups. Overall, the combination of Gillet 
and Zeale primer sets were most cost-effective to identify the widest taxonomic
range of prey as well as the desman itself, which could be further improved
stepwise by adding sequentially the outputs of Leray, Brandon-Mong and Meusnier
primers. These results are relevant for the conservation biology of this
endangered species as they allow a better characterization of its food and
habitat requirements.