PT  - JOURNAL ARTICLE
AU  - Maxime Galan
AU  - Jean-Baptiste Pons
AU  - Orianne Tournayre
AU  - Eric Pierre
AU  - Maxime Leuchtmann
AU  - Dominique Pontier
AU  - Nathalie Charbonnel
TI  - Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis
AID  - 10.1101/155721
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 155721
4099  - http://biorxiv.org/content/early/2017/06/26/155721.short
4100  - http://biorxiv.org/content/early/2017/06/26/155721.full
AB  - Assessing diet variability between species, populations and individuals is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a two-step PCR protocol enabling the ‘all at once’ taxonomic identification of bats and their arthropod preys for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed in triplicate. We compare the efficiency of DNA extraction methods and we evaluate the effectiveness of our protocol using the rate of bat identification success, taxonomic resolution, sensitivity, and amplification biases. Our strategy involves twice fewer steps than usually required in the other metabarcoding studies and reduces the probability to misassign preys to wrong samples. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. Our results illustrate the power of this approach to assess diet richness and variability within and between colonies. We therefore provide a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing’chirosurveillance’ and conservation strategies.