Tags

Type your tag names separated by a space and hit enter

Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis.
Mol Ecol Resour. 2018 May; 18(3):474-489.ME

Abstract

Assessing diet variability 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 short COI minibarcode and two-step PCR protocol enabling the "all at once" taxonomic identification of bats and their arthropod prey 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 using three replicates. We compare the efficiency of DNA extraction methods, and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity and amplification biases. Our parallel identification strategy of predators and prey reduces the risk of mis-assigning prey to wrong predators and decreases the number of molecular steps. 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. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing "chirosurveillance" and conservation strategies.

Authors+Show Affiliations

CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montferrier sur Lez Cedex, France.LabEx ECOFECT Ecoevolutionary Dynamics of Infectious Diseases, Université de Lyon, Lyon, France.CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montferrier sur Lez Cedex, France.CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montferrier sur Lez Cedex, France.Nature Environment, Surgères, France.LabEx ECOFECT Ecoevolutionary Dynamics of Infectious Diseases, Université de Lyon, Lyon, France. CNRS, Laboratoire de Biométrie et Biologie Évolutive, UMR5558, Université de Lyon, Université Lyon 1, Villeurbanne, France.CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montferrier sur Lez Cedex, France.

Pub Type(s)

Comparative Study
Journal Article

Language

eng

PubMed ID

29288544

Citation

Galan, Maxime, et al. "Metabarcoding for the Parallel Identification of Several Hundred Predators and Their Prey: Application to Bat Species Diet Analysis." Molecular Ecology Resources, vol. 18, no. 3, 2018, pp. 474-489.
Galan M, Pons JB, Tournayre O, et al. Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis. Mol Ecol Resour. 2018;18(3):474-489.
Galan, M., Pons, J. B., Tournayre, O., Pierre, É., Leuchtmann, M., Pontier, D., & Charbonnel, N. (2018). Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis. Molecular Ecology Resources, 18(3), 474-489. https://doi.org/10.1111/1755-0998.12749
Galan M, et al. Metabarcoding for the Parallel Identification of Several Hundred Predators and Their Prey: Application to Bat Species Diet Analysis. Mol Ecol Resour. 2018;18(3):474-489. PubMed PMID: 29288544.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis. AU - Galan,Maxime, AU - Pons,Jean-Baptiste, AU - Tournayre,Orianne, AU - Pierre,Éric, AU - Leuchtmann,Maxime, AU - Pontier,Dominique, AU - Charbonnel,Nathalie, Y1 - 2018/01/24/ PY - 2017/06/28/received PY - 2017/11/29/revised PY - 2017/12/23/accepted PY - 2017/12/31/pubmed PY - 2018/10/4/medline PY - 2017/12/31/entrez KW - Arthropoda KW - Chiroptera KW - environmental DNA (eDNA) KW - false positives KW - high-throughput sequencing KW - predator-prey interactions SP - 474 EP - 489 JF - Molecular ecology resources JO - Mol Ecol Resour VL - 18 IS - 3 N2 - Assessing diet variability 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 short COI minibarcode and two-step PCR protocol enabling the "all at once" taxonomic identification of bats and their arthropod prey 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 using three replicates. We compare the efficiency of DNA extraction methods, and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity and amplification biases. Our parallel identification strategy of predators and prey reduces the risk of mis-assigning prey to wrong predators and decreases the number of molecular steps. 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. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing "chirosurveillance" and conservation strategies. SN - 1755-0998 UR - https://www.unboundmedicine.com/medline/citation/29288544/Metabarcoding_for_the_parallel_identification_of_several_hundred_predators_and_their_prey:_Application_to_bat_species_diet_analysis_ L2 - https://doi.org/10.1111/1755-0998.12749 DB - PRIME DP - Unbound Medicine ER -