Data from: DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet
Ecological understanding of the role of consumer-resource interactions in natural food webs is limited by the difficulty of accurately and efficiently determining the complex variety of food types animals have eaten in the field. We developed a method based on DNA metabarcoding multiplexing and next...
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Data Archiving and Networked Services (DANS)
2013
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Online Access: | https://doi.org/10.5061/dryad.1br2n |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::e4e29f65d5a4eb3e15ed697d63b81476 2023-05-15T18:42:18+02:00 Data from: DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet De Barba, Marta Miquel, Christian Boyer, Frederic Mercier, Céline Rioux, Delphine Coissac, Eric Taberlet, Pierre De Barba, M. Miquel, C. Boyer, F. Mercier, C. Rioux, D. Coissac, E. Taberlet, P. 2013-01-01 https://doi.org/10.5061/dryad.1br2n undefined unknown Data Archiving and Networked Services (DANS) http://dx.doi.org/10.5061/dryad.1br2n https://dx.doi.org/10.5061/dryad.1br2n lic_creative-commons oai:easy.dans.knaw.nl:easy-dataset:84515 10.5061/dryad.1br2n oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:84515 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care Diet Analysis mitochondrial 16S gene invertebrate DNA sequences Rosaceae internal transcribed spacer Asteraceae DNA sequences Poaceae vertebrate DNA sequences Rosaceae DNA sequences Illumina HiSeq 2000 Cyperaceae DNA sequences mitochondrial 12S gene consumer-resource interactions Poaceae DNA sequences internal controls plant DNA sequences mitochondrial 12S and 16S genes Vertebrata Ursus arctos ITS 1 Arthropoda ITS 2 Asteraceae Cyperaceae chloroplast trnL (UAA) Spermatophyta Mollusca Trentino Italy envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2013 fttriple https://doi.org/10.5061/dryad.1br2n 2023-01-22T16:51:50Z Ecological understanding of the role of consumer-resource interactions in natural food webs is limited by the difficulty of accurately and efficiently determining the complex variety of food types animals have eaten in the field. We developed a method based on DNA metabarcoding multiplexing and next-generation sequencing to uncover different taxonomic groups of organisms from complex diet samples. We validated this approach on 91 faeces of a large omnivorous mammal, the brown bear, using DNA metabarcoding markers targeting the plant, vertebrate, and invertebrate components of the diet. We included internal controls in the experiments and performed PCR replication for accuracy validation in post-sequencing data analysis. Using our multiplexing strategy, we significantly simplified the experimental procedure and accurately and concurrently identified different prey DNA corresponding to the targeted taxonomic groups, with ≥60% of taxa of all diet components identified to genus/species level. The systematic application of internal controls and replication was a useful and simple way to evaluate the performance of our experimental procedure, standardize the selection of sequence filtering parameters for each marker data, and validate the accuracy of the results. Our general approach can be adapted to the analysis of dietary samples of various predator species in different ecosystems, for a number of conservation and ecological applications entailing large-scale population level diet assessment through cost effective screening of multiple DNA metabarcodes, and the detection of fine dietary variation among samples or individuals and of rare food items. GH_P3V5_P3MAV_P3Ast_P3Cyp_P3Poa_P3Ros_P3alignment_refDBcdSequence alignment of the chloroplast trnL (UAA) intron of 62 plantsalignment_refDBits2Sequence alignment of the internal transcribed spacer 2 (ITS2) of 30 plants of the family Rosaceae Dataset Ursus arctos Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care Diet Analysis mitochondrial 16S gene invertebrate DNA sequences Rosaceae internal transcribed spacer Asteraceae DNA sequences Poaceae vertebrate DNA sequences Rosaceae DNA sequences Illumina HiSeq 2000 Cyperaceae DNA sequences mitochondrial 12S gene consumer-resource interactions Poaceae DNA sequences internal controls plant DNA sequences mitochondrial 12S and 16S genes Vertebrata Ursus arctos ITS 1 Arthropoda ITS 2 Asteraceae Cyperaceae chloroplast trnL (UAA) Spermatophyta Mollusca Trentino Italy envir geo |
spellingShingle |
Life sciences medicine and health care Diet Analysis mitochondrial 16S gene invertebrate DNA sequences Rosaceae internal transcribed spacer Asteraceae DNA sequences Poaceae vertebrate DNA sequences Rosaceae DNA sequences Illumina HiSeq 2000 Cyperaceae DNA sequences mitochondrial 12S gene consumer-resource interactions Poaceae DNA sequences internal controls plant DNA sequences mitochondrial 12S and 16S genes Vertebrata Ursus arctos ITS 1 Arthropoda ITS 2 Asteraceae Cyperaceae chloroplast trnL (UAA) Spermatophyta Mollusca Trentino Italy envir geo De Barba, Marta Miquel, Christian Boyer, Frederic Mercier, Céline Rioux, Delphine Coissac, Eric Taberlet, Pierre De Barba, M. Miquel, C. Boyer, F. Mercier, C. Rioux, D. Coissac, E. Taberlet, P. Data from: DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet |
topic_facet |
Life sciences medicine and health care Diet Analysis mitochondrial 16S gene invertebrate DNA sequences Rosaceae internal transcribed spacer Asteraceae DNA sequences Poaceae vertebrate DNA sequences Rosaceae DNA sequences Illumina HiSeq 2000 Cyperaceae DNA sequences mitochondrial 12S gene consumer-resource interactions Poaceae DNA sequences internal controls plant DNA sequences mitochondrial 12S and 16S genes Vertebrata Ursus arctos ITS 1 Arthropoda ITS 2 Asteraceae Cyperaceae chloroplast trnL (UAA) Spermatophyta Mollusca Trentino Italy envir geo |
description |
Ecological understanding of the role of consumer-resource interactions in natural food webs is limited by the difficulty of accurately and efficiently determining the complex variety of food types animals have eaten in the field. We developed a method based on DNA metabarcoding multiplexing and next-generation sequencing to uncover different taxonomic groups of organisms from complex diet samples. We validated this approach on 91 faeces of a large omnivorous mammal, the brown bear, using DNA metabarcoding markers targeting the plant, vertebrate, and invertebrate components of the diet. We included internal controls in the experiments and performed PCR replication for accuracy validation in post-sequencing data analysis. Using our multiplexing strategy, we significantly simplified the experimental procedure and accurately and concurrently identified different prey DNA corresponding to the targeted taxonomic groups, with ≥60% of taxa of all diet components identified to genus/species level. The systematic application of internal controls and replication was a useful and simple way to evaluate the performance of our experimental procedure, standardize the selection of sequence filtering parameters for each marker data, and validate the accuracy of the results. Our general approach can be adapted to the analysis of dietary samples of various predator species in different ecosystems, for a number of conservation and ecological applications entailing large-scale population level diet assessment through cost effective screening of multiple DNA metabarcodes, and the detection of fine dietary variation among samples or individuals and of rare food items. GH_P3V5_P3MAV_P3Ast_P3Cyp_P3Poa_P3Ros_P3alignment_refDBcdSequence alignment of the chloroplast trnL (UAA) intron of 62 plantsalignment_refDBits2Sequence alignment of the internal transcribed spacer 2 (ITS2) of 30 plants of the family Rosaceae |
format |
Dataset |
author |
De Barba, Marta Miquel, Christian Boyer, Frederic Mercier, Céline Rioux, Delphine Coissac, Eric Taberlet, Pierre De Barba, M. Miquel, C. Boyer, F. Mercier, C. Rioux, D. Coissac, E. Taberlet, P. |
author_facet |
De Barba, Marta Miquel, Christian Boyer, Frederic Mercier, Céline Rioux, Delphine Coissac, Eric Taberlet, Pierre De Barba, M. Miquel, C. Boyer, F. Mercier, C. Rioux, D. Coissac, E. Taberlet, P. |
author_sort |
De Barba, Marta |
title |
Data from: DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet |
title_short |
Data from: DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet |
title_full |
Data from: DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet |
title_fullStr |
Data from: DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet |
title_full_unstemmed |
Data from: DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet |
title_sort |
data from: dna metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet |
publisher |
Data Archiving and Networked Services (DANS) |
publishDate |
2013 |
url |
https://doi.org/10.5061/dryad.1br2n |
genre |
Ursus arctos |
genre_facet |
Ursus arctos |
op_source |
oai:easy.dans.knaw.nl:easy-dataset:84515 10.5061/dryad.1br2n oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:84515 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.1br2n https://dx.doi.org/10.5061/dryad.1br2n |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.1br2n |
_version_ |
1766231948602114048 |