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The problem of omnivory: A synthesis on omnivory and DNA metabarcoding

Lookup NU author(s): Dr Jordan CuffORCiD



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


Dietary analysis using DNA metabarcoding is a powerful tool that is increasingly being used to further our knowledge of trophic interactions in highly complex food webs but is not without limitations. Omnivores, the most generalist of consumers, pose unique challenges when using such methods. Here, we provide the rationale to understand the problems associated with analysing the complex diets of omnivores. By reviewing existing metabarcoding studies of omnivorous diet, and constructing hypothetical scenarios arising from each, we outline that great caution is required when interpreting sequencing data in such cases. In essence, the problems of accidental consumption and secondary ingestion are significant sources of error when investigating omnivorous diets. The integration of multiple high throughput sequencing markers increases the taxonomic breadth of taxa detected but we reveal how some detections may be misleading. Disentangling which taxa have been deliberately or accidentally consumed by the focal omnivore is challenging and can falsely emphasise those that were not intentionally consumed, obscuring biologically meaningful interactions. Although we suggest ways to disentangle these issues, we urge that the results of such analyses should be interpreted with caution and all possible scenarios for the presence of biota within omnivores given due consideration.

Publication metadata

Author(s): Tercel MPTG, Symondson WOC, Cuff JP

Publication type: Article

Publication status: Published

Journal: Molecular Ecology

Year: 2021

Volume: 30

Issue: 10

Pages: 2199-2206

Print publication date: 09/05/2021

Online publication date: 27/03/2021

Acceptance date: 22/03/2021

Date deposited: 03/11/2023

ISSN (print): 0962-1083

ISSN (electronic): 1365-294X

Publisher: Wiley-Blackwell Publishing Ltd.


DOI: 10.1111/mec.15903


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Funder referenceFunder name
Biotechnology and Biological Sciences Research Council BB/M009122/1
Durrell Wildlife Conservation Trust MR/S502455/1
Natural Environment Research Council NE/L002434/1