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Updated: Jun 2, 2026
Laboratory Protocol for Genetic Gut Content Analyses of Aquatic Macroinvertebrates Using Group-specific rDNA Primers
Published on: October 5, 2017
A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces.
Emmanuel Corse1, Caroline Costedoat, Rémi Chappaz
1Aix-Marseille Université, CNRS, IRD, UMR 6116 - IMEP, Evolution Génome Environnement, Centre Saint-Charles, Case 36, 3 Place Victor Hugo, 13331 Marseille Cedex 3 Montpellier SupAgro, INRA, IRD, CIRAD, Centre de Biologie et de Gestion des Populations, Campus International de Baillarguet, CS30016, 34988 Montferrier-sur-Lez, France.
This study introduces a new DNA barcoding method for analyzing animal diets using faeces. The approach broadens prey identification, revealing distinct feeding behaviors in freshwater fish.
Area of Science:
- Ecology
- Molecular Biology
- Ichthyology
Background:
- Traditional animal diet analysis often requires prior knowledge of prey species.
- Teleost feeding behavior can evolve, making exhaustive prey listing challenging.
- DNA barcoding from faeces offers a promising, yet often limited, approach to diet analysis.
Purpose of the Study:
- To extend DNA barcoding for diet analysis to include a wide taxonomic range of potential prey items.
- To develop and validate a broadly applicable molecular method for fish diet analysis.
Main Methods:
- Design of 34 ecological clade-specific primer sets for European river ecosystems.
- Testing primers on isolated tissues and fish faeces using nested PCR for enhanced sensitivity.
- Sequencing and analysis of PCR products to confirm prey identification.
Main Results:
- The developed methodology successfully identified prey items in the faeces of three freshwater cyprinid species.
- Principal Component Analysis revealed distinct perilithon grazer and benthophagous feeding behaviors.
- Results align with existing literature on the feeding ecology of the studied fish species.
Conclusions:
- The new DNA barcoding method effectively broadens prey identification in diet analysis.
- The PCR-based approach is simple and generalizable to other freshwater organisms.
- This technique offers new perspectives for understanding freshwater food web dynamics.
