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Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

Eeva M Soininen1*, Alice Valentini2, Eric Coissac2, Christian Miquel2, Ludovic Gielly2, Christian Brochmann3, Anne K Brysting4, Jørn H Sønstebø3, Rolf A Ims1, Nigel G Yoccoz1 and Pierre Taberlet2

Author Affiliations

1 Department of Biology, University of Tromsø, N-9037 Tromsø, Norway

2 Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France

3 National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway

4 Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway

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Frontiers in Zoology 2009, 6:16  doi:10.1186/1742-9994-6-16

Published: 20 August 2009



In order to understand the role of herbivores in trophic webs, it is essential to know what they feed on. Diet analysis is, however, a challenge in many small herbivores with a secretive life style. In this paper, we compare novel (high-throughput pyrosequencing) DNA barcoding technology for plant mixture with traditional microhistological method. We analysed stomach contents of two ecologically important subarctic vole species, Microtus oeconomus and Myodes rufocanus, with the two methods. DNA barcoding was conducted using the P6-loop of the chloroplast trnL (UAA) intron.


Although the identified plant taxa in the diets matched relatively well between the two methods, DNA barcoding gave by far taxonomically more detailed results. Quantitative comparison of results was difficult, mainly due to low taxonomic resolution of the microhistological method, which also in part explained discrepancies between the methods. Other discrepancies were likely due to biases mostly in the microhistological analysis.


We conclude that DNA barcoding opens up for new possibilities in the study of plant-herbivore interactions, giving a detailed and relatively unbiased picture of food utilization of herbivores.