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DNA based characterization of the diet from digested samples: a reliability study in ruminants

Abstract : Characterizing the diet of ruminants at pasture in diversified grasslands is a difficult step that could be realized by using the DNA-based methods recently developed for assessing the composition of environmental samples (i.e. metabarcoding approach). In this study, we performed two experiments to assess the performance of this method. The diet was inferred from rumen and faecal samples after DNA extraction, subsequent amplification of a short fragment of chloroplast DNA with universal primers used for plant DNA identification (trnL approach), and sequencing of the PCR products using HighSeq Illumina system. The first experiment compared the results obtained from replicated extractions and PCRs performed on faecal samples from cattle with a diversified diet, and showed a high reproducibility of the method. The second experiment was designed to assess the semi-quantitative aspects of this approach. Five diets were allocated to five sheep fed ad libitum according to a 5 × 5 Latin square design. The diets were mixtures of green fodder differing by their white clover:ryegrass ratios (i.e., 0:100, 25:75, 50:50, 75:25 and 100:0). The analysis of rumen contents allowed a reliable estimation of the proportion of each species ingested, while the information was much less accurate from faecal samples. Technical and analytical solutions are currently tested in order to improve the quantitative information obtained from faecal samples
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  • HAL Id : hal-02743384, version 1
  • PRODINRA : 269842

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Vincent Niderkorn, Anne Farruggia, Marta de Barba, Delphine Rioux, René Baumont, et al.. DNA based characterization of the diet from digested samples: a reliability study in ruminants. 1. Joint Meeting of FAO-CIHEAM Mountain Pastures and Mediterranean Forages Resources Networks and Mountain Cheese Network, Jun 2014, Lempdes, France. 4 p. ⟨hal-02743384⟩

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