Using stomach contents for diet analysis of carnivores through DNA barcoding

Diet studies based exclusively on morphological analyses commonly show high percentages of unidentified items due to intense deterioration. In this study we explore the advantages and disadvantages of the application of DNA barcoding in the dietary studies of carnivores, using the Egyptian mongoose as a model species. To do so, we extracted and amplified DNA of samples from stomach contents, using the COI marker. We were able to identify six prey species that had already been mentioned in other studies, but we also identified five new species in the diet of this carnivore. Although we did not find contamination with the predator’s DNA, we reported five cases of cross-contamination among vertebrate items within the same stomach content, and 14 vertebrate tissues that were identified as arthropods and nematodes. This suggested that molecular identification of stomach contents must be carefully evaluated. Despite some problems with the DNA barcoding, this is a useful tool for determining the diet of carnivores, and thus should be considered as a complementary tool to morphological analysis.