Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey

05 Dec 2014. NUS professors described how to use trace DNA in fecal samples to infer diet using whole genome shotgun sequencing.                       

Fecal samples are of great value as they contain DNA from the diet, the gut lining of the host species, microbes and parasites. Based on new sequencing technologies, the team led by Prof Rudolf MEIER from the Lee Kong Chian Natural History Museum in NUS can now directly obtain millions of short DNA sequences from such complex samples (“metagenomics”), and use them to characterize the ecology of endangered species. They developed bioinformatics methods for characterizing the diet of phytophagous Red Shanked Douc Langurs by matching the millions of reads to plant sequences. They compared this approach to the commonly used “metabarcoding” approach where only certain genes are amplified and considered. They also showed that metagenomics has the advantage of yielding more precise plant identifications.

Such characterization of diet and other aspects of ecology using fecal samples are critical for studying endangered animals where getting direct observations in the field is difficult because the species are rare and shy. Recently, they have used the new bioinformatics techniques for reconstructing the diet of Singapore’s endangered banded leaf monkey population. The diet information could be used to plant favored food trees. The same techniques will also be used for many additional endangered species in Singapore. Some of the examples are leopard cats and pangolins.

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Photo of the red shanked douc langur. [Image credit: John SHA]

Reference

Srivathsan A, Sha JCM, Vogler A, Meier R. “Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus).” Molecular Ecology Resources (2014) DOI: 10.1111/1755-0998.12302.