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Who is eating what: diet assessment using next generation sequencing

Pompanon, Francois, Deagle, Bruce E., Symondson, William Oliver Christian, Brown, David Steven, Jarman, Simon N. and Taberlet, Pierre 2012. Who is eating what: diet assessment using next generation sequencing. Molecular Ecology 21 (8) , pp. 1931-1950. 10.1111/j.1365-294X.2011.05403.x

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The analysis of food webs and their dynamics facilitates understanding of the mechanistic processes behind community ecology and ecosystem functions. Having accurate techniques for determining dietary ranges and components is critical for this endeavour. While visual analyses and early molecular approaches are highly labour intensive and often lack resolution, recent DNA-based approaches potentially provide more accurate methods for dietary studies. A suite of approaches have been used based on the identification of consumed species by characterization of DNA present in gut or faecal samples. In one approach, a standardized DNA region (DNA barcode) is PCR amplified, amplicons are sequenced and then compared to a reference database for identification. Initially, this involved sequencing clones from PCR products, and studies were limited in scale because of the costs and effort required. The recent development of next generation sequencing (NGS) has made this approach much more powerful, by allowing the direct characterization of dozens of samples with several thousand sequences per PCR product, and has the potential to reveal many consumed species simultaneously (DNA metabarcoding). Continual improvement of NGS technologies, on-going decreases in costs and current massive expansion of reference databases make this approach promising. Here we review the power and pitfalls of NGS diet methods. We present the critical factors to take into account when choosing or designing a suitable barcode. Then, we consider both technical and analytical aspects of NGS diet studies. Finally, we discuss the validation of data accuracy including the viability of producing quantitative data.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Biosciences
Subjects: Q Science > QH Natural history > QH301 Biology
Uncontrolled Keywords: DNA barcoding; DNA metabarcoding; faeces; food webs; herbivory; predation
Publisher: Wiley
ISSN: 1365-294X (online)
Last Modified: 02 May 2019 12:00

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