A cost-efficient and simple protocol to enrich prey DNA from extractions of predatory arthropods for large-scale gut content analysis by Illumina sequencing

Molecular analysis of predator gut content is a popular tool to uncover food web structure and has greatly profited from the emergence of next-generation sequencing technology. However, the molecular recovery of prey spectra comes with many challenges, particularly the overabundance of predator DNA in extractions. When predator and prey are distantly related, predator-specific blocking primers can be used to preferentially amplify prey DNA. But this is difficult in the case of arthropods, where prey and predator are often closely related.
Here, we present a simple and cost-efficient protocol for high-throughput analysis of the gut content of predatory arthropods without the need for blocking primers. We test several factors for their potential to enrich prey DNA from extractions of predators, including size selection of DNA, selection of different body parts for extraction, and variation in extraction lysis time and PCR fragment length.
Using a locally abundant spider species (Hololen...