Scoop That Poop: Optimising Faecal Sample Pre-Processing for Parasite Metabarcoding

Molecular techniques such as DNA metabarcoding are increasingly used to characterise parasite communities. However, relatively few studies have examined how sample processing methods influence detection rates. We used faecal samples collected from free-roaming horses to evaluate how parasite density and pre-processing methods influenced quantification of parasite richness, community composition, and detection of different taxa. Methods that concentrated parasites substantially increased parasite detection, especially at the low infection levels often seen in wildlife. Specifically, we found that DNA extracts from larval coproculture and a newly developed egg concentration approach detected approximately twice as many species and genera as extracts made directly from faecal matter. Although parasite richness was consistently lower in these faecal subsamples, overall parasite communities were still similar between pre-processing methods. Ultimately, the optimal method depends on research constraints and goals. Working with parasite larvae is more time intensive, but lower cost as larval parasites can be extracted using a lysis buffer approach which performs similarly to commercial extraction kits. DNA extraction from faecal subsamples misses rare and common taxa but minimises field processing. Our novel egg concentration method offers a compromise between relatively rapid processing and high sensitivity.