Exploring non-invasive sampling of parasites by metabarcoding gastrointestinal nematodes in Madagascar frog species

Abstract

The diversity of Anuran parasites is poorly surveyed, despite arguably being one of the most important threats to anuran populations worldwide. Additionally, parasites also interact with a number of other stressors, such as invasive species, pollution, sedimentation and changing light conditions, caused by anthropogenic disturbance in natural habitats. We aimed to explore the use of metabarcoding, a new, non-invasive tool to survey the parasite assemblages in frogs in different environments facing different levels of anthropogenic pressure. We collected fecal samples from frogs across three different transects in Ranomafana National Park, located in southeastern Madagascar, and then used the 18S metabarcoding technique to identify nematode species from the collected fecal samples. We were able to find four different putative species, which were all identified to the genus level. In comparison to the literature on previous surveys done with traditional methods, the metabarcoding approach seems to provide similar diversity estimates and taxonomical accuracy. Our results suggest that non-invasive sampling and metabarcoding can provide a suitable tool for intestinal parasite surveys in anuran host populations.

Characterizing parasitic nematode faunas in faeces and soil using DNA metabarcoding

“…These molecular methods have proved useful in diagnostic settings, as well as for investigating the epidemiology and population genetics of these parasites [22]. More recently, high-throughput amplicon sequencing (metabarcoding) targeting different gene regions has been used to investigate the diversity and genetic structure of both free-living and parasitic nematode populations in a variety of environments and hosts (18S rDNA: [23][24][25][26][27][28]; cytochrome oxidase 1 (CO1): [23,29]; cytochrome B (cytB): [30]; ITS2 rDNA: [31][32][33][34]. Metabarcoding approaches allow the simultaneous identification of a wide range of GIN species, irrespective of life stage, from bulk environmental and faecal samples in a more time-and cost-effective manner than morphological surveys, making it an attractive method for identifying and monitoring occurrence of actual species of GINs in wild vertebrate populations.…”