A comprehensive understanding of trophic interactions in terrestrial ecosystems is crucial for ecological research and conservation. Recent advances in non-invasive methods, such as DNA metabarcoding, have enabled researchers to collect vast amounts of data on wild animal diets. However, sharing this data and metadata effectively and transparently presents new challenges. To address this, a new type of scholarly journal publication has emerged that aims to describe datasets rather than report research investigations. In this paper, we present a dataset of consumed prey species and parasites based on the metabarcoding of 113 faecal samples from the greater and lesser mouse-eared bats (Myotis myotis and Myotis blythii), along with a detailed description of the data sampling, laboratory analysis, and bioinformatics pipeline. Our dataset comprises 1018 unique Barcode Index Numbers (BINs) from 12 Classes and 43 Orders. In addition, we provide interactive Krona charts to visually summarize the taxonomic relationships and relative read abundance of the consumed prey species and parasites. This data can be used for meta-analysis, exploring new predator-prey and host-parasite interactions, studying inter and intraspecific ecological interactions, and informing protected area management, among other applications. By sharing this dataset, we hope to encourage other researchers to use it to answer additional ecological questions and advance our understanding of trophic interactions in terrestrial ecosystems.

metabarcoding, Myotis myotis, Myotis blythii, Bats (Chiroptera), predator-prey interactions, parasite-host interactions