Abstract
Biodiversity monitoring using metabarcoding is now widely used as a routine environmental management tool. However, despite the rapid advancement of third-generation high-throughput sequencing platforms, there are limited studies assessing the most suitable tools and approaches for environmental metabarcoding studies. We tested the utility of Oxford Nanopore Technologies MinION sequencing for short-read amplicon sequencing of mitochondrial COI mini-barcodes from a known composition of arthropod species and compared its performance with more commonly used Illumina NovaSeq sequencing. The mock arthropod species assemblage allowed us to optimise a bioinformatic filtering pipeline to identify arthropod species using MinION long reads. Using this pipeline, we identified host species and diet composition by sequencing droppings collected from five individual Irish brown long-eared bats (Plecotus auritus) roosts. We showed that MinION data provided a similar taxonomic assignment to NovaSeq but only if the reference species barcode database was accurate and comprehensive. The P. auritus diet inferred was as expected based on previous morphological and Illumina metabarcoding studies. We showed that less sequencing depth, but a higher number of biological samples were necessary for complete species composition detection by MinION. A relatively simple bioinformatic filtering tool such as NanoPipe could adequately retrieve both host species and diet composition. The biggest standing challenge was the reference database format transferability and comprehensiveness. This pipeline can be used to guide future metabarcoding studies using nanopore sequencing to minimise the cost and effort while optimising results.