Individual sorting and identification of thousands of insects collected in mass trapping biosurveillance programs is a labour intensive and time-consuming process. Metabarcoding, allows for the simultaneous identification of multiple individuals in a single mixed sample and has the potential to expedite this process. However, detecting all the species present in a bulk sample can be challenging, especially when under-represented non-native specimens are intercepted.

In this study, we quantified the effectiveness of DNA metabarcoding at detecting exotic species within six different mock communities of native and non-native species of European xylophagous cerambycid beetles. The main objective is to compare three different sequencing technologies (MinION, Illumina, and IonTorrent) to evaluate which one is the most suitable in this context. Although we did not observe significant differences in the total number of species detected between the three sequencing technologies, MinION detected a greater number of species on field-like samples. All three sequencing technologies achieved in detecting and identifying closely related species and species at low abundance. The capture method of insects in the field greatly influences sample preservation and detection. Individuals captured in traps containing monopropylene and water had lower DNA concentration, leading to lower species detection rates compared to individuals killed using just an insecticide without any collection medium.