DNA metabarcoding of environmental samples has rapidly become a valuable tool for ecological studies such as biodiversity and diet studies. To reveal the diversity in environmental samples such as soil, water, and faeces, this approach principally employs PCR amplification of environmental DNA with uniquely 5’ tagged universal primers for the target taxa group, followed by parallel
sequencing of all samples on a second generation sequencing platform. Despite this seemingly straightforward approach, there are a number of factors that need to be acknowledged and accounted for when using metabarcoding to detect diversity in environmental samples. Furthermore, the increasing number of studies and the range of questions addressed through the use of metabarcoding highlight the importance of continuous exploration and refinement of the
approach with the overall aim to optimise diversity detection while minimising the occurrence of errors. Centered around metabarcoding dietary studies of bat droppings and leech gut contents, this continuous exploration and refinement is reflected in both the work and structure of this thesis. After a thesis introduction and two chapters on environmental DNA and biodiversity monitoring, the next four chapters are ordered according to our exploration and increased knowledge on molecular dietary studies and experimental set-up of metabarcoding studies for sequencing on Illumina sequencing platforms.