DNA metabarcoding is a relatively new molecular tool for dietary analysis of wildlife populations for monitoring and conservation. Metabarcoding involves use of universal primers to amplify a
region of, for example, mitochondrial DNA (mtDNA) that is highly conserved within species and
variable among species (a “barcode”) extracted from an environmental sample. By utilizing
massively parallel sequencing of DNA extracted from predator feces, different prey mtDNA
barcodes can be sequenced simultaneously to reveal dietary patterns. Because predator DNA also
is abundant in their scats, sequences known as “blockers” are sometimes employed to block the
amplification of host mtDNA while allowing prey mtDNA to be amplified preferentially. Before
sequencing, a library must be constructed for each sample. Library construction involves
amplifying the mtDNA barcode region using universal primers and attaching unique identifiers or
indexes to those amplification products. In this study, we designed and tested four library-build
protocols on red fox (Vulpes vulpes) fecal samples. Two protocols used universal primers attached
to sample-specific inline tags, one treated with a blocker and the other without a blocker. The
other two protocols used the universal primer without inline tags, relying on a second step for
index attachment; one was treated with a blocker and the other without a blocker. We tested our
protocols with 3 mock fecal samples (mixtures of prey DNA of known content) and 38 red fox
fecal samples. We evaluated the performance of the four protocols based on total read numbers,
prey read numbers, and the number of species identified. All four protocols successfully identified
some of the prey species from the fox scats. Amplification without inline tag and with blocker
yielded the highest average number of prey reads and species identified. Thus, we conclude that
this protocol was the most efficient of the four.