1. Prey metabarcoding has become a popular tool in molecular ecology for
resolving trophic interactions at high resolution, from various sample
types and animals. To date, most predator-prey studies of small-sized
animals (<1 mm) have met the problem of overabundant predator
DNA in dietary samples by adding blocking primers/peptide nucleic acids.
These primers aim to limit the PCR amplification and detection of the
predator DNA but may introduce bias to the prey composition identified
by interacting with sequences that are similar to those of the predator.
2. Here we demonstrate the use of an alternative method to explore the
prey of small marine copepods using whole-body DNA extracts and deep,
brute force metabarcoding of an 18S rDNA fragment. 3. After processing
and curating raw data from two sequencing runs of varying depth (0.4 and
5.4 billion raw reads), we isolated 1.3 and 52.2 million prey reads,
with average depths of ~15 900 and ~120
000 prey reads per copepod individual, respectively. While data from
both sequencing runs were sufficient to distinguish dietary compositions
from disparate seasons, locations and copepod species, greater
sequencing depth led to better separation of clusters. 4. As computation
and sequencing are becoming ever more powerful and affordable, we expect
the brute force approach to become a general standard for prey
metabarcoding, as it offers a simple and affordable solution to
consumers that are impractical to dissect or unknown to science.