Advantages of the brute force method
We argue that for metabarcoding of dietary samples, the brute force method is superior to blocking primers by being simpler, cheaper, faster and offering a less biased result. It is simpler because, theoretically, the trophic interactions of any animal may be sampled and studied regardless of whether it is well known to science or just recently discovered. With a blocking-primer approach, the mandatory first step would be to have the targeted barcode of the consumer sequenced (unless it already exists). With sequence in hand, a site must be found that is unique and targets the consumer only. Site selection is difficult, however, because the blocking primer must be designed based on the sequences of both consumer (should match blocking primer perfectly) and putative prey (should be different enough to not bind the blocking primer). Ideally, one should also test the blocking primers against putative prey to make sure that the mismatches hinder hybridization. Services like TestProbe have been used to test blocking primers against broad databases like Silva (e.g. Ray et al., 2016), but it would be naive to expect that all putative prey sequences are available, especially for little known organisms sampled from frontier environments. Exactly how many nucleotide mismatches should be demanded, and at what point the blocking primers start affecting the amplification of other relevant sequences is unknown. PiƱol et al., (2015) found that amplification of non-target DNA was blocked even when the number of mismatches were 4 and 5 base pairs. Also, prey studies often utilize extra short sequences that sacrifice on taxonomic resolution to allow detection of prey from partly digested material. These factors make the blocking primer approach particularly problematic. Designing primers that solely block the consumer within a short stretch of DNA can be difficult, and there are no guarantees of finding out whether the study is doable before investments in sanger sequencing, blocking primer design or both have been made.