Conclusion
We developed and tested a pair of elongation arrest blocking primers, a
method which could potentially be replicated for other Teleosteans to
study their parasitic communities. Our elongation arrest blocking
primers led to a 66 % reduction in host DNA abundance in samples. This
ultimately enhanced the detection of parasitic taxa and significantly
reduced the amount of wasted sequencing. The combination of a
metataxonomic approach and blocking primers helped us detecting a
parasitic infection by the ciliate Nyctotherus sp. for one of the
first time in fish, while also facilitating the detection of four other
parasitic taxa in samples. However, other studies using annealing
inhibiting blocking primers and CRISPR-Cas Selective Amplicon Sequencing
(CCSAS) obtained a near complete inhibition of host DNA amplification.
Notably, the newly developed CCSAS method looks promising and should be
considered for future studies. When compared to our results, it seems
like CCSAS leads to a higher inhibition of amplification while requiring
a similar development path as elongation arrest blocking primers. Still,
using this approach on a larger amount of gut samples could lead to very
interesting results about the Eukaryotic microbiome of Amazonian
cichlids.