Metabarcoding in gut protozoology.

Amplicon-based next-generation sequencing (NGS) of ribosomal genes (metabarcoding) takes advantage of the fact that such genes (16S and 18S in prokaryotes and eukaryotes, respectively) are present in all nonviral organisms and are potent taxonomic markers – particularly for gut protozoa. Although metabarcoding applied to faecal DNA may not be a method that can be used diagnostically to rule out infection, it is a cost-effective screening tool that can provide detailed insight into gut microbiota diversity even at species/subtype level. Metabarcoding bypasses the limitations of traditional Sanger sequencing by enabling insight into intra-species genetic diversity and the delineation of mixed species/subtype infection. Coupled with knowledge on host specificity, a metabarcoding-generated taxonomic 16S+18S profile of a given faecal sample can largely identify the host from which it came. Next-generation sequencing (NGS) methods include whole-genome sequencing, metagenomic analysis, and amplicon-based NGS, all of which are gaining territory in parasitology. A modality of particular interest within the field of gut protozoology is exhaustive metabarcoding of ribosomal genes in a complex matrix such as faeces, by which method, amplicon-based NGS enables the detection and differentiation of both eukaryotic and prokaryotic organisms, circumventing Sanger sequencing-based limitations and representing a one-fits-most approach. Apart from being a tool to break the code of intracellular genetic variation and tell mixed species infections apart, metabarcoding can produce data that can serve to augment our understanding of the interplay between the organisms within the gut. [ABSTRACT FROM AUTHOR]