Navigating Blastocystis research – challenges in the next-generation sequencing era

Blastocystis research has grown rapidly with molecular tools, especially next-generation sequencing, increasing subtype discovery but raising methodological and taxonomic challenges. We assess subtype designation criteria, caution against lowering divergence thresholds without biological evidence, and propose minimum standards requiring near full-length small subunit ribosomal RNA data and replication to ensure nomenclatural stability and epidemiological comparability.