Assessing myxozoan diversity in fish: microscopy-based detection versus high-throughput amplicon sequencing

Accurately assessing the diversity of myxozoans (Cnidaria) continues to pose a significant taxonomic challenge. Here we evaluated the efficacy of microscopy-based detection in comparison to high-throughput amplicon sequencing by exhaustively screening 942 organ samples from 108 wild fish collected in Lake Weishan, China. Macroscopic and microscopic examination of various fish organs detected only three myxozoan species in 20.4% of the fish, whereas amplicon sequencing achieved 100% detection at the host level and identified 12,672 high-quality amplicon sequence variants (ASVs) that represent at least 102 distinct myxozoan species. Of these, 57 species could be matched to reference sequences, while the remaining 45 lineages constitute putative undescribed species. Species richness varied significantly among hosts (ranging from 24 to 77 species per fish species) and organs (ranging from 2 to 47 species per organ type within each fish species), with gills most frequently exhibiting the highest diversity. Seventy species were found in two or more fish species, and 77 species were detected in multiple organs. Our findings demonstrate that microscopy-based surveys substantially underestimate the diversity of myxozoans and offer the first quantitative framework for future large-scale ecological and pathological investigations of myxozoans.