Unravelling the phylogeny of a common intestinal protist: Intra-generic diversity of Endolimax

Endolimax nana is a common parasite of the human intestine, but members of the genus have also been reported in non-human hosts and in non-intestinal organs. Limited information is available regarding the genetic diversity of Endolimax, which is necessary to delineate species, host specificity and potential differences in clinical impact on the host. Here, we used cloning of PCR products followed by Sanger sequencing and next-generation PacBio Sequencing to sequence Endolimax-specific nuclear ribosomal genes. We furthermore undertook a phylogenetic analysis to gain additional insight into the taxonomy of Endolimax and related organisms. The new sequences confirmed that E. nana forms a discrete clade within the Archamoebae and is related to Endolimax piscium and Iodamoeba. However, we identified substantial sequence divergence within E. nana and the possible existence of two distinct clades. Whether these should be considered distinct taxa, ribosomal lineages, or variants within a single taxonomic entity awaits further sampling. Both of the sequencing approaches applied in the study helped us to improve our understanding of genetic diversity across Endolimax, and it is likely that next-generation sequencing technologies will facilitate the generation of Endolimax-specific DNA sequence data that will help complete our understanding its phylogenetic position and intrageneric diversity.