Fig. 1

Relationships among genotypes of Enterocytozoon bieneusi recorded in sambar deer in this study inferred from phylogenetic analysis of sequence data for the internal transcribed spacer (ITS) of nuclear ribosomal DNA by Bayesian inference (BI). Sequences from a range of distinct E. bieneusi genotypes from published papers were included for comparison in the analysis (see Additional file 3: Table S3; [33, 48,49,50]). Statistically significant posterior probabilities (pp) are indicated on branches. Individual GenBank accession numbers precede genotype designation (in italics), followed by sample and locality descriptions. Enterocytozoon bieneusi genotypes identified and characterised from faecal DNA samples in the present study are indicated in bold-type. Clades were assigned group names based on the classification system established by Drosten et al. [51], with Group 1 being further subdivided into Subgroups 1a to 1 h. The scale-bar represents the number of substitutions per site. The E. bieneusi genotypes PtEbIX (DQ85585) and CD8 (KJ668735) from dogs were used as outgroups. An asterisk (*) indicates a novel genotype characterised in the present study