Together with amoebae, flagellates belong to the phylum Sarcomastigophora. However, unlike amoebae, they use flagella for locomotion; the number of flagella is species-specific. The relative difficulty of identifying intestinal flagellates by microscopy is very much affected by the size of the organisms: the smallest species often go unobserved when present in low numbers; moreover, the active mobility that usually attracts the attention of microscopists can be missing if the specimen is not examined immediately after stool passage.
Intestinal flagellates of human interest are listed below, together with the stages that are useful for diagnosis:
- Giardia intestinalis (also called Giardia lamblia): cyst and trophozoite;
- Chilomastix mesnili: cyst and trophozoite;
- Retortamonas intestinalis (also called Embadomonas intestinalis): cyst and trophozoite;
- Enteromonas hominis (also called Tricercomonas hominis): cyst and trophozoite;
- Pentatrichomonas intestinalis (also called Trichomonas intestinalis): trophozoite only;
- Dientamoeba fragilis: trophozoite only.