Th relationships between the Encephalitozoon-like Septata intestinalis and other microsporidia that occur in humans, notably Encephalitozoon cuniculi and Encephalitozoon hellem, is insufficiently documented using morphological descriptions alone. To assess mutual relationships, we have examined other phenotypic as well as genetic aspects of S. intestinalis, obtained both from tissue culture and clinical specimens, in comparison with a number of other microsporidia. Phenotypic characterization was performed by analysis of the protein composition and antigenic structure of various microsporidian spores by SDS-PAGE and Western blotting. The genetic characterization consisted of the determination of the sequence of the S. intestinalis rrs gene encoding the small subunit ribosomal RNA (srRNA), restriction fragment length polymorphism (RFLP) analysis of amplified rrs genes and establishment of the degree of sequence identity between rrs genes of various microsporidian species. The unique sequence of rrs of S. intestinalis as well as the distinct RFLP and SDS-PAGE profiles indicate that S. intestinalis is clearly different from other human microsporidian species. However, its rrs gene shared about 90% sequence identity with rrs of both Encephalitozoon spp., E. cuniculi and E. hellem. This is remarkably higher than the about 70% identity observed between rrs of microsporidian species which belong to different genera and thus suggests that S. intestinalis should be regarded as a species of the genus Encephalitozoon. Western blots revealed a marked cross-reactivity between S. intestinalis and both species of Encephalitozoon which also stresses the close relationship between these organisms. It is concluded that S. intestinalis is so closely related to E. cuniculi, the type species of Encephalitozoon, that it should be reclassified as Encephalitozoon intestinalis.

Genes encoding small subunit ribosomal RNA (SSUrRNA) of 16 Blastocystis isolates from humans and other animals were amplified by the polymerase chain reaction, and the corresponding fragments were cloned and sequenced. Alignment of these sequences with the previously reported ones indicated the presence of 7 different sequence patterns in the highly variable regions of the small subunit ribosomal RNA. Phylogenetic reconstruction analysis using Proteromonas lacertae as the outgroup clearly demonstrated that the 7 groups with the different sequence patterns are separated to form independent clades, 5 of which consisted of the Blastocystis isolates from both humans (B. hominis) and other animals. The presence of 3 higher order clades was also clearly supported in the phylogenetic tree. However, a relationship among the 4 groups including these 3 higher order clades was not settled with statistical confidence. The remarkable heterogeneity of small subunit ribosomal RNAs among different Blastocystis isolates found in this study confirmed, with sequence-based evidence, that these organisms are genetically highly divergent in spite of their morphological identity. The highly variable small subunit ribosomal RNA regions among the distinct groups will provide useful information for the development of group-specific diagnostic primers.

The phylogenetic relationships of the microsporidian species Microgemma caulleryi, Pleistophora finisterrensis and Tetramicra brevifilum were investigated on the basis of restriction fragment length polymorphism (RFLP) analysis of PCR-amplified small-subunit rDNA (SSUrDNA). Using PCR primers specific for microsporidian SSUrDNA, a single product was obtained from each species, and heteroduplex analysis indicated a high degree of sequence homology among the 3 products. In RFLP analysis of the PCR-amplified SSUrDNA, the enzymes AluI and DdeI gave restriction patterns that differed among all 3 species. Phylogenetic analysis using restriction patterns as differential characters indicated that Microgemma caulleryi and Tetramicra brevifilum are more closely related to each other than to Pleistophora finisterrensis.

This study presents new findings concerning the evolution of the human pathogens, Trypanosoma brucei and T. cruzi, which suggest that these parasites have divergent origins and fundamentally different patterns of evolution. Phylogenetic analysis of 18S rRNA sequences places T. brucei in a clade comprising exclusively mammalian trypanosomes of African origin, suggesting an evolutionary history confined to Africa. T. cruzi (from humans and sylvatic mammals) clusters with trypanosomes specific to Old and New World bats, T. rangeli and a trypanosome species isolated from an Australian kangaroo. The origins of parasites within this clade, other than some of those from bats, lie in South America and Australia suggesting an ancient southern super-continent origin for T. cruzi, possibly in marsupials; the only trypanosomes from this clade to have spread to the Old World are those infecting bats, doubtless by virtue of the mobility of their hosts. Viewed in the context of palaeogeographical evidence, the results date the divergence of T. brucei and T. cruzi to the mid-Cretaceous, around 100 million years before present, following the separation of Africa, South America and Euramerica. The inclusion in this study of a broad range of trypanosome species from various different hosts has allowed long phylogenetic branches to be resolved, overcoming the limitations of many previous studies. Moreover, T. brucei and the other mammalian tsetse-transmitted trypanosomes appear, from these data, to be evolving several times faster than T. cruzi and its relatives.