Generation of a Microsporidia Species Attribute Database and Analysis of the Extensive Ecological and Phenotypic Diversity of Microsporidia

Abstract

Microsporidia are a large group of fungus-related obligate intracellular parasites. Though many microsporidia species have been identified over the past 160 years, depiction of the full diversity of this phylum is lacking. To systematically describe the characteristics of these parasites, we created a database of 1,440 species and their attributes, including the hosts they infect and spore characteristics. We find that microsporidia have been reported to infect 16 metazoan and 4 protozoan phyla, with smaller phyla being underrepresented. Most species are reported to infect only a single host, but those that are generalists are also more likely to infect a broader set of host tissues. Strikingly, polar tubes are threefold longer in species that infect tissues besides the intestine, suggesting that polar tube length is a determinant of tissue specificity. Phylogenetic analysis revealed four clades which each contain microsporidia that infect hosts from all major habitats. Although related species are more likely to infect similar hosts, we observe examples of changes in host specificity and convergent evolution. Taken together, our results show that microsporidia display vast diversity in their morphology and the hosts they infect, illustrating the flexibility of these parasites to evolve new traits. IMPORTANCE Microsporidia are a large group of parasites that cause death and disease in humans and many agriculturally important animal species. To fully understand the diverse properties of these parasites, we curated species reports from the last 160 years. Using these data, we describe when and where microsporidia were identified and what types of animals and host tissues these parasites infect. Microsporidia infect hosts using a conserved apparatus known as the polar tube. We observe that the length of this tube is correlated with the tissues that are being infected, suggesting that the polar tube controls where within the animals that the parasite infects. Finally, we show that microsporidia species often exist in multiple environments and are flexible in their ability to evolve new traits. Our study provides insight into the ecology and evolution of microsporidia and provides a useful resource to further understand these fascinating parasites.

Keywords: evolution; intracellular parasites; microbial ecology; microsporidia.

FIG 1

History and geography of microsporidia species discovery. (A) Number of new microsporidia species described per decade (n = 1,425 microsporidia species). (B) Number of microsporidia species found on each continent (n = 1,310 microsporidia species). (C to E) Geographical location of microsporidia, with each species depicted once for each locality where they have been reported. The number of species found in each locality is depicted as a heatmap, according to the scale at the bottom. Areas in gray indicate that no species have been reported. (C) Location of microsporidia species identified, by country and ocean. Numbers in blue circles describe species found in respective oceans (n = 1,310 microsporidia species). (D) Location of microsporidia species reported by province and territory within Canada (n = 45 microsporidia species). (E) Location of microsporidia species reported by state within the United States (n = 249 microsporidia species). The maps were generated in Excel (© GeoNames, Microsoft, Navinfo, TomTom, Wikipedia).

FIG 2

Microsporidia infect a diverse range of hosts from all major environments. Host taxonomy and environment were determined for each reported microsporidia species (see Materials and Methods). (A) Distribution of microsporidia hosts by metazoan (left) and protist (right) phyla. The number of host species in each phylum (blue) and the total number of extant species in each phylum (red) are shown. Phyla where the majority of microsporidia hosts are parasites are indicated (**) (n = 1,436 host species). (B) Number of described species from phyla reported to be infected by microsporidia (red) (n = 16 phyla) and those that have not been reported to be infected by microsporidia (blue) (n = 16 phyla). The Mann-Whitney U test was used to compare mean ranks between the groups. (C) Frequency of Chordata orders reported to be infected by microsporidia (n = 39 orders). (D) Venn diagram of the major environments that microsporidia hosts dwell in (n = 1,352 host species).

FIG 3

Microsporidia infect a diversity of tissues and species that infect more hosts tend to infect a broader set of tissues. (A and B) The tissues described to be infected by microsporidia were placed into 23 tissue types (see Materials and Methods). (A) The number of microsporidia species reported to infect each tissue type (n = 1,123 species). (B) Distribution of the number of tissue types infected by each microsporidia species (n = 1,020 species). (C) Distribution of the number of hosts infected by each microsporidia species (n = 1,435 species). (D) Proportion of species that infect more than one tissue compared to how many hosts are infected by that species (n = 1,078). Species that are described to have general or systemic infections are considered to infect more than one tissue. Significant difference between proportions were determined with pairwise chi-square tests, with Bonferroni P value correction (α = 0.05/6 comparisons = 8.3 × 10⁻³).

FIG 4

Microsporidia spores display a diversity of shapes, sizes, and polar tube lengths. (A and B) Spore shapes were placed into 20 morphology classes (see Materials and Methods and Table S3B in the supplemental material). (A) The frequency of spore shape type (n = 1,112 spores). (B) Spore length and width dimensions plotted for the six most common spore shapes (n = 816 spores). (C) Comparison of experimentally determined and calculated polar tubule lengths (n = 34 spores). (D) Median spore volume for uninucleate (n = 496) and binucleate (n = 287) spores. The P value was determined by the Mann-Whitney U test. (E) Comparison between experimental polar filament lengths and spore volume (n = 37 spores for uninucleate and 26 spores for binucleate). Correlation was calculated with Spearman r_s. (F) Relationship between polar tubule length and tissues infected. Median polar tube values are indicated in red. Significance was calculated using a paired t test between “Intestinal” species and “Other Tissues” species infecting the same host.

FIG 5

Bayesian 18S rRNA phylogeny of microsporidia species reveals four phenotypically diverse clades. (A) 18S rRNA phylogeny of 273 microsporidia species, inferred under a Bayesian framework (see Materials and Methods). Clades are colored and number of hosts indicated according to the legends at the right. Species not belonging to any of the four main clades are colored black. (B to D) Analysis of microsporidia phenotypes in each of the four major clades. (B) Frequency of host environments by clade. (C) Spore volume distribution by clade. (D) Calculated polar tube length distribution by clade. Significance evaluated using pairwise Mann-Whitney U-tests, with Bonferroni P value adjustments applied to correct for multiple testing (α = 0.05/6 = 8.3 × 10⁻³). (E) Number of hosts infected by microsporidia species from one, two, or three different clades (n = 406 microsporidia hosts).

FIG 6

Evolutionary relatedness of microsporidia phenotypes. (A) Distribution of species pairs according to sequence similarity (n = 36,315 comparisons). (B to F) Distribution of sequence pair similarity and frequency of shared host taxonomy (n = 34,980 comparisons) (B), environments (n = 33,670 comparisons) (C), infected tissues (n = 27,028 comparisons) (D), difference in spore volume (n = 31,878 comparisons) (E), and difference in calculated polar tube length (n = 17,955 comparisons) (F).