Towards a formal microsporidian taxonomy

Studying the dynamics of microsporidian replication in the host is challenging due the the lack of genetic tools, limitations on imaging in live animals, and the speed and stochastic nature of the invasion process. We have recently stumbled upon a strategy for live cell imaging of parasites in mammalian cultured cells, which bypasses some of the challenges described above, and allows us to track a single parasite from entry through replication in the host cell, and its ultimate spread to neighboring cells. Combined with other imaging techniques, such as ultrastructure expansion microscopy, we are gaining new insights into parasite replication and cell biology. In parallel, we have been using scRNA-seq to characterise the transcriptional landscape of microsporidian parasites throughout the lifecycle, and heterogeneity in host cell responses to infection. I will present our latest work in these areas, and discuss how these dynamics may differ between cell types and between microsporidian species.

Professor Damian Ekiert

Johns Hopkins University, US

Professor Damian Ekiert

Johns Hopkins University, US

Damian Ekiert completed his BA in Biology at the University of Chicago in 2005. He moved to the Scripps Research Institute in 2006 to carry out his PhD thesis work in the laboratory of Ian Wilson, studying the structural basis and influenza virus neutralisation by broadly neutralising antibodies. For his postdoctoral work, Damian moved to the University of California, San Francisco in 2012, under the mentorship of Jeffery Cox and Ronald Vale, where he shifted his focus to virulence factors in Mycobacterium tuberculosis. In 2017, Damian joined the faculty at NYU School of Medicine, where he established a research group in conjunction with Gira Bhabha, studying human-infecting microsporidian species, as well as a family of bacterial lipid transporters importance for virulence and cellular homeostasis. In 2024, Damian moved to Johns Hopkins University, where he is currently an Associate Professor in the Department of Biology.

Microsporidia are tiny, single-celled parasites similar to fungi that infect a wide range of animal species, from worms and honey bees to humans. In humans, these opportunistic pathogens can cause life-threatening infections in immunocompromised individuals. To initiate an infection, microsporidia harness a specialised harpoon-like invasion apparatus called the polar tube (PT) to gain entry into host cells. The PT is tightly coiled within the transmissible extracellular spore, and is about 20 times the length of the spore. Once triggered, the PT is rapidly ejected, within milliseconds, and is thought to penetrate the host cell, acting as a conduit for the transfer of infectious cargo into the host, to initiate infection. Once inside host cells, microsporidia create a niche which is permissive to their development. We combine optical microscopy, Volume electron microscopy and structural cell biology to decipher the 3-dimensional organisation, dynamics, and mechanism of the polar tube, parasite development, and host-parasite interactions.

Dr Gira Bhabha

Johns Hopkins University, US

Dr Gira Bhabha

Johns Hopkins University, US

Gira Bhabha completed her BA at the University of Chicago in 2005. She carried out her PhD at Scripps Research in La Jolla, California, where she focused on studying the role of protein dynamics in enzyme catalysis, under the mentorship of Peter Wright. Her postdoctoral work was carried out under the mentorship of Ron Vale and Yifan Cheng at the University of California, San Francisco, where she used cryo-EM, single molecule microscopy and biochemistry to study the structural basis of motility in the motor protein dynein. Gira began her independent career in 2017, leading a lab at NYU School of Medicine in New York City. The Bhabha lab works closely with the lab of Damian Ekiert; since their inception, the two labs have functioned synergistically as a single group. The Bhabha + Ekiert Labs study structural mechanisms and cell biology of microbes and their interactions with hosts, using integrative approaches including X-ray crystallography, cryo-electron microscopy, cryo-electron tomography, optical microscopy, biochemistry, microbiology and cell biology techniques. In 2024 Gira, Damian and their labs relocated to Johns Hopkins University in Baltimore, where she is an Associate Professor.

To explore microsporidian diversity in marine environments, we have examined samples from marine sediment and filtered marine planktonic communities. Our approach has been targeted, using microsporidia-specific primers to amplify SSU rRNA sequences from samples from the Pacific Northwest, Japan and the Caribbean. Novel taxa have been identified, highlighting the untapped diversity of microsporidia. Further understanding of microsporidian diversity was achieved by utilising the Protist Ribosomal Reference (PR2) database. PR2 consists of a large collection of taxonomically annotated eukaryotic SSU sequences with associated environmental metadata. We have comprehensively analysed sequences from both described and uncharacterised microsporidian taxa to better understand their taxonomy, along with their host and habitat distribution. This curated PR2 database is not only a comprehensive repository for microsporidia; it also allows us to predict where lineages from under-sampled clades (like short-branch microsporidia) could occur, identifying new environments to investigate.

Lilith R South, Patrick J Keeling and Naomi M Fast

Dr Naomi Fast

University of British Columbia, Canada

Dr Naomi Fast

University of British Columbia, Canada

Dr Naomi Fast is a molecular evolutionary biologist at the Biodiversity Research Centre at the University of British Columbia in Vancouver, Canada. Naomi's research explores eukaryotic microbial diversity and the implications of genome size reduction on cellular complexity. She takes a comparative evolutionary approach: examining microbial eukaryotes with tiny genomes (like the parasitic microsporidia and the red alga Cyanidioschyzon) and comparing their molecular machinery for processes like pre-mRNA splicing. More broadly, Naomi investigates the diversity of microsporidia and their relatives by environmental sampling, largely in marine sediment in the Pacific Northwest.

The study of microsporidia gene function has been hindered by a lack of genetic techniques. We have developed methods in C. elegans infected with its natural microsporidian parasite Nematocida parisii to perform genetic screens to select for drug resistance. We perform large-scale liquid cultures of C. elegans infected with N. parisii for multiple generations using increasing concentrations of two drugs, albendazole and dexrazoxane, with different mechanisms of action. We have isolated six isolates of N. parisii resistant to albendazole and three isolates resistant to dexrazoxane. Half of the albendazole-resistant isolates have genetic variants in beta-tubulin, the likely target of albendazole, and are resistant to multiple benzimidazole analogs, whereas the other three albendazole-resistant isolates show partial or no resistance to other benzimidazole analogs tested. We are currently analysing whole-genome sequencing data to identify potential causative genes for resistance in albendazole-resistant isolates without beta-tubulin mutations and in dexrazoxane-resistant isolates. The albendazole-resistant mutants with beta-tubulin mutations appear to be homozygous, suggesting that recombination occurred during selection. We are currently using albendazole- and dexrazoxane-resistant mutants to determine if sexual recombination between N. parisii can occur in a laboratory setting. Together, these genetic approaches will aid in characterising gene function in N. parisii and are likely applicable to the study of other microsporidia species.

Dr Aaron Reinke

University of Toronto, Canada

Dr Aaron Reinke

University of Toronto, Canada

Dr Reinke is an expert in studying microsporidia, which are widespread parasites that cause death and disease in humans and other animals. Dr Reinke started his independent research career in September 2017 in the Department of Molecular Genetics at the University of Toronto. Recent work from his lab includes identifying molecules that inhibit microsporidia infection, discovering a host protein necessary for microsporidia invasion, characterising a novel intergenerational immune response to microsporidia infection, and elucidating how the microbiome influences microsporidia infection. The lab has also studied microsporidia genomic evolution and host specificity, examining the extensive ecological and phenotypic diversity of microsporidia, analysing the genomic and phenotypic evolution of nematode-infecting microsporidia, finding conserved gene expression between related microsporidia and hosts, and demonstrating widespread functional loss of microsporidia proteins. Dr Reinke has also received several young investigator awards including a Sloan Research Fellowship in Computational & Evolutionary Molecular Biology.

Microsporidia are pathogens in both immune-deficient and immune-competent hosts; for instance, infection is seen in the setting of organ transplantation, human immunodeficiency infection, travel, children, and the elderly. Microsporidiosis is an increasing problem in patients with transplants, where clusters of infection due to latent infection in transplanted organs have been demonstrated. In the setting of immune suppression, they have been associated with increased morbidity and mortality. Microsporidiosis is an increasing problem in patients with transplants, where clusters of infection due to latent infection in transplanted organs have been demonstrated. Human infection has involved microsporidia from many different genera, eg Nosema, Vittaforma, Pleistophora, Encephalitozoon, Enterocytozoon, Septata (now Encephalitozoon), Trachipleistophora, Brachiola (now Anncaliia), and Tubulinosema. Infection can involve almost any organ system. Human pathogenic microsporidia are common in the environment having been found in surface water, municipal water supplies and in hospital and municipal wastewater samples. In addition, they are also found in zoonotic reservoirs. The prevalence of infection varies with geographic region and the diagnostic techniques used. Before the widespread use of combination active antiretroviral therapy (cART) in the United States the average prevalence of this infection in patients with HIV/AIDS and chronic diarrhoea was 30%. A meta-analysis of 131 published studies found a pooled prevalence of 14% for human gastrointestinal microsporidiosis using a random effects model. While it is clear that cART can hasten the resolution of microsporidiosis, the literature contains many reports that microsporidia persist despite cART (especially if the CD4 count remains low).

Dr Louis Weiss

Albert Einstein College, US

Dr Louis Weiss

Albert Einstein College, US

Louis M Weiss MD MPH is a Professor of Pathology and Medicine (Infectious Diseases), Vice Chair of Academic Affairs and Research for Pathology, and Co-Director of the Einstein Global Health Center at the Albert Einstein College of Medicine, Bronx, New York, USA. He received his MD from the Johns Hopkins University School of Medicine and MPH from the John Hopkins University School of Public Health and Hygiene. He is a Fellow of the American College of Physicians, American Academy of Microbiology, Infectious Diseases Society of America, and the Royal Society of Tropical Medicine and Hygiene. His laboratory primarily studies Toxoplasma gondii and microsporidia. He has published 250 papers and 35 book chapters on his research, and has edited several books including "The Microsporidia and Microsporidiosis", "Microsporidia: Pathogens of Opportunity", "Opportunistic Pathogens", and "Toxoplasma gondii: The Model Apicomplexan (1st, 2nd and 3rd editions)". He currently serves on the NIH Opportunistic Infections Advisory Panel.

At least five genera of microsporidia (Nosema, Vairimorpha, Pleistophora, Thelohania, and Endoreticulatus) infect silkworms and other lepidopteran species. The genus Nosema displays the highest diversity. Among 821 isolates we recently obtained, 30 were classified based on 18S rDNA and internal transcribed spacer (ITS) sequence analyses: 21 were assigned to Nosema, 5 to Beauveria, 2 to Endoreticulatus, and 1 to Amblyospora. Transovarial transmission (TOT) assessments of these 30 isolates revealed variable TOT rates ranging from 0% to 95%, with Nosema bombycis exhibiting the highest transmission efficiency. Microsporidia, particularly those within the genus Nosema, employ a conserved TOT mechanism in lepidopterans, initially infecting ovarian sheath cells, subsequently spreading to nurse cells, and ultimately invading oocytes. Species-specific differences in infection dynamics are evident: N. pernyi demonstrates higher parasite loads and early-stage replication within Antheraea pernyi oocytes, whereas N. bombycis produces mature spores uniformly in Bombyx mori. Vitellogenin (Vg), a key yolk precursor protein, is exploited by microsporidian parasites through interactions between spore wall proteins and specific Vg domains; RNAi-mediated knockdown of Vg significantly reduces parasite load. This molecular hijacking mechanism facilitates vertical transmission via the host’s nutrient transport system. Furthermore, Nosema infection induces structural reorganization in nurse cells, leading to the formation of membrane-bound vesicles that mediate spore transport into oocytes—a process distinct from classical endocytic pathways. Notably, N. bombycis demonstrates transovarial transmission in agriculturally significant pests such as Spodoptera litura and Helicoverpa armigera, underscoring its potential as a biological control agent for sustainable pest management.

Peitong Qiao 1, 2, Chunxia Wang 1, 2, Xuanang Yang 1, 2, Yingcan Qin1, 2, Yongzhi Kong 1, 2, Zishen Tang 1, 2, Tongyu Luo 1, 2, Tian Li 1, 2, *
1 State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China;
2 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China;

* Correspondence: lit@swu.edu.cn

Professor Tian Li

Southwest University, China

Professor Tian Li

Southwest University, China

Professor, State Key Laboratory of Resource Insects, Southwest University. Deputy Director, State Key Laboratory of Resource Insects, Southwest University. Director, Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University. Member of the Council of Chongqing Entomological Society, Chongqing Genetics Society and Chongqing Bioinformatics Society.

My research mainly focuses on microsporidian infection mechanisms, genomics and metagenomics, with an emphasis on mechanisms of vertical transmission and interactions with host cellular processes, including apoptosis, mitophagy, and mitochondrial dynamics. The findings from these researches have been published in in journals such as PLoS Pathogens, Virulence, Nucleic Acids Research, and BMC Genomics.

The western honey bee contributes critical pollination services to agricultural systems and significantly increases the fruit set, seed production, and yield of many important crop plants. It is anticipated that recent increases in colony mortality could result in productivity issues that have the potential to cause serious nutritional deficiencies for humans and significant economic losses worldwide. The microsporidian species Vairimorpha (Nosema) apis and Vairimorpha (Nosema) ceranae can cause individual pathology and mortality in honey bees and can contribute to colony-level disease and collapse in conjunction with other stressors. Fumagillin is the only effective therapeutic option currently registered and available for use against V. apis and V. ceranae. Fumagillin has since been demonstrated to be beneficial against a wide array of microsporidian species infecting diverse organisms, including humans. Despite its impressive success, caveats to continued use of fumagillin in bees are now evident, spurring significant efforts to find new treatment strategies to protect bees against microsporidia infection. Here, I will give a historical overview of microsporidia infection in bees and its treatment. I will then explore how microsporidia diversity at the cell and molecular level have raised significant barriers to finding novel anti-microsporidia strategies that are as broadly effective as Fumagillin. Examples will illustrate how whole-group or within-group rewiring of various cellular processes have resulted in loss of potential therapeutic targets as well as their transport mechanisms and processing machinery. Strategies for circumventing such obstacles and even taking advantage of novel attributes of microsporidia cell biology to identify novel therapeutics will be discussed.

Dr Jonathan Snow

Columbia University, US

Dr Jonathan Snow

Columbia University, US

Jonathan Snow is currently Professor and Chair of the Department of Biology of Barnard College, Columbia University. Dr Snow received his PhD in Biomedical Sciences from the University of California, San Francisco, and completed a postdoctoral fellowship at Children's Hospital Boston and Harvard Medical School. His graduate and postgraduate work focused on signal transduction, regulation of gene expression, and organismal stress responses in blood development of mammals. He subsequently became fascinated with the honey bee and changed his research focus to the study molecular mechanisms of disease in the key pollinator. Our current focus is on the biology, diagnosis, and treatment of the honey bee microsporidia parasite Vairimorpha (Nosema) ceranae. He continues his avocation as a beekeeper while teaching and maintaining an active research laboratory.

Hepatopancreatic microsporidiosis (HPM), a disease caused by microsporidian parasite Ecytonucleospora hepatopenaei or EHP, has become a serious threat to shrimp industry worldwide due to its effect on shrimp growth. HPM is associated with severe size variation and growth retardation, causing massive economic losses. EHP can infect several important shrimp species, such as black tiger shrimp Penaeus monodon, and Pacific white shrimp Penaeus vannamei. The primary target organ of EHP is hepatopancreas. Similar to other microsporidian species, EHP invade shrimp hepatopancreatic cells using spores, which germinate under particular conditions. During spore germination, the polar tube extrudes from the spore, pierce host cell membrane, and transfer its infectious materials into the host. Recently, our lab has identified that potassium hydrogen phthalate (KHP) and sodium hydrogen phthalate (NaHP) are able to induce the EHP spore germination, in vitro. We hypothesized that if the spores are germinated prior to encountering shrimp, the spores would lose their infectivity. To test this hypothesis, we pre-germinated spores with optimal concentrations of KHP, NaHP, and phloxine B. Pre-germinated spores were immersed into the aquarium containing naive P. vannamei post larvae. The EHP spores in 1X PBS were used as a control. After 14 days of immersion, the EHP infections were tested. The results showed that all pre-germinated spore groups had no infection, while the infection rate was 60 % in the control group. These results were confirmed by histology. Staining the hepatopancreatic tissues using a nuclear staining dye showed positive EHP infection in the control group, but not in the pre-germinated spore groups. Our results suggest that pre-germinated EHP spores lose their infectivity in the laboratory setting. The use of KHP and NaHP as anti-EHP agents need to be further tested in the farm setting.

Dr Pattana Jaroenlak

Chulalongkorn University, Thailand

Dr Pattana Jaroenlak

Chulalongkorn University, Thailand

Pattana is currently an assistant professor at the Department of Biochemistry, Faculty of Science, Chulalongkorn University in Bangkok, Thailand. He received a PhD in Biochemistry from Mahidol University. During his PhD, he worked at Centex Shrimp to sequence the whole genome of the shrimp microsporidian EHP and studied EHP virulence factors. He then joined New York University, School of Medicine for post-doctoral training. He worked on invasion mechanism of microsporidian species that infect humans and mosquitos. Recently, his lab at Chulalongkorn University aim to understand the invasion mechanism of EHP as well as how host cells respond to the EHP infections in shrimp.