Towards a formal microsporidian taxonomy

The 'Microsporidia' is currently considered a sub-phylum within the Rozellomycota, which contains 'long-branch' and 'short-branch' taxa, as defined by phylogenetic inference. These organisms are obligate parasites, requiring either a host cytoplasm or nucleus to be able to proliferate. Their initial discovery in the 1800s, beginning with Nosema bombycis from silkworm, has brought us to today's long list of candidates. Over 1000 putative microsporidium species are represented by only morphological data, where around 300 'formal' species are support by combined morphological and molecular data, and a further undefined number have been observed using molecular data alone. The availability of genomes has expanded greatly in recent years, including high quality telomere to telomere constructs, which give the field a new view of potential taxonomic value.

In this talk, I will provide an outline of the Microsporidia through history, using key examples to explore how a new committee, focal to the Microsporidia, may better define species, genes, family, and higher taxonomic criteria and delineation methods. This talk will kick off the two-day debate around rules and regulations that we might choose to employ when characterising a new microsporidium. Through better definition and regulation of microsporidian taxa, studies into pathology, evolution, and impact will all become more feasible, with clear benefits for health care, veterinary sciences, and ecological (One Health) understanding.

Dr Jamie Bojko

Teesside University, UK

Dr Jamie Bojko

Teesside University, UK

Dr Jamie Bojko is an Associate Professor in Disease Ecology at Teesside University's National Horizons Centre, and part of the Biodiscovery team. Jamie's research includes the taxonomic understanding of the Microsporidia - a group of obligate spore-forming pathogens with a wide host range. Jamie employs classic pathology tools (histology/electron microscopy) and experimental designs, coupled with the latest in genomic and bioinformatic techniques, to characterise novel pathogens across marine and terrestrial ecosystems. His focus has largely involved biological invasions, but the basis to all of his work resides in taxonomy.

Microsporidia, a vast phylum of obligate intracellular parasites classified as early branching Fungi, exhibit a remarkable ability to infect a wide variety of hosts, including over 220 genera of both vertebrates and invertebrates. To get an idea of the extent of the vastness of microsporidian diversity, we employed a data mining strategy to extract valuable insights from publicly available Panarthropod transcriptomic assembly projects. In total, more than 300 species across over 200 genera and 25 orders of panarthropod hosts were retrieved as 'potentially infected' with expected infection patterns. This not only underscores the ubiquity of these parasites across the Panarthropoda phylum, but also reveals environmental density with globally distributed host samples ranging from the wild to laboratory settings, including an insect cell line. Furthermore, we used a novel approach to to construct a multi-protein phylogeny using proteins extracted from the 'parasitised' assemblies and reference genomes. The resulting phylogenetic analysis not only confirmed the existence of established microsporidia clades and their typical hosts, but also unveiled potential novel clades. This study underscores the significance of data mining approaches in conjunction with traditional field studies, offering a promising avenue to elucidate the ecology and host spectrum of these often-overlooked parasites.

Dr Sam Edwards

Wageningen University, The Netherlands

Dr Sam Edwards

Wageningen University, The Netherlands

Sam Edwards is a postdoctoral researcher at Wageningen University, working with Vera Ros to uncover the molecular mechanisms behind baculovirus-driven behavioural manipulation in lepidopteran larvae. He earned his PhD in evolutionary ecology in December 2023 as Marie Curie H2020 fellow jointly at the University of Copenhagen and the University of Exeter, supervised by Henrik De Fine Licht and Bryony Williams. His doctoral research focused on obligate fungal and microsporidian pathogens of invertebrates. Prior to this, Sam contributed as a research scientist at the Universities of Melbourne, Liverpool, Oxford and Imperial College London, spanning projects from insect and primate sexual behaviour to bacterial endosymbiont genetics. His work integrates molecular and phylogenetic approaches to explore host-pathogen co-evolution across viruses, parasitoids, fungi, and microsporidia.

Microsporidia are of growing importance to public health and agriculture, yet many aspects of their biology and evolution remain poorly understood, in part due to their obligately intracellular lifestyle. Large-scale biodiversity genomics projects are transforming microsporidian research by incidentally generating parasite genomes when infected host individuals are sequenced. Using 40 such microsporidian genome assemblies that I have recently released, along with additional genomes assembled since, I will explore what these unexpected resources reveal about microsporidian biology and evolution. In particular, I discuss polyploidy in Microsporidia, how it can be reconciled with the life cycle, and patterns of genome evolution in the group. I also examine the microsporidian phylogeny from a whole-genome perspective and explore how genome-scale data can inform species delineation for these parasites.

Mr Amjad Khalaf

Wellcome Sanger Institute, UK

Mr Amjad Khalaf

Wellcome Sanger Institute, UK

Amjad Khalaf is a Palestinian and Italian PhD student in the Tree of Life programme at the Wellcome Sanger Institute, supervised by Professor Mark Blaxter and Dr Mara Lawniczak. His work focuses on microsporidian evolutionary genomics, specifically the origin of polyploidy in the group. He has generated 40 high-quality microsporidian genomes from serendipitously infected insect hosts, sequenced as part of the Darwin Tree of Life project. More broadly, he is interested in symbiosis and parasitism. His previous work includes investigating how Cucumber Mosaic Virus (CMV) alters aphid behaviour to increase its spread within a plant population, and studying mitochondrial dynamics in Drosophila spermatogenesis.

"Clades," defined as monophyletic groups sharing derived characters, and "grades," based on common morphological or functional traits, represent two distinct yet potentially complementary taxonomic approaches. The rise of sequence-based cladistics has often conflicted with traditional morphology-based taxonomy across many organisational groups, including the Microsporidia. This presentation examines how such conflicts have influenced practical taxonomy, focusing on two notable cases: Paranosema vs. Antonospora and Nosema vs. Vairimorpha (referring to honeybee microsporidia). Both cases are related to my research, and, besides, Nosema locustae, N apis and N. ceranae are famous for their applied and scientific importance. My points in brief: (i) Paranosema locustae, P grylli and P whitei, belong to one clade with solitary bee microsporidium Antonospora scoticae, but not to the genus Antonospora, (ii) Vairimorpha, like Nosema, remains a "holding" genus and a clade, and both honeybee microsporidia belong to this clade but not to the genus Vairimorpha. (iii) Given that the prime goal of taxonomy is to reflect biodiversity, in my view, Vairimorpha clade comprises several genera: Vairimorpha sensus stricto, Oligosporium and Rugispora to be retained, and more to be described. (iv) Our recent ultrastructural analysis justifies establishing a new genus for N apis. (v) In practical taxonomy I suggest following a golden rule: "create new genera for those lineages that do not correspond to the type taxon" (Bojko et al, 2022). (vi) Clades are not equivalent to taxa, and for now I advocate for a dual system indicating both the clade and formal taxon, thereby integrating phylogenetic insight with traditional classification.

Dr Yuliya Sokolova

National Institute on Deafness and Other Communication Disorders, USA

Dr Yuliya Sokolova

National Institute on Deafness and Other Communication Disorders, USA

Yuliya Sokolova graduated from the Invertebrate Zoology Department, School of Biology, Leningrad State University, Russia. She earned her PhD degree in Entomology at All-Russia Institute of Plant Protection, St Petersburg, in Irma Issi's lab; her PhD dissertation was dedicated to pathogenesis of microsporidiosis in lepidopterans with the focus on ultrastructural pathology. Postdoctoral study in Jim Fuxa's lab for Insect Pathology, Louisiana State University, USA, was devoted to biology and the lifecycle of Kneallhazia solenopsae, a microsporidium infecting fire ants. Afterwards, as a visiting scientist, for a couple of years, she studied apoptosis in microsporidia-infected macrophages in Liz Didier's Lab at Tulane University, LA. Then, Julia served as an electron microscopist in a core EM lab with a School of Veterinary Medicine, LSU in Baton Rouge. Since 2021 she working at NIH, an an electron microscopist in the Advanced Imaging Core. She has published about 80 peer reviewed papers on different aspects of microsporidia, mostly on ultrastructure and taxonomy. In 2019, at the Zoological Institute in St Petersburg, Julia defended her Doctor of Science Dissertation titled "Cellular organisation and biodiversity of microsporidia", which summarised her input in microsporidia research. Though her major research interests have now shifted to EM methodology, she continues working on microsporidia, yet at a slower pace.

Viruses of four families of arthropod-specific, large dsDNA viruses share a number of features. The viruses in these families are rod-shaped, have large, circular double-stranded DNA genomes and replicate in the nucleus of infected invertebrate cells. These shared characteristics and the presence of homologs encoding per os infectivity factors (pif genes), along with their absence from other viruses, suggest a common origin for the viruses in these families. Therefore, the class Naldaviricetes was recently proposed and later established by the International Committee on Taxonomy of Viruses (ICTV), accommodating these four families. Within this class of the ICTV approved the creation of the order Lefavirales for three of the four families, whose members carry homologs of the baculovirus genes for viral RNA polymerase subunits (late essential factors or lef genes), required for late gene expression. We further established a system for the binomial naming of the virus species in this order, in accordance with the 2019 ICTV decision to adopt a standardised nomenclature for all virus species. In this presentation, I will illustrate the history of baculovirus taxonomy and nomenclature, and use this example to show how ICTV study groups function and interact with the Executive Committee of ICTV.

Professor Monique van Oers

Wageningen University and Research, The Netherlands

Professor Monique van Oers

Wageningen University and Research, The Netherlands

Professor van Oers is the Chair of the Laboratory of Virology of Wageningen University in the Netherlands, and a member of the Academic Board of that university. Her main expertise lies in the biology, fundamental genomics and evolution of large DNA viruses of invertebrates. She applies fundamental research data for the biological control of insects pests and the optimisation of the baculovirus insect-cell expression system, which is used for the production of vaccines and gene therapy vectors. She coordinated the EU training network INSECT DOCTORS, aimed at improving insect mass-rearing. She is the President-Elect for the Society for Invertebrate Pathology (SIP) and the local organiser of the SIP-IOBC 2026 meeting in the Netherlands. She is invited to this Royal Society meeting to explain about the functioning of the Baculoviridae and Nudiviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV).