Microsporidia Genome Sequencing

Project Information

Microsporidia comprise a diverse class of over 1,200 species of intracellular pathogens that infect almost all animal phyla [1, 2]. At least 14 species of microsporidia can infect humans, and these infections can lead to death in immunocompromised patients. These pathogens belong within the fungal kingdom and are highly specialized, reduced fungi [3, 4]. As part of a NIAID approved white paper, we sequenced both human strains as well as those that infect model systems and insects. Analysis of genomes from this phyla will help define core sets of genes responsible for the common intracellular lifecycle and development, as well as genes specific to individual species which may define the host range for each species.

Very little sequence is available for microsporidia. The first full genome sequence reported is for one strain of Encephalitozoon cuniculi, which is 2.9 Mb. A second full genome sequence has just been described for the honeybee infecting species Nosema ceranae. Genomic surveys have been reported for Antonospora locustae (used as a pesticide for locusts) and Enterocytozoon bieneusi. ESTs have also been sequenced from Antonospora locustae and Edhazardia aedis. While these studies have been very informative, the field would greatly benefit from a comprehensive genomic examination of several species to gain more insight into their unique capabilities, their wide host range, and their persistence in various hosts.

We proposed to sequence the genomes of microsporidia species in two general classes: Class I species that are known to infect humans and Class II species that infect organisms that provide important models for research. Some of the Class II species also have zoonotic potential. Obtaining sufficiently quantities of pure DNA from obligate pathogens can be difficult. In addition to their medical and agricultural relevance, these species have been chosen because it is possible to procure enough pure DNA to perform the sequencing studies proposed below. The targeted species included: E. cuniculi, V. corneae, A. algerae, N. salmonis, P. neurophilia, P. theridion, E. aedis, V. culicis and N. parisii.

Project Consortium

Christina Cuomo, Broad Institute
Emily Troemel, University of California, San Diego
Patrick Keeling, University of British Columbia, Canada
Louis Weiss, Albert Einstein
Joe Heitman, Duke University
Naomi Fast, University of British Columbia, Canada
Saul Tzipori, Tufts Veterinary School
Elizabeth Didier, Tulane University
Michael Kent, Oregon State University
James Becnel, USDA
Lee Solter, University of Illinois
Anders Jorgensen, National Veterinary Institute, Norway


Didier ES, Weiss LM: Microsporidiosis: current status. Curr Opin Infect Dis 2006, 19:485-492.
Keeling PJ, Fast NM: Microsporidia: biology and evolution of highly reduced intracellular parasites. Annu Rev Microbiol 2002, 56:93-116.
Katinka MD, Duprat S, Cornillot E, Metenier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, et al: Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 2001, 414:450-453.
Keeling PJ, Luker MA, Palmer JD: Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi. Mol Biol Evol 2000, 17:23-31.

Photo Captions and Credits

The images on the home page are, from left to right:

1. and 3.: Developing N. parisii spore inside C. elegans
2. FISH staining of N. parisii inside C. elegans
4. and 5. N. parisii infecting the intestine of C. elegans.

All photos courtesy of Emily Troemel, UCSD.


This sequencing project was supported by the National Institute of Allergy and Infectious Disease, National Institutes of Health funded Genome Sequencing Center for Infectious Diseases at the Broad Institute.

Data access and citation

Genomes for all sequenced species are available in NCBI, on our ftp site, and in MicrosporidiaDb.  For use of this data, please cite:

Desjardins CA, Sanscrainte ND, Goldberg JM, Heiman D, Young S, Zeng Q, Madhani HD, Becnel JJ, Cuomo CA. Contrasting host-pathogen interactions and genome evolution in two specialist and generalist microsporidian pathogens of mosquitos. Nature Communications. 2015 May 13. 6:7121. doi: 10.1038/ncomms8121.

Bakowski MA, Priest M, Young S, Cuomo CA, Troemel ER. Genome Sequence of the Microsporidian Species Nematocida sp1 Strain ERTm6 (ATCC PRA-372).Genome Announc. 2014 Sep 18;2(5). pii: e00905-14. doi: 10.1128/genomeA.00905-14.

Pombert JF, Xu J, Smith DR, Heiman D, Young S, Cuomo CA, Weiss LM, Keeling PJ. 2013. Complete genome sequences from three genetically distinct strains reveal a high intra-species genetic diversity in the microsporidian Encephalitozoon cuniculi Eukaryotic Cell 12(4): 503-11.

Cuomo CA*, Desjardins CA*, Bakowski MA*, Goldberg J, Ma AT, Becnel JJ, Didier ES, Fan L, Heiman DI, Levin JZ, Young S, Zeng Q, Troemel ER. 2012. Microsporidia genome analysis reveals evolutionary strategies for obligate intracellular growth. Genome Research, 22(12): 2478-88.