Jean-Francois Pombert

  • Associate Professor of Biology
  • Academic Editor, PLOS ONE


Ph.D. in Biochemistry, Universite Laval 2008
Post-Doctoral Fellow in Genomics, Universite Laval 2007-2008
Post-Doctoral Fellow in Genomics, University of British Columbia 2008-2013

Research Interests

My research revolves mostly around comparative genomics, with an emphasis on finding the elements that distinguish obligate pathogens from their free-living relatives. I am particularly interested by key protists that could help us better understand the evolution of pathogenicity and by microbiomes and their associated diseases. I am also interested by unknown or poorly understood organisms and work with species widely dispersed across the Tree of Life.

Professional Affiliations & Memberships

  • American Association for the Advancement of Science (AAAS)
  • American Society for Microbiologists (ASM)
  • International Association for Dental Research (IADR), AADR division
  • International Society for Computational Biology (ISCB)
  • Society for Molecular Biology and Evolution (SMBE)


  • IIT College of Science Junior Research Excellence Award (2015)
  • FQRNT/Génome Québec Louis-Berlinguet Postdoctoral Fellowship (2008-2010)
  • Best Teacher, Department of Biochemistry and Microbiology, Universite Laval (2007)
  • CREFSIP Doctoral Scholarship (2001-2002)


  • 2018 Veseli IA, Mascarenhas dos Santos AC, Juárez O, Stark BC, Pombert JF. Complete genome sequence of Vitreoscilla sp. strain C1, source of the first bacterial hemoglobin. Microbiol Resour Announc. 2018. 7:e00922-18. DOI: 10.1128/MRA.00922-18
  • 2018 Game Changer – Next Generation Sequencing and its Impact on Food Microbiology. Ronholm, J., Bidawid, S., Torriani, S., eds. (2018). Lausanne: Frontiers Media. DOI: 10.3389/978-2-88945-463-1 ISBN: 978-2-88945-463-1 ISSN: 1664-8714
  • 2018 Mascarenhas dos Santos AC, Jie R, Antunes Godoy H, Alves M, Pombert JF. Complete genomes of the potential zoonotic pathogens Staphylococcus felis and Staphylococcus kloosii. Genome Announc. 2018. 6(20):e00404-18. PMID: 29773625 PMCID: PMC5958265 DOI: 10.1128/genomeA.00404-18.
  • 2017 Veseli IA, Tang C, Pombert JF. Complete genome of Staphylococcus lutrae ATCC 700373, a potential pathogen isolated from deceased otters. Genome Announc. 2017. 5(25):e00572-17. PMID: 28642379 PMCID: PMC5481585 DOI: 10.1128/genomeA.00572-17
  • 2017 Butler RR 3rd, Soomer-James J, Frenette M, Pombert JF. Complete genome sequences of two human oral microbiome commensals:Streptococcus salivarius ATCC 25975 and Streptococcus salivarius ATCC 27945. Genome Announc. 2017. 5(24):e00536-17. PMID: 28619805 PMCID: PMC5473274 DOI: 10.1128/genomeA.00536-17
  • 2017 Butler RR 3rd, Schill KM, Wang Y, Pombert JF. Genetic characterization of the exceptionally high heat resistance of the non-toxic surrogate Clostridium sporogenes PA 3679. Front. Microbiol. 2017. 8:545. PMID: 28421047 PMCID: PMC5376575 DOI: 10.3389/fmicb.2017.00545
  • 2017 Belkorchia A, Pombert JF, Polonais V, Parisot N, Delbac F, Brugère JF, Peyret P, Gaspin C, Peyretaillade E. Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes. DNA Research. 2017. 24(3):251-260. PMID: 28338834 PMCID: PMC5499648 DOI: 10.1093/dnares/dsx002
  • 2017 Wang J, Butler RR 3rd, Wu F, Pombert JF, Kilbane JJ 2nd, Stark BC. Enhancement of microbial biodesulfurization via genetic engineering and adaptive evolution. PLoS ONE. 2017. 12(1):e0168833. PMID: 28060828 DOI: 10.1371/journal.pone.0168833
  • 2017 del Campo, J, Pombert JF, Šlapeta J, Larkum A, Keeling PJ. The ‘other’ coral symbiont: Ostreobium diversity and distribution. ISME J. 2017. 11(1):296-299. PMID: 27420029 DOI: 10.1038/ismej.2016.101
  • 2016 Strassert JFH, Tikhonenkov DV, Pombert JF, Kolisko M, Tai V, Mylnikov AP and Keeling PJ. Moramonas marocensis gen. nov., sp. nov.: a jakobid flagellate isolated from desert soil with a bacteria-like, but bloated mitochondrial genome. Open Biol. 6:150239.
  • 2016 Butler RR 3rd, Wang J, Stark BC, and Pombert JF. Complete genome sequences of two interactive moderate thermophiles: Paenibacillus napthalenovorans 32O-Y and Paenibacillus sp. 32O-W. Genome Announc. 4(1):e01717-15.
  • 2016 Schill KM, Wang Y, Butler RR 3rd, Pombert JF, Reddy N, Skinner GE, and Larkin JW. Comparative analysis of Clostridium sporogenes PA3679 isolates obtained from different sources using pulsed-field gel electrophoresis (PFGE) and high-throughput sequencing. Appl Environ Microbiol. 82(1):384-393.
  • 2015 Pombert JF, Haag KL, Beidas S, Ebert D and Keeling PJ. The Ordospora colligata genome; evolution of extreme reduction in microsporidia and host-to-parasite horizontal gene transfer. mBio. 6(1):e02400-14.
  • 2014 Pombert JF, Blouin NA, Lane C, Boucias D and Keeling PJ. A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium. PLoS Genetics. 10(5): e1004355.
  • 2014 Sun Y and Pombert JF. Helicosporidia: A genomic snapshot of an early transition to parasitism. Acta Soc Bot Pol. 83(4):377–385.
  • 2014 Haag KL, James TY, Pombert JF, Larsson R, Schaer TMM, Refardt D and Ebert D. Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites. PNAS. 111(43): 15480-15485.
  • 2014 Peyretaillade E, Boucher D, Parisot N, Gasc C, Butler R, Pombert JF, Lerat E and Peyret P. Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems. Heredity. September 3rd, Advanced access.

Complete publication list »


  • Oral microbiome, Green algal genomics, Pathogen genomics


  • Comparative genomics, Computational biology/bioinformatics, High-throughput DNA sequencing