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Marc Monot Ph.D French


2013                        Ph.D. Microbiology                                             Paris 7University                               Paris, FR

2009                        Master Bioinformatics                                    Paris 7University                               Paris, FR

2000                       B.Sc Biochemistry                                               Preston University                             Preston, UK

Professional Experiences

Nomination in 2016 asAssociate Professorof the University of Sherbrooke, Canada.

Since 2018          Head of the Biomics Platform                  Institut Pasteur                                   Paris, FR

2010-2017          Permanent Scientist                                         Institut Pasteur                                   Paris, FR

                                    Laboratoire Pathogenèse des Batéries Anaérobies headed by Dr. B. Dupuy

2002-07                ResearchTechnician                                       Institut Pasteur                                   Paris, FR

Unité de Génétique Moléculaire Bactérienne headed by Dr S. T. Cole

Student Supervision

Ph.D.Student(2016-2020), MasterStudent (2011-2012), ResearchTechnician(2008-2010).


Invited Speaker: Sherbrooke University, Canada (2015).

Oral presentation: Core4Life, Barcelone (2019), France Génomique, France (2018),  Phage-Sur-Yvette, France (2017), Clostpath 8thPalm Cove, Australia (2013)

Poster presentations: Clostpath 6thRome, Italie (2009); ICDS Bled, Slovenia (2010); JOBIM Renne, France (2012) and Clostpath 9thFreiburg, Germany (2015) 


Member of the scientific evaluation comittee (Institut Pasteur 2015-17)

Editorial board member(Scientific Reports 2017-2019)

Scientific production

50 publications(10 in first or last author including 5 as corresponding author). 

H-index : 28,citations : 3237, HALdeposit.

Journal articles52 documents

  • Victoria Mesa, Marc Monot, Laurent Ferraris, Michel Popoff, Christelle Mazuet, et al.. Core-, pan- and accessory genome analyses of Clostridium neonatale: insights into genetic diversity. Microbial Genomics, Society for General Microbiology, 2022, 8 (5), pp.000813. ⟨10.1099/mgen.0.000813⟩. ⟨pasteur-03711097⟩
  • Imen Najjar, Laurence Motreff, Laurence Ma, Laure Lemée, Valérie Briolat, et al.. How Did Institut Pasteur’s NGS Core Facility, Biomics, Manage the Coronavirus Disease 2019 Crisis?. Journal of Biomolecular Techniques, Association of Biomolecular Resource Facilities, 2021, 32 (2), pp.jbt.21-3202-004. ⟨10.7171/jbt.21-3202-004⟩. ⟨pasteur-03371253⟩
  • Julian R. Garneau, Véronique Legrand, Martial Marbouty, Maximilian O. Press, Dean R. Vik, et al.. High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome. Scientific Reports, Nature Publishing Group, 2021, 11 (1), pp.18319. ⟨10.1038/s41598-021-97867-3⟩. ⟨pasteur-03369740⟩
  • Mamou Diallo, Nicolas Kint, Marc Monot, Florent Collas, Isabelle Martin-Verstraete, et al.. Transcriptomic and Phenotypic Analysis of a spoIIE Mutant in Clostridium beijerinckii. Frontiers in Microbiology, Frontiers Media, 2020, 11, pp.556064. ⟨10.3389/fmicb.2020.556064⟩. ⟨pasteur-03036263⟩
  • Olga Soutourina, Thomas Dubois, Marc Monot, Pavel Shelyakin, Laure Saujet, et al.. Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile. Frontiers in Microbiology, Frontiers Media, 2020, 11, pp.1939. ⟨10.3389/fmicb.2020.01939⟩. ⟨hal-02921326⟩
  • Laurent Bouillaut, Thomas Dubois, Michael Francis, Nadine Daou, Marc Monot, et al.. Role of the global regulator Rex in control of NAD + ‐regeneration in Clostridioides (Clostridium) difficile. Molecular Microbiology, Wiley, 2019, 111 (6), pp.1671-1688. ⟨10.1111/mmi.14245⟩. ⟨pasteur-02438283⟩
  • Thomas Dubois, Yannick D. N. Tremblay, Audrey Hamiot, Isabelle Martin-Verstraete, Julien Deschamps, et al.. A microbiota-generated bile salt induces biofilm formation in Clostridium difficile. npj Biofilms and Microbiomes, [London?]: Springer Nature published in partnership with Nanyang Technological University, 2019, 5 (1), ⟨10.1038/s41522-019-0087-4⟩. ⟨hal-02154613⟩
  • Isabelle Poquet, Laure Saujet, Alexis Canette, Marc Monot, Jovanna Mihajlovic, et al.. Clostridium difficile Biofilm: Remodeling Metabolism and Cell Surface to Build a Sparse and Heterogeneously Aggregated Architecture. Frontiers in Microbiology, Frontiers Media, 2018, 9, pp.2084. ⟨10.3389/fmicb.2018.02084⟩. ⟨pasteur-02015642⟩
  • Véronique Pantaleon, Marc Monot, Catherine Eckert, Sandra Hoys, Anne Collignon, et al.. Clostridium difficile forms variable biofilms on abiotic surface. Anaerobe, Elsevier Masson, 2018, 53, pp.34-37. ⟨10.1016/j.anaerobe.2018.05.006⟩. ⟨pasteur-02549240⟩
  • Anna Maikova, Johann Peltier, Pierre Boudry, Eliane Hajnsdorf, Nicolas Kint, et al.. Discovery of new type I toxin–antitoxin systems adjacent to CRISPR arrays in Clostridium difficile. Nucleic Acids Research, Oxford University Press, 2018, 46 (9), pp.4733-4751. ⟨10.1093/nar/gky124⟩. ⟨hal-01833638⟩
  • Julian R. Garneau, Ognjen Sekulovic, Bruno Dupuy, Olga Soutourina, Marc Monot, et al.. High Prevalence and Genetic Diversity of Large phiCD211 (phiCDIF1296T)-Like Prophages in Clostridioides difficile.. Applied and Environmental Microbiology, American Society for Microbiology, 2018, 84 (3), pp.e02164-17. ⟨10.1128/AEM.02164-17⟩. ⟨hal-02178884⟩
  • Julian Garneau, Florence Depardieu, Louis-Charles Fortier, David Bikard, Marc Monot. PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data. Scientific Reports, Nature Publishing Group, 2017, 7 (1), pp.8292. ⟨10.1038/s41598-017-07910-5⟩. ⟨pasteur-01613364⟩
  • Nicolas Kint, Claire Janoir, Marc Monot, Sandra Hoys, Olga Soutourina, et al.. The alternative sigma factor σ B plays a crucial role in adaptive strategies of Clostridium difficile during gut infection. Environmental Microbiology, Society for Applied Microbiology and Wiley-Blackwell, 2017, Special Issue on Pathogen and Antibiotic Resistance Ecology 19 (5), pp.1933 - 1958. ⟨10.1111/1462-2920.13696⟩. ⟨pasteur-01613370⟩
  • Bob G Blasdel, Anne Chevallereau, Marc Monot, Rob Lavigne, Laurent Debarbieux. Comparative transcriptomics analyses reveal the conservation of an ancestral infectious strategy in two bacteriophage genera.. ISME Journal, Nature Publishing Group, 2017, Advance online publication, ⟨10.1038/ismej.2017.63⟩. ⟨pasteur-01538822⟩
  • Brintha Girinathan, Marc Monot, Daniel Boyle, Kathleen N. Mcallister, Joseph A. Sorg, et al.. Effect of tcdR Mutation on Sporulation in the Epidemic Clostridium difficile Strain R20291. MSphere, American Society for Microbiology., 2017, 2 (1), pp.00383-16. ⟨10.1128/mSphere.00383-16⟩. ⟨pasteur-01613368⟩
  • Mark M Collery, Sarah A Kuehne, Shonna M Mcbride, Michelle L Kelly, Marc Monot, et al.. What's a SNP between friends: The influence of single nucleotide polymorphisms on virulence and phenotypes of Clostridium difficile strain 630 and derivatives.. Virulence, Taylor & Francis, 2016, ⟨10.1080/21505594.2016.1237333⟩. ⟨pasteur-01370882⟩
  • Anne Chevallereau, Bob G Blasdel, Jeroen de Smet, Marc Monot, Michael Zimmermann, et al.. Next-Generation "-omics" Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa.. PLoS Genetics, Public Library of Science, 2016, 12 (7), pp.e1006134. ⟨10.1371/journal.pgen.1006134⟩. ⟨pasteur-01350678⟩
  • Thomas Dubois, Marie Dancer-Thibonnier, Marc Monot, Audrey Hamiot, Laurent Bouillaut, et al.. Control of Clostridium difficile Physiopathology in Response to Cysteine Availability.. Infection and Immunity, American Society for Microbiology, 2016, 84 (8), pp.2389-405. ⟨10.1128/IAI.00121-16⟩. ⟨pasteur-01370880⟩
  • Gaelle André, Elise Haudecoeur, Emmanuelle Courtois, Marc Monot, Bruno Dupuy, et al.. Cpe1786/IscR of Clostridium perfringens represses expression of genes involved in Fe-S cluster biogenesis.. Research in Microbiology, Elsevier, 2016, ⟨10.1016/j.resmic.2016.03.002⟩. ⟨pasteur-01370878⟩
  • Imad Kansau, Amira Barketi-Klai, Marc Monot, Sandra Hoys, Bruno Dupuy, et al.. Deciphering Adaptation Strategies of the Epidemic Clostridium difficile 027 Strain during Infection through In Vivo Transcriptional Analysis. PLoS ONE, Public Library of Science, 2016, 11 (6), pp.e0158204. ⟨10.1371/journal.pone.0158204⟩. ⟨pasteur-01370713⟩
  • Christophe Brézillon, Michel Haustant, Susann Dupke, Jean-Philippe Corre, Angelika Lander, et al.. Capsules, Toxins and AtxA as Virulence Factors of Emerging Bacillus cereus Biovar anthracis. PLoS Neglected Tropical Diseases, Public Library of Science, 2015, 9 (4), pp.e0003455. ⟨10.1371/journal.pntd.0003455⟩. ⟨pasteur-01370745⟩
  • Corinne Levi-Meyrueis, Véronique Monteil, Odile Sismeiro, Marie-Agnès Dillies, Annie Kolb, et al.. Repressor activity of the RpoS/σS-dependent RNA polymerase requires DNA binding. Nucleic Acids Research, Oxford University Press, 2015, 43 (3), pp.1456 - 1468. ⟨10.1093/nar/gku1379⟩. ⟨pasteur-01370752⟩
  • François Wasels, Patrizia Spigaglia, Fabrizio Barbanti, Marc Monot, Laura Villa, et al.. Integration of erm (B)-containing elements through large chromosome fragment exchange in Clostridium difficile. Mobile Genetic Elements, Taylor & Francis, 2015, 5 (1), pp.12-16. ⟨10.1080/2159256X.2015.1006111⟩. ⟨pasteur-01370722⟩
  • Marc Monot, Catherine Eckert, Astrid Lemire, Audrey Hamiot, Thomas Dubois, et al.. Clostridium difficile: New Insights into the Evolution of the Pathogenicity Locus. Scientific Reports, Nature Publishing Group, 2015, 5, pp.15023. ⟨10.1038/srep15023⟩. ⟨hal-01271725⟩
  • Pierre Boudry, Ekaterina Semenova, Marc Monot, Kirill A. Datsenko, Anna Lopatina, et al.. Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile. mBio, American Society for Microbiology, 2015, 6 (5), pp.e01112-15. ⟨10.1128/mBio.01112-15⟩. ⟨pasteur-01370739⟩
  • François Wasels, Marc Monot, Patrizia Spigaglia, Fabrizio Barbanti, Laurence Ma, et al.. Inter- and intraspecies transfer of a Clostridium difficile conjugative transposon conferring resistance to MLSB.. Microbial Drug Resistance, Mary Ann Liebert, 2014, 20 (6), pp.555-60. ⟨10.1089/mdr.2014.0015⟩. ⟨pasteur-01370763⟩
  • Marc Monot, Mickael Orgeur, Emilie Camiade, Clément Brehier, Bruno Dupuy. COV2HTML: A Visualization and Analysis Tool of Bacterial Next Generation Sequencing (NGS) Data for Postgenomics Life Scientists. OMICS, Mary Ann Liebert, 2014, 18 (3), pp.184-195. ⟨10.1089/omi.2013.0119⟩. ⟨pasteur-01370754⟩
  • Ines Moura, Marc Monot, Chiara Tani, Patrizia Spigaglia, Fabrizio Barbanti, et al.. Multidisciplinary analysis of a nontoxigenic Clostridium difficile strain with stable resistance to metronidazole.. Antimicrobial Agents and Chemotherapy, American Society for Microbiology, 2014, 58 (8), pp.4957-60. ⟨10.1128/AAC.02350-14⟩. ⟨pasteur-01370760⟩
  • Pierre Boudry, C. Gracia, M. Monot, J. Caillet, L. Saujet, et al.. Pleiotropic Role of the RNA Chaperone Protein Hfq in the Human Pathogen Clostridium difficile. Journal of Bacteriology, American Society for Microbiology, 2014, 196 (18), pp.3234-3248. ⟨10.1128/JB.01923-14⟩. ⟨pasteur-02440841⟩
  • Amira Barketi-Klai, Marc Monot, Sandra Hoys, Sylvie Lambert-Bordes, Sarah A Kuehne, et al.. The flagellin FliC of Clostridium difficile is responsible for pleiotropic gene regulation during in vivo infection.. PLoS ONE, Public Library of Science, 2014, 9 (5), pp.e96876. ⟨10.1371/journal.pone.0096876⟩. ⟨pasteur-01370758⟩
  • Hedwig Kurka, Armin Ehrenreich, Wolfgang Ludwig, Marc Monot, Maja Rupnik, et al.. Sequence similarity of Clostridium difficile strains by analysis of conserved genes and genome content is reflected by their ribotype affiliation.. PLoS ONE, Public Library of Science, 2014, 9 (1), pp.e86535. ⟨10.1371/journal.pone.0086535⟩. ⟨pasteur-01370765⟩
  • Corinne Lévi-Meyrueis, Véronique Monteil, Odile Sismeiro, Marie-Agnès Dillies, Marc Monot, et al.. Expanding the RpoS/σS-network by RNA sequencing and identification of σS-controlled small RNAs in Salmonella.. PLoS ONE, Public Library of Science, 2014, 9 (5), pp.e96918. ⟨10.1371/journal.pone.0096918⟩. ⟨pasteur-01370762⟩
  • Imane El Meouche, Johann Peltier, Marc Monot, Olga Soutourina, Martine Pestel-Caron, et al.. Characterization of the SigD regulon of C. difficile and its positive control of toxin production through the regulation of tcdR.. PLoS ONE, Public Library of Science, 2013, 8 (12), pp.e83748. ⟨10.1371/journal.pone.0083748⟩. ⟨pasteur-01370779⟩
  • Claire Janoir, Cécile Denève, Sylvie Bouttier, Frédéric Barbut, Sandra Hoys, et al.. Adaptive strategies and pathogenesis of Clostridium difficile from in vivo transcriptomics.. Infection and Immunity, American Society for Microbiology, 2013, 81 (10), pp.3757-69. ⟨10.1128/IAI.00515-13⟩. ⟨pasteur-01370786⟩
  • Olga A Soutourina, Marc Monot, Pierre Boudry, Laure Saujet, Christophe Pichon, et al.. Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile.. PLoS Genetics, Public Library of Science, 2013, 9 (5), pp.e1003493. ⟨10.1371/journal.pgen.1003493⟩. ⟨pasteur-01370770⟩
  • Fátima C Pereira, Laure Saujet, Ana R Tomé, Mónica Serrano, Marc Monot, et al.. The spore differentiation pathway in the enteric pathogen Clostridium difficile.. PLoS Genetics, Public Library of Science, 2013, 9 (10), pp.e1003782. ⟨10.1371/journal.pgen.1003782⟩. ⟨pasteur-01370787⟩
  • Laure Saujet, Fátima C Pereira, Monica Serrano, Olga Soutourina, Marc Monot, et al.. Genome-Wide Analysis of Cell Type-Specific Gene Transcription during Spore Formation in Clostridium difficile. PLoS Genetics, Public Library of Science, 2013, 9 (10), pp.e1003756. ⟨10.1371/journal.pgen.1003756⟩. ⟨pasteur-01370780⟩
  • Ana Antunes, Emilie Camiade, Marc Monot, Emmanuelle Courtois, Frédéric Barbut, et al.. Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile.. Nucleic Acids Research, Oxford University Press, 2012, 40 (21), pp.10701-18. ⟨10.1093/nar/gks864⟩. ⟨pasteur-01370790⟩
  • Marc Monot, Caroline Boursaux-Eude, Marie Thibonnier, David Vallenet, Ivan Moszer, et al.. Reannotation of the genome sequence of Clostridium difficile strain 630.. Journal of Medical Microbiology, Society for General Microbiology, 2011, 60 (8), pp.1193-9. ⟨10.1099/jmm.0.030452-0⟩. ⟨pasteur-01370838⟩
  • Laure Saujet, Marc Monot, Bruno Dupuy, Olga Soutourina, Isabelle Martin-Verstraete. The key sigma factor of transition phase, SigH, controls sporulation, metabolism, and virulence factor expression in Clostridium difficile.. Journal of Bacteriology, American Society for Microbiology, 2011, 193 (13), pp.3186-96. ⟨10.1128/JB.00272-11⟩. ⟨pasteur-01370840⟩
  • Frédéric Barbut, Marc Monot, Antoine Rousseau, Sébastien Cavelot, Tabassome Simon, et al.. Rapid diagnosis of Clostridium difficile infection by multiplex real-time PCR.: Diagnosis of Clostridium difficile Infection and Identification of the Epidemic clone 027 by Multiplex Real-Time PCR. (Titre fichier auteur). European Journal of Clinical Microbiology and Infectious Diseases, Springer Verlag, 2011, 30 (10), pp.1279-85. ⟨10.1007/s10096-011-1224-z⟩. ⟨pasteur-01370849⟩
  • Pushpendra Singh, Philippe Busso, Alberto Paniz-Mondolfi, Nacarid Aranzazu, Marc Monot, et al.. Molecular drug susceptibility testing and genotyping of Mycobacterium leprae strains from South America.. Antimicrobial Agents and Chemotherapy, American Society for Microbiology, 2011, 55 (6), pp.2971-3. ⟨10.1128/AAC.00201-11⟩. ⟨pasteur-01370845⟩
  • Sheerazed Boulkroun, Laure Guenin-Macé, Maria-Isabel Thoulouze, Marc Monot, Anaïs Merckx, et al.. Mycolactone suppresses T cell responsiveness by altering both early signaling and posttranslational events.. Journal of Immunology, Publisher : Baltimore : Williams & Wilkins, c1950-. Latest Publisher : Bethesda, MD : American Association of Immunologists, 2010, 184 (3), pp.1436-44. ⟨10.4049/jimmunol.0902854⟩. ⟨pasteur-00594632⟩
  • Gaelle André, Elise Haudecoeur, Marc Monot, Kaori Ohtani, Tohru Shimizu, et al.. Global regulation of gene expression in response to cysteine availability in Clostridium perfringens.. BMC Microbiology, BioMed Central, 2010, 10 (1), pp.234. ⟨10.1186/1471-2180-10-234⟩. ⟨pasteur-00670625⟩
  • C A Molina-Torres, J Castro-Garza, J Ocampo-Candiani, M Monot, S T Cole, et al.. Effect of serial subculturing on the genetic composition and cytotoxic activity of Mycobacterium tuberculosis.. Journal of Medical Microbiology, Society for General Microbiology, 2010, 59 (4), pp.384-91. ⟨10.1099/jmm.0.015966-0⟩. ⟨pasteur-01370851⟩
  • G. Michael Taylor, Soren Blau, Simon Mays, Marc Monot, Oona Y.-C. Lee, et al.. Mycobacterium leprae genotype amplified from an archaeological case of lepromatous leprosy in Central Asia. Journal of Archaeological Science, Elsevier, 2009, 36 (10), pp.2408-2414. ⟨10.1016/j.jas.2009.06.026⟩. ⟨pasteur-01370863⟩
  • Marc Monot, Nadine Honoré, Thierry Garnier, Nora Zidane, Diana Sherafi, et al.. Comparative genomic and phylogeographic analysis of Mycobacterium leprae.: Phylogeography of leprosy (titre du fichier auteur). Nature Genetics, Nature Publishing Group, 2009, 41 (12), pp.1282-9. ⟨10.1038/ng.477⟩. ⟨pasteur-01370857⟩
  • Wafa Frigui, Daria Bottai, Laleh Majlessi, Marc Monot, Emmanuelle Josselin, et al.. Control of M. tuberculosis ESAT-6 secretion and specific T cell recognition by PhoP.. PLoS Pathogens, Public Library of Science, 2008, 4 (2), pp.e33. ⟨10.1371/journal.ppat.0040033⟩. ⟨pasteur-01370872⟩
  • Marc Monot, Nadine Honoré, Charlotte Balière, Baohong Ji, Samba Sow, et al.. Are variable-number tandem repeats appropriate for genotyping Mycobacterium leprae?. Journal of Clinical Microbiology, American Society for Microbiology, 2008, 46 (7), pp.2291-7. ⟨10.1128/JCM.00239-08⟩. ⟨pasteur-01370869⟩
  • Romulo Aráoz, Nadine Honoré, Sungae Cho, Jong-Pill Kim, Sang-Nae Cho, et al.. Antigen discovery: a postgenomic approach to leprosy diagnosis.. Infection and Immunity, American Society for Microbiology, 2006, 74 (1), pp.175-82. ⟨10.1128/IAI.74.1.175-182.2006⟩. ⟨pasteur-00204119⟩
  • Romulo Aráoz, Nadine Honoré, Sayera Banu, Caroline Demangel, Yakouba Cissoko, et al.. Towards an immunodiagnostic test for leprosy.. Microbes and Infection, Elsevier, 2006, 8 (8), pp.2270-6. ⟨10.1016/j.micinf.2006.04.002⟩. ⟨pasteur-01370874⟩
  • Marc Monot, Nadine Honoré, Thierry Garnier, Romulo Araoz, Jean-Yves Coppée, et al.. On the origin of leprosy.. Science, American Association for the Advancement of Science (AAAS), 2005, 308 (5724), pp.1040-2. ⟨10.1126/science/1109759⟩. ⟨pasteur-00204117⟩