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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

Menu Logo Principal CBGP Cirad IRD SupAgro Muse

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Charbonnel Nathalie


Immunoecology, genomics of host-parasite relationships and their consequences for the emergence of zoonoses


My research focuses on host-parasites interactions in the context of emerging zoonoses and pluriannual
demographic cycles. I aim to describe the spatio-temporal variability of these interactions and to decipher the neutral and adaptive mechanisms underlying their evolution. I am especially interested in studying the heterogeneity of hosts' immune responses, using phenotypic and genomic approaches.As an evolutionary ecologist, I combine different approaches to lead this research, including immunogenetics, zoonoses epidemiology and population genomics. I have worked a lot on rodents, helminths and hantaviruses, but I am now also interested in bats, microbiome (bacterial and fungal communities) and coinfections.

Recently, I have developed research on bat ecology. I am interested in studying bat population genetics and bat diet, using molecular approach. In particular, I would like to test whether win win strategies can be implemented for insectivore bat conservation biology and biological control against pest.

Research Group Membership - CBGP : Ecology and Evolution of Zoonoses

Recent publications (since 2016)

* Abbate, J., Galan, M., Razzauti, M., Sironen, T., Voutilainen, L., Henttonen, H., Gasqui, P., Cosson, J. F. and Charbonnel, N. (Submitted). Pathogen community composition and co-infection patterns in a wild community of rodents. PCI Ecology.

* Charbonnel, N., Galan, M., Tatard, C., Loiseau, A., Diagne, C. A., Dalecky, A., Parrinello, H., Rialle, S., Severac, D. and Brouat, C. (In_Revision). Differential immune gene expression associated with contemporary range expansion of two invasive rodents in Senegal. Nature Scientific Reports. doi:

* Fevola, C. et al. (In press). Geographical distribution of Ljungan virus in small mammals in Europe. Vector Borne and Zoonotic Diseases.

* Quéméré, E., Hessenauer, P., Galan, M., Fernandez, M., Merlet, J., Chaval, Y., Verheyden, H., Hewison, A. J. M., Morellet, N., Gilot-Fromont, E. and Charbonnel, N. (In revision). Fluctuating pathogen-mediated selection drives the maintenance of innate immune gene polymorphism in a widespread wild ungulate. doi: 10.1101/458216.

* Tournayre, O., Leuchtmann, M., Filippi-Codaccion, O., Trillat, M., Piry, S., Pontier, D., Charbonnel, N. and Galan, M. (In revision). In silico and empirical evaluation of twelve COI & 16S metabarcoding primer sets for insectivorous bat diet analysis. Ecology and Evolution. doi: 10.1101/742874.


* Madrières, S., Castel, G., Murri, S., Vulin, J., Marianneau, P. and Charbonnel, N. (2019). The needs for developing experiments on reservoirs in hantavirus research : accomplishments, challenges and promises for the future. Viruses-Basel, 11. doi:10.3390/v11070664.

* Tournayre, O., Pons, J. B., Leuchtmann, M., Leblois, R., Piry, S., Filippi-Codaccion, O., Loiseau, A., Duhayer, J., Garin, I., Mathews, F., Puechmaille, S., Pontier, D. and Charbonnel, N. (2019). Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum Western range. Ecology and Evolution, 9, 12272–12290. doi: 10.1002/ece3.5714.


* Dubois, A., Castel, G., Murri, S., Pulido, C., Pons, J. B., Benoit, L., Loiseau, A., Lakhdar, L., Galan, M., Marianneau, P. and Charbonnel, N. (2018). Bank vole immunoheterogeneity may limit nephropatia epidemica emergence in a French non-endemic region. Parasitology, 145, 393–407. doi: 10.1017/S0031182017001548.

* Galan, M., Pons, J. B., Tournayre, O., Pierre, E., Leuchtmann, M., Pontier, D. and Charbonnel, N. (2018). Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis. Molecular ecology resources, 18, 474-489. doi: 10.1111/1755-0998.12749.

* Rohfritsch, A., Galan, M., Gautier, M., Gharbi, K., Olsson, G. E., Gschloessl, B., Zeimes, C., VanWambeke, S., Vitalis, R. and Charbonnel, N. (2018). Preliminary insights into the genetics of bank vole tolerance to Puumala hantavirus in Sweden. Ecology and Evolution, 8, 11273–11292. doi:10.1002/ece3.4603.


* Diagne, C. A., Charbonnel, N., Henttonen, H., Sironen, T. and Brouat, C. (2017a). Serological survey of zoonotic viruses in invasive and native commensal rodents in Senegal, West Africa. Vector Borne and Zoonotic Diseases, 17, 730-733. doi: 10.1089/vbz.2017.2135.

* Diagne, C. A., Galan, M., Tamisier, L., D'Ambrosio, J., Dalecky, A., Bâ, K., Kane, M., Niang, Y., Diallo, M., Sow, A., Tatard, C., Loiseau, a., Fossati, O., Sembene, M., Cosson, J. F., Charbonnel, N. and Brouat, C. (2017b). Ecological and sanitary impacts of bacterial communities associated to biological invasions in African commensal rodent communities. Nature Scientific Report, 7, 14995. doi:10.1038/s41598-017-14880-1.

* Dubois, A., Castel, G., Murri, S., Pulido, C., Pons, J. B., Benoit, L., Loiseau, A., Lakhdar, L., Galan, M., Charbonnel, N. and Marianneau, P. (2017a). Experimental infections of wild bank voles (Myodes glareolus) from nephropatia epidemica endemic and non-endemic regions revealed slight differences in Puumala virological course and immunological responses. Virus research, 235, 67-72. doi: 10.1016/j.virusres.2017.04.004.

* Dubois, A., Galan, M., Cosson, J. F., Gauffre, B., Henttonen, H., Nieminaa, J., Razzauti, M., Voutilainen, L., Vitalis, R., Guivier, E. and Charbonnel, N. (2017b). Microevolution of Bank Voles (Myodes glareolus) at Neutral and Immune-Related Genes During a Multi-Annual Complete Dynamic Cycle : consequences for Puumala hantavirus epidemiology. Infection Genetics and Evolution, 49, 318–329. doi: 10.1016/j.meegid.2016.12.007.

* Diagne, C. A., Gilot-Fromont, E., Cornet, S., Husse, L., Doucouré, S., Dalecky, A., Bâ, K., Kane, M., Niang, Y., Diallo, M., Sow, A., Fossati-Gaschignard, O., Piry, S., Artige, E., Sembene, M., Brouat, C. and Charbonnel, N. (2017c). Contemporary variations of immune responsiveness during range expansion of two invasive rodents in Senegal. Oikos, 126, 435-446. doi: 10.1111/oik.03470.


* Cornet, S., Brouat, C., Diagne, C. A. and Charbonnel, N. (2016). EcoImmunology and bioinvasion: revisiting the EICA hypotheses. Evolutionary applications, 9, 952–962. doi:10.1111/eva.12406.

* Diagne, C. A., Ribas Salvador, A., Charbonnel, N., Dalecky, A., Tatard, C., Gauthier, P., Haukisalmi, V., Fossati, O., Bâ, K., Kane, M., Niang, Y., Diallo, M., Sow, A., Piry, S., Sembene, M. and Brouat, C. (2016). Parasites and invasions: changes in gastrointestinal helminth assemblages in invasive and native rodents in Senegal. International Journal Parasitology, 46, 857–869. doi: 10.1016/j.ijpara.2016.07.007.

* Galan, M., Razzauti, M., Bard, E., Brouat, C., Charbonnel, N., Dehne-Garcia, A., Loiseau, A., Tatard, C., Vignes, H., Vayssier-Taussat, M. and Cosson, J. F. (2016). 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife. mSystems, 1, e00032-00016. doi: 10.1128/mSystems.00032-16.

See also

Referee for scientific documents

Editorial board member : Nature Scientific Report (since 2014)

Journal reviews for Evolution; Genetics; Infection, Genetics and Evolution; Journal of Animal Ecology; Molecular Ecology; Functional Ecology; Proceedings of the Royal Society...

Funding agency reviews for the Wellcome trust, ANR, Région Aquitaine, International Science and Technology Centre of Moscou (research projects), Joint German-African Projects in Infectiology…


Scientific animation

Co-organizer of the 'Donneurs de Sciences' Group in CBGP (2018-)

Co-organizer of the 18th conference on Ecology and Evolution of Infectious Diseases EEID2020 (

Co-organizer of the molecular platform in CBGP (2016-2019)

Co-leader of the Interaction-Adaptation-Speciation scientific group (2006-2013) then of the Ecology and Evolution of Zoonoses scientific group in the CBGP (2015-2020)

Organisation of the weekly seminars of Evolution in Montpellier (2004-2005).

Organisation of scientific animation for children and non-scientific adults (Darwin year, 2009).

Creation of an educative game ‘Ori’Maki’ that helps understanding evolutionary processes.

Participation to television programs (Euronews and TF1)


Participation to PhD thesis committees and Master jury

Jury member for ‘Habilitation to lead researches’ (5)

PhD thesis (16)

PhD dissertation (24)

Master’s degree (7).


Administrative roles including Evaluation

Member of the scientific committee of the INRA- BPE (2013-2020)

Member of the scientific committee of the INRA- department EFPA (2012-2020)

Member of the scientific committee of the IRD- CSS3 (2012-2015)

Member of the Doctoral School SIBAGHE, co-supervision of HDR (2011-2014)