Chargée de Recherche, HDR


Université de Strasbourg / CNRS UMR7156
Génétique Moléculaire, Génomique, Microbiologie.   
Batiment IPCB, 4 Allée Konrad Roentgen, 67000 Strasbourg, France
67000 Strasbourg

  :      + 33 (0)3 68 85 19 73
 :      emilie.muller[at]unistra.fr

Research interests

  • Functional and comparative (meta)genomics of one-carbon compound metabolism
  • Eco-systems biology and multi-omic integration
  • Microbial community structure, function and evolution in polluted environments
  • Microbial ecology and lifestyle strategy


Oct. 2016 - present: Chargé de recherches au CNRS (CR2), Université de Strasbourg, France.
Dec. 2015 – Aug. 2016: Research associate at the Luxembourg Centre for Systems Biomedicine / University of Luxembourg.
Sept. 2013 – Nov. 2015: Senior post-doctoral researcher at the Luxembourg Centre for Systems Biomedicine / University of Luxembourg.
Sept. 2011 – Aug. 2013: Post-doctoral researcher at the Luxembourg Centre for Systems Biomedicine / University of Luxembourg.

Qualifications and training

January 2020: HDR diploma (Habilitation) . “Ecologie fonctionnelle des communautés microbiennes à l'âge de l'Anthropocène : de la réponse au stress à l’évolution des populations”. University of Strasbourg (France), UMR7156 UNISTRA-CNRS.
March 2011: PhD in Molecular and Cellular Biology. University of Strasbourg (France), UMR7156 UNISTRA-CNRS.
June 2007: Master “Géosciences, Environnement et Risques”, Speciality: Environmental Physics, Chemistry and Biology, University Louis Pasteur, Strasbourg (France).
June 2005: Bachelor in Biology, University Louis Pasteur, Strasbourg (France).

Current and recent research supports

  • 2017-2020 dehalofluidX (ANR): Function-driven, microfluidics-based discovery of novel microbial dehalogenases [Partner].
  • 2017-2018 MAD (IdEx Attractivité): Functional probing of fungal and bacterial DUF2156 domain-containing proteins in model organisms and microbiomes [Co-PI].
  • 2017-2019 2D-DCM (Ec2Co): Transport réactif du dichloromethane en aquifère de laboratoire [Partner].
  • 2014-2018 LEGeLiS (CORE Junior – FNR) Linking Environment - Genome - Lifestyle Strategy [PI, then external partner].

Scientific and academic responsabilities

  • Supervision
    • Mentoring of Ph.D. thesis:
      Shaman NARAYANASAMY (2014 – 2017), Cédric LACZNY (2014-2015), Hugo ROUME (2011-2013).
    • Supervision or co-supervision of Master and engineering school students (3 months – 7 months): Carmen LAZARO SANCHEZ (M2-2021), Margaux CHEMINAT (M1-2021), Victor HANSS (M2-2020), Caroline CHOUFA (M2-2018), Thomas LUTZ (ES-2017), Myriam ZEIMES (M2-2015), Jill BOHLER (M1-2012).
    • Supervision or co-supervision of final year Diploma: Carole PFISTER (2010), Elena IULIANI (2009), Charles-Benjamin GEITNER (2008), Elena IULIANI (2008).
    • Internships: Carmen LAZARO SANCHEZ (2018-2019), Marion LEMARE (2018).
  • Member of Dissertation Committees:
    • PhD thesis : L. HERMON, (2017, Université de Strasbourg - examinatrice interne) ; W. GOI CHIN LIN (2019, National University of Singapore – rapporteure) ; L. CARDONA (2020, AgroParisTech - examinatrice externe).
    • on-going thesis committee :  M.-L. UWIZEYE (University of Luxembourg) ; Q. BAPTISTE (INRAE d’Anthony, France) ; A. ESPINOSA PRIETO (Université de Strasbourg, France).
  • Teaching
    • at Université de Strasbourg (2020-present):
      • Génomique, practicals 48h/y, L3 Sciences de la vie : biologie moléculaire et cellulaire.
      • Purification en analyse des biomolécules, lectures 4h/y, practicals 32h/y, M2 Chimie : Chimie biologie et médicament
      • Ecologie moléculaire, lectures 3h/y, practicals 3h/y, tutorials 3h/y, M2 Sciences du vivant : Plantes, environnement et génie écologique
    • at University of Luxembourg (2012-2015):
      • Biotechnology - genetic engineering and recombinant DNA technology, 2h lecture in 2015,3rd year of Bachelor degree in Life Sciences.
      • Metabolomics and Metabolism: lecture 1h/y, practical 4h/y from 2012-2015, Master in integrated systems biology.
      • Practicals in Metabolomics: practicals 16h/y from 2012-2015, Master in integrated systems biology.
    • at Université de Strasbourg (2007-2011):
      • Basic Technics in Biology, 100h in 2011, 1st year Bachelor degree in Life Sciences in Psychology.
      • Basic Cellular Biology Practicals, 40h/y from 2007 to 2010, 1st year Bachelor degree in Psychology.
      • Human Genetics, 40h/y from 2007 to 2010, 1st year Bachelor degree in Psychology.
      • Medullary reflex Practicals, 30h in 2009, 2nd year Bachelor degree in Psychology.
      • Nervous system Histology Practicals, 40h in 2007, 1st year Bachelor degree in Psychology.
  • Regular reviewer activity for scientific journals and grant evaluation.

Honors and Awards

  • 2016: Received second, CNRS section 30, CR2 recruitment campaign
  • 2015: 2 years grant “CORE junior” from the Fonds National de la Recherche (Luxembourg).
  • 2011: 2 years grant “Aide Formation à la Recherche” from the Fonds National de la Recherche (Luxembourg).
  • 2011: PhD award “Région Alsace” from the “Société de Biologie de Strasbourg”
  • 2007: 3 years PhD Grant “Région Alsace”

List of Publications


Delogu, F., Kunath, B.J., Queirós, P.M., Halder, R., Lebrun, L.A., Pope P.B., May P., Widder, S., Muller E.E.L., Wilmes P. (2023) Forecasting the dynamics of a complex microbial community using integrated meta-omics. Nature Ecology and Evolution. https://doi.org/10.1038/s41559-023-02241-3

Prieto-Espinoza, M., Di Chiara Roupert, R., Muller, EEL., Vuilleumier, S., Imfeld, G. & Weill, S. (2023) Combining multi-phase flow and pathway-specific reactive transport modeling to investigate the impact of water table fluctuations on dichloromethane biodegradation. Adv Water Res, in press.

Muller, E.E.L. (2023) The social dimension of microbial niches. Nature Ecology & Evolution 7, 649-650.


Delogu, F., Kunath, B., Queiros,P., Halder, R., Lebrun, L., Pope, P., May, P., Widder, S., Muller,E.E.L. & Wilmes, P. (2022) Forecasting of a complex microbial community using meta-omics. bioRxiv, 2022-10.


Martinez Arbas, S., Bhanu Busi, S., Queiros, P., De Nies, L., Herold, M., May, P., Wilmes, P., Muller, E.E.L., Narayanasamy, S. Challenges, strategies and perspectives for reference-independent longitudinal multi-omic microbiome studies. Front. Genetics, 12, art. 858.

Martinez Arbas, S., Narayanasami, S., Herold, M., Lebrun, L., Hoopmann, M., Li, S., Lam, T., Kunath, B.,  Hicks, N., Liu, C., Price, L., Laczny, C., Gillece, J., Schupp, J., Keim, P., Moritz, R.,  Faust, K., Tang, H;, Ye, Y., Skupin, A., May, A., Muller, E.E.L. & Wilmes, P. (2020) Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nat. Microb., 6, 123-135.


Hayoun, K., Geersens, E., Laczny, C.C., Halder, R., Lázaro Sánchez, C., Manna, A., Bringel, F., Ryckelynck, M., Wilmes, P., Muller, E.E.L., Alpha-Bazin, B., Armengaud, J. & Vuilleumier, S. (2020)Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics. Microorganisms , 8, 1876.

Herold, M., Martinez Arbas, S., Narayanasami, S., Sheik, A., Kleine-Borgmann, L., Lebrun, L., Kunath, B., Roume, H., Bessarab, I., Williams, R., Gillece, J., Schupp, J., Keim, P., Jäger, C., Hoopmann, M., Moritz, R., Ye, Y., Li, S., Tang, H., Heintz-Buschart, A., May, P., Muller, E.E.L., Laczny, C. & Wilmes, P. (2020) Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance. Nat Commun,11, 5281.


Muller, E.E.L. (2019) Determining microbial niche breadth in the environment for better ecosystem fate predictions. mSystems4:e00080-19.


Shah P., Muller E.E.L., Lebrun L.A., Wampach L., Wilmes P. (2018) Sequential isolation of DNA, RNA, protein, and metabolite fractions from murine organs and intestinal contents for integrated omics of host–microbiota interactions. Special issue: Microbial Proteomics: Methods and Protocols.Methods in Molecular Biology, 1841:279-291.

Muller E.E.L., Faust, K., Widder, S., Herold, M., Martinez Arbas, S. & Wilmes, P. (2018) Using metabolic networks to resolve ecological properties of microbiomes. Curr. Opin. Sys. Biol. 8, 73-80.

Calusinska, M., Goux, X., Fossépré, M., Muller, E.E.L.,  Wilmes, P.,  Delfosse P. A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems. Biotechnol. biofuels. 11, art. 196.

Chaib De Mares, M., Jiménez, D.J., Palladino, G., Gutleben, J., Lebrun, L.A., Muller, E.E.L., Wilmes, P.,  Sipkema, D., van Elsas J.D. Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics. Scientific reports , 8, art. 11795.


Muller E.E.L.*, Narayanasamy, S.*, Zeimes, M., Laczny, C.C., Lebrun, L.A., Herold, M., Hicks, N.D., Gillece, J.D., Schupp, J.M., Keim, P., Wilmes, P. First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ. Stand. genomic sci., 12, art. 64 (*co-first authors).

Bringel, F., Postema, C.P., Mangenot, S., Bibi-Triki, S., Chaignaud, P., Farhan Ul Haque, M., Gruffaz, C., Hermon, L., Louhichi, Y., Maucourt, B., Muller, E.E.L., Nadalig, T., Lajus, A., Rouy, Z., Médigue, C., Barbe, V., Janssen, D.B. & Vuilleumier, S. (2017) Genome sequence of the dichloromethane-degrading bacterium Hyphomicrobium sp. strain GJ21. Genome Announc. 5, art. 00622-17

Svartström, O., Alneberg, J., Terrapon, N., Lombard, V., de Bruijn, I., Malmsten, J., Dalin, A-M., Muller E.E.L., Shah, P., Wilmes, P., Henrissat, B., Aspeborg, H. & Andersson, A.F. (2017) Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.ISME J., 11, 2538-2551.

Kaysen, A., Heintz-Buschart, A., Muller, E.E.L., Narayanasamy, S., Wampach, L., Laczny, C.C., Graf, N., Simon, A., Franke, K., Bittenbring, J., Wilmes, P. & Schneider, J.G. (2017) Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic stem cell transplantation. Transl. Res. 186;79:94.

 Wampach, L., Heintz-Buschart, A., Hogan, A., Muller, E.E.L., Narayanasamy, S., Laczny, C.C., Hugerth, L.W., Bindl, L., Bottu, J., Andersson, A.F., de Beaufort, C. & Wilmes, P. (2017) Colonization and succession within the human gut microbiome by archaea, bacteria and microeukaryotes during the first year of life. Front. Microbiol. 2;8:738.

Bradley, A.S., Swanson, P.K., Muller, E.L.L., Bringel, F., Caroll, S.M., Pearson, A., Vuilleumier, S., Marx, C.J. Hopanoid-free Methylobacterium extorquens DM4 overproduces carotenoids and has widespread growth impairment. PloS One e0173323.


Narayanasamy, S., Jarosz, Y., Muller, E.E.L., Laczny, C.C., Herold, M., Kaysen, A., Heintz-Buschart, A., May, P., Pinel, N. & Wilmes, P. (2016) IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses. Genome Biol.17:260.

Laczny, C.C., Muller, E.E.L., Heintz-Buschart, A., Herold, M., Lebrun, L.A., Hogan, A., May, P., de Beaufort, C. & Wilmes, P. (2016) Prioritization, recovery and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract. Front. Microbiol.7 - 884.

Sheik, A.R., Muller, E.E.L., Audinot, J.-N., Lebrun, L.A., Grysan, P., Guignard, C. & Wilmes, P. (2016) In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella. ISME J. 10, 1274–1279


Roume, H., Heintz-Buschart, A., Muller, E.E.L.,  May, P., Satagopam, V.P., Laczny, C.C., Narayanasamy, S., Lebrun, L.A., Hoopmann, M.R., Schupp, J.M., Gillece, J.D., Hicks, N.D., Engelthaler, D.M., Sauter, T., Keim, P.S., Moritz, R.L. & Wilmes, P.(2015) Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks.Biofilms and Microbiomes.1-15007.

Narayansamy, S., Muller, E.E.L., Sheik, A.R. & Wilmes, P.(2015) Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities. Microbial Biotechnol.8, 262-268.


Muller, E.E.L., Heintz-Buschart, A., Roume, H., Lebrun, L.A. & Wilmes, P.(2014) The sequential isolation of metabolites, RNA, DNA, and proteins from a single, undivided mixed microbial community sample.  Protocol Exchange. doi: 10.1038/protex.2014.051.

Muller, E.E.L.*, Pinel, N.*, Laczny, C.C., Hoopmann, M.R., Narayanasamy, S., Lebrun, L.A., Roume, H., Lin, J., May, P., Hicks, N.D., Heintz-Buschart, A., Wampach, L., Liu, C.M., Price, L.B., Gillece, J.D., Guignard, C., Schupp, J.M., Vlassis, N., Baliga, N.S., Moritz, R.L., Keim, P.S. & Wilmes, P. (2014) Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nat. Commun.5-5603 (*co-first authors).

Muller, E.E.L., Sheik, A.R. & Wilmes, P. (2014) Lipid-based biofuel production from wastewater. Curr. Opin. Biotechnol, Special issue: Chemical Biotech 2014. 30, 9-16.

Hugerth, L.W., Muller, E.E.L., Hu, Y., Lebrun, L.A., Roume, H., Lundin, D., Wilmes, P. & Andersson, A.F. (2014) Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. PLoS One, 9, e95567.

Sheik, A.R., Muller, E.E.L. & Wilmes, P. (2014) A hundred years of activated sludge: time for a rethink. Front. Microbiol.5, 47.

Gruffaz, C., Muller, E.E.L., Louhichi-Ilael, Y., Nelli, Y.R., Guichard, G. & Bringel, F. (2014) Genes of the N-methylglutamate pathway are essential for growth of Methylobacterium extorquens DM4 with monomethylamine. Appl. Environ. Microbiol.80,3541-3550.


Muller, E.E.L., Glaab E., May, P., Vlassis, N. & Wilmes, P. (2013) Condensing the omics fog of microbial communities. Trends Microbiol.21, 325-333.

Roume H., Heintz-Buschart, A, Muller, E.E.L. & Wilmes, P. (2013) Sequential Isolation of metabolites, RNA, DNA, and proteins from the same unique sample. Methods Enzymol.531, 219-236.

Roume, H., Muller, E.E.L., Cordes T., Hiller, K. & Wilmes, P. (2013) Biomolecular isolation methods for eco-systems biology.ISME J.7,110-121.


Muller, E.E.L. *, Pinel, N.*, Gillece, J.D., Schupp, J.M., Price, L.B., Engelthaler, D.M., Levantesi, C., Tandoi, V., Luong, K., Baliga, N.S., Korlach, J., Keim, P.S. & Wilmes, P. (2012) Genome sequence of "Candidatus Microthrix parvicella" Bio17-1, a long-chain-fatty-acid-accumulating filamentous Actinobacterium from a biological wastewater treatment plant. Journal of Bacteriology, 194, 6670-6671. (*co-first authors).

Marx, C.J., Bringel, F., Chistoserdova, L., Moulin, L., Ul Haque, M.F., Fleischman, D.E., Gruffaz, C., Jourand, P., Knief, C., Lee, M.C., Muller, E.E.L., Nadalig, T., Peyraud, R., Roselli, S., Russ, L., Goodwin, L.A., Ivanova, N., Kyrpides, N., Lajus, A., Land, M.L., Médigue, C., Mikhailova, N., Nolan, M., Woyke, T., Stolyar, S., Vorholt, J.A. & Vuilleumier, S. (2012) Complete genome sequences of six strains of the genus Methylobacterium. J Bacteriol 194, 4746-4748.


Vuilleumier, S., Nadalig, T., Ul Haque, M.F., Magdelenat, G., Lajus, A., Roselli, S., Muller, E.E.L., Gruffaz, C., Barbe, V., Médigue, C. & Bringel, F. (2011) Complete genome sequence of the chloromethane-degrading Hyphomicrobium sp. strain MC1. J. Bacteriol. 193, 5035-5036.

Muller, E.E.L., Hourcade, E., Louhichi-Jelail, Y., Hammann, P., Vuilleumier, S. & Bringel, F. (2011) Functional genomics of dichloromethane utilization in Methylobacterium extorquens DM4. Environ. Microbiol.13, 2518-2535.

Muller, E.E.L., Bringel, F. & Vuilleumier, S. (2011) Dichloromethane-degrading bacteria in the genomic age. Special issue: environmental microbiology, Res. Microbiol.  162, 869-876.


Vuilleumier, S., Chistoserdova, L., Lee, M.-C., Bringel, F., Lajus, A., Zhou, Y., Gourion, B., Barbe, V., Chang, J., Cruveiller, S., Dossat, C., Gillett, W., Gruffaz, C., Haugen, E., Hourcade, E., Levy, R., Mangenot, S., Muller, E.E.L, Nadalig, T., Pagni, M., Penny, C., Peyraud, R., Robinson, D.G., Roche, D., Rouy, Z., Saenampechek, C., Salvignol, G., Vallenet, D., Wu, Z., Marx, C.J., Vorholt, J.A., Olson, M. V., Kaul, R., Weissenbach, J., Médigue, C. & Lidstrom, M.E. (2009). Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources. PLoS ONE  4, e5584.