Chargée de Recherche (CRCN)


Université de Strasbourg / CNRS UMR7156
Laboratoire de Génétique Moléculaire, Génomique, Microbiologie.   
Département Micro-organismes, Génomes, Environnement                 
28 rue Goethe
F - 67000 Strasbourg

Tel :           + 33 (0)3 68 85 19 73
e-mail :      emilie.muller@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


25 peer-reviewed publications (see list below or full list of publications).
Researchgate profile at https://www.researchgate.net/profile/Emilie_Muller2


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.


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 3 Ph.D. thesis:
      Shaman NARAYANASAMY (2014 – 2017), Cédric LACZNY (2014-2015), Hugo ROUME (2011-2013).
    • Supervision or co-supervision of 5 final year Diploma and Master undergraduate students (3 months - 1 year each): Myriam ZEIMES (2015), Jill BOHLER (2012), Carole PFISTER (2010), Elena IULIANI (2009), Charles-Benjamin GEITNER (2009).
  • Teaching
    • at University of Luxembourg:
      • 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:
      • 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.
  • Reviewer activity for BBA General Subject, BMC research Notes, Cell factory, Environmental Microbiology, Environmental Microbiology Report, The ISME journal.
  • Evaluation expert for Minnesota Sea Grant (2015), BeNeLux Bioinformatics Conference (2015).

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


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.

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. mSystems 4: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.


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. (in press).

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.


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.

Shah, P., Heintz-Buschart, A., Lebrun, L.A., Muller, E.E.L. & Wilmes, P. (2016) Preparation of microbiome samples. Method. Mol. Biol. (in press).

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.