Dominique
Schneider

Enseignant Chercheur
Team GEM
[info]
Phone: 04 76 63 74 90
Address: Bâtiment Jean Roget, Domaine de la Merci
Office: 508a

My primary interest is to study the traits that determine the fit between organisms and their environment and the evolution of these traits by natural selection. Evolution is inherently complex owing to the high dimensionality of genomes and the multitude of interactions between genes, gene products, metabolites, and environmental factors including resources. To understand many adaptations, one must investigate changes in entire genomes and examine their consequences for global expression and organismal performance. Any study has therefore to be integrative and multidisciplinary and at the frontier of ecology, evolution, microbiology and genetics, including the fields of experimental evolution, microbial genetics and population genetics.

The developed research uses an unprecedented biological material: bacterial populations that evolved in a defined environment since now more than 30 years. This experimental evolution strategy, the longest-running on Earth, provides a living and complete fossil record including the ancestor cell and evolved clones that derived from this ancestor for more than 70,000 generations. This experiment is of course in the field of biology but is also a human adventure, and is related to philosophy, history of science and to many more fields.

Life is all about interactions, and therefore, social interactions are essential. Development of research and teaching projects aiming at improving social interactions and well-being are therefore also at the heart of evolution.

Research themes

The central research theme focuses on the investigation of the ecological and molecular mechanisms underlying the dynamics of bacterial evolutionary processes and the evolution of phenotypic traits, including adaptation to various environments, adaptive diversification, metabolic and biochemical abilities, and antibiotic resistance.
Experimental evolution strategies are developed and analyzed at various levels: i) phenotypic changes in relation to the interactions between genes, gene products and metabolites inside the cells, ii) between cell lineages, and iii) the link with environmental factors including resources and antibiotic pressure.

The main interest is to understand how genomic changes are related to metabolic and regulatory network dynamics to allow adaptation, diversification, co-existence of bacterial ecotypes and modifications of virulence and antibiotic resistance traits. Establishing the link between, on one hand, changes in genomes and expression profiles and, on the other hand, changes in phenotypes like fitness, metabolic and biochemical abilities and antibiotic resistance is a prerequisite to understand how natural selection is able to re-shape and improve entire genomes, and which functions are more plastic over evolutionary time. Using such an evolutionary perspective is fully complementary to most “Systems Biology” approaches and addresses how evolvable are genomic and network features and what are the molecular bases of such evolvability.

Keywords

Experimental evolution
Microbiology
Regulatory networks
Metabolic networks
Adaptation
Speciation

Publications

Main publications over the last 10 years:

Beslon G., and Schneider D. 2017. ISEE-Resistance: Using in silico experimental evolution to sensitize providers on antibiotic resistance. Antimicrobial Resistance and Infection Control 6(52):2-2.

Rocabert C., Knibbe C., Consuegra J., Schneider D., Beslon G. 2017, September. Environmental seasonality drives digital populations towards stable cross-feeding. In European Conference on Artificial Life (ECAL).

Couce A., Viraphong Caudwell L., Feinauer C., Hindré T., Feugeas J-P., Weigt M., Lenski R. E., Schneider D., and Tenaillon O. 2017. Mutator genomes decay despite sustained fitness gains in a long-term experiment with bacteria. Proc. Natl Acad. Sci. USA. 114, E9026-E9035.

Consuegra J., Plucain J., Gaffé J., Hindré T., and Schneider D. 2017. Genetic basis of exploiting ecological opportunity during the long-term diversification of a bacterial population. J. Mol. Evol. 85, 26-36.

Rocabert C., Knibbe C., Consuegra J., Schneider D., and Beslon G. 2017. Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification. PLoS Comput. Biol. 13(3):e1005459.

Pelosi L., Ducluzeau A-L., Loiseau L., Barras F., Schneider D., Junier I., and Pierrel F. 2016. Evolution of ubiquinone biosynthesis: multiple proteobacterial enzymes with various regioselectivities to catalyze three contiguous aromatic hydroxylation reactions. mSystems. 1(4):e00091-16.

Großkopf T.*, Consuegra J.*, Gaffé J., Willison J. C., Lenski R. E., Soyer O. S., and Schneider D. 2016. Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. BMC Evol Biol. 16:163.

Tenaillon O., Barrick J. E., Ribeck N., Deatherage D. E., Blanchard J. L., Dasgupta A., Wu G. C., Wielgoss S., Cruveiller S., Médigue C., Schneider D., and Lenski R. E. 2016. Tempo and mode of genome evolution in a 50,000-generation experiment. Nature. 536, 165-170.

Plucain J., Suau A., Cruveiller S., Médigue C., Schneider D., and Le Gac M. 2016. Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria. BMC Evol. Biol.16:86.

Shadoud L., Almahmoud I., Jarraud S., Etienne J., Larrat S., Schwebel C., Timsit J-F., Schneider D., and Maurin M. 2015. Hidden selection of bacterial resistance to fluoroquinolones in vivo: The case of Legionella pneumophila and humans. EBioMedicine. 2, 1179-1185.

Rudan M., Schneider D., Warnecke T., and Krisko A. 2015. RNA chaperones buffer deleterious mutations in E. coli. eLife. 10.7554/eLife.04745.

Caspar Y., Jeanty M., Blu J., Burchak O., Le Pihive E., Maigre L., Schneider D., Jolivalt C., Paris J-M., Hequet A., Minassian F., Denis J-N., and Maurin M. 2015. Novel synthetic bis-indolic derivatives with antistaphylococcal activity, including against MRSA and VISA strains. J. Antimicrob. Chemother. 70, 1727-1737.

Raeside C., Gaffé J., Deatherage D. E., Tenaillon O., Briska A. M., Ptashkin R. N., Cruveiller S., Médigue C., Lenski R. E., Barrick J. E., and Schneider D. 2014. Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli. mBio. 5(5):e01377-14.

Plucain J., Hindré T., Le Gac M., Tenaillon O., Cruveiller S., Médigue C., Leiby N., Harcombe W. R., Marx C. J., Lenski R. E., and Schneider D. 2014. Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli. Science. 343, 1366-1369.

Héquet A., Burchak O. N., Jeanty M., Le Pihive E., Maigre L., Bouhours P., Schneider D., Maurin M., Paris J-M., Denis J-N., and Jolivalt C. 2014. 1-(1H-indol-3-yl)ethanamine derivatives as potent Staphylococcus aureus NorA efflux pump inhibitors. ChemMedChem. 9, 1534-1545.

Sutera V., Levert M., Burmeister W. P., Schneider D., and Maurin M. 2014. Evolution toward high-level fluoroquinolone resistance in Francisella species. J. Antimicrob. Chemother. 69, 101-110.

Larose C., Prestat E., Cecillon S., Berger S., Malandain C., Lyon D., Ferrari C., Schneider D., Dommergue A., and Vogel T. M. 2013. Interactions between snow chemistry, mercury inputs and microbial population dynamics in an arctic snowpack. PLoS One. 8(11):e79972.

Le Gac M., Cooper T. F., Cruveiller S., Médigue C., and Schneider D. 2013. Evolutionary history and genetic parallelism affect correlated responses to evolution. Mol. Ecol. 22, 3292-3303.

Maharjan R. P.*, Gaffé J.*, Plucain J., Schliep M., Wang L., Feng L., Tenaillon O., Ferenci T., and Schneider D. 2013. A case of adaptation through a mutation in a tandem duplication during experimental evolution in Escherichia coli. BMC Genomics. 14, 441.

Wielgoss S., Barrick J. E., Tenaillon O., Wiser M. J., Dittmar W. J., Cruveiller S., Chane-Woon-Ming B., Médigue C., Lenski R. E., and Schneider D. 2013. Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load. Proc. Natl Acad. Sci. USA. 110, 222-227.

Beslon G., Batut B., Parsons D. P., Schneider D., and Knibbe C. 2013. An alife game to teach evolution of antibiotic resistance. Advances in Artificial Life, ECAL 12, 43-50.

Le Gac M., Plucain J., Hindré T., Lenski R. E., and Schneider D. 2012. Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with E. coli. Proc. Natl Acad. Sci. USA. 109, 9487-9492.

Hindré T., Knibbe C., Beslon G., and Schneider D. 2012. New insights into bacterial adaptive abilities by in vivo and in silico experimental evolution. Nature Rev. Microbiol. 10, 352-365.

Jamet A., Frapy E., Schneider D., Nassif X., and Martin P. 2012. A cell-contact-regulated operon is involved in genetic variability in Neisseria meningitidis. Res. Microbiol. 163, 192-199.

Wielgoss S., Barrick J. E., Tenaillon O., Cruveiller S., Chane-Woon-Ming B., Médigue C., Lenski R. E., and Schneider D. 2011. Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with Escherichia coli. Genes, Genomes, Genetics, G3 (Bethesda). 1, 183-186.

Khan A. I., Dinh D. M., Schneider D., Lenski R. E., and Cooper T. F. 2011. Negative epistasis between beneficial mutations in an evolving bacterial population. Science. 332, 1193-1196.

Gaffé J., McKenzie C., Maharjan R. P., Coursange E., Ferenci T., and Schneider D. 2011. Insertion Sequence-driven evolution of Escherichia coli in chemostats. J. Mol. Evol. 72, 398-412.

Burchak O. N., Le Pihive E., Maigre L., Guinchard X., Bouhours P., Jolivalt C., Schneider D., Maurin M., Paris J-M., and Denis J-N. 2011. Synthesis and evaluation of 1-(1H-indol-3-yl)ethanamine derivatives as new antibacterial agents. Bioorg. Med. Chem. 19, 3204-3215.

Larose C., Dommergue A., Marusczak N., Coves J., Ferrari C., and Schneider D. 2011. Bioavailable mercury cycling in polar snowpacks. Environ. Sci. Techn. 45, 2150-2156.

Charpentier X., Kay E., Schneider D., and Shuman H. 2011. Antibiotics and UV radiation induce competence for natural transformation in Legionella pneumophila. J. Bacteriol. 193, 1114-1121.

Crozat E., Hindré T., Kühn L., Garin J., Lenski R.E., and Schneider D. 2011. Altered Regulation of the OmpF porin by Fis in Escherichia coli during an evolution experiment and between B and K12 strains. J. Bacteriol. 193, 429-440.

Vergnes M., Ginevra C., Kay E., Normand P., Thioulouse J., Jarraud S., Maurin M., and Schneider D. 2011. Insertion Sequences as highly resolutive genomic markers for ST1 Legionella pneumophila Paris. J. Clin. Microbiol. 49, 315-324.

Gestin B., Valade E., Thibault F., Schneider D., and Maurin M. 2010. Phenotypic and genetic characterization of macrolide resistance in Francisella tularensis subsp. holarctica biovar I. J. Antimicrob. Chemother. 65, 2359-2367.

Larose C., Dommergue A., De Angelis M., Cossa D., Averty B., Marusczak N., Soumis N., Schneider D., and Ferrari C. 2010. Springtime changes in snow chemistry lead to new insights into mercury methylation in the Arctic. Geochim. Cosmochim. Acta. 74, 6263-6275.

Maharjan R., Zhou Z., Ren Y., Li Y., Gaffé J., Schneider D., McKenzie C., Reeves P., Ferenci T., and Wang L. 2010. Genomic identification of a novel mutation in hfq that provides multiple benefits in evolving glucose-limited populations of Escherichia coli. J. Bacteriol. 192, 4517-4521.

Meyer J.R., Agrawal A.A., Quick R.T., Dobias D.T., Schneider D., and Lenski R.E. 2010. Parallel changes in host resistance to viral infection during 45,000 generations of relaxed selection. Evolution. 64, 3024-3034.

Crozat E., Winkworth C., Gaffé J., Hallin P. F., Riley M. A., Lenski R. E., and Schneider D. 2010. Parallel genetic and phenotypic evolution of DNA superhelicity in experimental populations of Escherichia coli. Mol. Biol. Evol. 27, 2113-2128.

Larose C., Berger S., Ferrari C., Navarro E., Dommergue A., Schneider D.*, and Vogel T.M.* 2010. Microbial sequences retrieved from environmental samples from seasonal Arctic snow and meltwater from Svalbard, Norway. Extremophiles. 14, 205-212.

Dommergue A., Larose C., Fain X., Clarisse O., Foucher D., Hintelmann H., Schneider D., and Ferrari C. 2010. Deposition of mercury species in the Ny-Ålesund area (79°N) and their transfer during snowmelt. Environ. Sci. Techn. 44, 901-907.

Barrick J.E., Yu D.S., Yoon S.H., Jeong H., Oh T.K., Schneider D., Lenski R.E., and Kim J.F. 2009. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature. 461, 1243-1247.

Almahmoud I., Kay E., Schneider D., and Maurin M. 2009. Mutational paths towards increased fluoroquinolone-resistance in Legionella pneumophila. J. Antimicrob. Chemother. 64, 284-293.

Philippe N., Pelosi L., Lenski R.E., and Schneider D. 2009. Evolution of penicillin-binding protein 2 concentration and cell shape during a long-term experiment with Escherichia coli. J. Bacteriol. 191, 909-921.

Touchon M., Hoede C., Tenaillon O., Barbe V., Baeriswyl S., Bidet P., Bingen E., Bonacorsi S., Bouchier C., Bouvet O., Calteau A., Chiapello H., Clermont O., Cruveiller S., Danchin A., Diard M., Dossat C., El Karoui M., Frapy E., Garry L., Ghigo J-M., Gilles A-M., Johnson J., Le Bouguénec C., Lescat M., Mangenot S., Martinez-Jéhanne V., Matic I., Nassif X., Oztas S., Petit M-A., Pichon C., Rouy Z., Saint Ruf C., Schneider D., Tourret J., Vacherie B., Vallenet D., Médigue C., Rocha E., Denamur E. 2009. Organised genome dynamics in the Escherichia coli species: the path to adaptation. PLoS Genetics. 5(1), e1000344.

Rozen D.E., Philippe N., de Visser J.A., Lenski R.E., and Schneider D. 2009. Death and cannibalism in a seasonal environment facilitate bacterial coexistence. Ecol. Lett. 12, 34-44.

Teachings

In charge of two teaching modules:
- BIO305: Interactions of bacteria with their environment and host cells. Second-year university students.
- BIO531: Fundamental and Applied Microbiology. Master 2 students.

Teaching of:
Microbiology, genetics, molecular genetics, molecular biology, evolution, gene expression.

Partnerships

Collaborations:
- Richard Lenski, Michigan State University, USA
- Jeffrey Barrick, The University of Texas at Austin, USA
- Soeren Molin, Danish Technical University, Copenhagen, Denmark
- Orkun Soyer, University of Warwick, UK
- Guillaume Beslon, INRIA, Lyon
- Olivier Tenaillon, INSERM, Paris
- Claudine Médigue, Génoscope, Paris