Timothy M. Vogel Environmental Microbial Genomics Group

Logo GenomEnviron
Laboratoire Ampere
Ecole Centrale de Lyon . France
(33) 472 18 65 14

Education | Research Interests | Publications | Curriculum Vitae | More...

  Tim Vogel  
  Timothy M. Vogel

Environmental Microbial Genomics Group
Laboratoire Ampère, UMR CNRS 5005
Ecole Centrale de Lyon
Université de Lyon
36 avenue Guy de Collongue
69134 Ecully cedex

  Phone: (33) 4 72 18 65 14
Fax: (33) 4 78 43 37 17



Ph.D. Environmental Engineering (Microbiology), 1988, Stanford University
M.S. Environmental Engineering, 1983, Stanford University
B.S. Geology, 1979, University of Washington, Seattle.
B.S. Biological Oceanography, 1979, University of Washington, Seattle.


My environmental microbiology research concerns the ability of bacteria to adapt to different environments. An excellent model for this adaptation is the fate and effects of xenobiotic compounds. While my work on xenobiotic compounds has included work from soil bioremediation and groundwater treatment to degradation pathways, much of my current microbial ecology research is on the perturbations of microbial communities and the adaptation of microorganisms to xenobiotic compounds (either by mutation, gene transfer or gene shuffling). In addition, within gene transfer, my current research also includes the fate of DNA from transgenic plants - its movement, degradation and potential transfer to bacteria.

My environmental genomics (mostly metagenomics) involves exploring the functional and structural relationships between the environmental genetic resources within a given ecosystem (currently: polluted soil (chlorinated compounds and petroleum hydrocarbons, microbial fuel cells) and bacterial adaptation and evolution. High throughput techniques, such as microarrays and "next generation sequencing", are used to produce data that supports relevant hypotheses.

My environmental bioengineering work centers around the biodegradation of contaminants in the subsurface and the applications of microbial fuel cells (MFCs). Modeling is an important aspect of this work along with the application of modern molecular biology methods.

topPUBLICATIONS 2008-2015 (for a complete list of publications click here)

Zhu, C. Delmont, TO. Vogel, T M. Bromberg, Y. 2015. Functional Basis of Microorganism Classification. PLoS Computational Biology. 11: e1004472. DOI:10.1371/journal.pcbi.100447

Sanguino, L. Franqueville, L., Vogel, TM., Larose, C. 2015. Linking environmental prokaryotic viruses and their host through CRISPRs. FEMS Microbial. Ecol. 91: 10.1093/femsec/fiv046

Delmont, TO. Eren, AM. Maccario, L. Prestat, E. Esen, OC. Pelletier, E. Le Paslier, D. Simonet, P. Vogel, TM 2015. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. FRONTIERS IN MICROBIOLOGY 6:

Maccario L, Vogel TM and Larose C (2014) Potential drivers of microbial community structure and function in Arctic spring snow. Front. Microbiol. 5:413. doi: 10.3389/fmicb.2014.00413

Le Digabel, Y., Demanèche, S., Benoit, Y., Fayolle-Guichard, F., and Vogel, T.M. 2014. Ethyl tert-butyl ether (ETBE)-degrading microbial communities in enrichments from polluted environments. Journal of Hazardous Materials, 279 :502-510.

Nesme, J., Cécillon, S., Delmont, T.O., Monier, J-M., Vogel, T.M., Simonet, P. 2014. Large-Scale Metagenomic-Based Study of Antibiotic Resistance in the Environment Current Biology 24, 1–5, http://dx.doi.org/10.1016/j.cub.2014.03.036

Delmont, T.O., Francioli, D., Jacquesson, S., Laoudi, S., Mathieu, A., Nesme, J., Ceccherini, M.T., Nannipieri, P., Simonet, P., Vogel, T.M. 2014. Microbial community and unseen diversity development in inoculated sterile soil, Biology and Fertility of Soil, DOI: 10.1007/s00374-014-0925

Mathieu A, Vogel TM and Simonet P. 2014. The Future of Skin Metagenomics. Res Mic. 165:69-76. doi: 10.1016/j.resmic.2013.12.002.

Jacquiod S, Demanèche S, Delmont TO, Ausec L, Dunon V, Franqueville L, Mandic-Mulec I, Springael D, Vogel TM and Simonet P. 2014. Genetic screening of a fosmid metagenomic soil library using radio-labeled oligonucleotide probes. J. Biotechnol. (in press).  doi: 10.1016/j.jbiotec.2014.03.036.

Larose, C., Dommergue, A., Vogel, T.M. The Dynamic Arctic Snow Pack: An Unexplored Environment for Microbial Diversity and Activity. Biology, 2013, 2 (1), pp. 317-330. <http://dx.doi.org/10.3390/biology2010317>

Delmont, T.O., Simonet, P., Vogel, T.M. Mastering methodological pitfalls for surviving the metagenomic jungle.. BioEssays, 2013, 35 (8), pp. 744-54. <http://dx.doi.org/10.1002/bies.201200155>

Le Digabel, Y., Demanèche, S., Benoit, Y., Vogel, T.M., and Fayolle-Guichard, F. 2013. Ethyl tert-butyl ether (ETBE) biodegradation by a syntrophic association of Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP 2049 isolated from a polluted aquifer. Applied Microbiology and Biotechnology, 97:10531-10539

Bowman, J. S., C. Larose, T. M. Vogel and J. W. Deming. 2013. Selective occurrence of Rhizobiales in frost flowers on the surface of young sea ice near Barrow, Alaska and distribution in the polar marine rare biosphere. Environ. Microbiol. Reports 5:575-582.

Mathieu, A. Tom Delmont, T.O., Vogel, T.M., Patrick Robe, P., Nalin, R., Simonet, P. Life on Human Surfaces: Skin Metagenomics. PLoS ONE, 2013, 8 (6), pp. e65288. <http://dx.doi.org/10.1371/journal.pone.0065288>

Jacquiod, S., Franqueville, L., Cecillon, S., Vogel, T.M., Simonet, P. 2013. Soil Bacterial Community Shifts after Chitin Enrichment: An Integrative Metagenomic Approach. PLoS ONE 8: doi:10.1371/journal.pone.0079699

Delmont, T.O., Prestat,E., Keegan,K.P., Faubladier,M., Robe,P., Clark,I.M., Pelletier, E., Hirsch,P.R., Meyer,F., Gilbert,J.A., Le Paslier, D., Simonet, P., Vogel, T.M. 2012. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME Journal 6: 1677-1687.

Delmont, T.O., Simonet, P., Vogel, T.M. 2012. Describing microbial communities and performing global comparisons in the ‘omic era. ISME Journal 6: 1625-1628.

Eric Dugat-Bony, Corinne Biderre-Petit, Faouzi JAZIRI, Maude David, Jérémie Denonfoux, Delina Lyon, Jean-Yves Richard, Cyrille Curvers, Delphine Boucher, Timothy Vogel, Eric Peyretaillade, Pierre Peyret. In situ TCE degradation mediated by complex dehalorespiring communities during biostimulation processes. Microbial biotechnology, 2012, 5 (5 SI), pp. 642-653. <http://dx.doi.org/10.1111/j.1751-7915.2012.00339.x>

Gilbert, J., O'Dor, R., Vogel, T. 2011. Survey data are still vital to science. Nature 469:162. doi:10.1038/469162a

Delmont T.O., Robe P, Cecillon S, Clark I.M., Constancias F, Simonet P, Hirsch P.R., Vogel TM. 2011. Accessing Microbial Diversity for Soil Metagenomic Studies. Appl Environ Microbiol. In Press.

Nemir, A., David, M.M., Perrussel, R., Sapkota, A., Pascal Simonet, P., Jean-Michel Monier, J.M., Vogel, T.M. 2010. Comparative phylogenetic microarray analysis of microbial communities in TCE-contaminated soils. Chemosphere doi:10.1016/j.chemosphere.2010.03.036

Sapkota AR, Berger S, Vogel T.M. 2010. Human pathogens abundant in the bacterial metagenome of cigarettes. Environ Health Perspect. 118:351-6.

Héry M, Sanguin H, Perez Fabiel S, Lefebvre X, Vogel T.M., Paul E, Alfenore S. 2010. Monitoring of bacterial communities during low temperature thermal treatment of activated sludge combining DNA phylochip and respirometry techniques. Water Res. 2010 44:6133-43.

Pontiroli A, Ceccherini MT, Poté J, Wildi W, Kay E, Nannipieri P, Vogel T.M., Simonet P, Monier JM. 2010. Long-term persistence and bacterial transformation potential of transplastomic plant DNA in soil. Res Microbiol. 161:326-34.

Lyon, D., Buret, F., Vogel, TM, Monier JM. 2010. Is resistance futile? Changing external resistance does not improve microbial fuel cell performance, Bioelectrochemistry. 78: 2-7.

Lyon, D. Y., Monier, J-M.,  Dupraz, S., Freissinet, C., Simonet, P., and Vogel, T.M. 2010. Integrity and biological activity of DNA after UV exposure. Astrobiology, 10:285-92..

Larose, C., Sibel Berger, Christophe Ferrari, Elisabeth Navarro, Aurélien Dommergue, Dominique Schneider, Vogel, T.M. 2010.  Microbial sequences retrieved from environmental samples from seasonal Arctic snow and meltwater from Svalbard, Norway.  Extremophiles.14:205-12. DOI: 10.1007/s00792-009-0299-2

Malandain, C., Fayolle-Guichard, F., Vogel, T.M. 2010. Cytochromes P450-mediated degradation of  fuel oxygenates by environmental isolates; FEMS Microbial Ecology 72:289-96. 10.1111/j.1574-6941.2010.00847.x

Lyon, D. Y., Pivetal, J., Blanchard, L. and Vogel, T.M. 2010. Bioremediation via
In Situ Electrotransformation
, Bioremediation Journal, 14:109-119

Poté J, Ceccherini MT, Rosselli W, Wildi W, Simonet P and Vogel TM. 2010. Leaching and transformability of transgenic DNA in unsaturated soil columns. Ecotoxicology and Environmental Safety. 73:67-72.

Vogel T.M., Hirsch PR, Simonet P, Jansson J, , Tiedje JM, Van Elsas JD, Nalin R Philippot L, and Bailey MJ. 2009. Advantages of the metagenomic approach for soil exploration. Nature Reviews Microbiology 7, 756–757

Vogel T.M., Simonet P, Jansson J, Hirsch PR, Tiedje JM, Van Elsas JD, Bailey MJ, Nalin R and Philippot L. 2009. TerraGenome: a consortium for the sequencing of a soil metagenome. Nature Rev. Microbiol. 7: 252.

Demanèche, S., Philippot, L., David, M.M., Navarro, E., Vogel, T.M., Simonet, P. 2009. Characterization  of Denitrification Gene Clusters of Soil Bacteria via a Metagenomic Approach. Appl. Environ. Microbiol.75: 534-537

Demanèche, S., David, M.M., Navarro, E., Simonet, P., Vogel, T.M. 2009. Evaluation of functional gene enrichment in a soil metagenomic clone library. J. Microbiol. Methods76: 105-107

Poté, J., Mavingui, P., Navarro, E., Rosselli, W., Wildi, W., Simonet, P., M. Vogel, T.M. 2009.
Extracellular Plant DNA in Geneva Groundwater and Traditional Artesian Drinking Water Fountains. Chemosphere, 75: 498-504.

Pontiroli A, Rizzi A, Simonet P, Daffonchio D, Vogel TM and Monier JM. 2009. Visual evidence of horizontal gene transfer between plant and bacteria in the phytosphere of transplastomic tobacco. Appl. Environ. Microbiol. 75: 3314-3322.

van Elsas, J.D., Costa, R., Jansson, J., Sjöling, S., Bailey, M., Nalin, R., Vogel, T.M. and van Overbeek, L. 2008. The metagenomics of disease suppressive soils – experiences from the METACONTROL project. Trends in Biotechnol. 26:591-601. doi:10.1016/j.tibtech.2008.07.004

Smalla, K., Tebbe, C.C., van Elsas, J.D., Vogel, T.M. 2008. Microbial community networks. FEMS Microbial Ecology. 66:1-2. DOI: 10.1111/j.1574-6941.2008.00596.x

David M, Sapkota AR, Simonet P, Vogel T.M. 2008. A novel and rapid  method for synthesizing positive controls or standards for quantitative PCR. J. Microbiol. Methods. 73:73-77.

Demanèche S, Sanguin H, Poté J, Navarro E, Bernillon D, Mavingui P,  Wildi W, Vogel T.M. and Simonet P. 2008 Antibiotic resistant soil bacteria in transgenic plant fields. Proc Natl Acad. Sci. (USA) PNAS. 105:3957-3962.

Lefevre F, Robe P, Jarrin C, Ginolhac A, Zago C, Auriol D, Vogel T.M.,  Simonet P and Nalin R. Drugs from hidden bugs: Discovery from untapped  resources. Res. Microbiol. 159:153-161.

Rizzi A, Pontiroli A, Brusetti L, Borin S, Sorlini C, Abruzzes Ae,  Sacchi GA,   Vogel T.M., Simonet P, Bazzicalupo M, Nielsen KM, Monier  J.M and Daffonchio D. 2008. Strategy for In Situ Detection of Natural  Transformation-Based Horizontal Gene Transfer Events. Appl. Environ. Microbiol. 74: 1250-1254.


Professor, 2000 -The University of Lyon
R&D Project Manager, 1998- 2000, Rhodia Eco Services
Animateur Scientifique et Technique, 1994-1997, Rhône-Poulenc Industrialisation
Expert d'Environnement, 1992-1994, Rhône-Poulenc Industrialisation
Assistant Professor, 1988-1993 The University of Michigan.
Assistant Professor, 1987-1988, Michigan State University.
Acting Instructor, Fall 1985, Stanford University.
Research Assistant, 1981-1987, Stanford University.
Organic Geochemist, 1979-1982, U.S. Geological Survey.

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