Dirk Gevers

Postdoc
(Group member from 2003 until 2009)


+ 32 (0) 9 33 13 822

VIB / Ghent University
Bioinformatics & Systems Biology
Technologiepark 927
B-9052 Gent
BELGIUM

CV

Birthdate: 8 June 1976, Turnhout, Belgium.

June 2006 - now: Visiting postdoc at the Polz Lab, Civil & Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA: 'A population-level analysis of the bacterial species' (FWO travel grant)

Oktober 2004 - now: Postdoc 'From comparative genomics to a prokaryotic genomic taxonomy', Laboratory of Microbiology, Ghent University, Belgium (FWO post-doctoral grant)

January 2003 - September 2004: Postdoc 'Microbial comparative genomics', Bioinformatics & Evolutionary Genomics, Ghent University/VIB, Belgium (BOF/UGent post-doctoral grant).

October 1998 - December 2002: Ph.D. studies 'Transferable tetracycline resistance in lactic acid bacteria isolated from fermented dry sausage', Laboratory of Microbiology, Ghent University, Belgium (IWT post-graduate grant).

October 1996 - September 1998: Licentiate Biochemistry (M. Sc.), Ghent University, Belgium.

October 1994 - September 1996: Candidate Chemistry (B. Sc.), Limburg University (LUC), Diepenbeek, Belgium.

Research

My post-doctoral research is an interplay between comparative and evolutionary bioinformatics applied at the crossroads between prokaryotic taxonomy, ecology and population genetics. The research bridges between the research at Laboratory of Microbiology and the expertise in the Bioinformatics & Evolutionary Genomics group, both at the Ghent University, Faculty of Sciences. Currently I'm staying in the Polz lab at MIT to develop a different viewpoint on microbial evolution with inputs from environmental microbiology and population genetics. Specific topics of my research include:
  • Roadmap towards a prokaryotic genomic taxonomy: developing a bioinformatics toolbox for the detection of phylogenetic markers that can be used in multi-locus sequence schemes for high-throughput classification and identification, i.e. a genomic taxonomy. Applied to several model groups of bacteria representing different phylogenetic lineages: vibrios, lactic acid bacteria, burkholderias, ...
  • Population-level analysis of the bacterial species: in silico analysis of the sequence diversity and dynamics of a well-defined natural bacterial population, in order to increase our understanding of species and speciation in prokaryotes. Focus on the role of homologous recombination in the creation of genomic coherence.
  • Analysis of the Azorhizobium caulinodans genome with the aim of increasing our insight in the invasion, colonisation and signalisation between plant and bacteria (in collaboration with the plant-microbes group at PSB)

Papers

(29) Holder, J.W., Ulrich, J.C., DeBono, A.C., Godfrey, P.A., Desjardins, C.A., Zucker, J., Zeng, Q., Leach, A.L.B., Ghiviriga, I., Dancel, C., Abeel, T., Gevers, D., Kodira, C., Desany, B., Affourtit, J., Birren, B.W., Sinskey, A.J. (2011) Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development. PLoS Genet. 7(9):e1002219.

(28) Francis, I., Gevers, D., Karimi, M., Holsters, M. & Ver (2007) Linear plasmids and phytopathogenicity. Microbiology Monographs 7, 99-115 .

(27) Naser, S., Dawyndt, P., Hoste, B., Gevers, D., Vandemeulebroecke, K., Cleenwerck, I., Vancanneyt, M., Swings, J. (2007) Development of a rapid multilocus sequence analysis (MLSA)-based identification system for Lactobacillus using pheS and rpoA genes. Int. J. Syst. Evol. Microbiol. 57,2777–2789.

(26) van Hylckama Vlieg, J.E.T., Herbet, H. Starr, Gevers, D., Kelly, W.J., Swings, J., , Rademaker, J.L.W. (2007) Diversity Analysis of Dairy and Nondairy Lactococcus lactis Isolates, Using a Novel Multilocus Sequence Analysis Scheme and (GTG)5-PCR Fingerprinting. Appl. Environ. Microbiol. 73, 7128-7137.

(25) Gevers, D., Dawyndt, P., Vandamme, P., Willems, A., Vancanneyt, M., Swings, J., De Vos, P. (2006) Stepping stones towards a new prokaryotic taxonomy. Phil. Trans. R. Soc. B. 361(1475):1911-6.

(24) Jacobsen, L., Andersen, R.A., Hammer, K., Huys, G., Gevers, D., Wilcks, A. (2006) In vivo horizontal transfer of tetM and ermB resistance plasmids from food strains of Lactobacillus plantarum to Enterococcus faecalis in the gastrointestinal tract of gnotobiotic rats. FEMS Microbiol. Lett. (published online Oct 2, 2006).

(23) Gomez-Gil, B., Thompson, F.L., Sawabe, T., Vicente, A., Coelho, A., Gevers, D., Swings, J. (2006) The Genus Vibrio. in "The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, 3rd edition, release 3.x", Editors: M. Dworkin et al., Springer-Verlag, New York.

(22) Gevers, D., Van de Peer, Y. (2006) Gene duplicates in vibrio genomes. Invited book chapter in The Biology of Vibrios. Editors: Thompson, F.L., Austin, B. & Swings, J. ASM press. pp. 76-83.

(21) Thompson, F.L., Klose, K.E., Gevers, D., Avib, Group (2006) Meeting Report - Vibrio2005: the first International conference on the biology of Vibrios. J. Bacteriol. 188(13):4592-6.

(20) Heylen, K., Gevers, D., Vanparys, B., Wittebolle, L., Geets, J., Boon, N., De Vos, P. (2006) The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers. Environ. Microbiol. 8(11):2012-21.

(19) Heylen, K., Vanparys, B., Gevers, D., Wittebolle, L., Boon, N., De Vos, P. (2006) P. Nitric oxide (norB) gene sequence analysis in cultivated denitrifiers reveals discrepancies with nitrite oxide (nir) gene phylogeny. Environ. Microbiol. 9(4):1072-7..

(18) Ouadghiri, M., Vancanneyt, M., Naser, S., Gevers, D., Lefebvre, K., Swings, J., Amar, M. (2006) Lactic acid bacteria in raw milk and fermented skimmed milk lben sampled from different farms in Morocco. J. Appl. Microbiol. 106(2):486-95.

(17) Gevers, D., Coenye, T. (2005) Phylogenetic and genomic analysis. Invited book chapter in ASM Manual of Environmental Microbiology, 3th edition. Editors: Garland, J.L. & O'Connell, S. ASM press. p.157-168.

(16) * Coenye, T., * Gevers, D., Van de Peer, Y., Vandamme, P., Swings, J. (2005) Review: Towards a prokaryotic genomic taxonomy. Fems Microbiol. Rev. 29(2):147-67. *contributed equally

(15) Naser, S., Thompson, F.L., Hoste, B., Gevers, D., Vandemeulebroecke, K., Cleenwerck, I., Thompson, C. C., Vancanneyt, M., Swings, J. (2005) Phylogeny and Identification of Enterococcus Species Using atpA Gene Sequences. J. Clin. Micorbiol 43(5):2224-30.

(14) Gevers, D., Cohan, F.M., Lawrence, J.G., Spratt, B.G., Coenye, T., Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005) Re-evaluating prokaryotic species. Nature Rev. Micriobiol. 3(9):733-9.

(13) Thompson, F.L., Gevers, D., Thompson, C. C., Dawyndt, P., Naser, S., Hoste, B., Swings, J., (2005) Phylogeny and molecular identification of vibrios based on multilocus sequence analysis. Appl. Environ. Microbiol. 71(9):5107-15.

(12) Naser, S., Thompson, C. C., Hoste, B., Gevers, D., Dawyndt, P., Vancanneyt, M., Swings, J. (2005) Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology 151(Pt 7):2141-50.

(11) Gevers, D., Vandepoele, K., Simillion, C., Van de Peer, Y. (2004) Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol. 12(4):148-54.

(10) De Clerck, E, Gevers, D., Sergeant, K, Rodriguez-Diaz, M, Herman, L, Logan, N.A., Van Beeumen, J., De Vos, P. (2004) Genomic and phenotypic comparison of Bacillus fumarioli isolates from geothermal Antarctic soil and gelatine. Research in Microbiology 155(6):483-90.

(9) De Clerck, E, Gevers, D., De Ridder, K, De Vos, P. (2004) Screening of bacterial contamination during gelatine production by means of denaturing gradient gel electrophoresis, focussed on Bacillus and related endosporeforming genera. J. Appl. Microbiol. 96(6):1333-41.

(8) Gevers, D., Huys, G., Swings, J. (2003) In vitro conjugal transfer of tetracycline resistance from Lactobacillus isolates to other Gram-positive bacteria. FEMS Microbiol. Lett. 225(1):125-30.

(7) Masco, L., Huys, G., Gevers, D., Verbrugghen, L., Swings, J. (2003) Identification of Bifidobacterium species using rep-PCR fingerprinting. Syst. Appl. Microbiol. 26(4):557-63.

(6) Gevers, D., Masco, L., Baert, L., Huys, G., Debevere, J., Swings, J. (2003) Prevalence and diversity of tetracycline resistant lactic acid bacteria and their tet genes along the process line of fermented dry sausages. Syst. Appl. Microbiol. 26(2):277-83.

(5) Neysens, P., Messens, W., Gevers, D., Swings, J., De Vuyst, L. (2003) Biphasic kinetics of growth and bacteriocin production with Lactobacillus amylovorus DCE471 occur under stress conditions. Microbiology 149(Pt 4):1073-82.

(4) Gevers, D., Danielsen, M., Huys, G., Swings, J. (2003) Molecular characterization of tet (M) genes in Lactobacillus isolates from different types of fermented dry sausage. Applied and Environmental. Appl. Environ. Microbiol. 69(2):1270-5.

(3) Gevers, D., Huys, G., Swings, J. (2001) Applicability of rep- PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol. Lett. 205(1):31-6.

(2) Huys, G., Gevers, D., Temmerman, R., Cnockaert, M., Denys, R., Rhodes, G., Pickup, R., McGann, P., Hiney, M., Smith, P., Swings, J. (2001) Comparison of the antimicrobial tolerance of oxytetracycline-resistant heterotrophic bacteria isolated from hospital sewage and freshwater fishfarm water in Belgium. Syst. Appl. Microbiol. 24(1):122-30.

(1) Gevers, D., Huys, G., Devlieghere, F., Uyttendaele, M., Debevere, J., Swings, J. (2000) Isolation and identification of antibiotic resistant lactic acid bacteria from pre-packed sliced meat products. Syst. Appl. Microbiol. 23(2):279-84.











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Bioinformatics & Evolutionary Genomics
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B-9052 Gent
BELGIUM
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