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Dr. Theo Smits

Dr. Theo Smits

Dr. Theo Smits
ZHAW Life Sciences und Facility Management
Grüental
8820 Wädenswil

+41 (0) 58 934 52 93
theo.smits@zhaw.ch

Persönliches Profil

Tätigkeit an der ZHAW als

Dozent Genomik und Bioinformatik - Forschungsgruppe Umweltgenomik und Systembiologie

https://www.zhaw.ch/de/lsfm/institute-zentren/iunr/biologische-landwirtschaft/umweltgenomik-und-systembiologie/

Arbeits- und Forschungsschwerpunkte, Spezialkenntnisse

Genomik, Transcriptomik, Molekulare Biologie, Phylogenetik, Mikrobiologie, Mikrobielle Ökologie

Aus- und Fortbildung

1997-2001: PhD - Inst. of Biotechnology, ETH, Zürich, Switzerland
1991-1997: MSc Bioprocess Engineering (Orientation Microbiology/Molecular biology) – Wageningen University, Wageningen, The Netherlands

Beruflicher Werdegang

2007-2013: Scientific collaborator/PostDoc, Research Bacteriology, National Competence Center for Fire Blight, Agroscope Changins-Wädenswil, Switzerland
2005-2007: Research associate, Microbial Ecology Group, University of Konstanz, Konstanz, Germany
2002-2004: PostDoc, Laboratory of Environmental Biotechnology, EPFL, Lausanne, Switzerland
2001-2002: PostDoc, Laboratory of Soil Science, EPFL, Lausanne, Switzerland
1997-2001: PhD student, Institute of Biotechnology, ETH, Zürich, Switzerland

Projekte

Publikationen

Publikationen vor Tätigkeit an der ZHAW

*** Peer-reviewed papers ***

Marjan N. Kraak, Theo H. M. Smits, Birgit Kessler and Bernard Witholt, 1997. Polymerase C1 levels and poly(R-3-hydroxyalkanoate) synthesis in wild type and recombinant Pseudomonas strains. J. Bacteriol. 179 (16), 4985-4991.

Theo H. M. Smits, Martina Röthlisberger, Bernard Witholt and Jan B. van Beilen, 1999. Molecular cloning of alkane hydroxylase genes in Gram-negative and Gram-positive strains. Environ. Microbiol. 1 (4), 307-318.

Mercedes M. Marin, Theo H. M. Smits, Jan B. van Beilen and Fernando Rojo, 2000. The alkane hydroxylase gene of Burkholderia cepacia RR10 is under catabolite repression control. J. Bacteriol. 183 (14), 4202-4209.

Theo H. M. Smits, Markus A. Seeger, Bernard Witholt and Jan B. van Beilen, 2001. New alkane-responsive expression vectors for E. coli and Pseudomonas. Plasmid 46 (1), 16-24.

Jan B. van Beilen, Martin Neuenschwander, Theo H. M. Smits, Christian Roth, Stefanie B. Balada and Bernard Witholt, 2002. Rubredoxins involved in alkane oxidation. J. Bacteriol. 184 (6), 1722-1732.

Theo H. M. Smits, Stefanie B. Balada, Bernard Witholt and Jan B. van Beilen, 2002. Cloning and functional analysis of alkane hydroxylase genes from Gram-positive and Gram-negative strains. J. Bacteriol. 184 (6), 1733-1742.

Jan B. van Beilen, Theo H. M. Smits, Lyle G. Whyte, Susanne Schorcht, Martina Röthlisberger, Thorsten Plaggemeier, Karl-Heinrich Engesser and Bernard Witholt, 2002. Alkane hydroxylase homologues in Gram-positive strains. Environ. Microbiol. 4 (11), 676-682.

L. G. Whyte, T. H. M. Smits, D. Labbé, B. Witholt, C. W. Greer and J. B. van Beilen, 2002. Gene cloning and characterization of multiple alkane hydroxylase systems in Rhodococcus strains Q15 and NRRL B-16531. Appl. Environ. Microbiol. 68 (12), 5933-5942.

Theo H. M. Smits, Lukas Y. Wick, Hauke Harms and Christoph Keel, 2003. Characterization of surface hydrophobicity of filamentous fungi. Environ. Microbiol. 5 (2), 85-92.

Jan B. van Beilen, Frédéric Mourlane, Markus A. Seeger, Jasminka Kovac, Zhi Li, Theo H. M. Smits, Urban Fritsche and Bernard Witholt, 2003. Cloning of Baeyer-Villiger monooxygenases from Rhodococcus, Pseudomonas and Xanthobacter. Environ. Microbiol. 5 (3), 174-182.

Theo H. M. Smits, Bernard Witholt and Jan B. van Beilen, 2003. Functional characterization of genes involved in alkane oxidation by Pseudomonas aeruginosa. Anton. Leeuwenhoek 84 (3), 193-200.

Jan B. van Beilen, Zhi Li, Wouter A. Duetz, Theo H. M. Smits and Bernard Witholt, 2003. Diversity of alkane hydroxylase systems in the environment. Oil Gas Sci. Technol. Ref. IFP 58 (4), 427-440.

Akihiro Hara, Sang-Ho Baik, Kazuaki Syutsubo, Norihiko Misawa, Theo H. M. Smits, Jan B. van Beilen and Shigeaki Harayama, 2004. Cloning and functional analysis of alkB genes in Alcanivorax borkumensis SK2. Environ. Microbiol. 6 (3), 191-197.

Jan B. van Beilen, Mercedes M. Marin, Theo H. M. Smits, Martina Röthlisberger, Alessandro G. Franchini, Bernard Witholt and Fernando Rojo, 2004. Characterization of two alkane hydroxylase genes from the marine hydrocarbonoclastic bacterium Alcanivorax borkumensis. Environ. Microbiol. 6 (3), 264-273.

Theo H. M. Smits, Christiane Devenoges, Katia Szynalski, Julien Maillard and Christof Holliger, 2004. Development of a real-time PCR method for quantitation of the genera Dehalobacter, Dehalococcoides and Desulfitobacterium in microbial communities. J. Microbiol. Methods 57 (3), 369-378.

Jan B. van Beilen, Theo H. M. Smits, Franz Roos, Tobias Brunner, Stefanie B. Balada, Martina Röthlisberger and Bernard Witholt, Identification of an amino acid position that determines the substrate range of integral membrane alkane hydroxylases. J. Bacteriol. 187 (1), 85-91.

Stefanie Kohlmeyer, Theo H. M. Smits, Roseanne M. Ford, Christoph Keel, Hauke Harms and Lukas Y. Wick, 2005. Taking the fungal highway: mobilization of pollutant-degrading bacteria by fungi. Environ. Sci. Technol. 39, 4640-4646.

Sonja Weinitschke, Karin Denger, Theo H. M. Smits, Klaus Hollemeyer and Alasdair M. Cook, 2006. The sulfonated osmolite N-methyltaurine is dissimilated by Alcaligenes faecalis and by Paracoccus versutus with release of methylamine. Microbiology 152 (4), 1179-1185.

Karin Denger, Theo H. M. Smits and Alasdair M. Cook, 2006. L-cysteate sulpholyase, a widespread, pyridoxal 5’ phosphate desulphonative enzyme purified from Silicibacter pomeroyi DSS-3T. Biochem. J. 394 (3), 657-664.

Alasdair M. Cook, Karin Denger and Theo H. M. Smits, 2006. Dissimilation of C3-sulfonates. Arch. Microbiol. 185 (2), 83-90.

Andzelika K. Gorzynska, Karin Denger, Alasdair M. Cook and Theo H. M. Smits. 2006. Inducible transcription of genes involved in taurine uptake and dissimilation by Silicibacter pomeroyi DSS-3T. Arch. Microbiol. 185 (4), 402-406.

Heike Laue, Theo H. M. Smits, Ulrike K. Schumacher, Marina C. Claros, Ralf Hartemink and Alasdair M. Cook. 2006. Identification of Bilophila wadsworthia by specific PCR which targets the taurine:pyruvate aminotransferase gene. FEMS Microbiol. Lett. 261 (1), 74-79.

Jutta Mayer, Karin Denger, Theo H. M. Smits, Klaus Hollemeyer, Ulrich Groth and Alasdair M. Cook. 2006. N-acetyltaurine dissimilated via taurine by Delftia acidovorans NAT. Arch. Microbiol. 186 (1), 61-67.

Karin Denger, Theo H. M. Smits, and Alasdair M. Cook. 2006. Genome-enabled analysis of the utilization of taurine as sole source of carbon or nitrogen by Rhodobacter sphaeroides 2.4.1. Microbiology 152 (11), 3197-3206.

Marijke I. Baldock , Karin Denger, Theo H. M. Smits, and Alasdair M. Cook. 2007. Roseovarius sp. strain 217: aerobic taurine dissimilation via acetate kinase and acetyl-CoA ligase. FEMS Microbiol. Lett. 271 (2), 202-206.

Sonja Weinitschke, Karin Denger, Alasdair M. Cook and Theo H. M. Smits. 2007. The DUF81 protein TauE in Cupriavidus necator H16, a sulfite exporter in the metabolism of C2 sulfonates. Microbiology 153 (9), 3055-3060.

Alasdair M. Cook, Theo H. M. Smits, and Karin Denger. 2007. Organosulfonates and heterotrophic sulfite metabolism. In C. Dahl and C. G. Friedrich (eds.), Microbial Sulfur Metabolism. pp. 170-183. Springer-Verlag, Berlin-Heidelberg (D).

Karin Denger, Sonja Weinitschke, Theo H. M. Smits, David Schleheck, and Alasdair M. Cook, 2008. Bacterial sulfite dehydrogenases in organotrophic metabolism: separation and identification in Cupriavidus necator H16 and in Delftia acidovorans SPH-1. Microbiology 154 (1), 256-263.

Jutta Mayer, Karin Denger, Katrin Kaspar, Klaus Hollemeyer, Theo H. M. Smits, Thomas Huhn and Alasdair M. Cook. 2008. Assimilation of homotaurine-nitrogen by Burkholderia sp. and excretion of sulfopropanoate. FEMS Microbiol. Lett. 279 (1), 77-82.

Verena Rösch, Karin Denger, David Schleheck, Theo H. M. Smits and Alasdair M. Cook. 2008. Different bacterial strategies to degrade taurocholate. Arch. Microbiol. 190 (1) 11-18.

Zdenek Krejčik, Karin Denger, Sonja Weinitschke, Klaus Hollemeyer, Václav Pačes, Alasdair M. Cook, and Theo H. M. Smits. 2008. Sulfoacetate released during the assimilation of taurine-nitrogen by Neptuniibacter caesariensis: purification of sulfoacetaldehyde dehydrogenase. Arch. Microbiol. 190 (2), 159-168.

Theo H. M. Smits, Arne Hüttmann, David Lerner and Christof Holliger, 2009. Detection and quantification of bacteria involved in aerobic and anaerobic ammonium oxidation in an ammonium-contaminated aquifer. Biorem. J. 13 (1), 41-51.

Karin Denger, Jutta Mayer, Matthias Buhmann, Sonja Weinitschke, Theo H. M. Smits and Alasdair M. Cook, 2009. Bifurcated degradative pathway of sulfolactate in Roseovarius nubinhibens ISM via sulfoacetaldehyde acetyltransferase and (S)-cysteate sulfo-lyase. J. Bacteriol. 191 (18): 5648-5656.

Fabio Rezzonico, Theo H. M. Smits, Emilio Montesinos, Jürg E. Frey and Brion Duffy, 2009. Genotypic comparison of Pantoea agglomerans plant and clinical strains to address biosafety and taxonomic questions. BMC Microbiol. 9:204.

Theo H. M. Smits, Sebastian Jaenicke, Fabio Rezzonico, Tim Kamber, Alexander Goesmann, Jürg E. Frey and Brion Duffy, 2010. Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into pathogenicity. BMC Genomics, 11: 2.

Sonja Weinitschke, Pia I. Sharma, Ulrich Stingl, Alasdair M. Cook and Theo H. M. Smits, 2010. Gene clusters involved in isethionate degradation by terrestrial and marine bacteria. Appl. Environ. Microbiol. 76 (2): 618.621.

Zdenek Krejčik, Klaus Hollemeyer, Theo H. M. Smits and Alasdair M. Cook, 2010. Isethionate formation from taurine in Chromohalobacter salexigens involves taurine:2-oxoglutarate aminotransferase and sulfoacetaldehyde reductase. Microbiology, 156 (5): 1547-1555.

Theo H. M. Smits, Fabio Rezzonico, Tim Kamber, Jochen Blom, Alexander Goesmann, Jürg E. Frey and Brion Duffy, 2010. Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp. Mol. Plant-Microbe Interact. 23 (4): 384-393.

Jürgen Ruff, Theo H. M. Smits, Alasdair M. Cook and David Schleheck, 2010. Identification of two vicinal operons for the degradation of 2-aminobenzenesulfonate encoded on plasmid pSAH in Alcaligenes sp. strain O1. Microbiol. Res. 165: 288-299.

Theo H. M. Smits, Fabio Rezzonico, Cosima Pelludat, Alexander Goesmann, Jürg E. Frey and Brion Duffy, 2010. Genomic and phenotypic characterization of a non-pigmented variant of Pantoea vagans biocontrol strain C9-1 lacking the 530 kb megaplasmid pPag3. FEMS Microbiol. Lett. 308 (1): 48-54.

Sonja Weinitschke, Klaus Hollemeyer, Bernhard Kusian, Botho Bowien, Theo H. M. Smits and Alasdair M. Cook, 2010. Sulfoacetate degraded via novel sulfoacetyl-CoA and sulfoacetaldehyde in Cupriavidus necator H16. J. Biol. Chem. 285 (46): 35249-35254.

Theo H. M. Smits, Fabio Rezzonico, Tim Kamber, Alexander Goesmann, Carol A. Ishimaru, Virginia O. Stockwell, Jürg E. Frey and Brion Duffy, 2010. The genome sequence of the biocontrol agent Pantoea vagans C9-1. J. Bacteriol. 192 (24): 6486-6487.

Rachel Powney, Theo H. M. Smits, Tim Sawbridge, Beatrice Frey, Jochen Blom, Jürg E. Frey, Kim M. Plummer, Steven V. Beer, Joanne Luck, Brion Duffy and Brendan Rodoni, 2011. Genome sequence of an Erwinia amylovora strain with restricted pathogenicity to Rubus plants. J. Bacteriol. 193 (3):785-786.

Juliane Weger, Melanie Schanze, Maja Hilber-Bodmer, Theo H. M. Smits and Andrea Patocchi, 2011. First report of the -tubulin E198A mutation conferring resistance to methyl benzimidazole carbamates in European isolates of Monilinia fructicola. Plant Dis. 95(4): 497.

Theo H. M. Smits, Fabio Rezzonico and Brion Duffy, 2011. Evolutionary insights from Erwinia amylovora genomics. J. Biotechnol., 155 (1) 34-39.

Kerstin Brankatschk, Jochen Blom, Alexander Goesmann, Theo H. M. Smits and Brion Duffy, 2011. The genome of a European fresh vegetable food safety outbreak strain of Salmonella enterica subsp. enterica serovar Weltevreden. J. Bacteriol., 193 (8): 2066.

Theo H. M. Smits, Antoine Assal, Daniel Hunkeler and Christof Holliger, 2011. Anaerobic degradation of vinyl chloride in aquifer microcosms. J. Environ. Qual. 40 (3): 915-922.

Fabio Rezzonico, Theo H. M. Smits and Brion Duffy, 2011. Diversity and functionality of CRISPR regions in fire blight pathogen Erwinia amylovora. Appl. Environ. Microbiol. 77 (11): 3819-3829.

Theo H. M. Smits, Fabio Rezzonico, Tim Kamber, Alexander Goesmann, Carol A. Ishimaru, Jürg E. Frey, Virginia O. Stockwell and Brion Duffy, 2011. Metabolic versatility and antibiotic biosynthesis are distinguishing genomic features of the commercial fire blight antagonist Pantoea vagans C9-1. PLoS One 6: e22247.

Joël Pothier, Frank-Jörg Vorhölter, Jochen Blom, Alexander Goesmann, Alfred Pühler, Theo H. M. Smits and Brion Duffy, 2011. Complete sequence and comparative genomic analysis of a ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni. FEMS Microbiol. Lett. 323 (1): 52-60.

P. Lawrence Pusey, Virginia O. Stockwell, Catherine L. Reardon, Theo H. M. Smits and Brion Duffy, 2011. Antibiosis by Pantoea agglomerans biocontrol strain E325 against Erwinia amylovora on apple blossom stigmas. Phytopathology 101 (10): 1234-1241.

Theo H. M. Smits and Brion Duffy, 2011. Genomics of iron-acquisition in the plant pathogen Erwinia amylovora: insights in the biosynthetic pathway of the siderophore desferrioxamine E. Arch. Microbiol. 193 (10) 693-699.

Pieter de Maayer, Stephanus N. Venter, Tim Kamber, Brion Duffy, Teresa A. Coutinho and Theo H. M. Smits, 2011. Comparative genomics of the type VI secretion systems of Pantoea and Erwinia species reveals the presence of putative effector islands that may be translocated by the VgrG and Hcp proteins. BMC Genomics 12: 576.

Pablo Llop, Jordi Cabrefiga, Theo H. M. Smits, Tanja Dreo, Sivlia Barbé, Joanna Pulawska, Alain Bultreys, Jochen Blom, Brion Duffy, Emilio Montesinos and María M. López, 2011. Erwinia amylovora novel plasmid pEI70: complete sequence biogeography, and role in aggressiveness in the fire blight phytopathogen. PLoS One 6 (12): e28651.

Tim Kamber, Theo H. M. Smits, Fabio Rezzonico and Brion Duffy, 2012. Genomics and current genetic understanding of Erwinia amylovora and the fire blight antagonist Pantoea vagans. Trees Struct. Funct. 26 (1): 227-238.

Maja Hilber-Bodmer, Verena Knorst, Theo H. M. Smits and Andrea Patocchi, 2012. First report of Asian brown rot caused by Monilia polystroma on apricot in Switzerland. Plant Dis. 96: 146.

Pieter de Maayer, Way Yin Chan, Fabio Rezzonico, Andreas Bühlmann, Stephanus N. Venter, Jochen Blom, Alexander Goesmann, Jürg E. Frey, Theo H. M. Smits, Brion Duffy and Teresa A. Coutinho, 2012. Complete genome sequence of Pantoea ananatis LMG 5342 clinical isolate. J. Bacteriol. 194 (6): 1615-1616.

Kerstin Brankatschk, Jochen Blom, Alexander Goesmann, Theo H. M. Smits and Brion Duffy, 2012. Comparative genomic analysis of Salmonella enterica subsp. enterica serovar Weltevreden foodborne strains with other serovars. Int. J. Food Microbiol. 155 (3): 247-256.

Fabio Rezzonico, Virginia O. Stockwell, Mauro Tonolla, Brion Duffy and Theo H. M. Smits, 2012. Pantoea clinical isolates cannot be accurately assigned to species based on metabolic profiling. Transpl. Infect. Dis. 14(2): 220-221.

Tim Kamber, Teresa A. Lansdell, Virginia O. Stockwell, Carol A. Ishimaru, Theo H. M. Smits and Brion Duffy, 2012. Characterization of the antibacterial peptide herbicolin I biosythetic operon in Pantoea vagans biocontrol strain C9-1 and incidence in Pantoea species. Appl. Environ. Microbiol. 78(12):4412-4419.

Fabio Rezzonico, Theo H. M. Smits and Brion Duffy, 2012. Misidentification slanders Pantoea agglomerans as a serial killer. J. Hosp. Infect. 81(2):137-139.

Fabio Rezzonico, Theo H.M. Smits and Brion Duffy, 2012. Detection of AI-2 receptors in genomes of Enterobacteriaceae suggests a role of type-2 quorum sensing in closed ecosystems. Sensors 12(5): 6645-6665.

Manuela Filippini, Weihong Qi, Jochen Blom, Alexander Goesmann, Theo H. M. Smits and Homayoun Bagheri, 2012. Genome sequence of Fibrella aestuarina BUZ 2T, a filamentous marine bacterium. J. Bacteriol. 194(13):3555.

Rachel A. Mann, Jochen Blom, Andreas Bühlmann, Kim M. Plummer, Steven V. Beer, Jo A.Luck, Alexander Goesmann, Brendan C. Rodoni, Brion Duffy and Theo H. M. Smits, 2012. Comparative analysis of the integrative conjugative element of Rubus- and Spiraeoideae-infecting Erwinia amylovora strains gives indications to genome reduction during species evolution. Gene 504(1): 6-12.

Fabio Rezzonico, Andrea Braun-Kiewnick, Rachel A. Mann, Alexander Goesmann, Brendan C. Rodoni, Brion Duffy and Theo H. M. Smits, 2012. Lipopolysaccharide biosynthesis genes discriminate between Rubus- and Spiraeoideae-infective genotypes of Erwinia amylovora. Mol. Plant Pathol. 13(8): 975-984.

Mickael Malnoy, Stefan Martens, John L. Norelli, Marie-Anne Barny, George W. Sundin, Theo H. M. Smits and Brion Duffy, 2012. Applied genomics of fire blight: plant-pathogen interactions, evolution and translation into disease control strategies. Annu. Rev. Phytopathol. 50: 475-494.

Manuela Filippini, Weihong Qi, Sebastian Jaenicke, Alexander Goesmann, Theo H. M. Smits and Homayoun C. Bagheri, 2012. Genome sequence of filamentous bacterium Fibrisoma limi BUZ 3T. J. Bacteriol. 194(16): 4445.

Andrea Braun-Kiewnick, Andreas Lehmann, Fabio Rezzonico, Theo H. M. Smits and Brion Duffy, 2012. Development of molecular monitoring tools for strain- and species-specific detection of the fire blight biocontrol agent Pantoea agglomerans. J. Microbiol. Methods 90: 315-320.

Pieter de Maayer, Wai-Yin Chan, Jochen Blom, Stephanus N. Venter, Brion Duffy, Theo H. M. Smits and Teresa A. Coutinho, 2012. The large universal plasmid, LPP-1, plays a major role in the biological and ecological diversification of Pantoea spp. BMC Genomics 13: 625.



*** Other publications ***

Theo H. M. Smits, Fabio Rezzonico, Cosima Pelludat, Alexander Goesmann, Jürg E. Frey and Brion Duffy, 2009. Complete genome sequencing of Pantoea agglomerans strain C9-1. IOBC Bull. 43, 375-378.

Fabio Rezzonico, Theo H. M. Smits, Cosima Pelludat, Emilio Montesinos, Jürg E. Frey and Brion Duffy, 2009. Genotypic comparison of Pantoea agglomerans biocontrol and clinical isolates to address taxonomic and bio-safety questions. IOBC Bull. 43, 35-39.

Andrea Braun-Kiewnick, Andreas Lehmann, Theo H. M. Smits, Brion Duffy and Tanja Dreo, 2011. Environmental monitoring of Pantoea agglomerans biocontrol strain E325 in Swiss orchards. Acta Hort. 896: 73-76.

Tanja Dreo, Maja Ravnikar, Jürg E. Frey, Theo H. M. Smits and Brion Duffy, 2011. In silico analysis of variable number of tandem repeats in Erwinia amylovora genome. Acta Hort. 896: 115-118.

Tim Kamber, Theo H. M. Smits and Brion Duffy , 2011. Type VI secretion systems in Erwinia amylovora CFBP 1430. Acta Hort. 896: 211-213.

Fabio Rezzonico, Theo H. M. Smits and Brion Duffy, 2011. Record of past encounters with phages and plasmids delivers new insights about the origin and dispersal of fire blight pathogen Erwinia amylovora. Acta Hort. 896: 109-113.

Theo H. M. Smits, Fabio Rezzonico, Jürg E. Frey, Brion Duffy, Jochen Blom and Alexander Goesmann, 2011. Insights into evolution from comparative genomics of Erwinia amylovora and related species. Acta Hort. 896: 259-262.

Theo H. M. Smits, Fabio Rezzonico, Cosima Pelludat, Tim Kamber, Jürg E. Frey, Brion Duffy, Alexander Goesmann, Carol A. Ishimaru and Virginia O. Stockwell, 2011. The genome sequence of Pantoea vagans biocontrol strain C9-1. Acta Hort. 896: 233-236.