Prof. Dr. Theo Smits

Personal profile

Management role

Head, Research Group Environmental Genomics and Systems Biology

Position at the ZHAW

Lecturer Genomics and Bioinformatics - Research Group Environmental Genomics and Systems Biology

www.zhaw.ch/iunr/umweltgenomik

Expertise and research interests

Genomics, Transcriptomics, Molecular Biology, Phylogenetics, Microbiology, Microbial Ecology

Projects

• Modernes Biodiversitätsmonitoring mit Next-Generation Sequencing (NGS-Methoden) / Deputy project leader / Project ongoing
• EBDOmics – Comparative genomics of Enterobacter spp. causing Bulb Decay of Onions / Project leader / Project ongoing
• Wildstauden-Mischpflanzungen zur Förderung der Biodiversität (ober- und unterirdisch) und Humuserhalt im urbanen Raum / Team member / Project ongoing
• Preservation of Central Asian fruit tree forest ecosystems from bacterial pathogen Erwinia amylovora (fire blight) / Project co-leader / Project ongoing
• Genomics and transcriptomics of Erwinia and Pantoea / Project leader / Project ongoing
• Comparative genomics of the plant pathogen Xanthomonas arboricola pv. pruni and related xanthomonads / Team member / Project ongoing
• Fire Blight App for Central Asia / Project leader / Project completed
• Antibiotic resistances in Enterobacteria / Deputy project leader / Project completed
• Fighting bites with bytes: Promoting public health with crowdsourced tick prevention / Project leader / Project completed
• CarbonATE - microbiological methanation / Team member / Project completed
• Platform Health / Project co-leader / Project completed
• XhortOMICs: Diagnostic and epidemiological tools for the Xanthomonas hortorum species-level clade based on OMICs technologies / Project leader / Project completed
• Effect of cryopreservation on genome mutation rate - examples of grapevine / Project leader / Project completed
• Development of a fast and exact method for R. solanacearum detection in Swiss surface water samples / Team member / Project completed
• Off Flavour control in land-based salmon production / Team member / Project completed
• Characterization of nitrogen dynamics in an aquaponic system / Project leader / Project completed
• Comparative genomics to untangle insect pathogenicity in plant-associated pseudomonads / Project leader / Project completed
• Sepsis-Associated Microorganisms in Brazilian Ambulatories (SAMBA) / Project leader / Project completed

Publications

• Arend, Lavinia N.V.S.; Bergamo, Ricardo; Rocha, Fabiano B.; Bail, Larissa; Ito, Carmen; Baura, Valter A.; Balsanelli, Eduardo; Pothier, Joël F.; Rezzonico, Fabio; Pilonetto, Marcelo; Smits, Theo H.M.; Tuon, Felipe Francisco,

  2023.

  Dissemination of NDM-producing bacteria in Southern Brazil.

  Diagnostic Microbiology and Infectious Disease.

  106(2), pp. 115930.

  Available from: https://doi.org/10.1016/j.diagmicrobio.2023.115930

• Kurz, Mirjam; Kölz, Adrian; Gorges, Jonas; Carmona, Beatriz Pablo; Brang, Peter; Vitasse, Yann; Kohler, Martin; Rezzonico, Fabio; Smits, Theo H. M.; Bauhus, Jürgen; Rudow, Andreas; Hansen, Ole Kim; Vatanparast, Mohammad; Sevik, Hakan; Zhelev, Petar; Gömöry, Dusan; Paule, Ladislav; Sperisen, Christoph; Csilléry, Katalin,

  2023.

  Tracing the origin of Oriental beech stands across Western Europe and reporting hybridization with European beech : implications for assisted gene flow.

  Forest Ecology and Management.

  531(120801).

  Available from: https://doi.org/10.1016/j.foreco.2023.120801

• Gartmann, Florentina; Hügly, Julian; Krähenbühl, Nikita; Brinkmann, Nadine; Schmautz, Zala; Smits, Theo H. M.; Junge, Ranka,

  2023.

  Bioponics – an organic closed-loop soilless cultivation system : yields and characteristics compared to hydroponics and soil cultivation.

  Agronomy.

  13(6), pp. 1436.

  Available from: https://doi.org/10.3390/agronomy13061436

• Sulja, Arburon; Pothier, Joël F.; Blom, Jochen; Moretti, Chiaraluce; Buonaurio, Roberto; Rezzonico, Fabio; Smits, Theo H. M.,

  2022.

  Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734.

  BMC Genomics.

  23(742).

  Available from: https://doi.org/10.1186/s12864-022-08966-y

• Schmautz, Zala; Walser, Jean-Claude; Espinal, Carlos A.; Gartmann, Florentina; Scott, Benjamin; Pothier, Joël F.; Frossard, Emmanuel; Junge, Ranka; Smits, Theo H. M.,

  2022.

  Microbial diversity across compartments in an aquaponic system and its connection to the nitrogen cycle.

  Science of the Total Environment.

  852(158426).

  Available from: https://doi.org/10.1016/j.scitotenv.2022.158426

• Dia, Nay C.; Cottyn, Bart; Blom, Jochen; Smits, Theo H. M.; Pothier, Joël F.,

  2022.

  Differentiation of the Xanthomonas hortorum – Xanthomonas hydrangeae species complex using sensitive and selective LAMP assays.

  Frontiers in Agronomy.

  4(898778).

  Available from: https://doi.org/10.3389/fagro.2022.898778

• Ruinelli, Michela; Blom, Jochen; Smits, Theo H. M.; Pothier, Joël F.,

  2022.

  Comparative genomics of Prunus-associated members of the Pseudomonas syringae species complex reveals traits supporting co-evolution and host adaptation.

  Frontiers in Microbiology.

  13(804681).

  Available from: https://doi.org/10.3389/fmicb.2022.804681

• Smits, Theo H. M.; Arend, Lavinia N. V. S.; Cardew, Sofia; Tång-Hallbäck, Erika; Mira, Marcelo T.; Moore, Edward R. B.; Sampaio, Jorge L. M.; Rezzonico, Fabio; Pillonetto, Marcelo,

  2022.

  Resolving taxonomic confusion : establishing the genus Phytobacter on the list of clinically relevant Enterobacteriaceae.

  European Journal of Clinical Microbiology & Infectious Diseases.

  41(4), pp. 547-558.

  Available from: https://doi.org/10.1007/s10096-022-04413-8

• Maltseva, Elina R.; Zharmukhamedova, Galiya A.; Jumanova, Zhulduzay K.; Naizabayeva, Dinara A.; Berdygulova, Zhanna A.; Dmitriyeva, Karina A.; Soltanbekov, Sagi S.; Argynbayeva, Assel M.; Skiba, Yuriy A.; Malakhova, Natalya P.; Rezzonico, Fabio; Smits, Theo H.M.,

  2022.

  Assessment of fire blight introduction in the wild apple forests of Kazakhstan.

  Biodiversity.

  23(3-4), pp. 123-128.

  Available from: https://doi.org/10.1080/14888386.2022.2141880

• Knecht, Leandra E.; Born, Yannick; Pelludat, Cosima; Pothier, Joël F.; Smits, Theo H. M.; Loessner, Martin J.; Fieseler, Lars,

  2022.

  Spontaneous resistance of Erwinia amylovora against bacteriophage Y2 affects infectivity of multiple phages.

  Frontiers in Microbiology.

  13(908346).

  Available from: https://doi.org/10.3389/fmicb.2022.908346

• Dia, Nay C.; Van Vaerenbergh, Johan; Van Malderghem, Cinzia; Blom, Jochen; Smits, Theo H. M.; Cottyn, Bart; Pothier, Joël F.,

  2021.

  Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens.

  International Journal of Systematic and Evolutionary Microbiology.

  71(12).

  Available from: https://doi.org/10.1099/ijsem.0.005163

• Kurz, Mirjam; Carnal, Simon; Dafny-Yelin, Mery; Mairesse, Orly; Gottsberger, Richard A.; Ivanović, Milan; Grahovac, Mila; Lagonenko, Alexander L.; Drenova, Nataliya; Zharmukhamedova, Galiya; Doolotkeldieva, Tinatin; Smits, Theo H.M.; Rezzonico, Fabio,

  2021.

  Tracking the dissemination of Erwinia amylovora in the Eurasian continent using a PCR targeted on the duplication of a single CRISPR spacer.

  Phytopathology Research.

  3(18).

  Available from: https://doi.org/10.1186/s42483-021-00096-9

• Moretti, Chiaraluce; Rezzonico, Fabio; Orfei, Benedetta; Cortese, Chiara; Moreno‐Pérez, Alba; van den Burg, Harrold A.; Onofri, Andrea; Firrao, Giuseppe; Ramos, Cayo; Smits, Theo H.M.; Buonaurio, Roberto,

  2021.

  Synergistic interaction between the type III secretion system of the endophytic bacterium Pantoea agglomerans DAPP‐PG 734 and the virulence of the causal agent of olive knot Pseudomonas savastanoi pv. savastanoi DAPP‐PG 722.

  Molecular Plant Pathology.

  22(10), pp. 1209-1225.

  Available from: https://doi.org/10.1111/mpp.13105

• Mainetti, Tamara; Palmisano, Marilena; Rezzonico, Fabio; Stres, Blaž; Kern, Susanne; Smits, Theo H. M.,

  2021.

  Broad diversity of bacteria degrading 17ß-estradiol-3-sulfate isolated from river sediment and biofilm at a wastewater treatment plant discharge.

  Archives of Microbiology.

  203(7), pp. 4209-4219.

  Available from: https://doi.org/10.1007/s00203-021-02409-0

• Schmautz, Zala; Espinal, Carlos A.; Smits, Theo H. M.; Frossard, Emmanuel; Junge, Ranka,

  2021.

  Nitrogen transformations across compartments of an aquaponic system.

  Aquacultural Engineering.

  92(102145).

  Available from: https://doi.org/10.1016/j.aquaeng.2021.102145

• Schmautz, Zala; Espinal, Carlos A.; Bohny, Andrea M.; Rezzonico, Fabio; Junge, Ranka; Frossard, Emmanuel; Smits, Theo H. M.,

  2021.

  Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments.

  BMC Microbiology.

  21(12).

  Available from: https://doi.org/10.1186/s12866-020-02075-0

• Doering, Michael; Freimann, Remo; Antenen, Nadine; Roschi, Alexia; Robinson, Christopher T.; Rezzonico, Fabio; Smits, Theo; Tonolla, Diego,

  2021.

  Microbial communities in floodplain ecosystems in relation to altered flow regimes and experimental flooding.

  Science of the Total Environment.

  788(147497).

  Available from: https://doi.org/10.1016/j.scitotenv.2021.147497

• Dia, Nay C.; Rezzonico, Fabio; Smits, Theo H. M.; Pothier, Joël F.,

  2020.

  Complete or high-quality draft genome sequences of six Xanthomonas hortorum strains sequenced with short- and long-read technologies.

  Microbiology Resource Announcements.

  9(41), pp. e00828-20.

  Available from: https://doi.org/10.1128/MRA.00828-20

• Gétaz, Michael; Puławska, Joanna; Smits, Theo H.M.; Pothier, Joël F.,

  2020.

  Host–pathogen interactions between Xanthomonas fragariae and its host Fragaria × ananassa investigated with a dual RNA-Seq analysis.

  Microorganisms.

  8(8), pp. 1253.

  Available from: https://doi.org/10.3390/microorganisms8081253

• Gétaz, Michael; Blom, Jochen; Smits, Theo H. M.; Pothier, Joël F.,

  2020.

  Comparative genomics of Xanthomonas fragariae and Xanthomonas arboricola pv. fragariae reveals intra- and interspecies variations.

  Phytopathology Research.

  2020(2), pp. 17.

  Available from: https://doi.org/10.1186/s42483-020-00061-y

• Escursell, Mireia Marcé; Roschi, Alexia; Smits, Theo; Rezzonico, Fabio,

  2020.

  Characterization and direct molecular discrimination of rpsL mutations leading to high streptomycin resistance in Erwinia amylovora.

  Journal of Plant Pathology.

  103(Suppl 1), pp. 99-108.

  Available from: https://doi.org/10.1007/s42161-020-00600-8

• Murray, Alison E.; Freudenstein, John; Gribaldo, Simonetta; Hatzenpichler, Roland; Hugenholtz, Philip; Kämpfer, Peter; Konstantinidis, Konstantinos T.; Lane, Christopher E.; Papke, R. Thane; Parks, Donovan H.; Rossello-Mora, Ramon; Stott, Matthew B.; Sutcliffe, Iain C.; Thrash, J. Cameron; Venter, Stephanus N.; Whitman, William B.; Acinas, Silvia G.; Amann, Rudolf I.; Anantharaman, Karthik; Armengaud, Jean; Baker, Brett J.; Barco, Roman A.; Bode, Helge B.; Boyd, Eric S.; Brady, Carrie L.; Carini, Paul; Chain, Patrick S. G.; Colman, Daniel R.; DeAngelis, Kristen M.; de los Rios, Maria Asuncion; Estrada-de los Santos, Paulina; Dunlap, Christopher A.; Eisen, Jonathan A.; Emerson, David; Ettema, Thijs J. G.; Eveillard, Damien; Girguis, Peter R.; Hentschel, Ute; Hollibaugh, James T.; Hug, Laura A.; Inskeep, William P.; Ivanova, Elena P.; Klenk, Hans-Peter; Li, Wen-Jun; Lloyd, Karen G.; Löffler, Frank E.; Makhalanyane, Thulani P.; Moser, Duane P.; Nunoura, Takuro; Palmer, Marike; Parro, Victor; Pedrós-Alió, Carlos; Probst, Alexander J.; Smits, Theo H.M.; Steen, Andrew D.; Steenkamp, Emma T.; Spang, Anja; Stewart, Frank J.; Tiedje, James M.; Vandamme, Peter; Wagner, Michael; Wang, Feng-Ping; Hedlund, Brian P.; Reysenbach, Anna-Louise,

  2020.

  Roadmap for naming uncultivated archaea and bacteria.

  Nature Microbiology.

  5(8), pp. 987-994.

  Available from: https://doi.org/10.1038/s41564-020-0733-x

• Madhaiyan, Munusamy; Saravanan, Venkatakrishnan Sivaraj; Blom, Jochen; Smits, Theo; Rezzonico, Fabio; Kim, Soo-Jin; Weon, Hang-Yeon; Kwon, Soon-Wo; Whitman, William B.; Ji, Lianghui,

  2020.

  Phytobacter palmae sp. nov., a novel endophytic, N2 fixing, plant growth promoting Gammaproteobacterium isolated from oil palm (Elaeis guineensis Jacq.).

  International Journal of Systematic and Evolutionary Microbiology.

  70(2), pp. 841-848.

  Available from: https://doi.org/10.1099/ijsem.0.003834

• Oh, Woo Taek; Jun, Jin Woo; Giri, Sib Sankar; Yun, Saekil; Kim, Hyoun Joong; Kim, Sang Guen; Kim, Sang Wha; Kang, Jeong Woo; Han, Se Jin; Kwon, Jun; Kim, Ji Hyung; Smits, Theo H.M.; Park, Se Chang,

  2019.

  Pseudomonas tructae sp. nov., novel species isolated from rainbow trout kidney.

  International Journal of Systematic and Evolutionary Microbiology.

  69(12), pp. 3851-3856.

  Available from: https://doi.org/10.1099/ijsem.0.003696

• Smits, Theo H.M.,

  2019.

  The importance of genome sequence quality to microbial comparative genomics.

  BMC Genomics.

  20(662).

  Available from: https://doi.org/10.1186/s12864-019-6014-5

• Smits, Theo H.M.; Duffy, Brion; Blom, Jochen; Ishimaru, Carol A.; Stockwell, Virginia O.,

  2019.

  Pantocin A, a peptide-derived antibiotic involved in biological control by plant-associated Pantoea species.

  Archives of Microbiology.

  201(6), pp. 713-722.

  Available from: https://doi.org/10.1007/s00203-019-01647-7

• Eck, Mathilde; Sare, Abdoul; Massart, Sébastien; Schmautz, Zala; Junge, Ranka; Smits, Theo H. M.; Jijakli, M.,

  2019.

  Exploring bacterial communities in aquaponic systems.

  Water.

  11(2), pp. 260.

  Available from: https://doi.org/10.3390/w11020260

• Rutz, Dominik; Frasson, David; Sievers, Martin; Blom, Jochen; Rezzonico, Fabio; Pothier, Joël F.; Smits, Theo H.M.,

  2019.

  Comparative genomic analysis of the biotechnological potential of the novel species Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T.

  Diversity.

  2019(11), pp. 204.

  Available from: https://doi.org/10.3390/d11110204

• Ruinelli, Michela; Blom, Jochen; Smits, Theo; Pothier, Joël,

  2019.

  Comparative genomics and pathogenicity potential of members of the Pseudomonas syringae species complex on Prunus spp.

  BMC Genomics.

  20(172).

  Available from: https://doi.org/10.1186/s12864-019-5555-y

• Rutz, Dominik; Frasson, David; Sievers, Martin; Blom, Jochen; Rezzonico, Fabio; Pothier, Joël F.; Smits, Theo H. M.,

  2019.

  High-quality draft genome sequence of Pseudomonas reidholzensis strain CCOS 865T.

  Microbiology Resource Announcements.

  8(3).

  Available from: https://doi.org/10.1128/MRA.01502-18

• Smits, Theo H.M.; Rezzonico, Fabio; Frasson, David; Vesga, Pilar; Vacheron, Jordan; Blom, Jochen; Pothier, Joël F.; Keel, Christoph; Maurhofer, Monika; Sievers, Martin,

  2019.

  Updated genome sequence and annotation for the full genome of Pseudomonas protegens CHA0.

  Microbiology Resource Announcements.

  8(39).

  Available from: https://doi.org/10.1128/MRA.01002-19

• Rutz, Dominik; Frasson, David; Sievers, Martin; Blom, Jochen; Rezzonico, Fabio; Pothier, Joël; Smits, Theo,

  2018.

  High-quality draft genome sequence of pseudomonas wadenswilerensis CCOS 864T.

  Microbiology Resource Announcements.

  7(16).

  Available from: https://doi.org/10.1128/MRA.01059-18

• Pillonetto, Marcelo; Arend, Lavinia; Gomes, Suzie M. T.; Oliveira, Marluce A. A.; Timm, Loeci N.; Martins, Andreza F.; Barth, Afonso L.; Mazzetti, Alana; Hersemann, Lena; Smits, Theo H. M.; Mira, Marcelo T.; Rezzonico, Fabio,

  2018.

  Molecular investigation of isolates from a multistate polymicrobial outbreak associated with contaminated total parenteral nutrition in Brazil.

  BMC Infectious Diseases.

  18(397), pp. 1-11.

  Available from: https://doi.org/10.1186/s12879-018-3287-2

• Dennert, Francesca; Imperiali, Nicola; Staub, Cornelia; Schneider, Jana; Laessle, Titouan; Zhang, Tao; Wittwer, Raphaël; van der Heijden, Marcel G A; Smits, Theo H M; Schlaeppi, Klaus; Keel, Christoph; Maurhofer, Monika,

  2018.

  Conservation tillage and organic farming induce minor variations in Pseudomonas abundance, their antimicrobial function and soil disease resistance.

  FEMS Microbiology Ecology.

  94(8), pp. fiy075.

  Available from: https://doi.org/10.1093/femsec/fiy075

• Pillonetto, Marcelo; Arend, Lavinia N.; Faoro, Helisson; D'Espindula, Helena R. S.; Blom, Jochen; Smits, Theo H. M.; Mira, Marcelo T.; Rezzonico, Fabio,

  2018.

  Emended description of the genus phytobacter, its type species phytobacter diazotrophicus (Zhang 2008) and description of phytobacter ursingii sp. nov.

  International Journal of Systematic and Evolutionary Microbiology.

  68, pp. 176-184.

  Available from: https://doi.org/10.1099/ijsem.0.002477

• Gétaz, Michael; Krijger, Marjon; Rezzonico, Fabio; Smits, Theo; van der Wolf, Jan M.; Pothier, Joël F.,

  2018.

  Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description.

  Microbial Genomics.

  4(7).

  Available from: https://doi.org/10.1099/mgen.0.000189

• Smits, Theo; Duffy, Brion; Sundin, George; Zhao, Youfu; Rezzonico, Fabio,

  2017.

  Erwinia amylovora in the genomics era : from genomes to pathogen virulence, regulation, and disease control strategies.

  Journal of Plant Pathology.

  99(Special issue), pp. 7-23.

  Available from: https://doi.org/10.4454/jpp.v99i0.3917

• Rezzonico, Fabio; Duffy, Brion; Smits, Theo H.M.; Pothier, Joël F.,

  2017.

  Erwinia species identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry.

  Journal of Plant Pathology.

  99(Special issue), pp. 121-129.

  Available from: https://doi.org/10.4454/jpp.v99i0.3916

• Ishimaru, Carol; Lansdell, Teresa A.; Clardy, Jon; Duffy, Brion; Smits, Theo H.M.,

  2017.

  The histidine-reversible antibiotic herbicolin O produced by Pantoea vagans C9-1 is pantocin A.

  Journal of Plant Pathology.

  99(Special issue), pp. 91-97.

  Available from: https://doi.org/10.4454/jpp.v99i0.3910

• De Maayer, Pieter; Aliyu, Habibu; Vikram, Surendra; Blom, Jochen; Duffy, Brion; Cowan, Don A.; Smits, Theo H.M.; Venter, Stephanus N.; Coutinho, Teresa A.,

  2017.

  Phylogenomic, pan-genomic, pathogenomic and evolutionary genomic insights into the agronomically relevant enterobacteria Pantoea ananatis and Pantoea stewartii.

  Frontiers in Microbiology.

  8, pp. 1755.

  Available from: https://doi.org/10.3389/fmicb.2017.01755

• Frasson, David; Opoku, Michael; Picozzi, Tara; Torossi, Tania; Balada, Stefanie; Smits, Theo; Hilber, Urs,

  2017.

  Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidholzensis sp. nov. : two new species within the Pseudomonas putida group isolated from forest soil.

  International Journal of Systematic and Evolutionary Microbiology.

  67, pp. 2853-2861.

  Available from: https://doi.org/10.1099/ijsem.0.002035

• Kamber, Tim; Pothier, Joël; Pelludat, Cosima; Rezzonico, Fabio; Duffy, Brion; Smits, Theo,

  2017.

  Role of the type VI secretion systems during disease interactions of Erwinia amylovora with its plant host.

  BMC Genomics.

  16(628), pp. 1-12.

  Available from: https://doi.org/10.1186/s12864-017-4010-1

• Schmautz, Zala; Graber, Andreas; Jaenicke, Sebastian; Goesmann, Alexander; Junge, Ranka; Smits, Theo H. M.,

  2017.

  Microbial diversity in different compartments of an aquaponics system.

  Archives of Microbiology.

  199(4), pp. 613-620.

  Available from: https://doi.org/10.1007/s00203-016-1334-1

• Palmer, Marike; Steenkamp, Emma T.; Coetzee, Martin P.A.; Chan, Wai-Yin; van Zyl, Elritha; De Maayer, Pieter; Coutinho, Teresa A.; Blom, Jochen; Smits, Theo; Duffy, Brion; Venter, Stephanus N.,

  2017.

  Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella.

  Antonie van Leeuwenhoek.

  110(10), pp. 1287-1309.

  Available from: https://doi.org/10.1007/s10482-017-0852-4

• Kupferschmied, Peter; Chai, Tiancong; Flury, Pascale; Blom, Jochen; Smits, Theo; Maurhofer, Monika; Keel, Christoph,

  2016.

  Specific surface glycan decorations enable antimicrobial peptide resistance in plant-beneficial pseudomonads with insect-pathogenic properties.

  Environmental Microbiology.

  18(11), pp. 4265-4281.

  Available from: https://doi.org/10.1111/1462-2920.13571

• Rezzonico, Fabio; Smits, Theo; Born, Yannick; Blom, Jochen; Frey, Jürg E.; Goesmann, Alexander; Cleenwerck, Ilse; de Vos, Paul; Bonaterra, Anna; Duffy, Brion; Montesinos, Emilio,

  2016.

  Erwinia gerundensis sp. nov. : a cosmopolitan epiphyte originally isolated from pome fruit trees.

  International Journal of Systematic and Evolutionary Microbiology.

  66, pp. 1583-1592.

  Available from: https://doi.org/10.1099/ijsem.0.000920

• Kamber, Tim; Buchmann, Jan P.; Pothier, Joël; Smits, Theo; Wicker, Thomas; Duffy, Brion,

  2016.

  Fire blight disease reactome : RNA-seq transcriptional profile of apple host plant defence responses to Erwinia amylovora pathogen infection.

  Scientific Reports.

  6(21600).

  Available from: https://doi.org/10.1038/srep21600

• Flury, Pascale; Aellen, Nora; Ruffner, Beat; Péchy-Tarr, Maria; Fataar, Shakira; Metla, Zane; Dominguez-Ferreras, Ana; Bloemberg, Guido; Frey, Joachim; Goesmann, Alexander; Raaijmakers, Jos M; Duffy, Brion; Höfte, Monica; Blom, Jochen; Smits, Theo; Keel, Christoph; Maurhofer, Monika,

  2016.

  Insect pathogenicity in plant-beneficial pseudomonads : phylogenetic distribution and comparative genomics.

  ISME Journal: Multidisciplinary Journal of Microbial Ecology.

  10, pp. 2527-2542.

  Available from: https://doi.org/10.1038/ismej.2016.5

• Sirakov, Ivaylo Nikolaev; Lutz, Matthias; Graber, Andreas; Mathis, Alex; Staykov, Yordan; Smits, Theo H. M.; Junge, Ranka,

  2016.

  Potential for combined biocontrol activity against fungal fish and plant pathogens by bacterial isolates from a model aquaponic system.

  Water.

  8(11).

  Available from: https://doi.org/10.3390/w8110518

• Smits, Theo H.M.; Rezzonico, Fabio; Blom, Jochen; Goesmann, Alexander; Abelli, Azzurra; Kron Morelli, Roberto; Vanneste, Joël L.; Duffy, Brion,

  2015.

  Draft genome sequence of the commercial biocontrol strain Pantoea agglomerans P10c.

  Genome Announcements.

  3(6).

  Available from: https://doi.org/10.1128/genomeA.01448-15

• Smits, Theo H. M.; Pothier, Joël F.; Ruinelli, Michela; Blom, Jochen; Frasson, David; Koechli, Chantal; Fabbri, Carlotta; Brandl, Helmut; Duffy, Brion; Sievers, Martin,

  2015.

  Complete genome sequence of the cyanogenic phosphate-solubilizing Pseudomonas sp. strain CCOS 191 : a close relative of Pseudomonas mosseli.

  Genome Announcements.

  3(3).

  Available from: https://doi.org/10.1128/genomeA.00616-15

• De Maayer, Pieter; Chan, Wai-Yin; Martin, Douglas A.; Blom, Jochen; Venter, Stephanus N.; Duffy, Brion; Cowan, Don A.; Smits, Theo H. M.; Coutinho, Teresa A.,

  2015.

  Integrative conjugative elements of the ICEPan family play a potential role in Pantoea ananatis ecological diversification and antibiosis.

  Frontiers in Microbiology.

  6(576).

  Available from: https://doi.org/10.3389/fmicb.2015.00576

• Brankatschk, Kerstin; Kamber, Tim; Pothier, Joël F.; Duffy, Brion; Smits, Theo H.M.,

  2014.

  Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization.

  Microbial Biotechnology.

  7(6), pp. 528-544.

  Available from: https://doi.org/10.1111/1751-7915.12104

• Ismail, Emadeldeen; Blom, Jochen; Bultreys, Alain; Ivanovic, Milan; Obradovic, Aleksa; van Doorn, Joop; Bergsma-Vlami, Maria; Maes, Martine; Willems, Anne; Duffy, Brion; Stockwell, Virginia O.; Smits, Theo H.M.; Pulawska, Joanna,

  2014.

  A novel plasmid pEA68 of Erwinia amylovora and the description of a new family of plasmids.

  Archives of Microbiology.

  196(12), pp. 891-899.

  Available from: https://doi.org/10.1007/s00203-014-1028-5

• Weller-Stuart, Tania; Chan, Wai-Yin; Coutinho, Teresa A.; Venter, Stephanus N.; Smits, Theo H.M.; Duffy, Brion; Goszczynska, Teresa; Cowan, Don A.; de Maayer, Pieter,

  2014.

  Draft genome sequences for the onion center roth pathogen Pantoea ananatis PA4 and maize brown stalk rot pathogen P. ananatis BD442.

  Genome Announcements.

  2(4).

  Available from: https://doi.org/10.1128/genomeA.00750-14

• Bühlmann, Andreas; Dreo, Tanja; Rezzonico, Fabio; Pothier, Joël F.; Smits, Theo H. M.; Ravnikar, Maja; Frey, Jürg E.; Duffy, Brion,

  2014.

  Phylogeography and population structure of the biologically invasive phytopathogen Erwinia amylovora inferred using minisatellites.

  Environmental Microbiology.

  16(7), pp. 2112-2125.

  Available from: https://doi.org/10.1111/1462-2920.12289

• Smits, Theo H. M.; Guerrero-Prieto, Víctor M.; Hernández-Escarcega, Germán; Blom, Jochen; Goesmann, Alexander; Rezzonico, Fabio; Duffy, Brion; Stockwell, Virginia O.,

  2014.

  Whole-genome sequencing of Erwinia amylovora strains from México detects SNPs in rpsL conferring streptomycin resistance and in the avrRpt2 effector altering host interactions.

  Genome Announcements.

  2(1).

  Available from: https://doi.org/10.1128/genomeA.01229-13

• Smits, Theo H. M.; Rezzonico, Fabio; López, Maria M.; Blom, Jochen; Goesmann, Alexander; Frey, Jürg E.; Duffy, Brion,

  2013.

  Phylogenetic position and virulence apparatus of the pear flower necrosis pathogen Erwinia piriflorinigrans CFBP 5888T as assessed by comparative genomics.

  Systematic and Applied Microbiology.

  36(7), pp. 449-456.

  Available from: https://doi.org/10.1016/j.syapm.2013.04.003

• Barbé, Silva; Llop, Pablo; Blom, Jochen; Cabrefiga, Jose; Goesmann, Alexander; Duffy, Brion; Montesinos, E.; Smits, Theo H.M.; López, M. M.,

  2013.

  Complete sequence of Erwinia piriflorinigrans plasmids pEPIR37 and pEPIR5 and role of pEPIR37 in pathogen virulence.

  Plant Pathology.

  62(4), pp. 786-798.

  Available from: https://doi.org/10.1111/ppa.12002

• Bühlmann, Andreas; Pothier, F.; Rezzonico, Fabio; Smits, Theo H. M.; Andreou, Michael; Boonham, Neil; Duffy, Brion; Frey, Jürg E.,

  2013.

  Erwinia amylovora loop-mediated isothermal amplification (LAMP) assay for rapid pathogen detection and on-site diagnosis of fire blight.

  Journal of Microbiological Methods.

  92(3), pp. 332-339.

  Available from: https://doi.org/10.1016/j.mimet.2012.12.017

• Mann, Rachel A.; Smits, Theo H.M.; Bühlmann, Andreas; Blom, Jochen; Goesmann, Alexander; Frey, Jürg E.; Plummer, Kim M.; Beer, Steven V.; Luck, Joanne; Duffy, Brion; Rodoni, Brendan,

  2013.

  Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core.

  PLOS ONE.

  8(2).

  Available from: https://doi.org/10.1371/journal.pone.0055644

• Bühlmann, Andreas; Pothier, Joël F.; Tomlinson, Jennifer A.; Frey, Jürg F.; Boonham, N.; Smits, Theo H.M.; Duffy, Brion,

  2012.

  Genomics-informed design of loop-mediated isothermal amplification for detection of phytopathogenic Xanthomonas arboricola pv. pruni at the intraspecific level.

  Plant Pathology.

  62(2), pp. 475-484.

  Available from: https://doi.org/10.1111/j.1365-3059.2012.02654.x

• Gygax, Gregory; Ratnaweera, Nils; Tischhauser, Werner; Smits, Theo H. M.; Laube, Patrick; Ott, Thomas,

  2023.

  An oracle for the optimization of underconstrained compositions of neural networks : the tick hazard use case [paper].

  In:

  Schneider, Johannes Josef; Weyland, Mathias Sebastian; Flumini, Dandolo; Füchslin, Rudolf Marcel, eds.,

  Artificial Life and Evolutionary Computation.

  XV International Workshop on Artificial Life and Evolutionary Computation (WIVACE), Winterthur, Switzerland, 15-17 September 2021.

  Cham:

  Springer.

  pp. 24-31.

  Communications in Computer and Information Science ; 1722.

  Available from: https://doi.org/10.1007/978-3-031-23929-8_3

• Kaufmann, Moritz; Schüle, Martin; Smits, Theo; Pothier, Joël,

  2020.

  Typing plasmids with distributed sequence representation [paper].

  In:

  Schilling, Frank-Peter; Stadelmann, Thilo, eds.,

  Artificial Neural Networks in Pattern Recognition.

  9th IAPR TC 3 Workshop on Artificial Neural Networks for Pattern Recognition (ANNPR'20), Winterthur, Switzerland, 2-4 September 2020.

  Cham:

  Springer.

  pp. 200-210.

  Lecture Notes in Computer Science ; 12294.

  Available from: https://doi.org/10.1007/978-3-030-58309-5_16

• Smits, Theo H.M.; Guerrero-Prieto, V. M.; Hernandez-Escarcega, G.; Rezzonico, Fabio; Blom, J.; Goesmann, A.; Duffy, Brion; Stockwell, V. O.,

  2014.

  Comparative genomics of Erwinia amylovora isolates from Mexico [paper].

  In:

  XIII International Workshop on Fire Blight, Zurich, Switzerland, 2-5 July 2013.

  International Society for Horticultural Science.

  pp. 173-177.

  Available from: https://doi.org/10.17660/ActaHortic.2014.1056.27

• Rezzonico, Fabio; Smits, Theo H.M.; Holliger, Eduard, eds.,

  2014.

  Proceedings of the 13th international workshop on fire blight.

  13th International Workshop on Fire Blight, Zürich, 2-5 July 2013.

  Leuven:

  International Society for Horticultural Sciences.

  .

  ISBN 9789462610460.

• Gerber, Nicole; Fieseler, Lars; Hirsch, Sven; Neutsch, Lukas; Papadopoulou, Athina; Smits, Theo,

  2022.

  Zusammenarbeit und wissenschaftlicher Austausch sind der Schlüssel zu erfolgreicher Forschung : der ZHAW Health Research Hub bringt’s unter einen Hut.

  Clinicum.

  2022(6), pp. 80-81.

  Available from: https://doi.org/10.21256/zhaw-26376

• Murray, Alison E.; Freudenstein, John; Gribaldo, Simonetta; Hatzenpichler, Roland; Hugenholtz, Philip; Kämpfer, Peter; Konstantinidis, Konstantinos T.; Lane, Christopher E.; Papke, R. Thane; Parks, Donovan H.; Rossello-Mora, Ramon; Stott, Matthew B.; Sutcliffe, Iain C.; Thrash, J. Cameron; Venter, Stephanus N.; Whitman, William B.; Acinas, Silvia G.; Amann, Rudolf I.; Anantharaman, Karthik; Armengaud, Jean; Baker, Brett J.; Barco, Roman A.; Bode, Helge B.; Boyd, Eric S.; Brady, Carrie L.; Carini, Paul; Chain, Patrick S. G.; Colman, Daniel R.; DeAngelis, Kristen M.; de los Rios, Maria Asuncion; Estrada-de los Santos, Paulina; Dunlap, Christopher A.; Eisen, Jonathan A.; Emerson, David; Ettema, Thijs J. G.; Eveillard, Damien; Girguis, Peter R.; Hentschel, Ute; Hollibaugh, James T.; Hug, Laura A.; Inskeep, William P.; Ivanova, Elena P.; Klenk, Hans-Peter; Li, Wen-Jun; Lloyd, Karen G.; Löffler, Frank E.; Makhalanyane, Thulani P.; Moser, Duane P.; Nunoura, Takuro; Palmer, Marike; Parro, Victor; Pedrós-Alió, Carlos; Probst, Alexander J.; Smits, Theo; Steen, Andrew D.; Steenkamp, Emma T.; Spang, Anja; Stewart, Frank J.; Tiedje, James M.; Vandamme, Peter; Wagner, Michael; Wang, Feng-Ping; Yarza, Pablo; Hedlund, Brian P.; Reysenbach, Anna-Louise,

  2020.

  Author correction : roadmap for naming uncultivated archaea and bacteria.

  Nature Microbiology.

  6(1), pp. 136.

  Available from: https://doi.org/10.1038/s41564-020-00827-2

Publications before appointment at the 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.

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