Prof. Dr. Theo Smits

Network

ORCID digital identifier

ORCID ID: 0000-0002-1237-235X

Projects

• Comparative genomics tools for analysis and detailed description of the clinically relevant bacterial genus Phytobacter / Project leader / ongoing
• AQUAPEALTH: Harnessing soilless microbial communities to enhance plant health across different cultivation systems / Project leader / ongoing
• EBDOmics – Comparative genomics of Enterobacter spp. causing Bulb Decay of Onions / Project leader / completed
• Fire Blight App for Central Asia / Project leader / completed
• Antibiotic resistances in Enterobacteria / Deputy project leader / completed
• Fighting bites with bytes: Promoting public health with crowdsourced tick prevention / Project leader / completed
• CarbonATE - microbiological methanation / Team member / completed
• Platform Health / Co-project leader / completed
• Preservation of Central Asian fruit tree forest ecosystems from bacterial pathogen Erwinia amylovora (fire blight) / Co-project leader / completed
• Diagnostic and epidemiological tools for the Xanthomonas hortorum species-level clade based on OMICs technologies / Project leader / completed
• Development of a fast and exact method for R. solanacearum detection in Swiss surface water samples / Team member / completed
• Effect of cryopreservation on genome mutation rate - examples of grapevine / Project leader / completed
• Off Flavour control in land-based salmon production / Team member / completed
• Characterization of nitrogen dynamics in an aquaponic system / Project leader / completed
• Comparative genomics to untangle insect pathogenicity in plant-associated pseudomonads / Project leader / completed
• Sepsis-Associated Microorganisms in Brazilian Ambulatories / Project leader / completed
• Genomics and transcriptomics of Erwinia and Pantoea / Project leader / completed
• Comparative genomics of the plant pathogen Xanthomonas arboricola pv. pruni and related xanthomonads / Team member / completed

Publications

Articles in scientific journal, peer-reviewed

• Drenova, Nataliya V., Alexandr N. Ignatov, Fabio Rezzonico, Galina N. Bondarenko, Denis L Belkin, Maxim O. Kondratyev, Fevzi S.-U. Dzhalilov, and Theo H. M. Smits. 2026. "The rodZ Repeat Region of Erwinia Amylovora : Genetic Diversity and Possible Functional Implications." Journal of Plant Pathology, August. https://doi.org/10.1007/s42161-026-02257-1.
• Jordan, Sara, Joël F. Pothier, Pieter de Maayer, Brian H. Kvitko, Teresa A. Coutinho, and Theo H. M. Smits. 2026. "Genome Sequences of 71 Ecologically and Geographically Diverse Enterobacter Strains." Microbiology Resource Announcements 15 (8): e00334–26. https://doi.org/10.1128/mra.00334-26.
• Pillonetto, Marcelo, Maria Esther Graf, Geiziane A. Gonçalves, Debora N. O. Kulek, Ana Paula S. Chacon, Helki S. R. Pereira, Alexandre W. Losso, et al. 2026. "Sepsis Caused by Two Phytobacter Species : Clinical Cases and Polyphasic Characterization of an Emerging Enterobacteriaceae." ASM Case Reports 2 (4): e00051–25. https://doi.org/10.1128/asmcr.00051-25.
• Jordan, Sara, Pieter de Maayer, Theo H. M. Smits, and Teresa A. Coutinho. 2026. "Enterobacter Species : Opportunistic Human and Plant Pathogens with Plant‐Beneficial Traits." Molecular Plant Pathology 27 (3): e70231. https://doi.org/10.1111/mpp.70231.
• Kalbermatten, Claudio L., Sara Jordan, Joël F. Pothier, Hans-Joachim Nägele, Theo H. M. Smits, and Wolfgang Merkle. 2026. "Optimizing Trickle-Bed Reactor Performance for Hydrogenotrophic Methane Production in Power-to-Methane Systems." Process Biochemistry 163 (February): 66–76. https://doi.org/10.1016/j.procbio.2026.02.010.
• Jordan, Sara, Joël F. Pothier, Fabio Rezzonico, Brian H. Kvitko, Teresa A. Coutinho, and Theo H. M. Smits. 2026. "Kosakonia Beeri Sp. Nov. And Phytobacter Cepae Sp. Nov. Isolated from Onion (Allium Cepa)." International Journal of Systematic and Evolutionary Microbiology 76 (1). https://doi.org/10.1099/ijsem.0.007043.
• Mazzetti, Alana, Helena R. S. D'Espindula, Debora O. Kulek, Karen L. Jones, Letícia Kraft, Theo H. M. Smits, Fabio Rezzonico, Marcelo Távora Mira, and Marcelo Pillonetto. 2026. "Construction of a SuperSpectrum for Rapid Identification of Opportunistic Human Pathogens Belonging to the Genus Phytobacter Using Whole-Cell MALDI-TOF MS." Diagnostic Microbiology and Infectious Disease 115 (1): 117275. https://doi.org/10.1016/j.diagmicrobio.2026.117275.
• Orfei, Benedetta, Joël F. Pothier, Luca Scotti, Antonio Aceto, Chiaraluce Moretti, Roberto Buonaurio, and Theo H. M. Smits. 2026. "Transcriptome Analysis of Pseudomonas Syringae Pv. Tomato DAPP-PG 215 in Response to Silver Nanoparticles Exposure." Frontiers in Microbiology 16 (1714857). https://doi.org/10.3389/fmicb.2025.1714857.
• Feltin, Chloé, Sylvain Piry, Benoit Moury, Lola Chateau, Karine Berthier, Jonathan M. Jacobs, Jules Butchacas, et al. 2025. "Ecological Ubiquity and Phylogeny Drive Nestedness in Phages–Bacteria Networks and Shape the Bacterial Defensome." PLOS Pathogens 21 (12): e1013428. https://doi.org/10.1371/journal.ppat.1013428.
• Berdygulova, Zhanna A., Dinara A. Naizabayeva, Zhaniya M. Dosmagambet, Fabio Rezzonico, Theo H. M. Smits, and Elina R. Maltseva. 2025. "A Distinct Erwinia Amylovora Lineage in Kazakhstan Associated with a pEA29 Transposase Mutation." Journal of Plant Pathology, December. https://doi.org/10.1007/s42161-025-02099-3.
• Blank-Pachlatko, Jonathan, Nicola Rhyner, Theo H.M. Smits, Beatrice Kulli Honauer, and Kirsten Edelkraut. 2025. "Beyond Plants : How Soil Alterations Shape Restoration Success in Alpine Grasslands." Tuexenia 45 (November): 405–27. https://doi.org/10.14471/2025.45.012.
• Jordan, Sara, Joël F. Pothier, Pieter de Maayer, Kirk Broders, Brian H. Kvitko, Teresa A. Coutinho, and Theo Smits. 2025. "Design of Genus-Specific Semi-Nested Primers for Simple and Accurate Identification of Enterobacter Strains." BMC Microbiology 25 (1): 456. https://doi.org/10.1186/s12866-025-04175-1.
• De Maayer, Pieter, Teigra Green, Sara Jordan, Theo H. M. Smits, and Teresa A. Coutinho. 2025. "Pan-Genome Analysis of the Enterobacter Hormaechei Complex Highlights Its Genomic Flexibility and Pertinence as a Multidrug Resistant Pathogen." BMC Genomics 26 (1): 406. https://doi.org/10.1186/s12864-025-11590-1.
• Dia, Nay C., Bart Cottyn, Andrew Aspin, Bruno Studer, Theo H.M. Smits, and Joël F. Pothier. 2025. "Bacterial Leaf Spot of Hydrangea : On a "New Old" Disease and the Importance of Diagnostic Specificity to Reduce Cross-Reactivity and Improve Surveillance." PhytoFrontiers 5 (2): 138–43. https://doi.org/10.1094/PHYTOFR-10-24-0119-FI.
• Rezzonico, Fabio, Saykal Bobushova, Dali Gaganidze, Mahabat Konurbaeva, Sergey Mukhanov, Sara Jordan, Tinatin Sadunishvili, Nataliya Drenova, Theo Smits, and Tinatin Doolotkeldieva. 2024. "Epidemiological Description of Fire Blight Introduction Patterns to Central Asia and the Caucasus Region Based on CRISPR Spacer Typing and Genome Analysis." Phytopathology Research 6 (66). https://doi.org/10.1186/s42483-024-00283-4.
• Michel, Isabelle R., Débora Kulek, Lavinia N.V.S. Arend, Marcelo Pillonetto, Theo H.M. Smits, and Fabio Rezzonico. 2024. "Development of Two Quantitative PCR Assays for the Detection of Emerging Opportunistic Human Pathogens Belonging to the Genus Phytobacter in Routine Diagnostics." Diagnostic Microbiology and Infectious Disease 110 (4): 116556. https://doi.org/10.1016/j.diagmicrobio.2024.116556.
• Rezzonico, Fabio, Ofere Francis Emeriewen, Quan Zeng, Andreas Peil, Theo H.M. Smits, and George W. Sundin. 2024. "Burning Questions for Fire Blight Research : I. Genomics and Evolution of Erwinia Amylovora and Analyses of Host-Pathogen Interactions." Journal of Plant Pathology 106 (3): 797–810. https://doi.org/10.1007/s42161-023-01581-0.
• Gartmann, Florentina, Julian Hügly, Nikita Krähenbühl, Nadine Brinkmann, Zala Schmautz, Theo H. M. Smits, and Ranka Junge. 2023. "Bioponics – an Organic Closed-Loop Soilless Cultivation System : Yields and Characteristics Compared to Hydroponics and Soil Cultivation." Agronomy 13 (6): 1436. https://doi.org/10.3390/agronomy13061436.
• Maltseva, Elina R., Galiya A. Zharmukhamedova, Zhulduzay K. Jumanova, Dinara A. Naizabayeva, Zhanna A. Berdygulova, Karina A. Dmitriyeva, Botakoz Tezekbayeva, et al. 2023. "Fire Blight Cases in Almaty Region of Kazakhstan in the Proximity of Wild Apple Distribution Area." Journal of Plant Pathology 106 (3): 971–78. https://doi.org/10.1007/s42161-023-01416-y.
• Crosby, Katherine C., Mariah Rojas, Parul Sharma, Marcela A. Johnson, Reza Mazloom, Brian H. Kvitko, Theo H. M. Smits, et al. 2023. "Genomic Delineation and Description of Species and Within-Species Lineages in the Genus Pantoea." Frontiers in Microbiology 14 (1254999). https://doi.org/10.3389/fmicb.2023.1254999.
• Hon, Peiyun, Karrie K. K. Ko, Jonathan W. Z. Chia, Partha P. De, Theo H. M. Smits, Jiaming Low, Shawn Vasoo, and Clement K. M. Tsui. 2023. "Correction for Hon et Al., "Genomic Identification of Two Phytobacter Diazotrophicus Isolates from a Neonatal Intensive Care Unit in Singapore"." Microbiology Resource Announcements 12 (10): e00689–23. https://doi.org/10.1128/MRA.00689-23.
• Orfei, Benedetta, Joël F. Pothier, Linda Fenske, Jochen Blom, Chiaraluce Moretti, Roberto Buonaurio, and Theo H. M. Smits. 2023. "Race-Specific Genotypes of Pseudomonas Syringae Pv. Tomato Are Defined by the Presence of Mobile DNA Elements within the Genome." Frontiers in Plant Science 14 (1197706). https://doi.org/10.3389/fpls.2023.1197706.
• Kurz, Mirjam, Ormon Sultangaziev, David Szalatnay, Ishenbai Sodonbekov, Dinara A. Naizabayeva, Muqaddas Milikbekova, Solimshoh Akbarsho, et al. 2023. "An App for Apples : Citizen-Led Mapping of Fire Blight in Central Asia." Journal of Plant Pathology 106 (3): 967–70. https://doi.org/10.1007/s42161-023-01406-0.
• Hon, Peiyun, Karrie K.K. Ko, Jonathan C.W. Zhong, Partha P. De, Theo H. M. Smits, Jiaming Low, Shawn Vasoo, and Clement K.M. Tsui. 2023. "Genomic Identification of Two Phytobacter Diazotrophicus Isolates from a Neonatal Intensive Care Unit in Singapore." Microbiology Resource Announcements 12 (6): e00167–23. https://doi.org/10.1128/mra.00167-23.
• Arend, Lavinia N.V.S., Ricardo Bergamo, Fabiano B. Rocha, Larissa Bail, Carmen Ito, Valter A. Baura, Eduardo Balsanelli, et al. 2023. "Dissemination of NDM-Producing Bacteria in Southern Brazil." Diagnostic Microbiology and Infectious Disease 106 (2): 115930. https://doi.org/10.1016/j.diagmicrobio.2023.115930.
• Kurz, Mirjam, Adrian Kölz, Jonas Gorges, Beatriz Pablo Carmona, Peter Brang, Yann Vitasse, Martin Kohler, et al. 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). https://doi.org/10.1016/j.foreco.2023.120801.
• Maltseva, Elina R., Galiya A. Zharmukhamedova, Zhulduzay K. Jumanova, Dinara A. Naizabayeva, Zhanna A. Berdygulova, Karina A. Dmitriyeva, Sagi S. Soltanbekov, et al. 2022. "Assessment of Fire Blight Introduction in the Wild Apple Forests of Kazakhstan." Biodiversity 23 (3-4): 123–28. https://doi.org/10.1080/14888386.2022.2141880.
• Knecht, Leandra E., Yannick Born, Cosima Pelludat, Joël F. Pothier, Theo H. M. Smits, Martin J. Loessner, and Lars Fieseler. 2022. "Spontaneous Resistance of Erwinia Amylovora against Bacteriophage Y2 Affects Infectivity of Multiple Phages." Frontiers in Microbiology 13 (908346). https://doi.org/10.3389/fmicb.2022.908346.
• Sulja, Arburon, Joël F. Pothier, Jochen Blom, Chiaraluce Moretti, Roberto Buonaurio, Fabio Rezzonico, and Theo H. M. Smits. 2022. "Comparative Genomics to Examine the Endophytic Potential of Pantoea Agglomerans DAPP-PG 734." BMC Genomics 23 (742). https://doi.org/10.1186/s12864-022-08966-y.
• Schmautz, Zala, Jean-Claude Walser, Carlos A. Espinal, Florentina Gartmann, Benjamin Scott, Joël F. Pothier, Emmanuel Frossard, Ranka Junge, and Theo H. M. Smits. 2022. "Microbial Diversity across Compartments in an Aquaponic System and Its Connection to the Nitrogen Cycle." Science of the Total Environment 852 (158426). https://doi.org/10.1016/j.scitotenv.2022.158426.
• Dia, Nay C., Bart Cottyn, Jochen Blom, Theo H. M. Smits, and Joël F. Pothier. 2022. "Differentiation of the Xanthomonas Hortorum – Xanthomonas Hydrangeae Species Complex Using Sensitive and Selective LAMP Assays." Frontiers in Agronomy 4 (898778). https://doi.org/10.3389/fagro.2022.898778.
• Ruinelli, Michela, Jochen Blom, Theo H. M. Smits, and Joël F. Pothier. 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). https://doi.org/10.3389/fmicb.2022.804681.
• Smits, Theo H. M., Lavinia N. V. S. Arend, Sofia Cardew, Erika Tång-Hallbäck, Marcelo T. Mira, Edward R. B. Moore, Jorge L. M. Sampaio, Fabio Rezzonico, and Marcelo Pillonetto. 2022. "Resolving Taxonomic Confusion : Establishing the Genus Phytobacter on the List of Clinically Relevant Enterobacteriaceae." European Journal of Clinical Microbiology & Infectious Diseases 41 (4): 547–58. https://doi.org/10.1007/s10096-022-04413-8.
• Doering, Michael, Remo Freimann, Nadine Antenen, Alexia Roschi, Christopher T. Robinson, Fabio Rezzonico, Theo Smits, and Diego Tonolla. 2021. "Microbial Communities in Floodplain Ecosystems in Relation to Altered Flow Regimes and Experimental Flooding." Science of the Total Environment 788 (147497). https://doi.org/10.1016/j.scitotenv.2021.147497.
• Dia, Nay C., Johan Van Vaerenbergh, Cinzia Van Malderghem, Jochen Blom, Theo H. M. Smits, Bart Cottyn, and Joël F. Pothier. 2021. "Xanthomonas Hydrangeae Sp. Nov., A Novel Plant Pathogen Isolated from Hydrangea Arborescens." International Journal of Systematic and Evolutionary Microbiology 71 (12). https://doi.org/10.1099/ijsem.0.005163.
• Kurz, Mirjam, Simon Carnal, Mery Dafny-Yelin, Orly Mairesse, Richard A. Gottsberger, Milan Ivanović, Mila Grahovac, et al. 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). https://doi.org/10.1186/s42483-021-00096-9.
• Moretti, Chiaraluce, Fabio Rezzonico, Benedetta Orfei, Chiara Cortese, Alba Moreno‐Pérez, Harrold A. van den Burg, Andrea Onofri, et al. 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): 1209–25. https://doi.org/10.1111/mpp.13105.
• Mainetti, Tamara, Marilena Palmisano, Fabio Rezzonico, Blaž Stres, Susanne Kern, and Theo H. M. Smits. 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): 4209–19. https://doi.org/10.1007/s00203-021-02409-0.
• Schmautz, Zala, Carlos A. Espinal, Theo H. M. Smits, Emmanuel Frossard, and Ranka Junge. 2021. "Nitrogen Transformations across Compartments of an Aquaponic System." Aquacultural Engineering 92 (102145). https://doi.org/10.1016/j.aquaeng.2021.102145.
• Schmautz, Zala, Carlos A. Espinal, Andrea M. Bohny, Fabio Rezzonico, Ranka Junge, Emmanuel Frossard, and Theo H. M. Smits. 2021. "Environmental Parameters and Microbial Community Profiles as Indication towards Microbial Activities and Diversity in Aquaponic System Compartments." BMC Microbiology 21 (12). https://doi.org/10.1186/s12866-020-02075-0.
• Dia, Nay C., Fabio Rezzonico, Theo H. M. Smits, and Joël F. Pothier. 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): e00828–20. https://doi.org/10.1128/MRA.00828-20.
• Gétaz, Michael, Joanna Puławska, Theo H.M. Smits, and Joël F. Pothier. 2020. "Host–Pathogen Interactions between Xanthomonas Fragariae and Its Host Fragaria × Ananassa Investigated with a Dual RNA-Seq Analysis." Microorganisms 8 (8): 1253. https://doi.org/10.3390/microorganisms8081253.
• Gétaz, Michael, Jochen Blom, Theo H. M. Smits, and Joël F. Pothier. 2020. "Comparative Genomics of Xanthomonas Fragariae and Xanthomonas Arboricola Pv. Fragariae Reveals Intra- and Interspecies Variations." Phytopathology Research 2020 (2): 17. https://doi.org/10.1186/s42483-020-00061-y.
• Escursell, Mireia Marcé, Alexia Roschi, Theo Smits, and Fabio Rezzonico. 2020. "Characterization and Direct Molecular Discrimination of rpsL Mutations Leading to High Streptomycin Resistance in Erwinia Amylovora." Journal of Plant Pathology 103 (Suppl 1): 99–108. https://doi.org/10.1007/s42161-020-00600-8.
• Murray, Alison E., John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T. Konstantinidis, et al. 2020. "Roadmap for Naming Uncultivated Archaea and Bacteria." Nature Microbiology 5 (8): 987–94. https://doi.org/10.1038/s41564-020-0733-x.
• Madhaiyan, Munusamy, Venkatakrishnan Sivaraj Saravanan, Jochen Blom, Theo Smits, Fabio Rezzonico, Soo-Jin Kim, Hang-Yeon Weon, Soon-Wo Kwon, William B. Whitman, and Lianghui Ji. 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): 841–48. https://doi.org/10.1099/ijsem.0.003834.
• Rutz, Dominik, David Frasson, Martin Sievers, Jochen Blom, Fabio Rezzonico, Joël F. Pothier, and Theo H. M. Smits. 2019. "High-Quality Draft Genome Sequence of Pseudomonas Reidholzensis Strain CCOS 865T." Microbiology Resource Announcements 8 (3). https://doi.org/10.1128/MRA.01502-18.
• Smits, Theo H.M., Fabio Rezzonico, David Frasson, Pilar Vesga, Jordan Vacheron, Jochen Blom, Joël F. Pothier, Christoph Keel, Monika Maurhofer, and Martin Sievers. 2019. "Updated Genome Sequence and Annotation for the Full Genome of Pseudomonas Protegens CHA0." Microbiology Resource Announcements 8 (39). https://doi.org/10.1128/MRA.01002-19.
• Rutz, Dominik, David Frasson, Martin Sievers, Jochen Blom, Fabio Rezzonico, Joël F. Pothier, and Theo H.M. Smits. 2019. "Comparative Genomic Analysis of the Biotechnological Potential of the Novel Species Pseudomonas Wadenswilerensis CCOS 864T and Pseudomonas Reidholzensis CCOS 865T." Diversity 2019 (11): 204. https://doi.org/10.3390/d11110204.
• Ruinelli, Michela, Jochen Blom, Theo Smits, and Joël Pothier. 2019. "Comparative Genomics and Pathogenicity Potential of Members of the Pseudomonas Syringae Species Complex on Prunus Spp." BMC Genomics 20 (172). https://doi.org/10.1186/s12864-019-5555-y.
• Oh, Woo Taek, Jin Woo Jun, Sib Sankar Giri, Saekil Yun, Hyoun Joong Kim, Sang Guen Kim, Sang Wha Kim, et al. 2019. "Pseudomonas Tructae Sp. Nov., Novel Species Isolated from Rainbow Trout Kidney." International Journal of Systematic and Evolutionary Microbiology 69 (12): 3851–56. 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). https://doi.org/10.1186/s12864-019-6014-5.
• Smits, Theo H.M., Brion Duffy, Jochen Blom, Carol A. Ishimaru, and Virginia O. Stockwell. 2019. "Pantocin A, a Peptide-Derived Antibiotic Involved in Biological Control by Plant-Associated Pantoea Species." Archives of Microbiology 201 (6): 713–22. https://doi.org/10.1007/s00203-019-01647-7.
• Eck, Mathilde, Abdoul Sare, Sébastien Massart, Zala Schmautz, Ranka Junge, Theo H. M. Smits, and M. Jijakli. 2019. "Exploring Bacterial Communities in Aquaponic Systems." Water 11 (2): 260. https://doi.org/10.3390/w11020260.
• Gétaz, Michael, Marjon Krijger, Fabio Rezzonico, Theo Smits, Jan M. van der Wolf, and Joël F. Pothier. 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). https://doi.org/10.1099/mgen.0.000189.
• Rutz, Dominik, David Frasson, Martin Sievers, Jochen Blom, Fabio Rezzonico, Joël Pothier, and Theo Smits. 2018. "High-Quality Draft Genome Sequence of Pseudomonas Wadenswilerensis CCOS 864T." Microbiology Resource Announcements 7 (16). https://doi.org/10.1128/MRA.01059-18.
• Pillonetto, Marcelo, Lavinia Arend, Suzie M. T. Gomes, Marluce A. A. Oliveira, Loeci N. Timm, Andreza F. Martins, Afonso L. Barth, et al. 2018. "Molecular Investigation of Isolates from a Multistate Polymicrobial Outbreak Associated with Contaminated Total Parenteral Nutrition in Brazil." BMC Infectious Diseases 18 (397): 1–11. https://doi.org/10.1186/s12879-018-3287-2.
• Dennert, Francesca, Nicola Imperiali, Cornelia Staub, Jana Schneider, Titouan Laessle, Tao Zhang, Raphaël Wittwer, et al. 2018. "Conservation Tillage and Organic Farming Induce Minor Variations in Pseudomonas Abundance, Their Antimicrobial Function and Soil Disease Resistance." FEMS Microbiology Ecology 94 (8): fiy075. https://doi.org/10.1093/femsec/fiy075.
• Pillonetto, Marcelo, Lavinia N. Arend, Helisson Faoro, Helena R. S. D'Espindula, Jochen Blom, Theo H. M. Smits, Marcelo T. Mira, and Fabio Rezzonico. 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 (January): 176–84. https://doi.org/10.1099/ijsem.0.002477.
• Palmer, Marike, Emma T. Steenkamp, Martin P.A. Coetzee, Wai-Yin Chan, Elritha van Zyl, Pieter De Maayer, Teresa A. Coutinho, et al. 2017. "Phylogenomic Resolution of the Bacterial Genus Pantoea and Its Relationship with Erwinia and Tatumella." Antonie van Leeuwenhoek 110 (10): 1287–1309. https://doi.org/10.1007/s10482-017-0852-4.
• Smits, Theo, Brion Duffy, George Sundin, Youfu Zhao, and Fabio Rezzonico. 2017. "Erwinia Amylovora in the Genomics Era : From Genomes to Pathogen Virulence, Regulation, and Disease Control Strategies." Journal of Plant Pathology 99 (Special issue): 7–23. https://doi.org/10.4454/jpp.v99i0.3917.
• Ishimaru, Carol, Teresa A. Lansdell, Jon Clardy, Brion Duffy, and Theo H.M. Smits. 2017. "The Histidine-Reversible Antibiotic Herbicolin O Produced by Pantoea Vagans C9-1 Is Pantocin A." Journal of Plant Pathology 99 (Special issue): 91–97. https://doi.org/10.4454/jpp.v99i0.3910.
• Rezzonico, Fabio, Brion Duffy, Theo H.M. Smits, and Joël F. Pothier. 2017. "Erwinia Species Identification Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry." Journal of Plant Pathology 99 (Special issue): 121–29. https://doi.org/10.4454/jpp.v99i0.3916.
• De Maayer, Pieter, Habibu Aliyu, Surendra Vikram, Jochen Blom, Brion Duffy, Don A. Cowan, Theo H.M. Smits, Stephanus N. Venter, and Teresa A. Coutinho. 2017. "Phylogenomic, Pan-Genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea Ananatis and Pantoea Stewartii." Frontiers in Microbiology 8 (September): 1755. https://doi.org/10.3389/fmicb.2017.01755.
• Frasson, David, Michael Opoku, Tara Picozzi, Tania Torossi, Stefanie Balada, Theo Smits, and Urs Hilber. 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 (August): 2853–61. https://doi.org/10.1099/ijsem.0.002035.
• Kamber, Tim, Joël Pothier, Cosima Pelludat, Fabio Rezzonico, Brion Duffy, and Theo Smits. 2017. "Role of the Type VI Secretion Systems during Disease Interactions of Erwinia Amylovora with Its Plant Host." BMC Genomics 16 (628): 1–12. https://doi.org/10.1186/s12864-017-4010-1.
• Schmautz, Zala, Andreas Graber, Sebastian Jaenicke, Alexander Goesmann, Ranka Junge, and Theo H. M. Smits. 2017. "Microbial Diversity in Different Compartments of an Aquaponics System." Archives of Microbiology 199 (4): 613–20. https://doi.org/10.1007/s00203-016-1334-1.
• Flury, Pascale, Nora Aellen, Beat Ruffner, Maria Péchy-Tarr, Shakira Fataar, Zane Metla, Ana Dominguez-Ferreras, et al. 2016. "Insect Pathogenicity in Plant-Beneficial Pseudomonads : Phylogenetic Distribution and Comparative Genomics." Edited by International Society for Microbial Ecology. ISME Journal: Multidisciplinary Journal of Microbial Ecology 10: 2527–42. https://doi.org/10.1038/ismej.2016.5.
• Sirakov, Ivaylo Nikolaev, Matthias Lutz, Andreas Graber, Alex Mathis, Yordan Staykov, Theo H. M. Smits, and Ranka Junge. 2016. "Potential for Combined Biocontrol Activity against Fungal Fish and Plant Pathogens by Bacterial Isolates from a Model Aquaponic System." Water 8 (11). https://doi.org/10.3390/w8110518.
• Kupferschmied, Peter, Tiancong Chai, Pascale Flury, Jochen Blom, Theo Smits, Monika Maurhofer, and Christoph Keel. 2016. "Specific Surface Glycan Decorations Enable Antimicrobial Peptide Resistance in Plant-Beneficial Pseudomonads with Insect-Pathogenic Properties." Environmental Microbiology 18 (11): 4265–81. https://doi.org/10.1111/1462-2920.13571.
• Rezzonico, Fabio, Theo Smits, Yannick Born, Jochen Blom, Jürg E. Frey, Alexander Goesmann, Ilse Cleenwerck, et al. 2016. "Erwinia Gerundensis Sp. Nov. : A Cosmopolitan Epiphyte Originally Isolated from Pome Fruit Trees." International Journal of Systematic and Evolutionary Microbiology 66 (March): 1583–92. https://doi.org/10.1099/ijsem.0.000920.
• Kamber, Tim, Jan P. Buchmann, Joël Pothier, Theo Smits, Thomas Wicker, and Brion Duffy. 2016. "Fire Blight Disease Reactome : RNA-Seq Transcriptional Profile of Apple Host Plant Defence Responses to Erwinia Amylovora Pathogen Infection." Scientific Reports 6 (21600). https://doi.org/10.1038/srep21600.
• Smits, Theo H.M., Fabio Rezzonico, Jochen Blom, Alexander Goesmann, Azzurra Abelli, Roberto Kron Morelli, Joël L. Vanneste, and Brion Duffy. 2015. "Draft Genome Sequence of the Commercial Biocontrol Strain Pantoea Agglomerans P10c." Genome Announcements 3 (6). https://doi.org/10.1128/genomeA.01448-15.
• Smits, Theo H. M., Joël F. Pothier, Michela Ruinelli, Jochen Blom, David Frasson, Chantal Koechli, Carlotta Fabbri, Helmut Brandl, Brion Duffy, and Martin Sievers. 2015. "Complete Genome Sequence of the Cyanogenic Phosphate-Solubilizing Pseudomonas Sp. Strain CCOS 191 : A Close Relative of Pseudomonas Mosseli." Genome Announcements 3 (3). https://doi.org/10.1128/genomeA.00616-15.
• De Maayer, Pieter, Wai-Yin Chan, Douglas A. Martin, Jochen Blom, Stephanus N. Venter, Brion Duffy, Don A. Cowan, Theo H. M. Smits, and Teresa A. Coutinho. 2015. "Integrative Conjugative Elements of the ICEPan Family Play a Potential Role in Pantoea Ananatis Ecological Diversification and Antibiosis." Frontiers in Microbiology 6 (576). https://doi.org/10.3389/fmicb.2015.00576.
• Smits, Theo H. M., Víctor M. Guerrero-Prieto, Germán Hernández-Escarcega, Jochen Blom, Alexander Goesmann, Fabio Rezzonico, Brion Duffy, and Virginia O. Stockwell. 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). https://doi.org/10.1128/genomeA.01229-13.
• Brankatschk, Kerstin, Tim Kamber, Joël F. Pothier, Brion Duffy, and Theo H.M. Smits. 2014. "Transcriptional Profile of Salmonella Enterica Subsp. Enterica Serovar Weltevreden during Alfalfa Sprout Colonization." Microbial Biotechnology 7 (6): 528–44. https://doi.org/10.1111/1751-7915.12104.
• Ismail, Emadeldeen, Jochen Blom, Alain Bultreys, Milan Ivanovic, Aleksa Obradovic, Joop van Doorn, Maria Bergsma-Vlami, et al. 2014. "A Novel Plasmid pEA68 of Erwinia Amylovora and the Description of a New Family of Plasmids." Archives of Microbiology 196 (12): 891–99. https://doi.org/10.1007/s00203-014-1028-5.
• Weller-Stuart, Tania, Wai-Yin Chan, Teresa A. Coutinho, Stephanus N. Venter, Theo H.M. Smits, Brion Duffy, Teresa Goszczynska, Don A. Cowan, and Pieter de Maayer. 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). https://doi.org/10.1128/genomeA.00750-14.
• Bühlmann, Andreas, Tanja Dreo, Fabio Rezzonico, Joël F. Pothier, Theo H. M. Smits, Maja Ravnikar, Jürg E. Frey, and Brion Duffy. 2014. "Phylogeography and Population Structure of the Biologically Invasive Phytopathogen Erwinia Amylovora Inferred Using Minisatellites." Environmental Microbiology 16 (7): 2112–25. https://doi.org/10.1111/1462-2920.12289.
• Smits, Theo H. M., Fabio Rezzonico, Maria M. López, Jochen Blom, Alexander Goesmann, Jürg E. Frey, and Brion Duffy. 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): 449–56. https://doi.org/10.1016/j.syapm.2013.04.003.
• Barbé, Silva, Pablo Llop, Jochen Blom, Jose Cabrefiga, Alexander Goesmann, Brion Duffy, E. Montesinos, Theo H.M. Smits, and M. M. López. 2013. "Complete Sequence of Erwinia Piriflorinigrans Plasmids pEPIR37 and pEPIR5 and Role of pEPIR37 in Pathogen Virulence." Plant Pathology 62 (4): 786–98. https://doi.org/10.1111/ppa.12002.
• Bühlmann, Andreas, F. Pothier, Fabio Rezzonico, Theo H. M. Smits, Michael Andreou, Neil Boonham, Brion Duffy, and Jürg E. Frey. 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): 332–39. https://doi.org/10.1016/j.mimet.2012.12.017.
• Mann, Rachel A., Theo H.M. Smits, Andreas Bühlmann, Jochen Blom, Alexander Goesmann, Jürg E. Frey, Kim M. Plummer, et al. 2013. "Comparative Genomics of 12 Strains of Erwinia Amylovora Identifies a Pan-Genome with a Large Conserved Core." Plos One 8 (2). https://doi.org/10.1371/journal.pone.0055644.
• Bühlmann, Andreas, Joël F. Pothier, Jennifer A. Tomlinson, Jürg F. Frey, N. Boonham, Theo H.M. Smits, and Brion Duffy. 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): 475–84. https://doi.org/10.1111/j.1365-3059.2012.02654.x.

Book chapters, peer-reviewed

Coutinho, Teresa A, Pieter de Maayer, Sara Jordan, and Theo Smits. 2024. "Enterobacter." In Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB), Online, edited by William B. Whitman. Hoboken: Wiley. https://doi.org/10.1002/9781118960608.gbm01145.pub2.

Written conference contributions, peer-reviewed

• Gygax, Gregory, Nils Ratnaweera, Werner Tischhauser, Theo H. M. Smits, Patrick Laube, and Thomas Ott. 2023. "An Oracle for the Optimization of Underconstrained Compositions of Neural Networks : The Tick Hazard Use Case." Conference paper. In Artificial Life and Evolutionary Computation, edited by Johannes Josef Schneider, Mathias Sebastian Weyland, Dandolo Flumini, and Rudolf Marcel Füchslin, 24–31. Cham: Springer. https://doi.org/10.1007/978-3-031-23929-8_3.
• Kaufmann, Moritz, Martin Schüle, Theo Smits, and Joël Pothier. 2020. "Typing Plasmids with Distributed Sequence Representation." Conference paper. In Artificial Neural Networks in Pattern Recognition, edited by Frank-Peter Schilling and Thilo Stadelmann, 200–210. Cham: Springer. https://doi.org/10.1007/978-3-030-58309-5_16.
• Smits, Theo H.M., V. M. Guerrero-Prieto, G. Hernandez-Escarcega, Fabio Rezzonico, J. Blom, A. Goesmann, Brion Duffy, and V. O. Stockwell. 2014. "Comparative Genomics of Erwinia Amylovora Isolates from Mexico." Conference paper. In XIII International Workshop on Fire Blight, Zurich, Switzerland, 2-5 July 2013, 173–77. International Society for Horticultural Science. https://doi.org/10.17660/ActaHortic.2014.1056.27.
• Rezzonico, Fabio, Theo H.M. Smits, and Eduard Holliger, eds. 2014. Proceedings of the 13th International Workshop on Fire Blight. 13th International Workshop on Fire Blight, Zürich, 2-5 July 2013. Vol. 1. Leuven: International Society for Horticultural Science.

Other publications

• Orfei, Benedetta, Joël Pothier, Luca Scotti, Antonio Aceto, Chiaraluce Moretti, Roberto Buonaurio, and Theo Smits. 2026. "Correction: Transcriptome Analysis of Pseudomonas Syringae Pv. Tomato DAPP-PG 215 in Response to Silver Nanoparticles Exposure." Frontiers in Microbiology 17 (1809727). https://doi.org/10.3389/fmicb.2026.1809727.
• Rezzonico, Fabio, and Theo H. M. Smits. 2025. ""Citrobacter Bitternis" Ko et Al., 2015 and "Kluyvera Intestini" Tetz and Tetz, 2016 Are Heterotypic Synonyms of Phytobacter Diazotrophicus Zhang et Al., 2017." bioRxiv. https://doi.org/10.1101/2025.08.11.669625.
• Kurz, Mirjam, Adrian Kölz, Jonas Gorges, Beatriz Pablo Carmona, Peter Brang, Yann Vitasse, Martin Kohler, et al. 2023. "Corrigendum to "Tracing the Origin of Oriental Beech Stands across Western Europe and Reporting Hybridization with European Beech – Implications for Assisted Gene Flow" [for. Ecol. Manage. 531 (2023) 120801]." Forest Ecology and Management 537 (120942). https://doi.org/10.1016/j.foreco.2023.120942.
• Gerber, Nicole, Lars Fieseler, Sven Hirsch, Lukas Neutsch, Athina Papadopoulou, and Theo Smits. 2022. "Zusammenarbeit und wissenschaftlicher Austausch sind der Schlüssel zu erfolgreicher Forschung : der ZHAW Health Research Hub bringt's unter einen Hut." Clinicum 2022 (6): 80–81. https://doi.org/10.21256/zhaw-26376.
• Murray, Alison E., John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T. Konstantinidis, et al. 2020. "Author Correction : Roadmap for Naming Uncultivated Archaea and Bacteria." Nature Microbiology 6 (1): 136. https://doi.org/10.1038/s41564-020-00827-2.

Research data

• 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. European Nucleotide Archive.
• 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. Gene Expression Omnibus.
• Smits, Theo H. M.; Pothier, Joël F., 2018. Diversity of Xanthomonas fragariae with MLVA & CRISPR. European Nucleotide Archive.
• Dia, Nay C.; Van Vaerenbergh, Johan; Van Malderghem, Cinzia; Blom, Jochen; Smits, Theo H. M.; Cottyn, Bart; Pothier, Joël F., 2021. Complete genome sequences of four Xanthomonas hortorum species level clade strains sequenced with short- and long-read technologies. European Nucleotide Archive.

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