Prof. Dr. Theo Smits

Network

ORCID digital identifier

ORCID ID: 0000-0002-1237-235X

Projects

• 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

• Orfei, B., Pothier, J., Scotti, L., Aceto, A., Moretti, C., Buonaurio, R., & Smits, T. (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
• Jordan, S., de Maayer, P., Smits, T. H. M., & Coutinho, T. A. (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, C. L., Jordan, S., Pothier, J. F., Nägele, H.-J., Smits, T. H. M., & Merkle, W. (2026). Optimizing trickle-bed reactor performance for hydrogenotrophic methane production in power-to-methane systems. Process Biochemistry, 163, 66–76. https://doi.org/10.1016/j.procbio.2026.02.010
• Jordan, S., Pothier, J. F., Rezzonico, F., Kvitko, B. H., Coutinho, T. A., & Smits, T. H. M. (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, A., D’Espindula, H. R. S., Kulek, D. O., Jones, K. L., Kraft, L., Smits, T. H. M., Rezzonico, F., Mira, M. T., & Pillonetto, M. (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, B., Pothier, J. F., Scotti, L., Aceto, A., Moretti, C., Buonaurio, R., & Smits, T. H. M. (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, C., Piry, S., Moury, B., Chateau, L., Berthier, K., Jacobs, J. M., Butchacas, J., Fenske, L., Ebeling-Koning, L., Smits, T. H. M., Morris, C. E., & Torres-Barceló, C. (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, Z. A., Naizabayeva, D. A., Dosmagambet, Z. M., Rezzonico, F., Smits, T. H. M., & Maltseva, E. R. (2025). A distinct Erwinia amylovora lineage in Kazakhstan associated with a pEA29 transposase mutation. Journal of Plant Pathology. https://doi.org/10.1007/s42161-025-02099-3
• Blank-Pachlatko, J., Rhyner, N., Smits, T. H. M., Kulli Honauer, B., & Edelkraut, K. (2025). Beyond plants : how soil alterations shape restoration success in alpine grasslands. Tuexenia, 45, 405–427. https://doi.org/10.14471/2025.45.012
• Jordan, S., Pothier, J. F., de Maayer, P., Broders, K., Kvitko, B. H., Coutinho, T. A., & Smits, T. (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, P., Green, T., Jordan, S., Smits, T. H. M., & Coutinho, T. A. (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, N. C., Cottyn, B., Aspin, A., Studer, B., Smits, T. H. M., & Pothier, J. F. (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), 138–143. https://doi.org/10.1094/PHYTOFR-10-24-0119-FI
• Rezzonico, F., Bobushova, S., Gaganidze, D., Konurbaeva, M., Mukhanov, S., Jordan, S., Sadunishvili, T., Drenova, N., Smits, T., & Doolotkeldieva, T. (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, I. R., Kulek, D., Arend, L. N. V. S., Pillonetto, M., Smits, T. H. M., & Rezzonico, F. (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, F., Emeriewen, O. F., Zeng, Q., Peil, A., Smits, T. H. M., & Sundin, G. W. (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
• Maltseva, E. R., Zharmukhamedova, G. A., Jumanova, Z. K., Naizabayeva, D. A., Berdygulova, Z. A., Dmitriyeva, K. A., Tezekbayeva, B., Khassein, A., Skiba, Y. A., Malakhova, N. P., Ismagulova, G. A., Rezzonico, F., & Smits, T. H. M. (2023). Fire blight cases in Almaty Region of Kazakhstan in the proximity of wild apple distribution area. Journal of Plant Pathology, 106(3), 971–978. https://doi.org/10.1007/s42161-023-01416-y
• Gartmann, F., Hügly, J., Krähenbühl, N., Brinkmann, N., Schmautz, Z., Smits, T. H. M., & Junge, R. (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
• Crosby, K. C., Rojas, M., Sharma, P., Johnson, M. A., Mazloom, R., Kvitko, B. H., Smits, T. H. M., Venter, S. N., Coutinho, T. A., Heath, L. S., Palmer, M., & Vinatzer, B. A. (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, P., Ko, K. K. K., Chia, J. W. Z., De, P. P., Smits, T. H. M., Low, J., Vasoo, S., & Tsui, C. K. M. (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, B., Pothier, J. F., Fenske, L., Blom, J., Moretti, C., Buonaurio, R., & Smits, T. H. M. (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, M., Sultangaziev, O., Szalatnay, D., Sodonbekov, I., Naizabayeva, D. A., Milikbekova, M., Akbarsho, S., Bobushova, S., Doolotkeldieva, T., Rezzonico, F., & Smits, T. H. M. (2023). An app for apples : citizen-led mapping of fire blight in Central Asia. Journal of Plant Pathology, 106(3), 967–970. https://doi.org/10.1007/s42161-023-01406-0
• Hon, P., Ko, K. K. K., Zhong, J. C. W., De, P. P., Smits, T. H. M., Low, J., Vasoo, S., & Tsui, C. K. M. (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, L. N. V. S., Bergamo, R., Rocha, F. B., Bail, L., Ito, C., Baura, V. A., Balsanelli, E., Pothier, J. F., Rezzonico, F., Pilonetto, M., Smits, T. H. M., & Tuon, F. F. (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, M., Kölz, A., Gorges, J., Carmona, B. P., Brang, P., Vitasse, Y., Kohler, M., Rezzonico, F., Smits, T. H. M., Bauhus, J., Rudow, A., Hansen, O. K., Vatanparast, M., Sevik, H., Zhelev, P., Gömöry, D., Paule, L., Sperisen, C., & Csilléry, K. (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, E. R., Zharmukhamedova, G. A., Jumanova, Z. K., Naizabayeva, D. A., Berdygulova, Z. A., Dmitriyeva, K. A., Soltanbekov, S. S., Argynbayeva, A. M., Skiba, Y. A., Malakhova, N. P., Rezzonico, F., & Smits, T. H. M. (2022). Assessment of fire blight introduction in the wild apple forests of Kazakhstan. Biodiversity, 23(3-4), 123–128. https://doi.org/10.1080/14888386.2022.2141880
• Knecht, L. E., Born, Y., Pelludat, C., Pothier, J. F., Smits, T. H. M., Loessner, M. J., & Fieseler, L. (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, A., Pothier, J. F., Blom, J., Moretti, C., Buonaurio, R., Rezzonico, F., & Smits, T. H. M. (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, Z., Walser, J.-C., Espinal, C. A., Gartmann, F., Scott, B., Pothier, J. F., Frossard, E., Junge, R., & Smits, T. 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). https://doi.org/10.1016/j.scitotenv.2022.158426
• Dia, N. C., Cottyn, B., Blom, J., Smits, T. H. M., & Pothier, J. F. (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, M., Blom, J., Smits, T. H. M., & Pothier, J. 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). https://doi.org/10.3389/fmicb.2022.804681
• Smits, T. H. M., Arend, L. N. V. S., Cardew, S., Tång-Hallbäck, E., Mira, M. T., Moore, E. R. B., Sampaio, J. L. M., Rezzonico, F., & Pillonetto, M. (2022). Resolving taxonomic confusion : establishing the genus Phytobacter on the list of clinically relevant Enterobacteriaceae. European Journal of Clinical Microbiology & Infectious Diseases, 41(4), 547–558. https://doi.org/10.1007/s10096-022-04413-8
• Doering, M., Freimann, R., Antenen, N., Roschi, A., Robinson, C. T., Rezzonico, F., Smits, T., & Tonolla, D. (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, N. C., Van Vaerenbergh, J., Van Malderghem, C., Blom, J., Smits, T. H. M., Cottyn, B., & Pothier, J. F. (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, M., Carnal, S., Dafny-Yelin, M., Mairesse, O., Gottsberger, R. A., Ivanović, M., Grahovac, M., Lagonenko, A. L., Drenova, N., Zharmukhamedova, G., Doolotkeldieva, T., Smits, T. H. M., & Rezzonico, F. (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, C., Rezzonico, F., Orfei, B., Cortese, C., Moreno‐Pérez, A., van den Burg, H. A., Onofri, A., Firrao, G., Ramos, C., Smits, T. H. M., & Buonaurio, R. (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), 1209–1225. https://doi.org/10.1111/mpp.13105
• Mainetti, T., Palmisano, M., Rezzonico, F., Stres, B., Kern, S., & Smits, T. 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), 4209–4219. https://doi.org/10.1007/s00203-021-02409-0
• Schmautz, Z., Espinal, C. A., Smits, T. H. M., Frossard, E., & Junge, R. (2021). Nitrogen transformations across compartments of an aquaponic system. Aquacultural Engineering, 92(102145). https://doi.org/10.1016/j.aquaeng.2021.102145
• Schmautz, Z., Espinal, C. A., Bohny, A. M., Rezzonico, F., Junge, R., Frossard, E., & Smits, T. H. M. (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, N. C., Rezzonico, F., Smits, T. H. M., & Pothier, J. 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), e00828–20. https://doi.org/10.1128/MRA.00828-20
• Gétaz, M., Puławska, J., Smits, T. H. M., & Pothier, J. F. (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, M., Blom, J., Smits, T. H. M., & Pothier, J. F. (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, M. M., Roschi, A., Smits, T., & Rezzonico, F. (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, A. E., Freudenstein, J., Gribaldo, S., Hatzenpichler, R., Hugenholtz, P., Kämpfer, P., Konstantinidis, K. T., Lane, C. E., Papke, R. T., Parks, D. H., Rossello-Mora, R., Stott, M. B., Sutcliffe, I. C., Thrash, J. C., Venter, S. N., Whitman, W. B., Acinas, S. G., Amann, R. I., Anantharaman, K., et al. (2020). Roadmap for naming uncultivated archaea and bacteria. Nature Microbiology, 5(8), 987–994. https://doi.org/10.1038/s41564-020-0733-x
• Madhaiyan, M., Saravanan, V. S., Blom, J., Smits, T., Rezzonico, F., Kim, S.-J., Weon, H.-Y., Kwon, S.-W., Whitman, W. B., & Ji, L. (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), 841–848. https://doi.org/10.1099/ijsem.0.003834
• Smits, T. H. M., Rezzonico, F., Frasson, D., Vesga, P., Vacheron, J., Blom, J., Pothier, J. F., Keel, C., Maurhofer, M., & Sievers, M. (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, D., Frasson, D., Sievers, M., Blom, J., Rezzonico, F., Pothier, J. F., & Smits, T. H. M. (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
• Ruinelli, M., Blom, J., Smits, T., & Pothier, J. (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
• Rutz, D., Frasson, D., Sievers, M., Blom, J., Rezzonico, F., Pothier, J. F., & Smits, T. 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), 204. https://doi.org/10.3390/d11110204
• Oh, W. T., Jun, J. W., Giri, S. S., Yun, S., Kim, H. J., Kim, S. G., Kim, S. W., Kang, J. W., Han, S. J., Kwon, J., Kim, J. H., Smits, T. H. M., & Park, S. C. (2019). Pseudomonas tructae sp. nov., novel species isolated from rainbow trout kidney. International Journal of Systematic and Evolutionary Microbiology, 69(12), 3851–3856. https://doi.org/10.1099/ijsem.0.003696
• Smits, T. 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, T. H. M., Duffy, B., Blom, J., Ishimaru, C. A., & Stockwell, V. O. (2019). Pantocin A, a peptide-derived antibiotic involved in biological control by plant-associated Pantoea species. Archives of Microbiology, 201(6), 713–722. https://doi.org/10.1007/s00203-019-01647-7
• Eck, M., Sare, A., Massart, S., Schmautz, Z., Junge, R., Smits, T. H. M., & Jijakli, M. (2019). Exploring bacterial communities in aquaponic systems. Water, 11(2), 260. https://doi.org/10.3390/w11020260
• Gétaz, M., Krijger, M., Rezzonico, F., Smits, T., van der Wolf, J. M., & Pothier, J. 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). https://doi.org/10.1099/mgen.0.000189
• Rutz, D., Frasson, D., Sievers, M., Blom, J., Rezzonico, F., Pothier, J., & Smits, T. (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, M., Arend, L., Gomes, S. M. T., Oliveira, M. A. A., Timm, L. N., Martins, A. F., Barth, A. L., Mazzetti, A., Hersemann, L., Smits, T. H. M., Mira, M. T., & Rezzonico, F. (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, F., Imperiali, N., Staub, C., Schneider, J., Laessle, T., Zhang, T., Wittwer, R., van der Heijden, M. G. A., Smits, T. H. M., Schlaeppi, K., Keel, C., & Maurhofer, M. (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, M., Arend, L. N., Faoro, H., D’Espindula, H. R. S., Blom, J., Smits, T. H. M., Mira, M. T., & Rezzonico, F. (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, 176–184. https://doi.org/10.1099/ijsem.0.002477
• Palmer, M., Steenkamp, E. T., Coetzee, M. P. A., Chan, W.-Y., van Zyl, E., De Maayer, P., Coutinho, T. A., Blom, J., Smits, T., Duffy, B., & Venter, S. N. (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
• Rezzonico, F., Duffy, B., Smits, T. H. M., & Pothier, J. F. (2017). Erwinia species identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Journal of Plant Pathology, 99(Special issue), 121–129. https://doi.org/10.4454/jpp.v99i0.3916
• Ishimaru, C., Lansdell, T. A., Clardy, J., Duffy, B., & Smits, T. 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), 91–97. https://doi.org/10.4454/jpp.v99i0.3910
• Smits, T., Duffy, B., Sundin, G., Zhao, Y., & Rezzonico, F. (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
• De Maayer, P., Aliyu, H., Vikram, S., Blom, J., Duffy, B., Cowan, D. A., Smits, T. H. M., Venter, S. N., & Coutinho, T. A. (2017). Phylogenomic, pan-genomic, pathogenomic and evolutionary genomic insights into the agronomically relevant enterobacteria Pantoea ananatis and Pantoea stewartii. Frontiers in Microbiology, 8, 1755. https://doi.org/10.3389/fmicb.2017.01755
• Frasson, D., Opoku, M., Picozzi, T., Torossi, T., Balada, S., Smits, T., & Hilber, U. (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, 2853–2861. https://doi.org/10.1099/ijsem.0.002035
• Kamber, T., Pothier, J., Pelludat, C., Rezzonico, F., Duffy, B., & Smits, T. (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, Z., Graber, A., Jaenicke, S., Goesmann, A., Junge, R., & Smits, T. H. M. (2017). Microbial diversity in different compartments of an aquaponics system. Archives of Microbiology, 199(4), 613–620. https://doi.org/10.1007/s00203-016-1334-1
• Sirakov, I. N., Lutz, M., Graber, A., Mathis, A., Staykov, Y., Smits, T. H. M., & Junge, R. (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
• Flury, P., Aellen, N., Ruffner, B., Péchy-Tarr, M., Fataar, S., Metla, Z., Dominguez-Ferreras, A., Bloemberg, G., Frey, J., Goesmann, A., Raaijmakers, J. M., Duffy, B., Höfte, M., Blom, J., Smits, T., Keel, C., & Maurhofer, M. (2016). Insect pathogenicity in plant-beneficial pseudomonads : phylogenetic distribution and comparative genomics. ISME Journal: Multidisciplinary Journal of Microbial Ecology, 10, 2527–2542. https://doi.org/10.1038/ismej.2016.5
• Kupferschmied, P., Chai, T., Flury, P., Blom, J., Smits, T., Maurhofer, M., & Keel, C. (2016). Specific surface glycan decorations enable antimicrobial peptide resistance in plant-beneficial pseudomonads with insect-pathogenic properties. Environmental Microbiology, 18(11), 4265–4281. https://doi.org/10.1111/1462-2920.13571
• Rezzonico, F., Smits, T., Born, Y., Blom, J., Frey, J. E., Goesmann, A., Cleenwerck, I., de Vos, P., Bonaterra, A., Duffy, B., & Montesinos, E. (2016). Erwinia gerundensis sp. nov. : a cosmopolitan epiphyte originally isolated from pome fruit trees. International Journal of Systematic and Evolutionary Microbiology, 66, 1583–1592. https://doi.org/10.1099/ijsem.0.000920
• Kamber, T., Buchmann, J. P., Pothier, J., Smits, T., Wicker, T., & Duffy, B. (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, T. H. M., Rezzonico, F., Blom, J., Goesmann, A., Abelli, A., Kron Morelli, R., Vanneste, J. L., & Duffy, B. (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, T. H. M., Pothier, J. F., Ruinelli, M., Blom, J., Frasson, D., Koechli, C., Fabbri, C., Brandl, H., Duffy, B., & Sievers, M. (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, P., Chan, W.-Y., Martin, D. A., Blom, J., Venter, S. N., Duffy, B., Cowan, D. A., Smits, T. H. M., & Coutinho, T. 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). https://doi.org/10.3389/fmicb.2015.00576
• Smits, T. H. M., Guerrero-Prieto, V. M., Hernández-Escarcega, G., Blom, J., Goesmann, A., Rezzonico, F., Duffy, B., & Stockwell, V. 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). https://doi.org/10.1128/genomeA.01229-13
• Brankatschk, K., Kamber, T., Pothier, J. F., Duffy, B., & Smits, T. H. M. (2014). Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization. Microbial Biotechnology, 7(6), 528–544. https://doi.org/10.1111/1751-7915.12104
• Ismail, E., Blom, J., Bultreys, A., Ivanovic, M., Obradovic, A., van Doorn, J., Bergsma-Vlami, M., Maes, M., Willems, A., Duffy, B., Stockwell, V. O., Smits, T. H. M., & Pulawska, J. (2014). A novel plasmid pEA68 of Erwinia amylovora and the description of a new family of plasmids. Archives of Microbiology, 196(12), 891–899. https://doi.org/10.1007/s00203-014-1028-5
• Weller-Stuart, T., Chan, W.-Y., Coutinho, T. A., Venter, S. N., Smits, T. H. M., Duffy, B., Goszczynska, T., Cowan, D. A., & de Maayer, P. (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, A., Dreo, T., Rezzonico, F., Pothier, J. F., Smits, T. H. M., Ravnikar, M., Frey, J. E., & Duffy, B. (2014). Phylogeography and population structure of the biologically invasive phytopathogen Erwinia amylovora inferred using minisatellites. Environmental Microbiology, 16(7), 2112–2125. https://doi.org/10.1111/1462-2920.12289
• Smits, T. H. M., Rezzonico, F., López, M. M., Blom, J., Goesmann, A., Frey, J. E., & Duffy, B. (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), 449–456. https://doi.org/10.1016/j.syapm.2013.04.003
• Barbé, S., Llop, P., Blom, J., Cabrefiga, J., Goesmann, A., Duffy, B., Montesinos, E., Smits, T. 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), 786–798. https://doi.org/10.1111/ppa.12002
• Bühlmann, A., Pothier, F., Rezzonico, F., Smits, T. H. M., Andreou, M., Boonham, N., Duffy, B., & Frey, J. 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), 332–339. https://doi.org/10.1016/j.mimet.2012.12.017
• Mann, R. A., Smits, T. H. M., Bühlmann, A., Blom, J., Goesmann, A., Frey, J. E., Plummer, K. M., Beer, S. V., Luck, J., Duffy, B., & Rodoni, B. (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, A., Pothier, J. F., Tomlinson, J. A., Frey, J. F., Boonham, N., Smits, T. H. M., & Duffy, B. (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), 475–484. https://doi.org/10.1111/j.1365-3059.2012.02654.x

Book chapters, peer-reviewed

Coutinho, T. A., de Maayer, P., Jordan, S., & Smits, T. (2024). Enterobacter. In W. B. Whitman (Ed.), Bergey’s Manual of Systematics of Archaea and Bacteria (BMSAB), Online. Wiley. https://doi.org/10.1002/9781118960608.gbm01145.pub2

Written conference contributions, peer-reviewed

• Gygax, G., Ratnaweera, N., Tischhauser, W., Smits, T. H. M., Laube, P., & Ott, T. (2023). An oracle for the optimization of underconstrained compositions of neural networks : the tick hazard use case [Conference paper]. In J. J. Schneider, M. S. Weyland, D. Flumini, & R. M. Füchslin (Eds.), Artificial Life and Evolutionary Computation (pp. 24–31). Springer. https://doi.org/10.1007/978-3-031-23929-8_3
• Kaufmann, M., Schüle, M., Smits, T., & Pothier, J. (2020). Typing plasmids with distributed sequence representation [Conference paper]. In F.-P. Schilling & T. Stadelmann (Eds.), Artificial Neural Networks in Pattern Recognition (pp. 200–210). Springer. https://doi.org/10.1007/978-3-030-58309-5_16
• Smits, T. H. M., Guerrero-Prieto, V. M., Hernandez-Escarcega, G., Rezzonico, F., Blom, J., Goesmann, A., Duffy, B., & Stockwell, V. O. (2014). Comparative genomics of Erwinia amylovora isolates from Mexico [Conference paper]. XIII International Workshop on Fire Blight, Zurich, Switzerland, 2-5 July 2013, 173–177. https://doi.org/10.17660/ActaHortic.2014.1056.27
• Proceedings of the 13th international workshop on fire blight. (2014). In F. Rezzonico, T. H. M. Smits, & E. Holliger (Eds.), 13th International Workshop on Fire Blight, Zürich, 2-5 July 2013 (Vol. 1). International Society for Horticultural Sciences.

Other publications

• Rezzonico, F., & Smits, T. H. M. (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, M., Kölz, A., Gorges, J., Pablo Carmona, B., Brang, P., Vitasse, Y., Kohler, M., Rezzonico, F., Smits, T. H. M., Bauhus, J., Rudow, A., Hansen, O. K., Vatanparast, M., Sevik, H., Zhelev, P., Gömöry, D., Paule, L., Sperisen, C., & Csilléry, K. (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, N., Fieseler, L., Hirsch, S., Neutsch, L., Papadopoulou, A., & Smits, T. (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, A. E., Freudenstein, J., Gribaldo, S., Hatzenpichler, R., Hugenholtz, P., Kämpfer, P., Konstantinidis, K. T., Lane, C. E., Papke, R. T., Parks, D. H., Rossello-Mora, R., Stott, M. B., Sutcliffe, I. C., Thrash, J. C., Venter, S. N., Whitman, W. B., Acinas, S. G., Amann, R. I., Anantharaman, K., 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

• Smits, Theo H. M.; Pothier, Joël F., 2018. Diversity of Xanthomonas fragariae with MLVA & CRISPR. European Nucleotide Archive. Available from: https://www.ebi.ac.uk/ena/browser/view/PRJEB25730
• 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. Available from: https://www.ebi.ac.uk/ena/browser/view/PRJEB38813
• 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. Available from: https://www.ebi.ac.uk/ena/browser/view/PRJEB38812
• 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. Available from: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150636

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