Dr. Joël Pothier

Experience

• Postdoctoral researcher
  Agroscope
  09 / 2008 - 04 / 2013
• Postdoctoral researcher
  CNRS
  04 / 2008 - 07 / 2008

Network

ORCID digital identifier

ORCID ID: 0000-0002-9604-7780

Projects

• Local Adaptation and Sustainability in Grain Legume Cultivation with Soybean as a Proof of Principle / Project leader / ongoing
• Fungal Diversity in Bhutan’s Royal Botanical Park via Soil eDNA Metabarcoding and Visual Arts for Conservation and Communication / Project leader / ongoing
• A regenerative mulch mat made from regionally sourced biomass using fungal binding and saprophytic fungi for sustainable urban agriculture and viticulture / Project leader / ongoing
• Development of a biofungicide based on actinobacteria strains isolated from extreme Moroccan ecosystems to protect and improve tomato productivity / Project leader / ongoing
• CHIPOTS+: Chitin-Integrated Mycelium-Bound Substrate Blocks for Seedling Boosting / Project leader / completed
• Bioprospecting and genomics of actinobacteria isolated from the Marchica lagoon / Project leader / completed
• Massive detection of tomato brown rugose fruit virus by high-throughput sequencing / Project leader / completed
• EBDOmics – Comparative genomics of Enterobacter spp. causing Bulb Decay of Onions / Deputy project leader / completed
• Fire Blight App for Central Asia / Deputy project leader / completed
• Acceptance of an app for contact-tracing of SARS-CoV-2 in the Swiss population / Team member / completed
• A multidisciplinary project to understand the effect of chitin soil amendment on the plant response, natural microbial community and the fate of human pathogenic bacteria / Project leader / completed
• Silent pathway awakening to discover novel antibacterial compounds from actinomycetes / Co-project leader / completed
• MinION2FixID: fast and reliable legume root nodule bacteria identification using nanopore sequencing technology / Co-project leader / completed
• Diagnostic and epidemiological tools for the Xanthomonas hortorum species-level clade based on OMICs technologies / Co-project leader / completed
• Development of a fast and exact method for R. solanacearum detection in Swiss surface water samples / Co-project leader / completed
• Effect of cryopreservation on genome mutation rate - examples of grapevine / Deputy project leader / completed
• Characterization of nitrogen dynamics in an aquaponic system / Team member / completed
• Comparative genomics to untangle insect pathogenicity in plant-associated pseudomonads / Team member / completed
• Sepsis-Associated Microorganisms in Brazilian Ambulatories / Team member / completed
• MycoTOF – Determining mycotoxigenic molds and mycotoxins / Co-project leader / completed
• Sustainable production of high quality cherries for the European market / Project leader / completed
• DROPSA – Strategies to develop effective, innovative and practical approaches to protect major European fruit crops from pests and pathogens / Project leader / completed
• High-throughput proteomics of Thiodictyon synthrophicum strain Cad16T / Project leader / completed
• Genomics and transcriptomics of Erwinia and Pantoea / Team member / completed
• In-depth molecular analysis of stool and water samples collected in Kampala, Uganda / Project leader / completed
• MALDI-TOF MS for microorganism identification: from pattern recognition towards marker based approaches / Project leader / completed
• Comparative genomics of the plant pathogen Xanthomonas arboricola pv. pruni and related xanthomonads / Project leader / completed

Publications

Articles in scientific journal, peer-reviewed

• Jordan, S., Pothier, J. F., de Maayer, P., Kvitko, B. H., Coutinho, T. A., & Smits, T. H. M. (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
• 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
• 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
• Makechemu, M., Goto, Y., Schmid, M. W., Zbinden, H., Widrig, V., Kaufmann, M., Pothier, J. F., Keller, B., & Zipfel, C. (2025). Chitin soil amendment triggers systemic plant disease resistance through enhanced pattern‐triggered immunity. Plant Biotechnology Journal, 23(11), 5032–5044. https://doi.org/10.1111/pbi.70282
• 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
• Zhao, X., Overbeek, L. V., Burgess, C. M., Holden, N., Brennan, F., Johannessen, G. S., Allende, A., Höfte, M., Cottyn, B., Pothier, J. F., Schikora, A., & Uyttendaele, M. (2025). Human pathogenic microorganisms in fresh produce production : lessons learned when plant science meets food safety. Journal of Food Protection, 88(7), 100551. https://doi.org/10.1016/j.jfp.2025.100551
• 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
• Garcia, E., Soares, F., Rodrigues, C. O., Trovão, J., Pothier, J. F., Camelo, A., Espírito Santo, C., Dragnev, D., Petrova, E., Costa, J., & Bobev, S. (2024). Expansion of the host range of Xanthomonas euroxanthea : first occurence in sunflower in Bulgaria. Plant Disease, 109(4), 810–815. https://doi.org/10.1094/PDIS-08-24-1691-SC
• Pas, C., Fieseler, L., Pothier, J. F., & Briers, Y. (2024). Isolation, characterization, and receptor-binding protein specificity of phages PAS7, PAS59 and PAS61 infecting Shiga toxin-producing Escherichia coli O103 and O146. Scientific Reports, 14(26050). https://doi.org/10.1038/s41598-024-77463-x
• Dimaria, G., Mosca, A., Russo, M., Cubero, J., Pothier, J. F., Koebnik, R., & Catara, V. (2024). Draft genome sequence of Xanthomonas arboricola pv. pruni PVCT 262.1 isolated from Prunus dulcis in Italy. Microbiology Resource Announcements, 13(7), e0027324. https://doi.org/10.1128/mra.00273-24
• Kaufmann, M., Li, L., Van Poucke, C., Rhyner, N., De Tender, C., Uyttendaele, M., Heyndrickx, M., Zipfel, C., Pothier, J. F., & Bart, C. (2024). Soil type and associated microbiomes influences chitin's growth-promotion effect in lettuce. Phytobiomes Journal, 8(3), 248–261. https://doi.org/10.1094/PBIOMES-12-23-0132-R
• Costa, J., Pothier, J. F., Bosis, E., Boch, J., Kölliker, R., & Koebnik, R. (2023). A community-curated DokuWiki resource on diagnostics, diversity, pathogenicity and genetic control of Xanthomonads. Molecular Plant-Microbe Interactions, 37(3), 347–353. https://doi.org/10.1094/MPMI-11-23-0184-FI
• Kałużna, M., Prokić, A., Obradović, A., Weldon, W. A., Stockwell, V. O., & Pothier, J. F. (2023). Specific and sensitive detection tools for Xanthomonas arboricola pv. corylina, the causal agent of bacterial blight of hazelnut, developed with comparative genomics. Frontiers in Plant Science, 14(1254107). https://doi.org/10.3389/fpls.2023.1254107
• 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
• Li, L., Kaufmann, M., Makechemu, M., Van Poucke, C., De Keyser, E., Uyttendaele, M., Zipfel, C., Cottyn, B., & Pothier, J. F. (2023). Assessment of transcriptional reprogramming of lettuce roots in response to chitin soil amendment. Frontiers in Plant Science, 14(1158068). https://doi.org/10.3389/fpls.2023.1158068
• 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
• Pothier, J. F., Bolt, V., Arn, F., Frasson, D., Rhyner, N., & Sievers, M. (2023). High-quality draft genome sequence of Streptomyces albidoflavus CCOS 2040, isolated from a Swiss soil sample. Microbiology Resource Announcements, 12(3), e01225–22. https://doi.org/10.1128/mra.01225-22
• 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
• Silva, K. G., Martins, L., Teixeira, M., Pothier, J. F., & Tavares, F. (2022). DNA markers for detection and genotyping of Xanthomonas euroxanthea. Microorganisms, 10(6), 1078. https://doi.org/10.3390/microorganisms10061078
• Kałużna, M., & Pothier, J. F. (2022). Complete genome sequence data of two Xanthomonas arboricola strains isolated from blueberry plants displaying bacterial leaf blight in Poland. Phytopathology, 112(8), 1814–1818. https://doi.org/10.1094/PHYTO-11-21-0484-A
• 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
• Dia, N. C., Morinière, L., Cottyn, B., Bernal, E., Jacobs, Jonathan M., Koebnik, R., Osdaghi, E., Potnis, N., & Pothier, J. F. (2022). Xanthomonas hortorum – beyond gardens : current taxonomy, genomics, and virulence repertoires. Molecular Plant Pathology, 23(5), 597–621. https://doi.org/10.1111/mpp.13185
• Hakalová, E., Čechová, J., Tekielska, D. A., Eichmeier, A., & Pothier, J. F. (2022). Combined effect of thyme and clove phenolic compounds on Xanthomonas campestris pv. campestris and biocontrol of black rot disease on cabbage seeds. Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.1007988
• Pothier, J. F., Kałużna, M., Prokić, A., Obradovic, A., & Rezzonico, F. (2021). Complete genome and plasmid sequence data of three Xanthomonas arboricola pv. corylina strains, the bacterium responsible for bacterial blight of hazelnut. Phytopathology, 112(4), 956–960. https://doi.org/10.1094/PHYTO-08-21-0356-A
• 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
• Kałużna, M., Fischer‐Le Saux, M., Pothier, J., Jacques, M.-A., Obradović, A., Tavares, F., & Stefani, E. (2021). Xanthomonas arboricola pv. juglandis and pv. corylina: Brothers or distant relatives? : genetic clues, epidemiology, and insights for disease management. Molecular Plant Pathology, 22(12), 1481–1499. https://doi.org/10.1111/mpp.13073
• Cottyn, B., De Paepe, B., Dia, N., Van Malderghem, C., Pothier, J., & Van Vaerenbergh, J. (2021). First report of bacterial leaf spot of Hydrangea in retail nurseries in Belgium caused by strains assigned to a new Xanthomonas hortorum clade. New Disease Reports, 43(2), e12008. https://doi.org/10.1002/ndr2.12008
• Catara, V., Cubero, J., Pothier, J., Bosis, E., Bragard, C., Đermić, E., Holeva, M. C., Jacques, M.-A., Petter, F., Pruvost, O., Robène, I., Studholme, D. J., Tavares, F., Vicente, J. G., Koebnik, R., & Costa, J. (2021). Trends in molecular diagnosis and diversity studies for phytosanitary regulated Xanthomonas. Microorganisms, 9(4), 862. https://doi.org/10.3390/microorganisms9040862
• Fernandes, C., Martins, L., Teixeira, M., Blom, J., Pothier, J., Fonseca, N. A., & Tavares, F. (2021). Comparative genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis strains isolated from a single walnut host tree. Microorganisms, 9(3), 624. https://doi.org/10.3390/microorganisms9030624
• Arn, F., Frasson, D., Kroslakova, I., Rezzonico, F., Pothier, J., Riedl, R., & Sievers, M. (2020). Isolation and identification of actinomycetes strains from Switzerland and their biotechnological potential. Chimia, 74(5), 382–390. https://doi.org/10.2533/chimia.2020.382
• Puławska, J., Kałużna, M., Warabieda, W., Pothier, J. F., Gétaz, M., & van der Wolf, J. M. (2020). Transcriptome analysis of Xanthomonas fragariae in strawberry leaves. Scientific Reports, 10(20582). https://doi.org/10.1038/s41598-020-77612-y
• 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
• Martins, L., Fernandes, C., Blom, J., Dia, N. C., Pothier, J. F., & Tavares, F. (2020). Xanthomonas euroxanthea sp. nov. : a new xanthomonad species including pathogenic and non-pathogenic strains of walnut. International Journal of Systematic and Evolutionary Microbiology, 70(12), 6024–6031. https://doi.org/10.1099/ijsem.0.004386
• 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
• Rothen, J., Sapugahawatte, D. N., Li, C., Lo, N., Vogel, G., Foucault, F., Pflüger, V., Pothier, J., Blom, J., Daubenberger, C., & Ip, M. (2020). A simple, rapid typing method for Streptococcus agalactiae based on ribosomal subunit proteins by MALDI-TOF MS. Scientific Reports, 10(8788). https://doi.org/10.1038/s41598-020-65707-5
• Fossou, R. K., Pothier, J. F., Zézé, A., & Perret, X. (2020). Bradyrhizobium ivorense sp. nov. as a potential local bioinoculant for Cajanus cajan cultures in Côte d'Ivoire. International Journal of Systematic and Evolutionary Microbiology, 70(2), 1421–1430. https://doi.org/10.1099/ijsem.0.003931
• 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
• 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). 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, 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
• Luedin, S., Liechti, N., Cox, R. P., Danza, F., Frigaard, N.-U., Posth, N., Pothier, J. F., Roman, S., Storelli, N., Wittwer, M., & Tonolla, M. (2019). Draft genome sequence of Chromatium okenii isolated from the stratified alpine Lake Cadagno. Scientific Reports, 9(1), 1936. https://doi.org/10.1038/s41598-018-38202-1
• Rothen, J., Pothier, J. F., Foucault, F., Blom, J., Nanayakkara, D., Li, C., Ip, M., Tanner, M., Vogel, G., Pflüger, V., & Daubenberger, C. A. (2019). Subspecies typing of Streptococcus agalactiae based on ribosomal subunit protein mass variation by MALDI-TOF MS. Frontiers in Microbiology, 10(471). https://doi.org/10.3389/fmicb.2019.00471
• Schneeberger, P. H. H., Fuhrimann, S., Becker, S. L., Pothier, J. F., Duffy, B., Beuret, C., Frey, J. E., & Utzinger, J. (2019). Qualitative microbiome profiling along a wastewater system in Kampala, Uganda. Scientific Reports, 9(1), 17334. https://doi.org/10.1038/s41598-019-53569-5
• Luedin, S. M., Storelli, N., Danza, F., Roman, S., Wittwer, M., Pothier, J. F., & Tonolla, M. (2019). Mixotrophic growth under micro-oxic conditions in the purple sulfur bacterium "Thiodictyon syntrophicum". Frontiers in Microbiology, 10(384). https://doi.org/10.3389/fmicb.2019.00384
• Gétaz, M., Baeyen, S., Blom, J., Maes, M., Cottyn, B., & Pothier, J. F. (2018). High-quality draft genome sequences of five xanthomonas arboricola pv. fragariae isolates. Genome Announcements, 6(7). https://doi.org/10.1128/genomeA.01585-17
• 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
• Luedin, S. M., Pothier, J. F., Danza, F., Storelli, N., Frigaard, N.-U., Wittwer, M., & Tonolla, M. (2018). Complete genome sequence of "Thiodictyon syntrophicum" sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno. Standards in Genomic Sciences, 13(14). https://doi.org/10.1186/s40793-018-0317-z
• Knecht, L. E., Born, Y., Pothier, J. F., Loessner, M. J., & Fieseler, L. (2018). Complete genome sequences of erwinia amylovora phages vB_EamP-S2 and vB_EamM-Bue1. Microbiology Resource Announcements, 7(3). https://doi.org/10.1128/MRA.00891-18
• 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
• Fernandes, C., Blom, J., Pothier, J. F., & Tavares, F. (2018). High-quality draft genome sequence of xanthomonas arboricola pv. juglandis CPBF 1521, isolated from leaves of a symptomatic walnut tree in Portugal without a past of phytosanitary treatment. Microbiology Resource Announcements, 7(16). https://doi.org/10.1128/MRA.00887-18
• Fernandes, C., Blom, J., Pothier, J. F., & Tavares, F. (2018). High-Quality draft genome sequence of xanthomonas sp. strain CPBF 424, a walnut-pathogenic strain with atypical features. Microbiology Resource Announcements, 7(15). https://doi.org/10.1128/MRA.00921-18
• Normand, P., Nouioui, I., Pujic, P., Fournier, P., Dubost, A., Schwob, G., Klenk, H.-P., Nguyen, A., Abrouk, D., Herrera-Belaroussi, A., Pothier, J. F., Pflüger, V., & Fernandez, M. P. (2018). Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa. International Journal of Systematic and Evolutionary Microbiology, 68, 3001–3011. https://doi.org/10.1099/ijsem.0.002939
• 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
• Gétaz, M., Bühlmann, A., Schneeberger, P. H. H., Van Malderghem, C., Duffy, B., Maes, M., Pothier, J. F., & Cottyn, B. (2017). A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics. Plant Pathology, 66(7), 1094–1102. https://doi.org/10.1111/ppa.12665
• 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
• Gétaz, M., van der Wolf, J., Blom, J., & Pothier, J. F. (2017). Complete genome sequences of three isolates of Xanthomonas fragariae, the bacterium responsible for angular leaf spots on strawberry plants. Genome Announcements, 5(32). https://doi.org/10.1128/genomeA.00642-17
• Ruinelli, M., Blom, J., & Pothier, J. F. (2017). Complete genome sequence of Pseudomonas viridiflava CFBP 1590: isolated from diseased cherry in France. Genome Announcements, 5(30). https://doi.org/10.1128/genomeA.00662-17
• Rothen, J., Schindler, T., Pothier, J. F., Younan, M., Certa, U., Daubenberger, C., Pflüger, V., & Jores, J. (2017). Draft genome sequences of seven Streptococcus agalactiae strains isolated from Camelus dromedarius at the horn of Africa. Genome Announcements, 5(28). https://doi.org/10.1128/genomeA.00525-17
• Schneeberger, P. H. H., Pothier, J. F., Bühlmann, A., Duffy, B., Beuret, C., Utzinger, J., & Frey, J. E. (2017). Development and evaluation of a bioinformatics approach for designing molecular assays for viral detection. Plos One, 12(5). https://doi.org/10.1371/journal.pone.0178195
• Konavko, D., Malchev, S., Pothier, J. F., Jundzis, M., Moročko-Bičevska, I., & Rezzonico, F. (2016). Diversity and host range of Pseudomonas in fruit tree species in Latvia. Acta Horticulturae, 1149, 25–30. https://doi.org/10.17660/ActaHortic.2016.1149.5
• Kałużna, M., Willems, A., Pothier, J. F., Ruinelli, M., Sobiczewski, P., & Puławska, J. (2016). Pseudomonas cerasi sp. nov. (non Griffin, 1911) isolated from diseased tissue of cherry. Systematic and Applied Microbiology, 39(6), 370–377. https://doi.org/10.1016/j.syapm.2016.05.005
• Schneeberger, P. H. H., Becker, S. L., Pothier, J. F., Duffy, B., N'Goran, E. K., Beuret, C., Frey, J. E., & Utzinger, J. (2016). Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire : a proof-of-concept study. Infection, Genetics and Evolution, 40, 389–397. https://doi.org/10.1016/j.meegid.2015.08.044
• Ruinelli, M., Schneeberger, P. H. H., Ferrante, P., Bühlmann, A., Scortichini, M., Vanneste, J. L., Duffy, B., & Pothier, J. F. (2016). Comparative genomics-informed design of two LAMP detection assays for detection of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae and discrimination of isolates belonging to the pandemic biovar 3. Plant Pathology, 66(1), 140–149. https://doi.org/10.1111/ppa.12551
• Puławska, J., Kuzmanović, N., Willems, A., & Pothier, J. F. (2016). Pararhizobium polonicum sp. nov. isolated from tumors on stone fruit rootstocks. Systematic and Applied Microbiology, 39(3), 164–169. https://doi.org/10.1016/j.syapm.2016.03.002
• 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
• Palacio-Bielsa, A., López-Soriano, P., Bühlmann, A., van Doorn, J., Pham, K., Cambra, M. A., Berruete, I. M., Pothier, J. F., Duffy, B., Olmos, A., & López, M. M. (2015). Evaluation of a real-time PCR and a loop-mediated isothermal amplification for detection of Xanthomonas arboricola pv. pruni in plant tissue samples. Journal of Microbiological Methods, 112, 36–39. https://doi.org/10.1016/j.mimet.2015.03.005
• 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
• Ziegler, D., Pothier, J. F., Ardley, J., Kouakou Fossou, R., Pflüger, V., de Meyer, S., Vogel, G., Tonolla, M., Howieson, J., Reeve, W., & Perret, X. (2015). Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS. Applied Microbiology and Biotechnology, 99(13), 5547–5562. https://doi.org/10.1007/s00253-015-6515-3
• 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
• 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
• van der Wolf, J. M., Nijhuis, E. H., Kowalewska, M. J., Saddler, G. S., Parkinson, N., Elphinstone, J. G., Pritchard, L., Toth, I. K., Lojkowska, E., Potrykus, M., Waleron, M., de Vos, P., Cleenwerck, I., Pirhonen, M., Garlant, L., Hélias, V., Pothier, J. F., Pflüger, V., Duffy, B., et al. (2014). Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum). International Journal of Systematic and Evolutionary Microbiology, 64, 768–774. https://doi.org/10.1099/ijs.0.052944-0
• Vandroemme, J., Cottyn, B., Pothier, J. F., Pflüger, V., Duffy, B., & Maes, M. (2013). Xanthomonas arboricola pv. fragariae : what's in a name?. Plant Pathology, 62(5), 1123–1131. https://doi.org/10.1111/ppa.12028
• Socquet-Juglard, D., Duffy, B., Pothier, J. F., Christen, D., Gessler, C., & Pattochi, A. (2013). Identification of a major QTL for Xanthomonas arboricola pv. pruni resistance in apricot. Tree Genetics & Genomes, 9(2), 409–421. https://doi.org/10.1007/s11295-012-0562-z
• 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
• Socquet-Juglard, D., Kamber, T., Pothier, J. F., Christen, D., Gessler, C., Duffy, B., & Patocchi, A. (2013). Comparative RNA-Seq analysis of early-infected peach leaves by the invasive phytopathogen Xanthomonas arboricola pv. pruni. Plos One, 8(1). https://doi.org/10.1371/journal.pone.0054196
• 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

Written conference contributions, peer-reviewed

• 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
• Kałużna, M., Willems, A., Pothier, J. F., Ruinelli, M., Sobiczewski, P., & Puławska, J. (2016). Characterization and genetic diversity of causal agent of stone fruit bacterial canker Pseudomonas cerasi : a new pathogen of cherry [Conference paper]. II International Workshop on Bacterial Diseases of Stone Fruits and Nuts, 1149, 9–14. https://doi.org/10.17660/ActaHortic.2016.1149.2

Other publications

• 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
• Pothier, J. F. (2024). Viren-Diagnostik für den Gemüsesektor : frühzeitige Viruserkennung dank der Kombination molekularer Methoden. IUNR Magazin, 2024(01), 22–23. https://doi.org/10.21256/zhaw-30617
• Aspin, A., Cole, J., & Pothier, J. (2023). PM 7/65 (2) Xanthomonas fragariae. Wiley. https://doi.org/10.1111/epp.12916
• Costa, J., Pothier, J. F., Boch, J., Stefani, E., & Koebnik, R. (2022). Integrating science on Xanthomonas and Xylella for integrated plant disease management. Microorganisms, 11(1), 6. https://doi.org/10.3390/microorganisms11010006
• Stefani, E., Loreti, S., Costa, J., Cunty, A., & Pothier, J. F. (2021). PM 7/120 (2) Pseudomonas syringae pv. actinidiae. Wiley. https://doi.org/10.1111/epp.12782
• Costa, J., Pothier, J. F., Boch, J., Stefani, E., Jacques, M.-A., Catara, V., & Koebnik, R. (2021). Integrating science on Xanthomonadaceae for sustainable plant disease management in Europe. Molecular Plant Pathology, 22(12), 1461–1463. https://doi.org/10.1111/mpp.13150
• Luedin, S. M., Storelli, N., Danza, F., Roman, S., Wittwer, M., Pothier, J., & Tonolla, M. (2018). Anoxygenic photosynthesis and dark carbon metabolism under micro-oxic conditions in the purple sulfur bacterium "Thiodictyon syntrophicum" nov. strain Cad16T. bioRxiv. https://doi.org/10.1101/420927
• Saponari, M., Gétaz, M., Palkovics, L., Kuzmanović, N., Puławska, J., Ruinelli, M., Pothier, J., Obradović, A., Boscia, D., Végh, A., & Kałużna, M. (2017). Bacterial diseases. In J. Quero-García, A. Iezzoni, J. Puławska, & G. Lang (Eds.), Cherries : botany, production and uses. CAB International.

Research data

• 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.
• Smits, Theo H. M.; Pothier, Joël F., 2018. Diversity of Xanthomonas fragariae with MLVA & CRISPR. European Nucleotide Archive.
• 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.
• Fernandes, Camila; Blom, Jochen; Pothier, Joël F.; Tavares, Fernando, 2018. High-quality draft genome sequences of distinct Xanthomonas spp. isolated from a single walnut tree host. 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.

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