Publications of R. Garrido Oter

Chesneau, G.; Herpell, J.; Garrido Oter, R.; Hacquard, S.: From synthetic communities to synthetic ecosystems: exploring causalities in plant-microbe-environment interactions. New Phytologist 245 (2), pp. 496 - 502 (2025)

Ordon, J.; Logemann, E.; Maier, L.-P.; Lee, T.; Dahms, E.; Oosterwijk, A.; Flores-Uribe, J.; Miyauchi, S.; Paoli, L.; Stolze, S. C. et al.; Nakagami, H.; Felix, G.; Garrido-Oter, R.; Ma, K.-W.; Schulze-Lefert, P.: Conserved immunomodulation and variation in host association by Xanthomonadales commensals in Arabidopsis root microbiota. Nature Plants (2025)

Basak, A. K.; Piasecka, A.; Hucklenbroich, J.; Tuerksoy, G. M.; Guan, R.; Zhang, P.; Getzke, F.; Garrido-Oter, R.; Hacquard, S.; Strzalka, K. et al.; Bednarek, P.; Yamada, K.; Nakano, R. T.: ER body-resident myrosinases and tryptophan specialized metabolism modulate root microbiota assembly. New Phytologist 241, pp. 329 - 342 (2024)

Loo, E. P. I.; Durán, P.; Pang, T. Y.; Westhoff, P.; Deng, C.; Durán, C.; Lercher, M.; Garrido Oter, R.; Frommer, W. B.: Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis. Cell Host & Microbe 32 (4), pp. 543 - 556.e6 (2024)

Ordon, J.; Thouin, J.; Nakano, R. T.; Ma, K.-W.; Zhang, P.; Huettel, B.; Garrido Oter, R.; Schulze-Lefert, P.: Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota. Nature Microbiology (2024)

Getzke, F.; Hassani, M. A.; Crüsemann, M.; Malisic, M.; Zhang, P.; Ishigaki, Y.; Böhringer, N.; Jiménez Fernández, A.; Wang, L.; Ordon, J. et al.; Ma, K.-W.; Thiergart, T.; Harbort, C. J.; Wesseler, H.; Miyauchi, S.; Garrido-Oter, R.; Shirasu, K.; Schäberle, T.F.; Hacquard, S.; Schulze-Lefert, P.: Co-functioning of bacterial exometabolites drives root microbiota establishment. Proceedings of the National Academy of Sciences of the United States of America 120 (15), e2221508120 (2023)

Bourceret, A.; Guan, R.; Dorau, K.; Mansfeldt, T.; Omidbakhshfard, A.; Medeiros, D. B.; Fernie, A. R.; Hofmann, J.; Sonnewald, U.; Mayer, J. et al.; Gerlach, N.; The RECONSTRUCT consortium; Bucher, M.; Garrido Oter, R.; Spaepen, S.; Schulze-Lefert, P.: Maize Field Study Reveals Covaried Microbiota and Metabolic Changes in Roots over Plant Growth. mBio, e02584-21 (2022)

Durán, P.; Flores-Uribe, J.; Wippel, K.; Zhang, P.; Guan, R.; Melkonian, B.; Melkonian, M.; Garrido Oter, R.; Zhang, P.: Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota. Nature Communications 13 (406) (2022)

Meyer, F.; Fritz, A.; Deng, Z.-L.; Koslicki, D.; Lesker, T. R.; Gurevich, A.; Robertson, G.; Alser, M.; Antipov, D.; Beghini, F. et al.; Bertrand, D.; Brito, J. J.; Brown, C. T.; Buchmann, J.; Buluc, A.; Chen, B.; Chikhi, R.; Clausen, P. T. L. C.; Cristian, A.; Dabrowski, P. W.; Darling, A. E.; Egan, R.; Eskin, E.; Georganas, E.; Goltsman, E.; Gray, M. A.; Hansen, L. H.; Hofmeyr, S.; Huang, P.; Irber, L.; Jia, H.; Jorgensen, T. S.; Kieser, S. D.; Klemetsen, T.; Kola, A.; Kolmogorov, M.; Korobeynikov, A.; Kwan, J.; LaPierre, N.; Lemaitre, C.; Li, C.; Limasset, A.; Malcher-Miranda, F.; Mangul, S.; Marcelino, V. R.; Marchet, C.; Marijon, P.; Meleshko, D.; Mende, D. R.; Milanese, A.; Nagarajan, N.; Nissen, J.; Nurk, S.; Oliker, L.; Paoli, L.; Peterlongo, P.; Piro, V. C.; Porter, J. S.; Rasmussen, S.; Rees, E. R.; Reinert, K.; Renard, B.; Robertsen, E. M.; Rosen, G. L.; Ruscheweyh, H.-J.; Sarwal, V.; Segata, N.; Seiler, E.; Shi, L.; Sun, F.; Sunagawa, S.; Sorensen, S. J.; Thomas, A.; Tong, C.; Trajkovski, M.; Tremblay, J.; Uritskiy, G.; Vicedomini, R.; Wang, Z.; Wang, Z.; Wang, Z.; Warren, A.; Willassen, N.; Yelick, K.; You, R.; Zeller, G.; Zhao, Z.; Zhu, S.; Zhu, J.; Garrido-Oter, R.; Gastmeier, P.; Hacquard, S.; Haeussler, S.; Khaledi, A.; Maechler, F.; Mesny, F.; Radutoiu, S.; Schulze-Lefert, P.; Smit, N.; Strowig, T.; Bremges, A.; Sczyrba, A.; McHardy, A. C.: Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods 19 (4), pp. 429 - 440 (2022)

Nobori, T.; Cao, Y.; Entila, F.; Dahms, E.; Tsuda, Y.; Garrido Oter, R.; Tsuda, K.: Dissecting the cotranscriptome landscape of plants and their microbiota. EMBO Reports 23, e55380 (2022)

Durán, P.; Reinstädler, A.; Rajakrut, A.; Hashimoto, M.; Garrido Oter, R.; Schulze-Lefert, P.; Panstruga, R.: A fungal powdery mildew pathogen induces extensive local and marginal systemic changes in the Arabidopsis thaliana microbiota. Environmental Microbiology 23 (10), pp. 6292 - 6308 (2021)

Durán, P.; Reinstaedler, A.; Rajakrut, A.; Hashimoto, M.; Garrido Oter, R.; Schulze-Lefert, P.; Panstruga, R.: A fungal powdery mildew pathogen induces extensive local and marginal systemic changes in the Arabidopsis thaliana microbiota. SI 23 (10), pp. 6292 - 6308 (2021)

Ma, K.-W.; Niu, Y.; Jia, Y.; Ordon, J.; Copeland, C.; Emonet, A.; Geldner, N.; Guan, R.; Stolze, S. C.; Nakagami, H. et al.; Garrido-Oter, R.; Schulze-Lefert, P.: Coordination of microbe–host homeostasis by crosstalk with plant innate immunity. Nature Plants (2021)

Mahdi, L. K.; Miyauchi, S.; Uhlmann, C.; Garrido-Oter, R.; Langen, G.; Wawra, S.; Niu, Y.; Guan, R.; Robertson-Albertyn, S.; Bulgarelli, D. et al.; Parker, J. E.; Zuccaro, A.: The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. The ISME Journal (2021)

Shimasaki, T.; Masuda, S.; Garrido-Oter, R.; Kawasaki, T.; Aoki, Y.; Shibata, A.; Suda, W.; Shirasu, K.; Yazaki, K.; Nakano, R. T. et al.; Sugiyama, A.: Tobacco Root Endophytic Arthrobacter Harbors Genomic Features Enabling the Catabolism of Host-Specific Plant Specialized Metabolites. mBio 12 (3), e00846-21 (2021)

Winkelmueller, T. M.; Entila, F.; Anver, S.; Piasecka, A.; Song, B.; Dahms, E.; Sakakibara, H.; Gan, X.; Kułak, K.; Sawikowska, A. et al.; Krajewski, P.; Garrido-Oter, R.; Tsiantis, M.; Fukushima, K.; Schulze-Lefert, P.; Laurent, S.; Bednarek, P.; Tsuda, K.: Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species. The Plant Cell, koab073 (2021)

Wippel, K.; Tao, K.; Niu, Y.; Zgadzaj, R. L.; Kiel, N.; Guan, R.; Dahms, E.; Zhang, P.; Jensen, D. B.; Logemann, E. et al.; Radutoiu, S.; Schulze-Lefert, P.; Garrido Oter, R.: Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota. Nature Microbiology (2021)

Zhang, J.; Liu, Y.-X.; Guo, X.; Qin, Y.; Garrido-Oter, R.; Schulze-Lefert, P.; Bai, Y.: High-throughput cultivation and identification of bacteria from the plant root microbiota. Nature Protocols 16 (2), pp. 988 - 1012 (2021)

Zhang, P.; Spaepen, S.; Bai, Y.; Hacquard, S.; Garrido-Oter, R.: Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities. ISME Communications 73 (1), p. 1 (2021)

Harbort, C. J.; Hashimoto, M.; Inoue, H.; Niu, Y.; Guan, R.; Rombolà, A. D.; Kopriva, S.; Voges, M. J. E. E. E.; Sattely, E. S.; Garrido-Oter, R. et al.; Schulze-Lefert, P.: Root-secreted coumarins and the microbiota interact to improve iron nutrition in Arabidopsis. Cell Host & Microbe 28, pp. 825 - 837 (2020)

Thiergart, T.; Durán, P.; Ellis, T.; Vannier, N.; Garrido-Oter, R.; Kemen, E.; Roux, F.; Alonso-Blanco, C.; Agren, J.; Schulze-Lefert, P. et al.; Hacquard, S.: Root microbiota assembly and adaptive differentiation among European Arabidopsis populations. Nature Ecology & Evolution 4 (1), pp. 122 - 131 (2020)

Berens, M. L.; Wolinska, K. W.; Spaepen, S.; Ziegler, J.; Nobori, T.; Nair, A.; Krüler, K.; Winkelmueller, T. M.; Wang, Y.; Mine, A. et al.; Becker, D.; Garrido-Oter, R.; Schulze-Lefert, P.; Tsuda, K.: Balancing trade-offs between biotic and abiotic stress responses through leaf age-dependent variation in stress hormone cross-talk. Proceedings of the National Academy of Sciences of the United States of America 116, pp. 2364 - 2373 (2019)

Thiergart, T.; Zgadzaj, R.; Bozsóki, Z.; Garrido-Oter, R.; Radutoiu, S.; Schulze-Lefert, P.: Lotus japonicus symbiosis genes impact microbial interactions between symbionts and multikingdom commensal communities. mBio 10, e01833-19 (2019)

Wang, Y.; Garrido-Oter, R.; Wu, J.; Winkelmueller, T. M.; Agler, M.T.; Colby, T.; Nobori, T.; Kemen, E.; Tsuda, K.: Site-specific cleavage of bacterial MucD by secreted proteases mediates antibacterial resistance in Arabidopsis. Nature Communications 10, 2853 (2019)

Wippel, K.; Schulze-Lefert, P.; Garrido Oter, R.: Rhizobien in der Pflanzenmikrobiota: Evolution der Wurzelknöllchensymbiose und Nutzen der Mikrobiota für den Pflanzenwirt. Biologie in unserer Zeit 49 (6), pp. 426 - 434 (2019)

Zhang, J.; Liu, Y.-X.; Zhang, N.; Hu, B.; Jin, T.; Xu, H.; Qin, Y.; Yan, P.; Zhang, X.; Guo, X. et al.; Hui, J.; Cao, S.; Wang, X.; Wang, C.; Wang, H.; Qu, B.; Fan, G.; Yuan, L.; Garrido-Oter, R.; Chu, C.; Bai, Y.: NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nature Biotechnology 37 (6), pp. 676 - 684 (2019)

Durán, P.; Thiergart, T.; Garrido-Oter, R.; Agler, M.T.; Kemen, E.; Schulze-Lefert, P.; Hacquard, S.: Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival. Cell 175 (4), pp. 973 - + (2018)

Garrido Oter, R.; Nakano, R. T.; Dombrowski, N.; Ma, K.-W.; AgBiome Team, T.; McHardy, A.; Schulze-Lefert, P.: Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia. Cell Host & Microbe 24, pp. 155 - 167 (2018)

Meyer, F.; Hofmann, P.; Belmann, P.; Garrido Oter, R.; Fritz, A.; Sczyrba, A.; McHardy, A. C.: AMBER: Assessment of Metagenome BinnERs. GigaScience 7 (6), giy069 (2018)

Robbins, C.; Thiergart, T.; Hacquard, S.; Garrido Oter, R.; Gans, W.; Peiter, E.; Schulze-Lefert, P.; Spaepen, S.: Root-associated bacterial and fungal community profiles of Arabidopsis thaliana are robust across contrasting soil P levels. Phytobiomes 2 (1), pp. 24 - 34 (2018)

Dombrowski, N.; Schlaeppi, K.; Agler, M.T.; Hacquard, S.; Kemen, E.; Garrido Oter, R.; Wunder, J.; Coupland, G.; Schulze-Lefert, P.: Root microbiota dynamics of perennial Arabis alpina are dependent on soil residence time but independent of flowering time. The ISME Journal 11, 10.1038/ismej.2016.109, pp. 43 - 55 (2017)

Hacquard, S.; Spaepen, S.; Garrido-Oter, R.; Schulze-Lefert, P.: Interplay Between Innate Immunity and the Plant Microbiota. Annual Review of Phytopathology (55), pp. 565 - 589 (2017)

Sczyrba, A.; Hofmann, P.; Belmann, P.; Koslicki, D.; Janssen, S.; Droge, J.; Gregor, I.; Majda, S.; Fiedler, J.; Dahms, E. et al.; Bremges, A.; Fritz, A.; Garrido-Oter, R.; Jorgensen, T. S.; Shapiro, N.; Blood, P. D.; Gurevich, A.; Bai, Y.; Turaev, D.; DeMaere, M. Z.; Chikhi, R.; Nagarajan, N.; Quince, C.; Meyer, F.; Balvociute, M.; Hansen, L. H.; Sorensen, S. J.; Chia, B. K. H.; Denis, B.; Froula, J. L.; Wang, Z.; Egan, R.; Don Kang, D.; Cook, J. J.; Deltel, C.; Beckstette, M.; Lemaitre, C.; Peterlongo, P.; Rizk, G.; Lavenier, D.; Wu, Y.-W.; Singer, S. W.; Jain, C.; Strous, M.; Klingenberg, H.; Meinicke, P.; Barton, M. D.; Lingner, T.; Lin, H.-H.; Liao, Y.-C.; Silva, G. G. Z.; Cuevas, D. A.; Edwards, R. A.; Saha, S.; Piro, V. C.; Renard, B. Y.; Pop, M.; Klenk, H.-P.; Goker, M.; Kyrpides, N. C.; Woyke, T.; Vorholt, J. A.; Schulze-Lefert, P.; Rubin, E. M.; Darling, A. E.; Rattei, T.; McHardy, A. C.: Critical Assessment of Metagenome Interpretation — a benchmark of metagenomics software. Nature methods 14, pp. 1063 - 1071 (2017)

Hacquard, S.; Kracher, B.; Hiruma, K.; Muech, P. C.; Garrido Oter, R.; Thon, M. R.; Weimann, A.; Damm, U.; Dallery, J.-F.; Hainaut, M. et al.; Henrissat, B.; Lespinet, O.; Sacristan, S.; Ver Loren van Themaat, E.; Kemen, E.; McHardy, A. C.; Schulze-Lefert, P.; O'Connell, R. J.: Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi. Nature Communications 7, 11362 (2016)

Zgadzaj, R. L.; Garrido Oter, R.; Jensen, D. B.; Koprivova, A.; Schulze-Lefert, P.; Radutoiu, S.: Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. Proceedings of the National Academy of Sciences of the United States of America PNAS, Proceedings of the National Academy of Sciences 113 (49), pp. E7996 - E8005 (2016)

Bai, Y.; Mueller, D. B.; Srinivas, G.; Garrido Oter, R.; Potthoff, E.; Rott, M.; Dombrowski, N.; Muench, P. C.; Spaepen, S.; Remus-Emsermann, M. et al.; Huettel, B.; McHardy, A. C.; Vorholt, J. A.; Schulze-Lefert, P.: Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528 (7582), pp. 364 - 369 (2015)

Bulgarelli, D.; Garrido Oter, R.; Muench, P. C.; Weiman, A.; Droege, J.; Pan, Y.; McHardy, A. C.; Schulze-Lefert, P.: Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley. Cell Host & Microbe 17 (3), pp. 392 - 403 (2015)

Hacquard, S.; Garrido Oter, R.; González, A.; Spaepen, S.; Ackermann, G.; Lebeis, S.; McHardy, A. C.; Dangl, J. L.; Knight, R.; Ley, R. et al.; Schulze-Lefert, P.: Microbiota and Host Nutrition across Plant and Animal Kingdoms. Cell Host & Microbe 17 (5), pp. 603 - 613 (2015)

Schlaeppi, K.; Dombrowski, N.; Garrido Oter, R.; Ver Loren van Themaat, E.; Schulze-Lefert, P.: Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proceedings of the National Academy of Sciences of the United States of America 111 (2), pp. 585 - 592 (2014)