Publications

Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags
Daniel, B. B. J., Steiger, Y., Sintsova, A., Field, C. M., Nguyen, B. D., Schubert, C., Cherrak, Y., Sunagawa, S., Hardt, W.-D., Vorholt, J. A. (2024).
https://doi.org/10.1038/s41564-024-01634-9
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations
Sintsova, A., Ruscheweyh, H.-J., Field, C. M., Feer, L., Nguyen, B., Daniel, B., Hardt, W.-D., Vorholt, J. A., Sunagawa, S. (2024).
https://doi.org/10.1093/bioinformatics/btae078
Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens
Pfeilmeier, S., Werz, A., Ote, M., Vorholt, J. A., et al. (2024).
https://doi.org/10.1038/s41564-023-01555-z
Identifying microbiota community patterns important for plant protection using synthetic communities and machine learning
Emmenegger, B., Massoni, J., Pestalozzi, C. M., Bortfeld-Miller, M., Maier, B. A., Vorholt, J. A. (2023).
https://doi.org/10.1038/s41467-023-43793-z
From microbiome composition to functional engineering, one step at a time
Burz, S. D., Causevic, S., Dal Co, A., Dmitrijeva, M., Vonaesch, P., Vorholt, J., et al. (2023).
https://doi.org/10.1128/mmbr.00063-23
The microbiota conditions a gut milieu that selects for wild-type Salmonella Typhimurium virulence
Gül, E., Hardt, W.-D., et al. (2023).
https://doi.org/10.1371/journal.pbio.3002253
Metabolic interaction models recapitulate leaf microbiota ecology
Schäfer, M., Pacheco, A., Künzler, R., Bortfeld-Miller, M., Field, C. M., Vayena, E., Hatzimanikatis, V., Vorholt, J. (2023).
https://doi.org/10.3929/ethz-b-000621167
Resolving metabolic interaction mechanisms in plant microbiomes
Pacheco, A. R., Vorholt, J. A. (2023).
https://doi.org/10.1016/j.mib.2023.102317
Mapping phyllosphere microbiota interactions in planta to establish genotype-phenotype relationships
Schäfer, M., Vogel, C.M., Bortfeld-Miller, M., Mittelviefhaus, M., Vorholt, J.A. (2022).
https://doi.org/10.1038/s41564-022-01132-w
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