Publications

Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions
Causevic, S., Dubey, M., Morales, M., Salazar, G., Sentchilo, V., Carraro, N., Ruscheweyh, H.-J., Sunagawa, S., van der Meer, J. R. (2024).
https://doi.org/10.1038/s41467-024-46933-1
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
An engineered bacterial symbiont allows noninvasive biosensing of the honey bee gut environment
Chhun, A., Moriano-Gutierrez, S., Zoppi, F., Cabirol, A., Engel, P., Schaerli, Y. (2024).
https://doi.org/10.1371/journal.pbio.3002523
Microfluidic approaches in microbial ecology
Ugolini, G. S., Wang, M., Secchi, E., Pioli, R., Ackermann, M., Stocker, R. (2024).
https://doi.org/10.1039/D3LC00784G
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
Oxidative stress changes interactions between 2 bacterial species from competitive to facilitative
Di Martino, R., Picot, A., Mitri, S. (2024).
https://doi.org/10.1371/journal.pbio.3002482
Host-derived organic acids enable gut colonization of the honey bee symbiont Snodgrassella alvi
Quinn, A., El Chazli, Y., Escrig, S., Daraspe, J., Neuschwander, N., McNally, A., Genoud, C., Meibom, A., Engel, P. (2024).
https://doi.org/10.1038/s41564-023-01572-y
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
Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers
Baud, G. L. C., Prasad, A., Ellegaard, K. M., Engel, P. (2023).
https://doi.org/10.1186/s13059-023-03131-4
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