Sunagawa, S. Archives

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

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

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

Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota

Hoces, D., Greter, G., Arnoldini, M., Stäubli, M., Moresi, C., Sintsova, A., Slack, E., et al. (2023).

https://doi.org/10.7554/eLife.81212

Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments

Ruscheweyh, H.-J., Milanese, A., Paoli, L., Karcher, N., Sunagawa, S., et al. (2022).

https://doi.org/10.1186/s40168-022-01410-z

Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle

Hoces, D., Lan, J., Sun, W., Geiser, T., Stäubli, M., Barazzone, E., Arnoldini, M., Challa, T.D., Klug, M., Kellenberger, A., Nowok, S., Faccin, E., Macpherson, A.J., Stecher, B., Sunagawa, S., Zenobi, R., Hardt, W.-D., Wolfrum, C., Slack, E. (2022).

https://doi.org/10.1371/journal.pbio.3001743

mOTUs: Profiling Taxonomic Composition, Transcriptional Activity and Strain Populations of Microbial Communities

Ruscheweyh, H.-J., Milanese, A., Paoli, L., Sintsova, A., Mende, D. R., Zeller, G., Sunagawa, S. (2021).

https://doi.org/10.1002/cpz1.218

mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes

Salazar, G., Ruscheweyh, H.-J., Hildebrand, F., Acinas, S. G., Sunagawa, S. (2021).

https://doi.org/10.1093/bioinformatics/btab465