Publications

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
The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves
Pfeilmeier, S., Petti, G. C., Bortfeld-Miller, Daniel, B., Field, C. M., Sunagawa, S., Vorholt, J. A. (2021).
https://doi.org/10.1038/s41564-021-00929-5
High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains
Zünd, M., Ruscheweyh, H.-J., Field, C. M., Meyer, N., Cuenca, M., Hoces, D., Hardt, W.-D., Sunagawa, S. (2021).
https://doi.org/10.1186/s40168-021-01033-w
Space, time and microdiversity: towards a resolution revolution in microbiomics
Paoli, L., Sunagawa, S. (2020).
doi: 10.1111/1758-2229.12897