Assistant Professor Yassine Cherrak

Research Interest

The gastrointestinal tract is colonized by trillions of microbes. This dense and highly complex microbial community is known as the gut microbiota. The gut microbiota community plays a pivotal role in maintaining host homeostasis, contributing to processes such as digestion, immune function, and even mood regulation. A fundamental aspect of the gut microbiota is also its capacity to defend the host against the invasion of exogenous bacteria. This protection is referred to as colonization resistance and is often attributed to specific commensal bacteria exerting benefiting functions.

Our laboratory investigates the mechanisms by which protective commensal strains confer colonization resistance and explores how enteric pathogens can bypass this defense, establish themselves in the gut, and cause disease. We are also interested in understanding how the dynamic interplay between the microbiota and invading pathogens is shaped by environmental factors, such as host immune status and diet. Insights gained from this research will not only increase our understanding of how the gut microbiota can acts as a protective barrier but also help developing precise microbiome-based intervention mitigate gastrointestinal diseases.

Recent Publications

1. Cherrak, Y#., Abi Younes, A., Perez-Molphe-Montoya, E., Maurer, L., Yilmaz, K., Enz, U., ... & Hardt, W. D. (2025). Neutrophil recruitment during intestinal inflammation primes Salmonella elimination by commensal E. coli in a context-dependent manner. Cell Host & Microbe, 33(3), 358-372. #co-corresponding author
2. Santamaria de Souza, N., Cherrak, Y., Andersen, T. B., Vetsch, M., Barthel, M., Kroon, S., ... & Hardt, W. D. (2025). Context-dependent change in the fitness effect of (in) organic phosphate antiporter glpT during Salmonella Typhimurium infection. Nature Communications, 16(1), 1912.
3. Cherrak, Y#,*., Salazar, M. A*., Näpflin, N., Malfertheiner, L., Herzog, M. K. M., Schubert, C., ... & Hardt, W. D. (2024). Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut. Nature Microbiology, 9(10), 2696-2709. #co-corresponding author, *co-first author.
4. Cherrak, Y#., Salazar, M. A., Yilmaz, K., Kreuzer, M., & Hardt, W. D. (2024). Commensal E. coli limits Salmonellagut invasion during inflammation by producing toxin-bound siderophores in a tonB-dependent manner. PLoS Biology, 22(6), e3002616. #co-corresponding author
5. Daniel, B. B., Steiger, Y., Sintsova, A., Field, C. M., Nguyen, B. D., Schubert, C., Cherrak, Y., ... & Vorholt, J. A. (2024). Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags. Nature Microbiology, 9(4), 1103-1116.
6. Kandolo, O., Cherrak, Y., Filella-Merce, I., Le Guenno, H., Kosta, A., Espinosa, L., ... & Durand, E. (2023). Acinetobacter type VI secretion system comprises a non-canonical membrane complex. PLoS Pathogens, 19(9), e1011687.
7. Cherrak, Y*., Filella-Merce*, I., Schmidt, V*., Byrne, D., Sgoluppi, V., Chaiaheloudjou, R., ... & Durand, E. (2021). Inhibiting type VI secretion system activity with a biomimetic peptide designed to target the baseplate wedge complex. MBio, 12(4), 10-1128. *co-first author.
8. Cherrak, Y*., Flaugnatti, N*., Durand, E., Journet, L., & Cascales, E. (2019). Structure and activity of the type VI secretion system. Microbiology spectrum, 7(4), 10-1128. *co-first author.
9. Rapisarda, C*., Cherrak, Y*., Kooger, R*., Schmidt, V., Pellarin, R., Logger, L., ... & Fronzes, R. (2019). In situ and high‐resolution cryo‐EM structure of a bacterial type VI secretion system membrane complex. The EMBO journal, 38(10), e100886. *co-first author.
10. Cherrak, Y*., Rapisarda, C*., Pellarin, R., Bouvier, G., Bardiaux, B., Allain, F., ... & Durand, E. (2018). Biogenesis and structure of a type VI secretion baseplate. Nature Microbiology, 3(12), 1404-1416. *co-first author.
11. Nguyen, V. S., Logger, L., Spinelli, S., Legrand, P., Huyen Pham, T. T., Nhung Trinh, T. T., Cherrak, Y., ... & Cambillau, C. (2017). Type VI secretion TssK baseplate protein exhibits structural similarity with phage receptor-binding proteins and evolved to bind the membrane complex. Nature Microbiology, 2(9), 1-9.