Following extensive resection, the remaining small intestine may be of insufficient length to absorb nutrients, leading to short bowel syndrome (SBS). SBS is associated with significant malnutrition, and patients must take lifelong supplements. Funded by the Marie Skłodowska-Curie Actions programme, the SBS-microbe project aims to shed light on SBS pathogenesis, focusing on microbiota, metabolic and cellular changes occurring after resection. Researchers plan to develop in vitro models to study disease progression and the role of host−microbiota interactions. The identification of SBS drivers will unveil key targets for triggering intestinal homeostasis.