Identification of microbial and cellular biomarkers for Short Bowel Syndrome in a combined in vitro-in vivo study

Project Information

SBS-microbe

Grant agreement ID: 101067622

DOI

10.3030/101067622

Project closed

EC signature date 25 July 2022

Start date 1 January 2023

End date 31 December 2024

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 175 920,00

Coordinated by

UNIVERSITEIT GENT
Belgium

Periodic Reporting for period 1 - SBS-microbe (Identification of microbial and cellular biomarkers for Short Bowel Syndrome in a combined in vitro-in vivo study)

Reporting period: 2023-01-01 to 2024-12-31

Summary of the context and overall objectives of the project

SBS-microbe is a multidisciplinary translational project aimed at expanding our knowledge on a rare but severe condition named Short Bowel Syndrome (SBS). In adults, SBS mostly occurs upon an extensive small intestinal resection, eventually resulting in intestinal failure. The alterations at both the cellular and microbial level induced by the resection contribute to severe side effects such as nutrient malabsorption and lactic acidosis, thereby compromising the patient’s quality of life. In this context, SBS-microbe aims at describing microbial, metabolic and cellular hallmarks of SBS. Specifically, the project focused on the following objectives:
• Objective 1: develop an in vitro model for human gastrointestinal tract comprising representative small intestinal and colonic microbiota and applicable to mimic intestinal resections, using the state-of-the-art technology of the Simulator of Human Intestinal Microbial Ecosystem (SHIME) (WP1);
• Objective 2: investigate in vitro the alterations occurring in the intestinal microbial ecology solely induced by reduced intestinal length, in an adapted SHIME model and identify key microbial altered metabolites associated to SBS (WP1);
• Objective 3: validate the in vitro identified SBS-associated microbial alterations against SBS patients’ data (WP2);
• Objective 4: study the impact of the altered microbiota on the integrity of the epithelial layer and barrier protection and decipher the involved cellular mechanisms, through the development of intestinal epithelial cellular models and their stimulation with samples from SHIME set-up (WP3).

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The project has achieved most of its objectives and milestones for the period with only part of the analysis still ongoing but in finalization.
In WP1, we developed a SI-M-SHIME model to mimic the oro-gastrointestinal tract in healthy condition, inoculated with saliva and fecal samples of healthy donors (five in total), performed in separate runs. The microbial composition and metabolic activity was validated against the original inoculum and literature data. Once established the SI-M-SHIME model was adapted to mimic a jejuno-colonic anastomosis to simulate SBS type II condition. Bacterial composition and metabolic activity was assessed for each compartment along time, before and after the simulated resection. In WP2 we recruited SBS patients and analyzed the fecal bacterial composition and metabolic activity (n collaboration with Prof. Tim Vanuytsel, UZ Leuven). The comparison of the patients’ data with those resulted from the SHIME model will allow to identify common SBS signatures. Last, in WP3 we developed two in vitro cellular models to mimic the small intestinal and colon epithelium. In particular, we optimized two differentiated triple co-culture models composed of entero-/colono-cytes, goblet and enteroendocrine-like cell lines. By stimulating these models with the SHIME suspensions of the corresponding gut compartment before and after the resection, we identified alterations in the epithelial functions associated to the SBS-microbiota.
For this study, several original scientific publications are currently in preparation and a review article was published in the high-impact journal FEMS Microbiology Reviews (doi: 10.1093/femsre/fuad022).

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Numerous progresses have been made by the international scientific community in the characterization of Short Bowel Syndrome (SBS) pathogenesis. Nonetheless, the high level of inter-individual variability in microbiome composition, the differences in clinical aspects and treatments, the difficult access to human samples and the challenges of longitudinal studies, restrain the possibilities for a mechanistic study of the SBS pathogenesis and its evolution in vivo. This project allow a multidisciplinary and mechanistic investigation in physiologic-like conditions of the alterations induced by an extensive small intestinal resection, leading to SBS, both at microbial and cellular level. In particular, SBS-microbe results in: i) an expanded mechanistic knowledge with the identification of cellular and/or microbial signatures that are specific to SBS; (ii) significant technological advances in the development of digestive technology and cellular models that more accurately mimic conditions of SBS and (iii) an increased awareness of the role of gut microbiota in the maintenance of healthy status and etiology of disease; (iv) national and international collaborations for excellent and innovative research.