Comprehensive toolkit integrating lifestyle and clinical questionnaires with gut microbiota profiling via rectal swabs: application in intensive care cirrhotic patients.

The study of gut microbiota is now an essential dimension in many clinical studies. For instance, microbiota diversity investigation can help us to better manage cirrhotic patients by the identification of markers of severity and the identification of possible sources of pathogens. Conducting clinical research on gut microbiota for fragile patients in intensive care units, such as cirrhotic patients, poses significant challenges. In this study, we developed a comprehensive toolkit for investigating gut microbiota in fragile patients using rectal swabbing combined with straightforward lifestyle and clinical questionnaires. We applied this prospective approach to 49 well-phenotyped cirrhotic patients as a function of their compensation status (compensated patients with outpatients' recruitment vs decompensated patients in intensive care units). Our results, consistent with the literature, showed that liver function impairment is associated with lower microbiota diversity. Additionally, we monitored aerobic microbiota in decompensated cirrhotic patients, observing the invasion of extended spectrum beta-lactamase (ESBL)-producing in the gut's aerobic microbiota prior to severe infection caused by these pathogens. We propose this pragmatic methodology for larger cohort studies, aiming to enhance the monitoring of immunocompromised patients by using microbiota analysis as a predictive tool for the severity of associated pathologies and the identification of agents responsible for severe infections.