Outcomes of Outpatients in an Gut Microbiota Clinic

Overview

The gut microbiota plays a crucial role in human health, influencing metabolism, immunity, and pathogen resistance. Research has linked microbiome dysbiosis to various intestinal and extra-intestinal disorders, prompting interest in therapeutic strategies like fecal microbiota transplantation (FMT), which is now standard for recurrent Clostridioides difficile infection and shows promise for other conditions. Despite its potential, the clinical integration of microbiome research remains limited due to biological complexity, lack of clinician awareness, and the absence of standardized guidelines. Meanwhile, patient demand for microbiome-based interventions is rising, leading some to seek non-scientific alternatives with potential health risks. Since 2016, the Gut Microbiota Clinic at Fondazione Policlinico Gemelli has provided personalized microbiota-based treatments, collaborating with specialists across disciplines. The clinic primarily serves patients with gastrointestinal and extra-intestinal disorders and employs a multidisciplinary approach. This study aims to characterize the clinical and microbiological and cytokine profiles of patients attending the clinic and establish a microbiological database. Primary and secondary endpoints include microbiota composition changes and clinical outcomes assessed through validated diagnostic tools.

The gut microbiota is a key mediator of various human functions, including metabolism, the immune system, and resistance to pathogen colonization. A growing body of scientific research has demonstrated-initially through association studies and subsequently through mechanistic experiments-that gut microbiome dysbiosis is linked to a wide range of both intestinal and extra-intestinal disorders. Recent evidence indicates that the gut microbiota is part of a complex network of interactions involving other host microbial communities and the immune system. In particular, the oral-gut axis has emerged as a key pathway through which the oral microbiota may influence gut microbial composition and function. Furthermore, host-microbiota interactions are mediated by immune mechanisms, including cytokine production and systemic inflammatory responses, linking microbiota composition to disease pathophysiology and clinical outcomes. This body of evidence has led to the exploration of gut microbiome modulation as a therapeutic strategy, such as fecal microbiota transplantation (FMT), which has become a standard treatment for recurrent Clostridioides difficile infection and has also shown promise for several other indications, including ulcerative colitis, irritable bowel syndrome, and metabolic syndrome. Furthermore, there is increasing interest in leveraging the gut microbiome as a diagnostic tool in clinical practice for various applications, including disease diagnosis, prognosis, and risk assessment; prediction of patient response to specific therapies; guidance and personalization of microbiome-targeted interventions such as probiotics or FMT; and monitoring the effectiveness of these treatments. Despite this enthusiasm, however, the integration of microbiome research advancements into routine clinical practice remains generally limited. This gap can be attributed to several factors, primarily the complexity of microbiome biology, the limited knowledge of gut microbiota among most healthcare professionals, and the absence of established guidelines and infrastructures for the clinical application of microbiome research. In contrast to the relatively slow adoption of microbiome research by clinicians, there is growing enthusiasm and high expectations among various patient groups for the rapid implementation of microbiota-related findings in clinical practice. This discrepancy poses the risk of patients seeking alternative, non-scientific solutions due to the lack of medical guidance. As a result, many individuals turn to non-medical sources, often found online, which may expose them to potential health risks and significant financial costs. Since 2016, the Gut Microbiota Clinic has been active within the CEMAD (Center for Digestive Diseases) at Fondazione Policlinico Gemelli. This clinic was established to address the needs of patients with gut microbiota imbalances, offering personalized therapeutic approaches based on microbiota profiling, which is assessed using a commercially available test. In particular, Fondazione Policlinico Gemelli collaborates with the company XBIOGEM for the production and supply of gut microbiota tests. The clinic primarily evaluates patients with gastrointestinal disorders (e.g., irritable bowel syndrome, inflammatory bowel diseases, and colitis induced by oncological treatments) as well as other conditions (e.g. patients with autoimmune disorders or patients undergoing oncological treatments). It operates through close collaboration with specialists from other medical fields, depending on the patient's condition (e.g., gastroenterologists, rheumatologists, dermatologists, infectious disease specialists, etc.), and follows a multidisciplinary approach involving dietitians and psychologists/psychiatrists as needed. This clinic is highly specialized and innovative and, to the best of our knowledge, is the first dedicated clinic of its kind worldwide. The aim of our study is to describe the characteristics of patients attending the Gut Microbiota Clinic at Fondazione Policlinico Gemelli and to establish a clinical and microbiological database. This initiative seeks to bridge the gap between the vast diagnostic and therapeutic potential of the gut microbiome and its practical application in routine clinical care. OBJECTIVES Primary Objective The primary objective is to describe the clinical and microbiological characteristics of patients attending the Gut Microbiota Clinic at Fondazione Policlinico Gemelli. Secondary Objectives * To describe changes in microbiota composition in patients undergoing microbiota testing as part of routine clinical practice after receiving standard treatments. * To assess clinical changes by evaluating follow-up consultations with the referring specialist (e.g., rheumatologist or dermatologist) for patients with extra-intestinal conditions, or through the judgment of the responsible physician. When applicable, validated diagnostic scores specific to the relevant condition (e.g., Mayo Score for ulcerative colitis, CDAI for Crohn's disease, or IBS-SSS for irritable bowel syndrome, PFS and OS for oncological patients) will be used. * To establish a microbiological database. ENDPOINTS Primary Endpoint The primary endpoint is the assessment of the clinical and microbiological characteristics of patients attending the Gut Microbiota Clinic at Fondazione Policlinico Gemelli. Secondary Endpoints Changes in gut microbiota composition and cytokine profile in patients undergoing the test as part of routine clinical practice, following treatment administered according to standard clinical care.