Principles and practice guidelines of microbiota medicine

As an emerging branch of clinical medicine, microbiota medicine has attracted worldwide attention from clinicians, medical educators, patient communities, and industry. However, this developing field still lacks consensus on its fundamental principles as well as guidelines for clinical and educational practice. An expert panel was convened by the journal Microbiota Medicine Research at the 2025 CHINAGUT Conference to develop the principles and practice guidelines of microbiota medicine.The expert panel is comprised of 48 clinicians from China, Singapore, Japan, India, and Italy. After the face-to-face meeting for discussion of draft, one round of voting and editing for the statements and comments were performed to reach consensus for all statements. The expert panel completed the online anonymous voting and revisions. The finalized guideline includes 15 consensus statements (Figure 1), addressing fundamental aspects of microbiota medicine, including disciplinary definition, diagnostic and therapeutic principles, multidisciplinary collaboration models, ethical and regulatory considerations, and core competencies and medical education frameworks.

Statement 1: Microbiota medicine is an emerging clinical discipline that investigates microbiota–host interactions to develop evidence-based strategies for disease prevention, diagnosis, and treatment, while advancing clinical practice and medical education.

Statement 2: Microbiota dysbiosis-related diseases comprise a group of disorders in which their onset and/or progression are associated with dysbiosis and may be ameliorated through microbiota reconstruction.

Statement 3: The pathophysiological mechanisms underlying host–microbiota interactions often involve abnormal processes such as inflammation, immune dysregulation, and metabolic disturbance.

Statement 4: The clinical suspicion of gut microbiota dysbiosis should be primarily based on patient history, medication use, symptoms and signs, and standard clinical investigations. At present, microbiome sequencing reports should not be used as the basis for clinical diagnosis.

Statement 5: The application of microbiome sequencing should be defined across research, clinical, and consumer domains. Each of these contexts should be guided by clear standards of evidence and recommendations for appropriate use.

Statement 6: Microbiota-based interventions, such as FMT and selected prebiotic or probiotic approaches, offer potential therapeutic options for dysbiosis-related diseases.

Statement 7: Clinical decisions regarding microbiota-based therapies should be guided by the patient condition and adherence to standardized evaluation and reporting frameworks such as the PRIM 2024 recommendations.

Statement 8: High-quality clinical care in microbiota medicine requires multidisciplinary expertise, robust clinical infrastructure, and advanced diagnostic systems.

Statement 9: Establishing integrative teams that span disciplines, institutions, and geographic regions can substantially improve the management of complex microbiota dysbiosis-related diseases by overcoming the limitations of single-specialty expertise.

Statement 10: In the multidisciplinary management of microbiota dysbiosis-related diseases, the attending physician acts as the primary coordinator, integrating clinical information, collecting medical history, and facilitating case discussions. Shared decision-making with the patient should be undertaken after multidisciplinary consultation and consensus on the management plan.

Statement 11: Multidisciplinary discussions in microbiota medicine should safeguard patient privacy and prioritize patient welfare, guided by the principles of beneficence and non-maleficence.

Statement 12: When local medical resources for microbiota medicine are limited, digital health or telemedicine platforms should be employed to establish multidisciplinary collaborative networks. When clinically indicated, coordinated emergency support or cross-institutional referral pathways should be activated.

Statement 13: Clinical decision-making in microbiota medicine must prioritize patient benefit, and refrain from commercially driven practices that lack evidence-based efficacy, undermine clinical priorities, or violate ethical or regulatory standards.

Statement 14: Microbiota medicine should be incorporated into undergraduate and postgraduate medical education to foster interdisciplinary competence and prepare future physicians for microbiome-based clinical practice.

Statement 15: Physicians in microbiota medicine should demonstrate core competencies in theoretical knowledge, technical skills, and communication competence, with the capacity to coordinate multidisciplinary care using integrative approaches (Figure 2).The publication of the Principles and Practice Guidelines of Microbiota Medicine: Statements from the CHINAGUT Conference provides a foundational consensus for clinical practice, education, and future research in this rapidly evolving field. The authors note that the guidelines will be updated in response to clinical feedback, technological advances, and developments in artificial intelligence, supporting the transition of microbiota medicine from conceptual innovation to standardized and reproducible clinical application.