The new method of fecal microbiota transplantation, based on automatic facilities and washing processes, was coined as washed microbiota transplantation (WMT). The first recommendations on WMT were released as Nanjing Consensus report by the fecal microbiota transplantation (FMT)-standardization Study Group in 2019. This is the second consensus report on WMT by the expert group of the CHINAGUT Conference. Delphi and grading of recommendations assessment, development, and evaluation (GRADE) systems were used to develop the consensus and appraise the quality of evidence and grading of recommendations. The present consensus named as Nanjing Consensus Ⅱ with 28 statements was developed according to the preferred reporting items for microbiotherapy guidelines in 2024 (PRIM 2024) for improving the clinical use of WMT. The expert panel ranked the top 10 indications of WMT rather than voting on Clostridioides difficile infection. This consensus will promote the multidisciplinary application of WMT and advance the development of microbiota medicine.
The growing recognition of the microbiome's role in human health has propelled the emergence of microbiota medicine—a new discipline integrating microbiology, multi-omics, and clinical science. Advances in sequencing, data integration, and interventions such as fecal microbiota transplantation (FMT) have transitioned the field from observational association towards therapeutic exploration across a spectrum of diseases. However, key challenges remain in establishing causal mechanisms, ensuring reproducible biomarkers, and bridging the efficacy gap between FMT for recurrent Clostridioides difficile infection (CDI) and other complex disorders. The trajectory of microbiota medicine points towards its maturation into a structured clinical discipline, moving from broad ecological modulation towards targeted, mechanism-based interventions that require interdisciplinary collaboration and robust translational frameworks. This review aims to provide a comprehensive overview of recent advances in microbiota medicine, spanning from its indications, therapeutic modalities, and diagnostic evidence to the disciplinary challenges and future prospects that will shape the field.