Research has shown that imbalances in the human gut microbiome are linked not only to gastrointestinal diseases but also to metabolic disorders, immune dysregulation, and even neurological conditions. Chang Gung Memorial Hospital has now completed 339 cases of fecal microbiota transplantation (FMT). Combining clinical and molecular testing, the hospital has launched Taiwan’s “Gut Microbiome Whole-Genome Analysis” technology, which helps physicians assess the risk of diseases such as colitis, colorectal cancer, and Parkinson’s disease.

In 2022 and 2023, the United States approved the first microbiome-based therapeutic drugs globally—Rebyota and Vowst—marking the official start of the “microbiome medicine era.” Taiwan’s National Science and Technology Council is actively promoting the “Microbiome Research and Application for Precision Health Program,” integrating academic, research, and clinical resources to build a local microbial strain database and develop clinical applications.

Since 2019, Chang Gung Memorial Hospital has completed 339 FMT treatments. For patients with difficult-to-treat or recurrent Clostridioides difficile infection (CDI), a single FMT procedure achieved a clinical success rate of 85.4%, significantly higher than the roughly 30% success rate of traditional antibiotic therapy, with a lower recurrence rate.

By restoring gut microbial balance, FMT offers new therapeutic opportunities for high-risk populations, such as patients with inflammatory bowel disease, long-term users of immunosuppressants or antibiotics, elderly patients, and cancer patients. The newly introduced “Gut Microbiome Whole-Genome Analysis” technology in Taiwan can analyze over 140,000 microbial species and antibiotic resistance genes, ushering in a new era of precision gut medicine.

Li Po-Hsien, Director of the Microbiome Therapy Center at Linkou Chang Gung Memorial Hospital, explained that the analysis uses a Laboratory Developed Test (LDT) to sequence 50–60 million gene fragments at once, comparing them against a database of over 140,000 microbial species and 6,400 antibiotic resistance genes, creating a personalized “gut health map” for each individual.

Li emphasized that microbial diversity is a key indicator of gut health. Reduced diversity often signals an imbalanced gut ecosystem, which studies have linked to increased risks of obesity, diabetes, inflammatory bowel disease, and depression. Early detection of such imbalances allows for risk prevention and nutritional adjustments, facilitating personalized health management strategies.

Li shared a clinical case of a young woman with ulcerative colitis who had suffered for two years from severe abdominal pain, frequent diarrhea, and bloody stools. She showed little improvement from multiple medications, was forced to take unpaid leave, and became homebound. Initially suspected of having concurrent difficult-to-treat CDI, repeated tests were negative, leaving the diagnosis at an impasse.

The hospital’s laboratory team broke through traditional diagnostic frameworks using advanced MALDI-TOF MS mass spectrometry technology, comparing over 9,000 protein spectra. They identified the true pathogen as Clostridium innocuum. Targeted antibiotic treatment completely resolved her abdominal pain and diarrhea, with no recurrence, and her intestinal mucosa fully healed.

Huang Chiung-Guei, Director of the Department of Laboratory Medicine at Linkou Chang Gung Memorial Hospital, noted that precise identification helps physicians quickly distinguish between Clostridium innocuum and CDI, ensuring hidden pathogens are accurately targeted and preventing treatment delays caused by incorrect medication. This achievement not only improves clinical decision-making but also positions Taiwan as a leader in rapid gut pathogen identification internationally.

Cheng-Hsun Chiu, Deputy Superintendent of Linkou Chang Gung Memorial Hospital, stated that the gut functions as the body’s “second genome,” affecting immunity, metabolism, and mental health. By integrating microbiome therapy with genomic testing, Chang Gung is realizing the vision of precision medicine in the gut, offering patients a chance for renewed health and opening a new chapter for public well-being.

Resource: 長庚完成 339 例腸道微菌叢植入治療！再新推「腸道微菌叢全基因分析」技術