Safety and efficacy of a novel fecal microbiota transplantation method using hydrogen nanobubble water without antibiotics or bowel cleansing in children with autism spectrum disorder: an open-label, single-arm study demonstrating improvements in core and comorbidity symptoms

Background Autism spectrum disorder (ASD) is rising in prevalence, but effective treatments for its core symptoms remain limited. Fecal microbiota transplantation (FMT) has shown promise; however, conventional methods often require antibiotics and bowel cleansing, raising concerns regarding safety and sustainability. We developed a novel FMT method using hydrogen nanobubble water and investigated its efficacy and safety. Methods This prospective, single-arm, before-and-after comparative study enrolled 30 children aged 5–12 years with ASD, selected according to inclusion and exclusion criteria. SHIN-1, a Good Manufacturing Practice (GMP)-grade prepared fecal microbial solution from a healthy screened donor, was suspended in hydrogen nanobubble water and administered via enema. Primary outcome was the Social Responsiveness Scale-2 (SRS-2), with objectivity confirmed using Gazefinder as an eye-tracking system. Secondary outcomes included sensory profile [Short Sensory Profile (SSP)], gastrointestinal symptoms [Gastrointestinal Symptom Rating Scale [GSRS], Bristol Stool Form Scale [BSFS]] and Patient Health Questionnaire-4 items (PHQ-4). Statistical analyses employed paired t-tests or Wilcoxon signed-rank tests ( α = 0.05). Results At 30 weeks, fecal microbiota reconstitution was observed, with increases in short-chain fatty acid–producing and typically taxa abundant in developing children. SRS-2 scores decreased 29% ( p < 0.001), sustained at one year. The classification is as follows; 19 severe cases improved to mild and 6 to normal. Improvements were greater in children without gastrointestinal disorders (45% vs. 24%). Social Communication and Interaction (SCI), Restricted Interests and Repetitive Behavior (RRB), and subscales improved uniformly; sensory, gastrointestinal, and emotional symptoms improved by 30%–61%. No adverse events occurred. Conclusion This novel hydrogen nanobubble water–based FMT method was safe and effective, reducing both core and peripheral symptoms of ASD and suggesting broad benefits via the gut microbiota–brain axis. Clinical Trial Registration: https://jrct.mhlw.go.jp/en-latest-detail/jRCTs031230041 .