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We conducted a Phase 1 clinical trial of an Investigational New Drug involving 2 weeks of oral vancomycin (to kill unhealthy gut bacteria), followed by a bowel cleanse and then Full Spectrum Microbiota (FSM) from healthy donors to create a healthy GI microbiome. We treated children ages 7-17 years who had ASD and moderate or severe gastrointestinal problems. We administered MTT in two stages: an oral or rectal dose, followed by 7-8 weeks of oral administration. There was an 82% reduction in GI symptoms, and a 25% reduction in autism symptoms. Their bacterial diversity significantly increased, from 25% below normal to normal. At the 8-week follow-up, the improvements in GI symptoms, ASD symptoms, and microbiome diversity were stable. At the two-year follow-up, most of the GI improvements remained, and there was a 47% reduction in ASD symptoms compared to baseline.