The investigators propose to investigate Microbiota Transfer Therapy (MTT) for treating children with Autism Spectrum Disorder (ASD) and gastrointestinal problems (primarily constipation and/or diarrhea). MTT involves a combination of 10 days of oral vancomycin (an antibiotic to kill pathogenic bacteria), followed by a bowel cleanse, followed by 12 weeks of Fecal Microbiota (FM).

For children ages 5-17 years with Autism Spectrum Disorder and gastrointestinal problems, a Phase 2 clinical trial will evaluate the safety, tolerability, and efficacy of MTT. The three parts of this trial are described below.

Part 1: Randomized Trial The trial will begin with a randomized, double-blind, placebo-controlled trial which will include a 2-week treatment with oral vancomycin (Group A) or placebo (Group B), then 1 day of Miralax to cleanse the bowel of vancomycin and bacteria/feces (both groups), followed by oral administration of FM (Group A) or placebo (Group B). An initial high dose of FM (or placebo) for two days will be followed by a lower maintenance dose of FM or placebo for 12 weeks.

Part 2: Extension (Group A) and Treatment (Group B)

• For Group A there will be 12-week observation period
• For Group B, there will be treatment similar to that received by the treatment group in Part 1 (partial cross-over, open-label), except that they will not receive vancomycin. So, they will be treated with Miralax followed by an initial high dose of FM for 2 days, and then a maintenance dose of FM for 12 weeks. The purpose of this arm is to determine if vancomycin is necessary or not.

Part 3: Follow-up There will be a follow-up evaluation at 6, 12, and 18 months after treatment ends, to determine long-term safety and efficacy.

Participant duration will be approximately 6.5 months for treatment, and follow-up at 6, 12 and 18 months after treatment ends.

Study duration will be approximately 4 years, including IRB approvals, training staff, recruiting, clinical trial, data analysis, and reporting.

Inclusion Criteria for Children with ASD

1. Child aged 5-17 years
2. Diagnosis of autism per the Childhood Autism Rating Scale 2 (CARS-2) and either the Autism Diagnostic Interview-Revised (ADI-R) or the Autism Diagnostic Observation Schedule 2 (ADOS 2).
3. GI disorder as defined below that has lasted for at least 3 years.
4. No changes in medications, supplements, diet, therapies, or education in last 3 months, and no intention to change them during the clinical trial.
5. General good physical health aside from gastrointestinal problems
6. Ability to swallow pills (without chewing)

Exclusion Criteria for Children with ASD

1. Antibiotics in last 3 months (does not apply to topical antibiotics)
2. Probiotics in last 2 months, or fecal transplant in last 12 months
3. Single-gene disorder (Fragile X, etc.)
4. Major brain malformation
5. Tube feeding
6. Severe gastrointestinal problems that require immediate treatment (life-threatening)
7. Ulcerative Colitis, Crohn's Disease, diagnosed Celiac Disease, Eosinophilic Gastroenteritis, or similar conditions
8. Severely underweight/malnourished (per physician clinical judgement)
9. Unstable, poor health; seizure disorder that is not responsive to treatment or not on stable management or complex type; or other health conditions that would significantly increase their risk of adverse effects (per physician clinical judgement)
10. Recent or scheduled surgeries
11. Current participation in other clinical trials
12. Females who are pregnant or who are sexually active without effective birth control.
13. Allergy or intolerance to vancomycin or Miralax
14. Clinically significant abnormalities at baseline on two blood safety tests: Comprehensive Metabolic Panel and Complete Blood Count with Differential.
15. Psychotropic medication daily use - Current or within past 2 months - which are known to interfere in gastrointestinal function
16. Evidence of significant impairment of immune system, or taking medications that can compromise the immune system, and thus increase risk if exposed to multiple-drug resistant bacteria.

Randomized, double-blind, placebo-controlled study.