Inclusion Criteria:  Diagnosis of Autism Spectrum Disorder Parent or Legally Authorized Representative willing and able to provide informed consent A reliable caregiver who can report side effects and communicate effectively with the research team Stable medications in the two months prior to enrollment Currently receiving interventions in the community/school for ASD If female and of childbearing potential, must be willing to utilize at least one highly effective method of birth control for the duration of the study. This includes condoms with spermicide, oral birth control pills, contraceptive implants, intra-uterine devices, or diaphragms. Subjects not of reproductive potential will be exempt (e.g. post-menopausal, surgically sterilized) If male, and partner is of childbearing potential, must be willing to utilize at least one highly effective method of birth control for the duration of the study. This includes condoms with spermicide, oral birth control pills, contraceptive implants, intra-uterine devices, or diaphragms. Subjects not of reproductive potential will be exempt (surgically sterilized)  Exclusion Criteria:  Female subjects who are pregnant, nursing, or intend to become pregnant during the study period. Subjects whose caregivers are unable/unwilling to cooperate with the protocol requirements. Subject will be excluded who are suffering with Rett syndrome and Childhood Disintegrative Disorder. Other serious co-morbid medical disorders affecting brain function and behaviour, including uncontrolled seizures. Subjects unable to refrain from taking non-study antibiotics for the period of the study. Subjects diagnosed with cancer, except small localized basal cell carcinoma. Subjects known to abuse alcohol or drugs. Subjects who have undergone gastric bypass or total colectomy, or who are scheduled for these procedures. Infection with HIV. Infection with Hepatitis B or C. Allergy to benzodiazepine. Inability to stop loperamide, diphenoxylate/atropine, or cholestyramine before the study Unable to stop opiate treatment unless on a stable dose including PRN dosing, and no dose increase planned for the duration of the study Known positive stool cultures for enteropathogens including, but not limited to Shigella, Salmonella, and Campylobacter within 30 days before enrollment. Known stool studies positive for ova and/or parasites in 30 days prior to enrollment. Planned travel outside United States during study period. Hypersensitivity to vancomycin Renal insufficiency Colitis