The investigators propose to investigate Microbiota Transfer Therapy (MTT) for treating patients with Pitt-Hopkins Syndrome (PTHS) and gastrointestinal problems (constipation, bloating, abdominal pain). MTT involves a combination of 10 days of oral vancomycin (an antibiotic to kill pathogenic bacteria), followed by 1 day of bowel cleanse using magnesium citrate, followed by 4 days of high dose MTP-101P with an antacid, followed by 12 weeks of a lower maintenance dose of MTP-101P with an antacid.

For children 5-17 years old and adults 18-55 years old with Pitt-Hopkins Syndrome (PTHS) and Gastrointestinal (GI) problems who have attempted two standard-of-care (SOC) GI treatments with no alleviation of symptoms. This is a Phase 2 clinical trial that will evaluate the safety, tolerability, and efficacy of a powder version of Microbiota Transfer Therapy (MTT) called MTP-101P. The three parts of this trial are described below.

Part 1: Placebo-Controlled Treatment (14 Weeks) The trial will begin with a randomized, double-blind, placebo-controlled trial which will include a 10-day treatment with oral vancomycin (or placebo), then 1 day of magnesium citrate to cleanse the bowel of vancomycin and bacteria/feces (all participants, since its bowel-emptying effect cannot be blinded), followed by 4 days of initial high dose of MTP-101P taken daily 5 minutes after antacid, and then 12 weeks of a lower maintenance dose of MTP-101P taken daily 5 minutes after an antacid.

Group A: Real Treatment vs. Group B: Placebo vancomycin, real magnesium citrate, placebo MTP-101P, real antacid.

Part 2: Open-Label Observation and Cross-Over (14 weeks) Group A: Observation over the next 14 weeks (no additional treatment). Group A completes the study at the end of part 2.

Group B: They will receive the same treatment that Group A received in part 1. This includes 10 days of vancomycin, magnesium citrate, and an initial high dose of MTP-101P for 4 days taken daily 5 minutes after an antacid, and then a lower dose of MTP-101P for 12 weeks taken daily 5 minutes after antacid.

Part 3: Follow Up Group B: There will be a follow-up evaluation 14 weeks post-treatment after the end of Part 2, to assess long-term efficacy and possible adverse effects.

Inclusion Criteria:

1. Children ages 5 to <18 years and adults ages 18 to < 55 years with Pitt Hopkins Syndrome (verified by genetic testing)
2. GI disorder as defined below that has lasted for at least 2 years.
3. No changes in medications, supplements, diet, or therapies in the 2 months prior to start of treatment, and no intention to change treatments during Part 1 (all participants) and Part 2 (group B) of the clinical trial. The only exception is GI medications, which may be reduced if symptoms reduce, and any changes during the study will be documented.
4. Review of last year of medical records by the study physician.
5. At least two previous trials of "standard of care" GI treatments that did not alleviate GI symptoms (constipation, diarrhea, bloating, gas, reflux, and/or abdominal pain). Standard of care treatments include laxatives, stool softeners, enemas, suppositories, or similar medications.

Exclusion Criteria:

1. Antibiotics in 2 months prior to start of treatment (topical antibiotics are allowed)

2. Probiotics in 2 months prior to start of treatment, or fecal transplant in last 12 months. Foods naturally containing probiotics such as yogurt are allowed.

3. Tube feeding may be an exclusion criterion if the participant requires an unusual diet such as a liquid diet with low fiber.

4. Current severe gastrointestinal problems that require immediate hospital treatment (life-threatening)

5. Ulcerative Colitis, Crohn's Disease, diagnosed Celiac Disease, Eosinophilic Gastroenteritis, or similar conditions

6. Unstable, poor health (based on study physician's opinion), or active malignancy or infection.

7. Recent or scheduled abdominal surgeries

8. Current participation in other clinical trials

9. Females who are pregnant or who are at risk of pregnancy and sexually active with a male partner without effective birth control. We will conduct a pregnancy test on all female participants 12 years and older as part of the screening and at each clinical visit.

   Males who are sexually active with a female partner without highly effective birth control (IUD or birth control hormones).

10. Allergy or intolerance to the study medications: vancomycin, magnesium citrate, milk powder with chocolate flavoring (which are included in MTP-101P), or the antacid.

11. Clinically significant abnormalities at baseline on the blood safety tests, and confirmed on a second test. The tests include Comprehensive Metabolic Panel, and Complete Blood Count with Differential. Note that some abnormalities may occur due to PTHS, so only those likely to significantly increase risk in this study would be grounds for exclusion, at the discretion of the study physician. See detailed discussion at the end of this section on Interpreting Laboratory Results. re. Eligibility for Admission to Study.

12. 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.

13. Substantially decreased kidney function, as evidenced by estimated glomerular filtration rate of <60 mL/min/1.73 m2. This is not normally reported for children on standard laboratory metabolic panels, so in those cases we will use the National Kidney Foundations Pediatric Glomerular filtration rate (GFR) Calculator to calculate the pediatric GFR based on age/height, the Blood urea nitrogen (BUN) and serum creatinine from our standard Comprehensive Metabolic Panel (CMP). [https://www.kidney.org/professionals/kdoqi/gfr\_calculatorped\] This calculator uses the Creatinine-based "Bedside Schwartz" equation (2009) that seems to be the most commonly used calculation for this purpose.

14. Participants who are breastfeeding.