The Use of Probiotic Dietary Supplementation to Alter the Intestinal Microbiota and Improve Growth in Children With Short Bowel Syndrome

1. Introduction and Purpose: The goal of this project is to improve linear growth and weight gain in children with short bowel syndrome by changing their intestinal microbiota and ultimately intestinal bacterial metabolism.
2. Background: Short bowel syndrome (SBS) occurs when there is insufficient intestinal mass to support normal growth and development. Approximately 35 babies out of every 100,000 live birth are affected by SBS in North America, and these infants remain dependent on intravenous, parenteral nutrition (PN) for a prolonged period of time. One of the major challenges these children face is achieving sufficient linear growth and weight gain despite receiving calories in excess of that required by age matched healthy children. Problems with poor intestinal absorption and motility and increased inflammation all contribute to poor growth in these patients. An important factor in the healthy function of the remaining small bowel is the intestinal microbial community. It is known that depletion of certain groups of beneficial gut bacteria, and their metabolic by-products, specifically short-chain fatty acids (SCFAs) can lead to intestinal inflammation, malabsorption, and less efficient use of consumed calories.

The long-term objective of the study is to determine how to effectively change the gut microbiota in children with SBS to restore a healthy balance and maximize growth and development. Although children with SBS have known disturbances to their intestinal microbiota, it is unclear whether providing an oral probiotic is an effective approach to correct these disturbances.

Aim 1: To determine if probiotic supplementation can significantly modulate gut microbiota and improve growth in SBS patients.

Aim 2: To determine levels of fecal SCFAs in children with SBS, including those receiving probiotics. 3. Study description: All eligible children will be consented at the time of an outpatient clinic visit or during an inpatient stay. Enrolled participants will then be randomized to "placebo" where they will receive the standard of care medical and nutritional treatment for short bowel syndrome in addition to 1mL of pure MCT (medium chain triglyceride) oil daily for 3 months, or "probiotic therapy" where they will receive a combination of Lactobacillus rhamnosus (5 billion colony-forming units per day) and Lactobacillus johnsonii,(200 million colony-forming units per day) daily for 3 months in addition to the standard of care. Randomization will not be blinded. The probiotics were chosen because they have been well studied in infants and children and both of these species have been found to be deficient in children with SBS and poor growth. The placebo was chosen because it is the only inactive ingredient included in the suspension of the probiotic, it is odorless and tasteless, and has no known side effects. The probiotic and MCT oil will be given daily either orally or through an existing gastrostomy tube. Patients who drop out of the study, or who are withdrawn will not be replaced, and the data from these subjects will be included as part of the analysis in an intention-to-treat manner.

Stool (approximately 200mg per sample) will be collected at 3 separate time points for each patient (at the beginning, middle and end of the study). Stool will be collected either during an inpatient stay or at an outpatient clinic visit. If a patient is unable to provide a stool sample, the family can collect one at home and it can be frozen and brought in at the time of the next clinic visit. A frozen sample can be used for 16S rRNA sequencing and metabolomics analysis, but not for SCFA concentration. Microbial gDNA can be recovered from stool that has been frozen for up to 6 months, with similar sequencing results compared to freshly processed stool. If a fresh sample is provided, a portion will be used to determine the concentration of SCFAs. Stool used for 16S rRNA sequencing and metabolomics will be kept frozen until analysis is performed. A one-time stool collection will also be obtained from 10 control patients with short bowel syndrome who are growing well and will be used for 16S rRNA and metabolomics analysis.