Elemental Diet and Gut Microbiome

The gut microbiome is the collection of microbes residing inside the gastrointestinal (GI) tract. The involvement of the gut microbiome has been demonstrated in multiple diseases processes including irritable bowel syndrome, small intestinal bacterial overgrowth (SIBO), Crohn's disease, and ulcerative colitis among many other diseases. A "healthy" diverse gut microbiome is associated with a better response to infections and immunopathogenic insults.

Many factors can affect the gut microbiome including medications, age, disease states and diet. Among these factors, diet is the easiest factor that can be modified to improve the gut microbiome. However, conducting dietary trials is challenging due to the inability to fully standardize what subjects eat even with strict dietary instructions. Moreover, individual preferences/allergies, the source of dietary ingredients, freshness, and food preparation are important steps which affect the diet and are challenging to standardize among subjects in a diet trial. This has led to significant ambiguity regarding the true extent and depth of dietary modifications on gut microbiome.

Apart from vitamins and micronutrients, the three main food macronutrients in the human diet are carbohydrates, protein and fat. Upon digestion, carbohydrates are broken into monosaccharides, proteins into amino acids and fats mainly into fatty acids. Elemental diets contain all daily required vitamins, micronutrients and macronutrients. The ingredients are readily digestible (carbohydrates, amino acids and medium chain fatty acids) and are absorbed within the proximal small bowel. One main disadvantage of elemental diets such as Vivonex is their unpalatability which has limited their use. A palatable elemental diet can be a very valuable tool to enable us to assess the effects of diet on the gut microbiome as it bypasses several confounding effects in dietary trials such as food allergies, individual digestion variability, completeness of the diet ingredients, and food preparation.

SIBO is a condition in which the gut microbiome plays an integral role and is defined by abnormal and excessive numbers of bacteria in the small bowel.4 Interest in SIBO has been fueled by the ever-increasing awareness of the human microbiome and its potential relationships to human health and disease. SIBO is a preferred condition to assess the effects of elemental diet on the gut microbiome, given the known role of the gut microbiome in SIBO. Those with SIBO experience a range of intestinal and extraintestinal symptoms including diarrhea, nausea, bloating, abdominal pain, and excess gas.

Commonly, SIBO has been defined by two methods: direct culture of small bowel aspirates, and indirect assessment using carbohydrate (e.g. lactulose or glucose) breath testing. SIBO is generally treated with antibiotics. Low fermentable and elemental diets also have positive effects in SIBO. Based on the potential effects of diet on the gut microbiome, we hypothesize that a two-week period of an elemental diet can change the gut microbiome in SIBO subjects.

Inclusion criteria

• • Participant must be able to understand and provide informed consent

• Males and Females ≥18-85
• Female subjects of childbearing potential must have a negative pregnancy test upon study entry
• Female (and male) subjects with reproductive potential, must agree to use FDA approved methods of birth control for the duration of the study
• Subject self-reports experiencing SIBO symptoms within 30 days
• Positive (abnormal) lactulose breath test for SIBO on visit 1 (day -7) as defined as:

• Rise of hydrogen ≥ 20ppm within 90 minutes on LBT OR
• A methane level ≥10 ppm at any point during the 120-minute LBT

Exclusion criteria

• • Inability or unwillingness of a participant to give written informed consent or comply with study protocol

• Pregnancy or lactating
• Type 1 or type 2 diabetes
• Active or ongoing infection that requires antibiotics other than the participants known prophylactic medications (i.e. active infection or antibiotic use in the last 1 month)
• Any condition that, in the opinion of the investigator, contraindicates participation in this study will be excluded from study participation.
• History of known Phenylketonuria (PKU) disease
• Non-English-speaking participants