Functional Characterization of Gastrointestinal Microbiome in Neonates

There are a paucity of data characterizing functional assessment of the interaction of gastrointestinal (GI) microbiome with the GI tract during development in the neonate. A healthy GI microbiome depends on pioneering microbiota obtained from the mother at birth.  Those pioneers act as gatekeepers supplying bactericides to defend against pathogens and produce substrates for intestinal cells as well as substrates for the proper succession of other commensal GI microbiota. We developed assays to monitor such functional development in feces.  The assays are focused on function of the microbiota to produce short-chain fatty acids, B vitamins, and lactate in feces.  Other assays measure function of the GI microbiome interaction with the gut immune system by monitoring lactoferrin, calprotectin, and an array of cytokines in stool samples. A third set of assays is established to monitor digestion of milk by the infant. A measure of caloric content, triglycerides, protein, glucose, lactose, fructose, and bile acids in fecal samples will be performed. Infants born prematurely are at a disadvantage for gut development because their mothers GI -, breast-, and vaginal microbiomes have not yet shifted to that observed in mothers late in their 3rd trimester.   The functional assessment of the GI microbiome of the infant born prematurely has not yet been compared to that of stool samples from the term neonate. Linear stool samples of the premature infant may permit analyses of healthy progression toward that of the term baby and could provide a predictor and novel biomarker of a premature infant failing to advance and regressing toward a diagnosis of necrotizing enterocolitis. The GI microbiome is dependent on microbiomes of the mother, their length of gestation and their use of antibiotics, vaginal or cesarean delivery, the onset and type feeding tolerance, antibiotic use, and geography.  We need to assess infants in various regions and on different types of feeding. It will be important to know concurrent treatments such as antibiotic therapeutics or gut rest.  Although this is a characterization study, we are hopeful it will provide novel biomarkers from fecal samples of health and disease.