Temporal and Spatial Changes in the Microbiome Following Pediatric Severe Traumatic Brain Injury.

OBJECTIVES: The microbiome may be affected by trauma and critical illness. Many studies of the microbiome in critical illness are restricted to a single body site or time point and confounded by preexisting conditions. We report temporal and spatial alterations in the microbiome of previously healthy children with severe traumatic brain injury (TBI). DESIGN: We collected oral, rectal, and skin swabs within 72 hours of admission and then twice weekly until ICU discharge. Samples were analyzed by 16S rRNA gene amplicon sequencing. Children undergoing elective outpatient surgery served as controls. Alpha and beta diversity comparisons were performed with Phyloseq, and differentially abundant taxa were predicted using Analysis of Composition of Microbiomes. SETTING: Five quaternary-care PICUs. PATIENTS: Patients less than 18 years with severe TBI requiring placement of an intracranial pressure monitor. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Three hundred twenty-seven samples were analyzed from 23 children with severe TBI and 35 controls. The community composition of initial oral (F = 3.2756, R2 = 0.0535, p = 0.012) and rectal (F = 3.0702, R2 = 0.0649, p = 0.007) samples differed between TBI and control patients. Rectal samples were depleted of commensal bacteria from Ruminococcaceae, Bacteroidaceae, and Lachnospiraceae families and enriched in Staphylococcaceae after TBI (p < 0.05). In exploratory analyses, antibiotic exposure, presence of an endotracheal tube, and occurrence of an infection were associated with greater differences of the rectal and oral microbiomes between TBI patients and healthy controls, whereas enteral nutrition was associated with smaller differences (p < 0.05). CONCLUSIONS: The microbiome of children with severe TBI is characterized by early depletion of commensal bacteria, loss of site specificity, and an enrichment of potential pathogens. Additional studies are needed to determine the impact of these changes on clinical outcomes.

Pilot Study of the Effect of Plant-Based Enteral Nutrition on the Gut Microbiota in Chronically Ill Tube-Fed Children.

BACKGROUND: Dietary intake sharply impacts the structure and function of the gut microbiota, which is important for childhood health. However, little is known about the microbiota of children who cannot eat by mouth. Standard enteral formulas for supplemental nutrition are low in fiber and high in processed sugars and are commonly associated with gastrointestinal side effects. In this pilot study, we examined the effects of plant-based enteral nutrition (PBEN) upon the gut bacteria of chronically ill children. METHODS: Ten children (median age 3.5 years, age range 2-8 years) dependent upon conventional enteral formula were transitioned to PBEN for 2 months. Microbial diversity within fecal samples collected before and after PBEN was assessed by 16S ribosomal RNA gene sequence analysis and was compared with rectal swabs from healthy children. Fecal short-chain fatty acids and bile acids were measured in parallel. RESULTS: Relative to control samples, fecal samples from study subjects were depleted of commensals (eg, Faecalibacterium) and enriched with pathogens (eg, Enterococcus). Postintervention samples from study subjects were more similar to healthy controls. Most subjects experienced PBEN-induced alterations in the gut microbiota, but these changes varied significantly across individuals. Clinical diaries indicated that PBEN was well tolerated, with improvement in symptoms noted in several subjects. CONCLUSION: Results from this pilot study suggest that PBEN is well tolerated and could improve the health of the microbiota in chronically ill children. This trial provides a rationale for systematic evaluation of PBEN in clinical trials of children who require supplemental nutrition.