Flourish: Exploring the Early Infant Gut Microbiome

Flourish Study: A Randomized, Three-Arm Longitudinal Clinical Study of Microbiome-Guided Interventions in Cesarean-Born Infants

The goal of this clinical trial is to learn whether microbiome analysis, education, and personalized recommendations can improve gut health and reduce early markers of immune-related conditions in infants aged 0-3 months delivered via Cesarean section. The study aims to determine whether these interventions can increase beneficial bacteria, decrease C-section-associated microbiome signatures, reduce opportunistic pathogens, and improve functional potential for HMO digestion and SCFA production. The study also seeks to assess whether improvements in microbiome composition are associated with a reduced prevalence of early atopic symptoms.

Researchers will compare three groups: a full intervention arm that receives microbiome reports, coaching, personalized recommendations, and educational materials; a limited intervention arm that receives simplified reports and basic recommendations; and a control arm that receives no results until study completion. This design allows evaluation of both a comprehensive intervention and a more scalable, minimal-results model.

Participants will:

1. Provide six microbiome stool samples over a 24-month period.
2. Provide additional small stool samples at two timepoints for exploratory metabolomic analysis.
3. Receive microbiome reports and guidance according to their assigned study arm.
4. Complete surveys on infant health history, symptoms, diet, and environmental exposures.
5. Participate in standardized eczema assessment(s) administered by a Nurse Practitioner and evaluated by a Pediatric Allergy Specialist if any symptoms are reported.

This study seeks to demonstrate that targeted microbiome support can positively shift gut microbial development in C-section infants and may reduce risks linked to the early stages of the atopic march. Findings may inform scalable strategies for delivering microbiome-based support in early life and improve long-term health outcomes for this high-risk population.

Inclusion Criteria:

• Infants are qualified for this study if they are 0 to 3 months of age at time of enrollment.
• Infants must have been delivered via Cesarean delivery (C-section), either scheduled or emergent.
• Infants must have been at least 36 weeks gestation at time of delivery.
• Infants and their caregivers must reside in the United States with a US mailing address.

Exclusion Criteria:

• Infants can not have been given probiotic supplements in their life at recruitment. This includes probiotic powder or supplements or formula with probiotic addition or multivitamin with probiotic addition.
• Twin and multiple birth infants are not accepted in this study.
• Infants cannot have the following existing health conditions:
• Gastrointestinal conditions: Hirschsprung disease, eosinophilic gastrointestinal disorders (EGID) including eosinophilic esophagitis (EoE), necrotizing enterocolitis (NEC), short bowel syndrome (SBS)
• Immune or auto-immune conditions: Severe Combined Immunodeficiency (SCID), human immunodeficiency virus (HIV)), excluding eczema and rashes
• Congenital conditions: cleft lip or cleft palate, congenital heart disease, cerebral palsy, fragile X syndrome, down syndrome, spina bifida, cystic fibrosis, phenylketonuria (PKU), congenital hypothyroidism (CHT), galactosaemia)
• Blood disorders (sickle cell disease, thalassemia, hemophilia)
• Infant or any immediate family member has previously received results from an at-home microbiome stool test (excluding standard clinical diagnostic testing such as stool culture or pathogen testing)