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NCT Number: NCT07333482

Flourish: Exploring the Early Infant Gut Microbiome

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.

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Key information

Conditions

Microbiota Dermatitis Eczema Gut Microbiome Microbiome Skin Diseases Skin Diseases, Eczematous Skin and Connective Tissue Diseases

Age range

0 month–3 month

Sex eligibility

All sexes

Study type

Interventional

Phase

Not applicable

Primary location

Seeding Labs INC

Austin, Texas, 78749, United States

Location status: Recruiting

Location contact

Kim Sukhum, PhD

CONTACT

[email protected]

502-437-9588

Who can participate

Healthy volunteers accepted: Yes

Only the study team can determine whether someone qualifies for participation.

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)

Treatment and study plan

Tailored Recommendations

Dietary Supplement

Recommendations are tailored to the infant's microbiome composition, functional gene profiles (e.g., HMO digestion and SCFA production pathways), age, feeding method, and reported symptoms.

Guidance may include evidence-based suggestions related to probiotic use, prebiotic intake, and age-appropriate nutritional strategies intended to support healthy gut microbiome development. All recommendations are educational in nature, optional, and provided for consideration by parents or caregivers. No supplements are provided directly as part of the study, and no supplementation is required for study participation.

Recommendations are updated over time as new microbiome data are collected and are delivered according to study arm assignment. The full intervention arm receives comprehensive, personalized recommendations with interpretive support, while the limited intervention arm receives probiotic recommendations only designed to model a scalable laboratory-developed test (LDT)-style approach.

Consult Call

Behavioral

Participants assigned to the full intervention arm will receive scheduled consult calls with a trained microbiome specialist as part of the study intervention. These are conducted remotely and are designed to support participant understanding of microbiome reports, review educational content, and discuss microbiome-informed recommendations in the context of the infant's age, feeding practices, and reported symptoms.

For participants in the full intervention arm, consult calls may include discussion of microbiome-guided recommendations related to diet, supplementation, and lifestyle factors. Participants in the limited intervention arm may elect to receive a call with a licensed Nurse Practitioner for the purpose of interpreting their static microbiome report only; these calls do not include personalized recommendations or discussion of broader health symptoms. Participants in the control arm do not receive consult calls during the active study period.

Educational Email Series

Behavioral

Participants assigned to the full intervention arm will receive a structured educational email series delivered longitudinally over the course of the study. The email series provides evidence-based education on early infant gut microbiome development and its relationship to immune and allergic health outcomes, with links to blog articles summarizing current peer-reviewed research.

Topics include Cesarean delivery and microbiome seeding, breastfeeding and human milk oligosaccharides, formula selection, probiotic use, antibiotic exposure, gut maturation, introduction of solid foods and allergens, eczema and the atopic march, food sensitivities, environmental microbial exposure, and general strategies to support infant gut health during early life.

The educational email series is informational only and does not include individualized medical advice. Participants in the limited intervention and control arms do not receive the educational email series during the active study period.

Primary outcomes

  1. Microbiota Composition

    Time frame: 24 months

    Changes in gut microbiota composition, including relative abundance of beneficial bacterial taxa such as Bifidobacterium, assessed using shotgun metagenomic sequencing.

  2. C-Section-Associated Microbiome Signatures

    Time frame: 24 months

    Changes in the relative abundance of microbial taxa and signatures previously associated with Cesarean delivery, assessed longitudinally using shotgun metagenomic sequencing.

  3. Opportunistic and Potentially Pathogenic Microbial Abundance

    Time frame: 24 months

    Changes in the relative abundance of opportunistic and potentially pathogenic microbial taxa over time, assessed using shotgun metagenomic sequencing.

  4. Functional Microbiome Capacity

    Time frame: 24 months

    Changes in microbial functional gene pathways related to human milk oligosaccharide (HMO) digestion and short-chain fatty acid (SCFA) production, assessed using metagenomic functional profiling.

  5. Eczema Incidence / Atopic Symptoms

    Time frame: 24 months

    Incidence of eczema and other early atopic symptoms assessed via parent-reported surveys and standardized eczema assessment when symptoms are reported.

Secondary outcomes

  1. HMO Digestion Functional Capacity

    Time frame: 24 months

    Changes in the abundance of microbial functional gene pathways involved in human milk oligosaccharide (HMO) digestion, assessed using shotgun metagenomic sequencing and functional gene annotation.

    Unit of Measure:

    Relative abundance of HMO digestion-related functional gene pathways

  2. SCFA Production Functional Capacity

    Time frame: 24 months

    Changes in the abundance of microbial functional gene pathways involved in short-chain fatty acid (SCFA) production, assessed using shotgun metagenomic sequencing and functional gene annotation.

    Unit of Measure:

    Relative abundance of SCFA production-related functional gene pathways

  3. Parent-Reported Infant Health Outcomes

    Time frame: 24 months

    Parent-reported infant health outcomes collected via longitudinal surveys, including gastrointestinal symptoms, infections, medication use, and feeding practices.

Other outcomes

  1. Stool Metabolomic Profiles

    Time frame: 24 months

    Description:

    Exploratory characterization of stool metabolite profiles collected at select time points, assessed using untargeted metabolomic analysis.

    Unit of Measure:

    Relative abundance of detected stool metabolites

    Measurement Tool:

    Untargeted stool metabolomics

    Time Frame:

    Select time points through 24 months

Study contacts

Contact information is provided by the study sponsor or research team.

Claudia Nakama, MPH

CONTACT

[email protected]

‪512-827-9765‬

Kimberley Sukhum, PhD

CONTACT

[email protected]

‪512-827-9765‬

Sponsors and collaborators

Lead sponsor

Seeding Inc

Industry

Collaborators

  • Laboratory Corporation of America

Registry information

Official study title

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

Important dates

Study start
2026
Primary completion
2028
Study completion
2028
First posted
Jan 12, 2026
Registry last updated
Feb 24, 2026

OpenTrials presents study information sourced from ClinicalTrials.gov. The official registry record should be consulted for the latest information.

View the official ClinicalTrials.gov record (opens in a new tab)

This listing is for discovery and informational purposes only. It is not medical advice, does not guarantee that a study is recruiting, and does not determine eligibility. Contact the study team and a qualified healthcare professional when considering participation.

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