Improving immune-related health outcomes post-cesarean birth with a gut microbiome-based program: A randomized controlled trial

Abstract

Background: Infants born via Cesarean section (C-section) often have a distinct gut microbiome and higher risks of atopic and immune-related conditions than vaginally delivered infants. We evaluated whether a microbiome-based program could shift gut microbiome composition and improve microbiome-associated health outcomes in C-section born infants. Methods: This open-label, randomized, controlled trial included full-term C-section-born infants aged 0–3 months, randomized to an intervention (n = 25) or control arm (n = 29). Over 6 months, the intervention arm received two microbiome reports, personalized recommendations based on their microbiome, educational materials, and coaching calls focused on microbiome health. Parents reported health conditions via surveys. Primary outcome: Difference between study arms in relative abundance of key gut microbiome taxa and functional genes. Other outcomes: Changes in a C-section index—a taxonomy-based metric comparing C-section-associated taxa to vaginally-associated taxa—and prevalence of atopic conditions. Results: Compared to controls, the intervention arm had higher Bifidobacterium (p =.025, q =.121) and higher abundance of genes associated with human milk oligosaccharide degradation (e.g., α-L-fucosidase, p =.019, q =.046) at timepoint 2. In the intervention arm, the C-section index decreased to a level similar to vaginally born infants (p =.807, q =.807). At the end of the intervention, atopic dermatitis prevalence was lower in the intervention arm than in controls (odds ratio, 0.17 [95% CI, 0.023–0.723], p =.031). Conclusion: A personalized microbiome-based program can modulate the gut microbiome of C-section-born infants and may reduce the risk of atopic conditions (ClinicalTrials.gov: NCT06424691).