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).

Keywords: atopic dermatitis; bifidobacterium; cesarean section; gut; infant gut; microbiome.

FIGURE 1

Participant study flow and study design. (A) Progression of participants from recruitment to analysis. (B) Participant flow from enrollment to exit. Participants were randomized into intervention (green) and control (purple) arms. The intervention arm received bi‐weekly educational emails and coaching calls every 4 weeks (green triangles). Data collection occurred at time point 1 (~2 weeks post‐randomization) and time point 2 (10–12 weeks after time point 1). Exit surveys were completed at time point 3.

FIGURE 2

Changes in microbial community structure and alpha and beta diversity post‐intervention. (A) Relative abundance of the 20 most abundant microbial taxa at the genus level. Less abundant taxa were grouped and are shown as “Other”. Each vertical bar represents an individual sample, and sample order is consistent across top and bottom panels to allow for individual‐level comparisons. (B) Shannon diversity index for control and intervention arms. (C, D) Non‐metric multidimensional scaling (NMDS) plots based on Bray‐Curtis distances, illustrating the clustering of microbial communities for each sample in (C) control and (D) intervention arm. Ellipses represent the standard error around group centroids for each time point, and the black arrows connect group centroids between time point 1 and time point 2 with the arrowhead pointing to time point 2. Samples from the same individual are joined by gray arrows with the arrowhead pointing to time point 2. (E) Boxplots of MDS1 from a NMDS analysis based on Bray‐Curtis dissimilarities. Boxplots show the median, interquartile range, and individual data points for each arm and time point. Points from the same individual are connected by lines to illustrate within‐subject changes over time. The Wilcoxon signed‐rank test was used to assess statistical significance between time points, and the Mann–Whitney U test and PERMANOVA were used to assess statistical significance between arms. p values were adjusted for multiple comparisons using the BH method (q values, 10 tests). *q < .1, ***q < .01; n.s., not significant.

FIGURE 3

Key taxa and HMO‐degrading gene abundances change over time and between control and intervention arm. Relative abundance of (A) Bifidobacterium and (B) Enterobacteriaceae; and gene abundance (measured in RPKM) of (C) α‐L‐fucosidase and (D) 2,3‐2,6‐a‐sialidase. Boxplots show the median, interquartile range, and individual data points for each arm and time point. The Wilcoxon signed‐rank test was used to assess statistical significance between time points, and the Mann–Whitney U test was used to assess statistical significance between arms. p values were adjusted for multiple comparisons using the BH method (q values, 48 tests for taxa and 24 tests for genes). *q < .1, **q < .05, ***q < .01, n.s., not significant.

FIGURE 4

Reduced C‐section index in the intervention arm. (A, B) Non‐metric multidimensional scaling (NMDS) plots based on Bray‐Curtis distances shaded by C‐section index. Plots show the clustering of microbial communities for time point 1 (circles) and time point 2 (triangles) in (A) the control arm and (B) the intervention arm. Ellipses represent standard error around the group centroids for each time point. (C) C‐section index across time points 1 and 2 in the control and intervention arms, shown alongside a group of C‐section‐delivered and vaginally‐delivered infants from Shao et al. (2019): Time point 1 at 21 days, time point 2 between 100 and 365 days. The Wilcoxon signed‐rank test was used to assess statistical significance between time points, and the Mann–Whitney U test was used to assess statistical significance between arms. p values were adjusted for multiple comparisons using the BH method (q values, 4 tests). *q < .1, ***q < .01, n.s., not significant.

FIGURE 5

Infants with atopic dermatitis have a higher C‐section index and altered gut microbiome composition. (A) Percentage of infants with different health conditions across time points. The left panel shows the percentage of infants with any condition, and the central panel shows the percentage of infants with atopic dermatitis (AD) and/or any food reaction. (B–D) Association between AD status at time point 2 and (B) C‐section index, relative abundance of (C) Bifidobacterium and (D) Enterobacteriaceae. The Mann–Whitney U test was used to assess statistical significance between the AD and non‐AD groups. p values were adjusted for multiple comparisons using the BH method (q values, 3 tests). *q < .1, **q < .05.