Factors influencing the infant gut microbiome at age 3-6 months: Findings from the ethnically diverse Vitamin D Antenatal Asthma Reduction Trial (VDAART)

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Abstract

Background:

The gut microbiome in infancy influences immune system maturation, and may have an important impact on allergic disease risk.

Objective:

We sought to determine how prenatal and early life factors impact the gut microbiome in a relatively large, ethnically diverse study population of infants at age 3 to 6 months, who were enrolled in Vitamin D Antenatal Asthma Reduction Trial, a clinical trial of vitamin D supplementation in pregnancy to prevent asthma and allergies in offspring.

Methods:

We performed 16S rRNA gene sequencing on 333 infants' stool samples. Microbial diversity was computed using the Shannon index. Factor analysis applied to the top 25 most abundant taxa revealed 4 underlying bacterial coabundance groups; the first dominated byFirmicutes(Lachnospiraceae/Clostridiales), the second byProteobacteria(Klebsiella/Enterobacter), the third byBacteriodetes, and the fourth byVeillonella. Scores for coabundance groups were used as outcomes in regression models, with prenatal/birth and demographic characteristics as independent predictors. Multivariate analysis, using all microbial community members, was also conducted.

Results:

White race/ethnicity was associated with lower diversity but higherBacteroidetescoabundance scores. C-section birth was associated with higher diversity, but decreasedBacteroidetescoabundance scores.Firmicutesscores were higher for infants born by C-section. Breast-fed infants had lower proportions ofClostridiales. Cord blood vitamin D was linked to increasedLachnobacterium, but decreasedLactococcus.

Conclusions:

The findings presented here suggest that race, mode of delivery, breast-feeding, and cord blood vitamin D levels are associated with infant gut microbiome composition, with possible long-term implications for immune system modulation and asthma/allergic disease incidence.

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