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


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.


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.


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.


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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