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

J Allergy Clin Immunol. 2017 Feb;139(2):482-491.e14. doi: 10.1016/j.jaci.2016.08.045. Epub 2016 Oct 13.


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 by Firmicutes (Lachnospiraceae/Clostridiales), the second by Proteobacteria (Klebsiella/Enterobacter), the third by Bacteriodetes, and the fourth by Veillonella. 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 higher Bacteroidetes coabundance scores. C-section birth was associated with higher diversity, but decreased Bacteroidetes coabundance scores. Firmicutes scores were higher for infants born by C-section. Breast-fed infants had lower proportions of Clostridiales. Cord blood vitamin D was linked to increased Lachnobacterium, but decreased Lactococcus.

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.

Keywords: C-section; Infant gut microbiome; breast-feeding; race.

Publication types

  • Clinical Trial

MeSH terms

  • Bacteria / genetics*
  • Biodiversity
  • Breast Feeding
  • Cesarean Section
  • Female
  • Fetal Blood / metabolism
  • Humans
  • Hypersensitivity / microbiology*
  • Infant
  • Intestines / microbiology*
  • Male
  • Microbiota*
  • RNA, Ribosomal, 16S / genetics*
  • Risk Factors
  • Sequence Analysis, RNA
  • Vitamin D / metabolism
  • White People


  • RNA, Ribosomal, 16S
  • Vitamin D