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

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

Author information

  • 1Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
  • 2Jackson Laboratory, Farmington, Conn.
  • 3Department of Medicine, Brigham and Women's Hospital, Boston, Mass.
  • 4Department of Medicine, Boston University School of Medicine, Boston, Mass.
  • 5Division of Allergy, Immunology and Pulmonary Medicine, Washington University School of Medicine, St Louis, Mo.
  • 6Kaiser Permanente, San Diego, Calif.
  • 7Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass. Electronic address:



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 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.


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.


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.


C-section; Infant gut microbiome; breast-feeding; race

[Available on 2018-02-01]
[PubMed - in process]
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