title: Factors influencing the infant gut microbiome at age 3-6 months: Findings from the ethnically diverse Vitamin D Antenatal Asthma Reduction Trial (VDAART).
abstract: 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.
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
authors.forename: Joanne E
authors.initials: JE
authors.lastname: Sordillo
authors.affiliation: Jackson Laboratory, Farmington, Conn.
authors.forename: Yanjiao
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: McGeachie
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
authors.forename: John
authors.initials: J
authors.lastname: Ziniti
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
authors.forename: Nancy
authors.initials: N
authors.lastname: Lange
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
authors.forename: Nancy
authors.initials: N
authors.lastname: Laranjo
authors.affiliation: Department of Medicine, Brigham and Women's Hospital, Boston, Mass.
authors.forename: Jessica R
authors.initials: JR
authors.lastname: Savage
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
authors.forename: Vincent
authors.initials: V
authors.lastname: Carey
authors.affiliation: Department of Medicine, Boston University School of Medicine, Boston, Mass.
authors.forename: George
authors.initials: G
authors.lastname: O'Connor
authors.affiliation: Department of Medicine, Boston University School of Medicine, Boston, Mass.
authors.forename: Megan
authors.initials: M
authors.lastname: Sandel
authors.affiliation: Division of Allergy, Immunology and Pulmonary Medicine, Washington University School of Medicine, St Louis, Mo.
authors.forename: Robert
authors.initials: R
authors.lastname: Strunk
authors.affiliation: Division of Allergy, Immunology and Pulmonary Medicine, Washington University School of Medicine, St Louis, Mo.
authors.forename: Leonard
authors.initials: L
authors.lastname: Bacharier
authors.affiliation: Kaiser Permanente, San Diego, Calif.
authors.forename: Robert
authors.initials: R
authors.lastname: Zeiger
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
authors.forename: Scott T
authors.initials: ST
authors.lastname: Weiss
authors.affiliation: Jackson Laboratory, Farmington, Conn.
authors.forename: George
authors.initials: G
authors.lastname: Weinstock
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
authors.forename: Diane R
authors.initials: DR
authors.lastname: Gold
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass. Electronic address: reaal@channing.harvard.edu.
authors.forename: Augusto A
authors.initials: AA
authors.lastname: Litonjua
mesh_terms: D001419:Bacteria / Q000235:genetics*; D044822:Biodiversity; D001942:Breast Feeding; D002585:Cesarean Section; D005260:Female; D005312:Fetal Blood / Q000378:metabolism; D006801:Humans; D006967:Hypersensitivity / Q000382:microbiology*; D007223:Infant; D007422:Intestines / Q000382:microbiology*; D008297:Male; D064307:Microbiota; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012307:Risk Factors; D017423:Sequence Analysis, RNA; D014807:Vitamin D / Q000378:metabolism; D044465:White People
chemical_list: D012336:RNA, Ribosomal, 16S; D014807:Vitamin D
keywords: C-section; Infant gut microbiome; breast-feeding; race