Supplementary Materials

Supplementary Material for:

Antibiotics, birth mode, and diet shape microbiome maturation during early life

Nicholas A. Bokulich, Jennifer Chung, Thomas Battaglia, Nora Henderson, Melanie Jay, Huilin Li, Arnon D. Lieber, Fen Wu, Guillermo I. Perez-Perez, Yu Chen, William Schweizer, Xuhui Zheng, Monica Contreras, Maria Gloria Dominguez-Bello, Martin J. Blaser*

*Corresponding author. Email: martin.blaser{at}nyumc.org

Published 15 June 2016, Sci. Transl. Med. 8, 343ra82 (2016)
DOI: 10.1126/scitranslmed.aad7121

This PDF file includes:

  • Materials and Methods
  • Fig. S1. LEfSe analysis of differentially abundant taxa between vaginally born, predominantly breast-fed (n = 15) and cesarean-delivered, predominantly formula-fed children (n = 7) from 1 to 6 months of life.
  • Fig. S2. Antibiotic exposures did not alter short-term α-diversity in individual subjects.
  • Fig. S3. Functional maturation of the microbiome is delayed by antibiotic exposure.
  • Fig. S4. Functional maturation of the microbiome is altered by formula feeding.
  • Fig. S5. Enumeration of 16S ribosomal RNA genes in fecal specimens in children at 1 and 12 months of age, by quantitative polymerase chain reaction.
  • Fig. S6. Average RA of Bacteroides in children in relation to feeding and delivery mode in the first 2 years of life.
  • Fig. S7. Cesarean section exerts a modest impact on microbiota maturation.
  • Fig. S8. Infant diet alters microbiota composition and maturation over the first 2 years of life.
  • Fig. S9. RA heatmap of major taxa in 296 maternal samples.
  • Fig. S10. Development of diversity of Bifidobacterium and Bacteroides OTUs in children in early life.
  • Table S1. Baseline characteristics of the 53 mothers in the study.
  • Table S2. Baseline characteristics of the 43 infants in the study.
  • Table S3. Prenatal antimicrobial use by class and purpose.
  • Table S4. Perinatal antibiotic use by class and indication.
  • Table S5. Postnatal antimicrobial use by class and age of child.
  • Table S6. LLM estimates of antibiotic treatment, diet, and delivery effects on α-diversity.
  • Table S7. Permutational MANOVA scores of antibiotic, diet, and delivery effects on unweighted UniFrac distance β-diversity.
  • Table S8. Permutational MANOVA scores of antibiotic, diet, and delivery effects on weighted UniFrac distance β-diversity.
  • Table S9. LLM estimates of antibiotic, diet, and delivery effects on microbiome maturation MAZ scores.
  • Table S10. LLM estimates of antibiotic, diet, and delivery effects on PICRUSt-predicted metagenome maturation MAZ scores.
  • References (5665)

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