Natural history of the infant gut microbiome and impact of antibiotic treatments on strain-level diversity and stability

The gut microbiome plays a key role in human health. This community is dynamic during the first three years of life, before stabilizing to an adult-like state. However, relatively little is known about the impact of environmental factors on the developing human gut microbiome. Here we report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, approximately half of whom received multiple courses of antibiotics during the first three years of life. While the gut microbiome of most vaginally born children was dominated by Bacteroides species, we found that all four children born by Cesarean section and approximately 20% of vaginally born children lacked Bacteroides in * To whom correspondence should be addressed. xavier@molbio.mgh.harvard.edu. †Co-senior authors ‡Current address: Janssen Human Microbiome Institute, Janssen Research and Development, Cambridge, MA 02142, USA. §The investigators in the DIABIMMUNE Study Group are listed in the Supplementary Material. Author contributions: M.Y. performed 16S and metagenomic data analysis. M.Y, H.V., E.S.L., and R.J.X. assembled and wrote the paper. H.S., A.H., T.H., S.J.R., and M.K. designed the cohort study and collected clinical samples. M.Y., and D.G. designed DNA sequencing experiments and sample management pipelines. M.Y., T.V., E.A.F., C.H., H.V., D.G. and E.S.L. led method and research development. E.S.L., M.K., and R.J.X. served as principal investigators. Competing interests: The authors declare no competing financial interests. Data and materials availability: The NCBI BioProject ID for these data is PRJNA290381. HHS Public Access Author manuscript Sci Transl Med. Author manuscript; available in PMC 2017 June 15. Published in final edited form as: Sci Transl Med. 2016 June 15; 8(343): 343ra81. doi:10.1126/scitranslmed.aad0917. A uhor M anscript