Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery

Abstract

Human microbial communities are characterized by their taxonomic, metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to determine the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites and assess the effect of the mode of delivery and its potential confounders or modifiers. A cohort of pregnant women in their early third trimester (n = 81) were prospectively enrolled for longitudinal sampling through 6 weeks after delivery, and a second matched cross-sectional cohort (n = 81) was additionally recruited for sampling once at the time of delivery. Samples across multiple body sites, including stool, oral gingiva, nares, skin and vagina were collected for each maternal–infant dyad. Whole-genome shotgun sequencing and sequencing analysis of the gene encoding the 16S rRNA were performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogeneous across all body sites at delivery, with the notable exception of the neonatal meconium. However, by 6 weeks after delivery, the infant microbiota structure and function had substantially expanded and diversified, with the body site serving as the primary determinant of the composition of the bacterial community and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with the cesarean mode of delivery in some body sites (oral gingiva, nares and skin; R2 = 0.038), this was not true for neonatal stool (meconium; Mann–Whitney P > 0.05), and there was no observable difference in community function regardless of delivery mode. For infants at 6 weeks of age, the microbiota structure and function had expanded and diversified with demonstrable body site specificity (P < 0.001, R2 = 0.189) but without discernable differences in community structure or function between infants delivered vaginally or by cesarean surgery (P = 0.057, R2 = 0.007). We conclude that within the first 6 weeks of life, the infant microbiota undergoes substantial reorganization, which is primarily driven by body site and not by mode of delivery.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Neonatal (at birth) microbial community structure.
Figure 2: The microbiota of infants at 6 weeks of age demonstrates body site specificity.
Figure 3: Failure to demonstrate a significant effect of mode of delivery on the infant microbiota across body sites and over time.
Figure 4: Taxonomic profiles of infant and maternal microbiomes from stool and oral gingiva, according to mode of delivery and time.
Figure 5: Expansion and diversification of microbial community structure and function in infants by 6 weeks of age.
Figure 6: Infant microbial community function with clinical metadata in a generalized linear model.

Accession codes

Primary accessions

BioProject

Sequence Read Archive

References

  1. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).

  2. Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Aagaard, K. et al. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One 7, e36466 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Costello, E.K. et al. Bacterial community variation in human body habitats across space and time. Science 326, 1694–1697 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Turnbaugh, P.J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031 (2006).

    Article  PubMed  Google Scholar 

  6. Ravel, J. et al. Vaginal microbiome of reproductive-age women. Proc. Natl. Acad. Sci. USA 108 (Suppl. 1), 4680–4687 (2011).

    Article  PubMed  Google Scholar 

  7. Ridaura, V.K. et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341, 1241214 (2013).

    Article  CAS  PubMed  Google Scholar 

  8. Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55–60 (2012).

    Article  CAS  PubMed  Google Scholar 

  9. Morgan, X.C. et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13, R79 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Schulz, M.D. et al. High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity. Nature 514, 508–512 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Gordon, H.A. & Pesti, L. The gnotobiotic animal as a tool in the study of host microbial relationships. Bacteriol. Rev. 35, 390–429 (1971).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Olszak, T. et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science 336, 489–493 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Wesemann, D.R. et al. Microbial colonization influences early B lineage development in the gut lamina propria. Nature 501, 112–115 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Gomez de Agüero, M. et al. The maternal microbiota drives early postnatal innate immune development. Science 351, 1296–1302 (2016).

    Article  CAS  PubMed  Google Scholar 

  15. Ivanov, I.I. et al. Induction of intestinal TH17 cells by segmented filamentous bacteria. Cell 139, 485–498 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Smith, P.M. et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341, 569–573 (2013).

    Article  CAS  PubMed  Google Scholar 

  17. Atarashi, K. et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331, 337–341 (2011).

    Article  CAS  PubMed  Google Scholar 

  18. Costello, E.K., Carlisle, E.M., Bik, E.M., Morowitz, M.J. & Relman, D.A. Microbiome assembly across multiple body sites in low-birthweight infants. mBio 4, e00782–13 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Feng, X.L., Xu, L., Guo, Y. & Ronsmans, C. Factors influencing rising cesarean section rates in China between 1988 and 2008. Bull. World Health Organ. 90, 30–39 (2012).

    Article  PubMed  Google Scholar 

  20. Osterman, M.J.K. & Martin, J.A. Trends in low-risk cesarean delivery in the United States, 1990–2013. Natl. Vital Stat. Rep. 63, 1–16 (2014).

    PubMed  Google Scholar 

  21. Almqvist, C., Cnattingius, S., Lichtenstein, P. & Lundholm, C. The impact of birth mode of delivery on childhood asthma and allergic diseases—a sibling study. Clin. Exp. Allergy 42, 1369–1376 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Black, M., Bhattacharya, S., Philip, S., Norman, J.E. & McLernon, D.J. Planned repeat cesarean section at term and adverse childhood health outcomes: a record-linkage study. PLoS Med. 13, e1001973 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. American College of Obstetricians and Gynecologists (College) & Society for Maternal–Fetal Medicine. Safe prevention of the primary cesarean delivery. Am. J. Obstet. Gynecol. 210, 179–193 (2014).

  24. Dominguez-Bello, M.G. et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc. Natl. Acad. Sci. USA 107, 11971–11975 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  25. Biasucci, G. et al. Mode of delivery affects the bacterial community in the newborn gut. Early Hum. Dev. 86 (Suppl. 1), 13–15 (2010).

    Article  PubMed  Google Scholar 

  26. Fallani, M. et al. Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding and antibiotics. J. Pediatr. Gastroenterol. Nutr. 51, 77–84 (2010).

    Article  PubMed  Google Scholar 

  27. Azad, M.B. et al. Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. CMAJ 185, 385–394 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  28. Barber, E.L. et al. Indications contributing to the increasing cesarean delivery rate. Obstet. Gynecol. 118, 29–38 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  29. David, L.A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559–563 (2014).

    Article  CAS  PubMed  Google Scholar 

  30. Koenig, J.E. et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. USA 108 (Suppl. 1), 4578–4585 (2011).

    Article  PubMed  Google Scholar 

  31. Jost, T., Lacroix, C., Braegger, C.P., Rochat, F. & Chassard, C. Vertical mother–neonate transfer of maternal gut bacteria via breastfeeding. Environ. Microbiol. 16, 2891–2904 (2014).

    Article  CAS  PubMed  Google Scholar 

  32. Azad, M. et al. Impact of maternal intrapartum antibiotics, method of birth and breastfeeding on gut microbiota during the first year of life: a prospective cohort study. BJOG Int. J. Obstet. Gynaecol. 123, 983–993 (2015).

    Article  CAS  Google Scholar 

  33. Ardeshir, A. et al. Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems. Sci. Transl. Med. 6, 252ra120 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Dufrene, M. & Legendre, P. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol. Monogr. 67, 345–366 (1997).

    Google Scholar 

  35. Koren, O. et al. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150, 470–480 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. La Rosa, P.S. et al. Patterned progression of bacterial populations in the premature infant gut. Proc. Natl. Acad. Sci. USA 111, 12522–12527 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Aagaard, K. et al. The placenta harbors a unique microbiome. Sci. Transl. Med. 6, 237ra65 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Antony, K.M. et al. The pre-term placental microbiome varies in association with excess maternal gestational weight gain. Am. J. Obstet. Gynecol. 212, 653.e1–653.e16 (2015).

    Article  Google Scholar 

  39. Collado, M.C., Rautava, S., Aakko, J., Isolauri, E. & Salminen, S. Human gut colonization may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci. Rep. 6, 23129 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Bäckhed, F. et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17, 852 (2015).

    Article  CAS  PubMed  Google Scholar 

  41. Knights, D. et al. Bayesian community-wide culture-independent microbial source tracking. Nat. Methods 8, 761–763 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Penders, J. et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118, 511–521 (2006).

    Article  PubMed  Google Scholar 

  43. Vatanen, T. et al. Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165, 842–853 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Dominguez-Bello, M.G. et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat. Med. 22, 250–253 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Galley, J.D., Bailey, M., Kamp Dush, C., Schoppe-Sullivan, S. & Christian, L.M. Maternal obesity is associated with alterations in the gut microbiome in toddlers. PLoS One 9, e113026 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Mueller, N.T. et al. Birth-mode-dependent association between pre-pregnancy maternal weight status and the neonatal intestinal microbiome. Sci. Rep. 6, 23133 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Chu, D.M. et al. The early infant gut microbiome varies in association with a maternal high-fat diet. Genome Med. 8, 77 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Hu, J. et al. Diversified microbiota of meconium is affected by maternal diabetes status. PLoS One 8, e78257 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Ridlon, J.M., Kang, D.J., Hylemon, P.B. & Bajaj, J.S. Bile acids and the gut microbiome. Curr. Opin. Gastroenterol. 30, 332–338 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  50. Kennedy, D.O. B vitamins and the brain: mechanisms, dose and efficacy—a review. Nutrients 8, 68 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Gibson, M.K. et al. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nat. Microbiol. 1, 16024 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Bokulich, N.A. et al. Antibiotics, birth mode and diet shape microbiome maturation during early life. Sci. Transl. Med. 8, 343ra82 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. DiGiulio, D.B. et al. Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular- and culture-based investigation. PLoS One 3, e3056 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Steel, J.H. et al. Bacteria and inflammatory cells in fetal membranes do not always cause preterm labor. Pediatr. Res. 57, 404–411 (2005).

    Article  PubMed  Google Scholar 

  55. Jiménez, E. et al. Isolation of commensal bacteria from umbilical cord blood of healthy neonates born by cesarean section. Curr. Microbiol. 51, 270–274 (2005).

    Article  CAS  PubMed  Google Scholar 

  56. Jiménez, E. et al. Is meconium from healthy newborns actually sterile? Res. Microbiol. 159, 187–193 (2008).

    Article  CAS  PubMed  Google Scholar 

  57. Ardissone, A.N. et al. Meconium microbiome analysis identifies bacteria correlated with premature birth. PLoS One 9, e90784 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  58. Hansen, R. et al. First-pass meconium samples from healthy-term vaginally delivered neonates: an analysis of the microbiota. PLoS One 10, e0133320 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Fallani, M. et al. Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centers. Microbiology 157, 1385–1392 (2011).

    Article  CAS  PubMed  Google Scholar 

  60. Yassour, M. et al. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci. Transl. Med. 8, 343ra81 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. La Rosa, P.S. et al. Hypothesis testing and power calculations for taxonomic-based human microbiome data. PLoS One 7, e52078 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Aagaard, K. et al. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB J. 27, 1012–1022 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Caporaso, J.G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Schmieder, R. & Edwards, R. Fast identification and removal of sequence contamination from genomic and metagenomic data sets. PLoS One 6, e17288 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Edgar, R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).

    Article  CAS  PubMed  Google Scholar 

  66. Haas, B.J. et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21, 494–504 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Cole, J.R. et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37, D141–D145 (2009).

    Article  CAS  PubMed  Google Scholar 

  68. DeSantis, T.Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  70. Segata, N. et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9, 811–814 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8, e1002358 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Le Chatelier, E. et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541–546 (2013).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors gratefully acknowledge the support of the NIH Director's New Innovator Award (DP2 DP21DP2OD001500; K.M. Aagaard), the NIH–NINR (NR014792-01; K.M. Aagaard), the NIH National Children's Study Formative Research (N01-HD-80020; K.M. Aagaard), the Burroughs Welcome Fund Preterm Birth Initiative (K.M. Aagaard), the March of Dimes Preterm Birth Research Initiative (K.M. Aagaard), the Baylor College of Medicine Medical Scientist Training Program (NIH NIGMS T32 GM007330; D.C. and K.M. Aagaard), the National Institute of General Medical Sciences (T32GM088129; D.M.C.), Baylor Research Advocates for Student Scientists (D.M.C.) and the Human Microbiome Project funded through the NIH Director's Common Fund at the National Institutes of Health (as part of NIH RoadMap 1.5; K.M. Aagaard). All sequencing and adaptation of protocols for WGS sequencing were performed by the Baylor College of Medicine Human Genome Sequencing Center (BCM–HGSC), which is funded by direct support from the National Human Genome Research Institute (NHGRI) at NIH (U54HG004973 (BCM); R. Gibbs, Principal Investigator). The authors also thank the staff members who were directly involved in clinical recruitment and specimen processing (M. Moller, B. Boggan, R. Benjamin, J. Chen, C. Cook and D. Racusin). The authors are grateful to M. Belfort, J. Versalovic, T. Savidge, R.A. Luna, D. Racusin, M. Suter and K. Meyer for critical review of the manuscript.

Author information

Authors and Affiliations

Authors

Contributions

D.M.C. and K.M. Aagaard designed and conceived the study; K.M. Aagaard and K.M. Antony assembled the cohort and developed the infrastructure to obtain swabs, samples and clinical metadata from all samples; K.M. Aagaard and K.M. Antony recruited and sampled all subjects; A.L.P., D.M.C. and M.D.S. prepared samples for sequencing of the gene encoding16S rRNA and for WGS sequencing; D.M.C., J.M. and K.M. Aagaard performed and supervised all analysis and statistical modeling; and D.M.C. and K.M. Aagaard wrote the manuscript, with contributions from J.M., A.L.P., K.M. Antony and M.D.S.

Corresponding author

Correspondence to Kjersti M Aagaard.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Figures

Supplementary Figures 1–16 (PDF 5996 kb)

Supplementary Tables

Supplementary Tables 1–12 (XLSX 5234 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Chu, D., Ma, J., Prince, A. et al. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat Med 23, 314–326 (2017). https://doi.org/10.1038/nm.4272

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nm.4272

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing