Planting the seed: Origins, composition, and postnatal health significance of the fetal gastrointestinal microbiota

Crit Rev Microbiol. 2017 May;43(3):352-369. doi: 10.1080/1040841X.2016.1211088. Epub 2016 Dec 8.


It has long been assumed that establishment of the fetal microbiome commences with the birthing process. However, recent studies have found bacterial DNA in umbilical cord blood, placenta, amniotic fluid, meconium, and fetal membranes in healthy normal pregnancies, leading to suggestions that the seeding of the fetal microbiome may commence in utero long before delivery. The origins of the microbiota of the fetal gastrointestinal (GI) tract have not yet been conclusively determined, although bacterial translocation from the maternal circulation, or ascension from the vagina, are both likely to be contributing pathways. Mother-to-child efflux of bacteria during pregnancy has the potential to markedly influence postnatal health, as the composition of gut microbiota determines production of important metabolites which are absorbed systemically and which modify immune function and development. Hence, the importance of understanding the colonization of the fetal GI microbiome is becoming clear, although few studies have investigated the origins, dynamics, and timing of the fetal microbiome. This is the topic of this review. By gaining a deeper understanding of the mechanisms underpinning fetal microbiome seeding, strategies may be developed to optimize fetal immune development and reduce the risk of adverse health and developmental outcomes.

Keywords: Microbiome; metabolome; neonate; developmental origins; intrauterine infection.

Publication types

  • Review

MeSH terms

  • Animals
  • Anti-Bacterial Agents / therapeutic use
  • Cesarean Section
  • Female
  • Gastrointestinal Microbiome*
  • Gastrointestinal Tract / embryology*
  • Gastrointestinal Tract / immunology
  • Gastrointestinal Tract / microbiology
  • Humans
  • Infant, Newborn
  • Meconium / microbiology*
  • Mouth / microbiology
  • Prebiotics
  • Pregnancy
  • Probiotics / pharmacology
  • Vagina / microbiology


  • Anti-Bacterial Agents
  • Prebiotics