Bacterial Colonization of the Newborn Gut, Immune Development, and Prevention of Disease

Nestle Nutr Inst Workshop Ser. 2017;88:23-33. doi: 10.1159/000455210. Epub 2017 Mar 27.


We now know that the fetus does not reside in a sterile intrauterine environment but is exposed to commensal bacteria from the maternal gut which cross the placenta and infiltrate the amniotic fluid. This exposure to colonizing bacteria continues at birth and during the first year of life, and it has a profound influence on lifelong health. Why is this important? Cross talk with colonizing bacteria in the developing neonatal intestine helps in the initial adaptation of the infant to extrauterine life, particularly in acquiring immune homeostasis, and provides protection against disease expression (e.g., allergy, autoimmune disease, and obesity) later in life. Colonizing intestinal bacteria are critical to the development of host defense during the neonatal period. Disrupted colonization (dysbiosis) due to cesarean section delivery, perinatal antibiotics, or premature delivery may adversely affect the development of host defense mechanisms in the gut and predispose to inflammation leading to increased susceptibility to disease later in life. Clinical evidence suggests that babies born by cesarean section have higher incidence rates of allergy, type 1 diabetes, and obesity. Infants given repeated antibiotic regimens are more likely to have asthma as adolescents. This observation helps to explain the disease paradigm shift in children from developed countries.

Publication types

  • Review

MeSH terms

  • Anti-Bacterial Agents / adverse effects
  • Asthma
  • Bacteria / growth & development*
  • Cesarean Section / adverse effects
  • Disease Susceptibility / microbiology*
  • Dysbiosis / complications
  • Gastrointestinal Microbiome / immunology
  • Gastrointestinal Microbiome / physiology*
  • Humans
  • Hypersensitivity
  • Immunity / physiology*
  • Infant
  • Infant, Newborn
  • Inflammation


  • Anti-Bacterial Agents