Acquisition of Gut Flora in the Infant

In "The “Forgotten Organ”: Gut Flora and Its Role in Immune Function" , it became clear that the origins of much disease in the body, including autoimmune disease, begins with the status of the microorganisms that are present in the gut.  Disease results when the essential gut flora becomes damaged and imbalanced, causing disruptions in the function of the immune system.  Damage to the essential flora may also allow the overgrowth of opportunistic flora or permit transitional flora to cause disease.  In understanding how damage to the gut flora occurs, it is important to examine the process by which gut flora is acquired at the very beginning of life.  Problems in the acquisition process can predispose an infant to an imbalance of gut flora that will impact health and the development of disease throughout life. Acquisition of Gut Flora

In the unborn child, it was once believed that the gut was sterile.  However, recent research suggests that colonization of the gut begins when the unborn child swallows amniotic fluid containing microbes from the mother's gut.  The majority of the colonization of the gut occurs during the birthing process when the infant is further exposed to a large amount of bacteria from the mother.  If the mother's flora is damaged or imbalanced, this will be passed on to the infant.

Type of Delivery

The process of gut colonization with flora is influenced by method of delivery, with vaginal delivery resulting in significantly faster rates of colonization.  Infants born by Cesarean section have lower numbers of Bifidobacteria and Bacteroides, important groups of essential flora, compared to vaginally born infants.  The gut flora of infants born by Cesarean section may be disturbed for up to 6 months, compared to 1 month for infants delivered vaginally.  This is significant because the early composition of the gut flora is known to impact development of the immune system and balance between Th1 and Th2 immunity (see this article for more information).

Infant Feeding (i.e. Diet)

The feeding method, or diet, of an infant also influences the gut flora by providing a source of nutrition that allows for the growth and function of flora and providing a source of continued colonization of microorganisms from the environment.  For babies that are breastfed, bacteria from the feeding environment will be transferred from the mother's skin and milk ducts.  For those that are bottle-fed, bacteria will be transferred from the dried powder and the equipment and water used to prepare the formula.  Breastfed newborns carry a more stable and uniform population of gut flora compared to bottle-fed infants.  The impact of breastfeeding on immediate and long-term health has been well-studied with the results indicating that breastfeeding has many protective health benefits.  One of the main reasons behind why breastfeeding is so health-promoting is because of its effects on the gut flora.  Attempts to make formulas more similar to breast milk involve adding probiotics (live bacteria), prebiotics (oligosaccharides), and other components to make the microbiota composition similar to that of breast milk.  The type of infant feeding is critical in influencing the composition of the gut flora, thereby affecting development of the immune system and long-term health.

Antibiotic Use

 The use of antibiotics in the perinatal period, before birth by the mother and after birth by the breastfeeding mother or infant, has a dramatic effect on the colonization of the gut flora.  The diversity of the gut flora is reduced in infants whose mothers received antibiotics during pregnancy or while breastfeeding.  Antibiotic use by the mother is also significant because the antibiotics will damage the gut flora of the mother and this damaged flora is then passed to the infant during the acquisition process.  Antibiotic use by the infant in the immediate period after birth has been shown to severely disrupt the gut flora in a way that lasts for months up to several years and has an impact on the child's long-term health.


The major factors that influence the colonization of gut flora in the infant include the status of the mother's gut flora (as this will be passed to the infant), the method of delivery, type of feeding, and antibiotic use.  There are also other factors that play a role, including the infant's overall environment, hygiene, and perinatal stress.  The colonization of the gut flora at the beginning of life is significant because the gut flora impacts the development of the immune system, has a major role in immune system functioning (80-85% of the immune system is in the gut), and thereby influences the process by which autoimmune and metabolic disease occurs.  Disease begins in the gut and it starts at the very beginning of life!


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Biasucci, G., Rubini, M., Riboni, S., Morelli, L., Bessi, E., & Retetangos, C. (2010). Mode of delivery affects the bacterial community in the newborn gut. Early Human Development, 86(Suppl 1), 13 - 5. 

Gronlund, M., Lehtonen O., Eerola E., & Kero, P. (1999). Fecal microflora in healthy infants born by different methods of delivery: permanent changes in intestinal flora after cesarean delivery. Journal of Pediatric Gastroenterology and Nutrition, 28, 19–25.

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