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Promoting and Protecting the Gastrointestinal Newborn Microbiome Through Breastfeeding Practices

Johnson, Jessica M. MSN, RN, PNP-PC; Adams, Ellise D. PhD, CNM; O'Neal, Pamela V. PhD, RN

Author Information
The Journal of Perinatal & Neonatal Nursing: July/September 2020 - Volume 34 - Issue 3 - p 222-230
doi: 10.1097/JPN.0000000000000498
  • Free


Breastfeeding is known to promote the health and survival of the newborn, and breast milk contains all required nutrients and bacteria to promote a healthy newborn gastrointestinal (GI) microbiome.1,2 A microbiome is a community of microbes living on and in the human body.3 The development of the newborn GI microbiome most likely begins during pregnancy and continues throughout the postpartum period. Many factors impact this development. Breast milk plays a key role in establishing a healthy newborn GI microbiome, protecting the infant's health by promoting homeostasis and supporting immunologic functions.4 The purpose of this clinical article is to discuss the impact of breast milk and breastfeeding on the newborn GI microbiome. A review of breast milk development and composition, the newborn GI microbiome, and how healthcare professionals can influence breastfeeding practices to promote the healthy development of the newborn GI microbiome will be discussed.


Breast milk has a unique composition that cannot be duplicated in manufactured formulas.5 Breast milk is dynamic, meaning the composition changes to meet the needs of the newborn. Breast milk is rich in macronutrients, micronutrients, and bacteria to aid in the development of the newborn GI microbiome.6 See Figure 1, which is an illustration of breast milk composition.

Figure 1.
Figure 1.:
Breast milk composition. Illustration by Marina Gibson and used with permission.

Breast milk development and composition

Breast milk provides optimal nutrition and hydration for the infant who is exclusively breastfed. The process of breast milk development begins in the mammary gland, and then it is transported by lactiferous ducts. During pregnancy, these ducts expand as a response to estrogen, growth hormone, cortisol, and prolactin.7 Progesterone influences breast alveoli to multiply and expand in the mammary glands. Prolactin causes the breasts to fill with milk. In the first few weeks of the infant's life, there is a positive relationship between maternal prolactin levels and milk production.8 Oxytocin is responsible for the letdown reflex that allows milk to flow along the lactiferous ducts.8 Oxytocin is stimulated when the infant is placed on the breast and begins to feed and through skin-to-skin contact between mother and infant. Oxytocin also has a psychological component. It can be released on the basis of the mother's feelings, such as lovingly thinking about the newborn or in response to the newborn's cries. In addition, oxytocin release can induce feelings of calm for the mother. During periods of stress, oxytocin release is inhibited and can affect the mother's ability to let down. Through skin-to-skin contact and breastfeeding, oxytocin and prolactin are released, which enhances the nurturing mother-infant relationship.8 The breasts will swell in the final weeks of pregnancy due to the presence of colostrum. The colostrum secreted in the first 48 to 72 hours after birth is rich in immunoglobulins. These immunoglobulins contain a high concentration of proteins, which support the immunity of the infant during the transition from intrauterine to extrauterine life when various exposures are encountered.

Macronutrients consist of carbohydrates, proteins, and fats. Specific carbohydrates in breast milk include oligosaccharides, which are often referred to as human milk oligosaccharides (HMOs).4,9 The HMOs are carbohydrates naturally found only in breast milk and they function as prebiotics. Breast milk HMOs do not serve a direct purpose for the newborn but serve a prebiotic function to stimulate the growth of Bifidobacterium and Bacteroides.10,11 Naturally occurring HMOs also inhibit pathogenic bacteria from adhering to mucosal surfaces, as well as promote Bifidobacteria and support immune development. Bifidobacteria is one of the first commensal bacteria to colonize the newborn GI microbiome and supports GI mucosal integrity. Synthetic oligosaccharide prebiotics are added to some formula preparations and have demonstrated similar GI pH and bifidogenic effects to naturally occurring HMOs; however, their effects on the establishment of the microbiome and immune system development still require further research.11,12 Naturally occurring HMOs enhance the GI epithelial barrier function; however, the prebiotic oligosaccharides added to formula are structurally different and may not provide the same protection.12 Proteins, such as secretory IgA and lactoferrin, fight off pathogenic bacteria and promote a healthy GI microbiome. Lipids and fats are additional maternal factors that are the main source of energy for the newborn and the infant.1

Micronutrients in breast milk are vitamins and minerals. The most common vitamins are A, B1, B2, B6, B12, and D. These vitamins aid the newborn in the development of healthy vision, the central nervous system, cells, bones, and teeth.13 A diet low in vitamins is associated with lower intelligence quotient scores, reduced school success, and behavioral problems.13 Essential minerals found in breast milk include iron, zinc, selenium, copper, iodine, calcium, magnesium, phosphorus, potassium, and sodium.14,15 Iron deficiency in the prenatal and early infancy period is associated with long-term neurobehavioral damage that may be irreversible.13 The role of these micronutrients is to promote brain and bone development and hormonal regulation in the newborn.

Bacteria are a key component of breast milk.2,5,6,13 Breast milk bacteria play an active role in the colonizing of the newborn GI tract and establishing the GI microbiome. Bacteria such as Lactobacillus, Staphylococcus, Streptococcus, Enterococcus, and Bifidobacteria are healthy, commensal bacteria found in breast milk, and these same bacteria have been identified in the newborn GI microbiome.6

The composition of breast milk is complex and diverse. Breast milk provides essential nutrients and bacteria for the newborn to grow and develop. It also supports the establishment of a stable GI microbiome. Breast milk composition changes over time to maximize the nutrient and bacterial needs of the growing infant to support the continued development of the GI microbiome. This change in breast milk naturally occurs on the basis of the developmental needs of the newborn.5 As the newborn grows and the microbiome becomes established, different bacteria become more abundant to further develop the newborn GI microbiome. Breast milk contains prebiotics (HMOs) and probiotics (immunoglobulins) that promote an intact GI mucosa. The presence of HMOs, which are naturally found in breast milk, promotes the growth of Bifidobacteria. As a specific example of the role of commensal bacteria, Bifidobacteria modulates the intestinal mucosal barrier, which is the first line of defense against pathogens.12Bifidobacteria promotes immunologic and inflammatory responses to decrease vulnerability to infectious agents and optimize the health of the newborn.12

Newborn GI microbiome

The newborn GI microbiome is dynamic and complex, and breastfeeding supports the colonization of the newborn GI microbiome. The key function of the GI microbiome is to be protective, promote healthy homeostasis, and support immunologic functions. The newborn GI microbiome changes over time, and the GI microbiome differs from childhood to adulthood. After birth, various external exposures can alter the newborn GI microbiome. These exposures can positively or negatively impact bacterial diversity and abundance.

Bacteria enter and colonize the newborn GI system by a variety of mechanisms. Bacterial transference occurs through placental transmission and the swallowing of amniotic fluid in utero, during the birth process, and in breastfeeding.5,16–18 Bacterial differences are observed by the birth route. Commonly, newborns born vaginally are colonized with Enterobacteriaceae, staphylococci, and Escherichia coli (E coli).11 After a few days, these newborns will have increased anaerobic bacteria such as Bifidobacteria, Bacteroides, Lactobacillus, and Prevotella, and many of these bacteria resemble maternal vaginal flora.19 Newborns born by cesarean birth have a GI microbiome that contains Staphylococcus and Corynebacterium, which is similar to maternal skin bacteria.19 The GI microbiome of breastfed infants differs from that of formula-fed (FF) infants and will be described in detail later. Primarily, vaginally born and breastfed infants have increased commensal bacteria that promote infant health and prevent pathogenic bacteria from proliferating and contributing to negative health outcomes. Healthcare practices that influence breastfeeding can be moderated and mediated to promote the development of commensal bacteria within the newborn GI microbiome.


Understanding the role that breastfeeding plays in the development of the newborn GI microbiome, healthcare providers can also consider the impact of breastfeeding practices on bacterial development. Of particular interest, the effects of infant feeding type, skin-to-skin care, rooming-in, and pacifier use will be addressed concerning their uses in breastfeeding establishment and microbiome development. These 4 healthcare practices are elements of the Baby-Friendly Hospital Initiative, which was developed by the World Health Organization and United Nations Children's Fund, to promote early initiation and continuation of breastfeeding worldwide.20,21 This initiative was used as a proven, evidence-based backdrop for understanding the impact of healthcare practices surrounding breastfeeding on newborn GI microbiome development.20–22

Type of infant feeding

Infant feeding patterns and diet composition are recognized as pivotal factors in the healthy development of the newborn GI microbiome, and breastfeeding is recognized as the best practice for the healthy establishment of the newborn GI microbiome.23 Breast milk is colonized with bacteria to help seed the newborn's GI tract.10 Bacteria in breast milk change over time on the basis of gestational age, maternal health factors, and as a response to the newborn's needs.10 Breastfed newborns have a different GI microbiome composition than their FF peers. Bifidobacterium and Bacteroides are the predominant bacteria in the breastfed newborn GI microbiome.23 Breast milk HMOs stimulate the growth of Bifidobacterium and Bacteroides. Bifidobacteria protects against the colonization of pathogenic bacteria and provides immune and inflammatory support by enhancing the newborn GI mucosa.10 Because of the prebiotic influence of the HMOs and the probiotic influence of the breast milk bacteria, breastfed newborns demonstrate a more stable GI microbiome than FF newborns.10

Formula feeding alters the newborn GI microbiome development and may be associated with negative health outcomes. Significant microbiome differences were seen by 3 to 4 months of life in FF compared with their breastfed counterparts.24 These differences were seen with any supplementation and there appeared to be a dose response with infants receiving any formula. Formula-fed infant microbiomes have a lower relative abundance of Bifidobacteria and a higher abundance of Enterobacteria at 3 and 4 months when compared with exclusively breastfed infants.24 Formula feeding leads to higher biodiversity in the infant GI microbiome, and the increased presence of potential pathogens, such as E coli and Clostridium. Clostridium has been indicated in the development of atopic disorders such as asthma, allergies, and eczema.23 Formula supplementation can alter the GI microbiome and can interfere with the supply-demand chain of breast milk production. Because of these effects, breast milk expression and supplementation may be more beneficial.22 Whenever formula supplementation is necessary, encouraging the mother to express breast milk can stimulate milk supply.22

Breast milk bacteria are different between feeding at the breast and feeding expressed breast milk.5 Newborn oral bacteria affect breast milk composition through a reciprocal relationship where the newborn's oral bacteria influence the breast milk microbiome.5 The breast milk expression process involves the physical expression, storage, and warming of the breast milk for feeding. During this process, the composition of the breast milk may be damaged. Freezing degrades the immunological components of breast milk.25 Heating above normal body temperatures can damage nutrients and immunologic properties.26

Exclusive breastfeeding can have a significant and potentially lifelong effect on newborn health. Interruptions to early microbiome development are associated with metabolic and immunologic pathologies.10 Dysbiosis, or the disruption of the newborn GI microbiome, has been implicated in disorders such as asthma, allergies, eczema, celiac disease, autoimmune disorders, and hypertension.10,13 Even brief exposure to formula during the neonatal period can alter or contribute to dysbiosis of the newborn GI microbiome and increase the risk of being overweight or developing atopic disorders.10,23,24 Increasing exclusive breastfeeding for 6 months and continuing breastfeeding for 1 to 2 years by 10% could reduce the incidence of childhood disorders such as asthma, leukemia, type 1 diabetes, childhood obesity, otitis media, diarrhea, necrotizing enterocolitis, and pneumonia.27 This reduction in childhood disorders could translate into healthcare savings of at least $312 million in the United States.27

Skin-to-skin care

Skin-to-skin care and early initiation of breastfeeding both help establish the newborn GI microbiome.22 Skin-to-skin care involves placing the undressed newborn on the bare chest of the mother as soon as both are medically stable for at least 1 hour or until the first successful breastfeeding event.22 Through skin-to-skin contact, infant stress can be reduced, establishment of breastfeeding can begin, microbial transfer from mother-to-infant can occur through breastfeeding and skin contact, and the healthy development of the newborn GI microbiome can be protected.

Skin-to-skin care has many benefits including demonstrated reductions in newborn stress, improved thermoregulation, less crying time, and lower incidence of hypoglycemia.28–30 Higher levels of infant stress have demonstrated increased intestinal permeability.31 This stress-related increased permeability can result in dysbiosis of the microbiome; however, prebiotic HMOs and the probiotic Bifidobacteria can reinforce this mucosal layer and help preserve GI mucosal integrity.11,12 Breast milk enhances the mucosal integrity and skin-to-skin contact reduces the incidence of intestinal permeability and together they encourage commensal newborn GI microbiome development.

Skin-to-skin contact also promotes initiating the first breastfeeding within the first hour after birth.22 When mothers feel successful with early breastfeeding, they are more likely to continue, which can impact the length of exclusivity of breastfeeding.28 In addition, the release of oxytocin through skin-to-skin contact and breastfeeding may enhance the mother's ability and drive to breastfeed.28

Concerning microbial transfer from mother to newborn, consider the effect of skin-to-skin contact on vaginally born and cesarean newborns. Newborns born via cesarean delivery have a different newborn GI microbiome than newborns born vaginally. The cesarean newborn GI microbiome increases the risk for immunologic and metabolic health problems.32,33 However, through immediate skin-to-skin contact beginning in the operating room, bacteria can be passed from the mother to the newborn but at a lower frequency than that obtained through vaginal birth.33 Newborns receiving immediate skin-to-skin care in the operating room had a lower rate of neonatal intensive care admission.34 Overall, the maternal microbiome is a key shaper of the newborn GI microbiome. Newborn GI microbiome development can be affected by the mode of birth and feeding method. By initiating immediate skin-to-skin contact as soon as the newborn and the mother are medically stable, the newborn GI microbiome development can be protected through reduced infant stress, microbial skin transfer from mother to infant, and through early initiation of breastfeeding.


Rooming-in involves allowing well mothers and newborns to stay together as much as possible.22 Rooming-in allows the mother to learn the newborn's cues and how to respond.35 In addition, rooming-in promotes bonding, skin-to-skin, and the establishment of breastfeeding, which promotes overall health including microbiome health.35 In the well, term newborn, scheduled feeding is not advised, rather healthcare professionals can help the mother establish an understanding of feeding cues and respond to those feeding cues appropriately by feeding on demand.22 Rooming-in has demonstrated an increase in the proportion of newborns exclusively breastfed at day 4 of life.36 This improvement in breastfeeding during the rooming-in hospital stay can reduce the risk of hyperbilirubinemia.35 In addition, environmental exposures can impact microbiome development. Cohabitation increases the sharing of microbes and reinforces the infant receiving a microbiome more similar to the mother's.11,12 Rooming-in enhances the mother's ability to respond to the infant's needs and increases contact to promote the development of the newborn GI microbiome.

Pacifier use

Pacifiers may influence breastfeeding success and increase environmental exposures to the developing newborn GI microbiome. The research findings are mixed on the effect of pacifiers on breastfeeding success.22,36 However, the American Academy of Pediatrics supports introducing a pacifier at mother's discretion after breastfeeding is established.37

Pacifiers can also introduce environmental exposures to the newborn GI microbiome development. Since the pacifier comes into contact with other surfaces, microbes from those surfaces can be passed directly to the infant. One study has demonstrated that after parents put the pacifier in their mouth to clean it, microbes from the parental oral microbiome are transferred to the infant.11 Another study noted that pacifiers in the neonatal intensive care unit had microbial colonies more similar to the hospital surfaces and that the microbiome of the infant in the neonatal intensive care unit resembled their hospital environment.38 Pacifier use can affect breastfeeding success and introduce environmental exposures. Breastfeeding exclusivity, skin-to-skin care, rooming-in, and pacifier use affect breastfeeding rates and newborn GI microbiome development.


The newborn GI microbiome is a valuable commodity. In this article, factors influencing the newborn GI microbiome have been identified as birth practices: maternal, newborn, infant and child nutrition, and environmental factors. The newborn's future health is also highly influenced by the development of a balanced newborn GI microbiome. Newborns are considered a vulnerable population39 and incapable of self-management related to factors that influence the GI microbiome. Because of this vulnerability, and because the GI microbiome is a valuable commodity, those charged with the care of the newborn must implement strategic measures to promote breastfeeding practices and to protect the newborn GI microbiome. Strategic measures, throughout the childbearing year, will be described in this discussion.

While not every woman chooses to breastfeed, those who do need adequate support and guidance. Simply put, if breastfeeding is linked to the healthy development of the GI microbiome, healthcare professionals have a responsibility to design and implement practices that support and promote the breastfeeding dyad. Figure 2 illustrates the relationship between healthcare provider influences on breastfeeding and the development of the newborn GI microbiome.

Figure 2.
Figure 2.:
Newborns, breastfeeding, and the GI microbiome. GI indicates gastrointestinal. This figure is available in color online (

Professional healthcare organizations support the initiation of breastfeeding within the first hour of life, exclusive breastfeeding for 6 months, and continuation of breastfeeding for 12 months.40–43 These standards provide the basis for breastfeeding care practices implemented by healthcare providers throughout the antepartum, intrapartum, postpartum, and community setting, and will facilitate homeostasis of the newborn GI microbiome.

The American College of Obstetricians and Gynecologists, the American Academy of Pediatrics, the American Academy of Family Physicians, the National Association of Pediatric Nurse Practitioners, and the United States Surgeon General recommend that providers of perinatal care obtain and implement the skill of breastfeeding anticipatory guidance and support for all childbearing women, especially those who choose to breastfeed.40,41,44–47 Anticipatory guidance minimizes barriers and assists in facilitating breastfeeding through education about the benefits of breastfeeding; education about the mechanics of breastfeeding to minimize complications; and assisting the mother to structure professional, peer, and familial support during breastfeeding.44,47

Higher maternal breastfeeding self-efficacy contributes to breastfeeding initiation, increased breastfeeding duration, and positive breastfeeding outcomes.42,44,48 Maternal breastfeeding self-efficacy is a woman's belief and perceived confidence in the ability to breastfeed and manage breastfeeding difficulties and complications from birth until a self-determined time in the life of the child.44 Therefore, anticipatory guidance and breastfeeding support for women will contribute to maternal self-efficacy and are essential tasks for providers of perinatal care.

Breastfeeding strategies in the antepartum period to increase maternal breastfeeding self-efficacy would include emotional support by listening to maternal concerns and providing encouragement when concerns are identified. Prior to birth, healthcare professionals can provide education to facilitate the development of breastfeeding skills such as positioning, latching, and recognizing infant cues. As mothers understand strategies, other than breastfeeding, to calm the infant, complications associated with breastfeeding can be minimized.44,48,49 Improving maternal self-efficacy, in turn, benefits the newborn GI microbiome. One example of this is maternal teaching that a full latch will produce the best composition of breast milk to enhance newborn nutrition.7 When mother and infant are supported to have a full, appropriate latch, the macronutrients, micronutrients, and bacteria in breast milk adapt to the infant's needs.5

In the intrapartum period, practices that are associated with successful breastfeeding include skin-to-skin care immediately after birth.50 Healthcare professionals in hospital setting can design workflow processes in the intrapartum setting to facilitate skin-to-skin care for vaginal and cesarean births. Evidenced-based policies for skin-to-skin care will standardize care that promotes breastfeeding and in turn the newborn skin and GI microbiome.20–22

Postpartum policies to improve breastfeeding success and promote the newborn GI microbiome include the practices of rooming-in22 and avoiding pacifiers.40,47 The American Academy of Pediatrics recommends introducing a pacifier after breastfeeding is well-established, usually 3 to 4 weeks of age.40 Rooming-in promotes the bond between mother and infant and provides mother the best opportunity to identify feeding cues. Policies to support rooming-in and avoiding pacifiers promote the newborn GI microbiome by avoiding potentially harmful environmental bacteria and at the same time promoting successful breastfeeding.

Healthcare providers in the community setting can continue to support the breastfeeding dyad through promoting healthy maternal and newborn/infant/child nutrition. The first 1000 days of life are critical to the neurologic development of a child.13 Breast milk is known to provide beneficial microbial communities that promote the GI microbiome of the newborn, infant, and child and contributes to neurobehavioral development.13 Also, the introduction of solid foods to the infant before 4 months of age may increase the risk of obesity.13 Protecting the newborn GI microbiome through breastfeeding duration and exclusivity may be a protective factor against adverse neurobehavioral outcomes and obesity.13 Therefore, healthcare providers in pediatric and primary care settings can provide education to families about extending breastfeeding and delaying solid foods until after 4 months of age.

Effective practice strategies to support breastfeeding and the newborn GI microbiome are facilitated by improved healthcare provider education and sound quality improvement and research findings. Formal academic settings for all healthcare providers can revise curriculum to include content identifying breastfeeding as a key method of establishing, promoting, and protecting the newborn GI microbiome. Leaders in the healthcare setting can provide continuing education about practical methods of promoting newborn GI microbiome homeostasis through effective breastfeeding. Healthcare providers can develop quality improvement projects to assess the implementation of policies relating to breastfeeding initiation, exclusivity, skin-to-skin care, rooming-in, and avoiding pacifiers regarding their effect on the newborn GI microbiome.21 Healthcare leaders can facilitate the development of research studies to inform the connection between breastfeeding and the development of the newborn GI microbiome. For example, a cohort study to compare the newborn GI microbiome of breastfed infants with formula-fed infants throughout the first year of life would provide valuable information about the development of the newborn microbiome. Additional studies might also include longer-term GI microbiome effects and their related health outcomes.


The provision of breastfeeding support and resources will assist in removing barriers, decreasing complications, and increasing the longevity of the breastfeeding relationship. In turn, these interventions promote the newborn GI microbiome. Promoting homeostasis and protection of the newborn GI microbiome may be one of the least described benefits of breastfeeding that contributes to the long-term health of the newborn.


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breastfeeding; microbiome; newborn

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