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Breastfeeding Helps Seed Infant Gut Microbiota

by Bianca Garilli, ND

Within the first few hours of birth, bacteria are introduced to the infant gut through multiple vectors including maternal skin and vaginal exposure, breast milk, and the external environment. These initial exposures leave a life-long bacterial footprint that can be detected into adulthood.  The importance of early gut imprinting on long term health is substantial and has been well documented.  It includes protection against respiratory and gastrointestinal tract infections, a reduction of atopic disease incidence, and is a protective factor for leukemia, celiac disease, diabetes, obesity and inflammatory bowel disease (IBD). Breastfeeding also has been shown to have a positive impact on improving newborn neurodevelopment, decreasing risk of sudden infant death syndrome and reducing overall infant mortality.1,2 A prospective study published in JAMA Pediatrics by Pannaraj et al investigated the vertical transfer of bacteria from maternal breast milk and areolar skin to the infant gut and looked at factors that influence changes in the infant gut microbiome over the first year of life.

Key Points

Fluctuations in infant gut microbiome composition

As Pannaraj notes, various factors impact the initial seeding of, and subsequent shifts in, the infant microbiome over the first 12 months of life; the most influential being the age of the infant, breast milk versus formula feeding, timing of formula introduction, and timing of solid food introduction.2Results from Pannaraj’s study of 228 healthy mothers and babies from 121 families, found that the microbiome composition differed amongst the infants depending on the source and duration of the infant’s initial exposures which may come from a variety of sources including contact with microbes from the mother’s skin and birth canal, the external environment and, most importantly, exposure to microbes from breastfeeding.  Infants primarily breastfed (defined as breast feeding more than 75% of the time) during the first 30 days of life were found to receive a mean of 27.7% of their bacteria from breast milk and 10.4% from areolar skin, making up nearly 40% of the total infant gut bacteria.In all primarily breastfed infants up to one year of age, 18.5% of the microbial community was derived from breast milk and 5.2% from areolar bacteria compared with only 5.7% of the bacteria from breast milk and less than 0.001% from areolar skin in the infants who were breast fed less than 75% of the time.

Effects of solid food introduction

Evidence indicates that maturation from infant to adult pattern microbiome usually occurs upon reduction and cessation of breast feeding and with the introduction of solid food.  Data from the Pannaraj study indicates that solid food introduction prior to four months of age precipitates an earlier maturation of the toddler’s gut microbiome.  It was further found that the primarily breast fed infants had lower levels of genes associated with bacteria involved in energy metabolism, sphingolipid metabolism and glycan biosynthesis and metabolism while infants with earlier solid food introduction deviated towards a microbiome profile favoring increased function related to xenobiotic biodegradation and metabolism.  Although the exact significance of these findings is still unclear, particularly on how the timing of microbiome maturation may affect childhood and adult health, reviewing findings from several other studies may help to add additional perspective.

These findings include3

  • The microbiome of infants follows a natural progression of maturation
    • The early microbiome is composed of bacteria which facilitate lactate utilization and are replaced by anaerobic organisms upon solid food introduction
    • These anaerobic bacteria play a role in the metabolism of the newly introduced solid food
  • This maturation process is thought to “educate” the immature immune system and program the metabolic system setting the stage for future health

Early introduction of solid foods accelerates the maturation process of the gut microbiome by theoretically cutting down on the time that the immune and metabolic systems have to “learn” appropriate processes for supporting life-long health.2  However, this theory remains controversial.

Information on the timing of solid food introduction and subsequent effect on future health outcomes can be found in a Cochrane Review.4 The 2016 review did not find any health benefits, or risks, associated with solid food introduction between the ages of 4-6 months nor did they find any evidence to disagree with current international health recommendations to exclusively breast feed for the first 6 months of life.  However, it should also be noted that the Cochrane Review did not study the diversity of the microbiome but rather the outcomes of the various timings of solid food introduction on the subjects’ health. Further research should be conducted to elucidate risks or benefits associated with early solid food introduction and life-long health outcomes related to the characteristics of the infant gut microbiome maturation shift.

Why is this Clinically Relevant? 

  • The infant gut microbiome footprint can be detected into adulthood and this initial seeding influences childhood and adult health
  • Evidence continues to support the central role of breastfeeding in the seeding of the infant gut microbiome
  • In infants breast fed at least 75% of the time, the infant gut microbiome receives up to 40% of its bacteria from maternal breast milk and areolar skin
  • Infant gut microbiome shifts towards a mature state with solid food introduction and reduction of breast milk exposure

View the abstract


  1. Brahm P, Valdes V. The benefits of breastfeeding and associated risks of replacement with baby formula. Rev Chil Pediatr. 2017;88(1):7-14.
  2. Pannaraj P et al. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome. JAMA Pediatr. 2017;171(7):647-654.
  3. Mueller N et al. The infant microbiome development: mom matters. Trends Mol Med. 2015;21(2):109–117.
  4. Smith HA, Becker GE.  Early additional food and fluids for healthy breastfed full-term infants. Cochrane Database Syst Rev. 2016;(8):CD006462.

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