The Infants Microbiome and Its Impact on Health
Written By Microbiome Plus+

The Infants Microbiome and Its Impact on Health

Older scientists used to believe that the gut is sterile until birth. However, today’s research contradicts this former belief showing that bacteria colonize the baby’s gut while it is still in the mother’s womb. Where do these bacteria come from? These microbes probably reach the baby’s gut when it swallows the fluid (called amniotic fluid) present in the bag of waters. Moreover, the skin of the baby is coated with a waxy substance that is shed into the bag of waters. This waxy coating also acts as a rich medium to fuel the growth of gut bacteria in the “womb baby.” [2] In fact, this waxy coating may also help keep life-threatening GI infections like necrotizing enterocolitis (as occurs in premature babies) at bay. Also, the early green stool of the fetus called meconium serves as a source of gut bacteria in the “womb baby.” [1]

Is early bacterial dwelling of the gut vital to a baby’s and child’s health? What are the factors that influence a baby’s gut microbiome and how do they contribute to health or disease? Let’s delve deeper into the answers.

Caesarean delivery alters the Gut Microbial Composition in early life

During vaginal birth, the newly born baby acquires most of the friendly bugs from the mother’s birth canal. In contrast, C-section deprives the baby of the beneficial microbes that reside in a mother’s vaginal canal. [2] These babies instead pick up bad bacteria from the mother’s skin and mouth, and also from the hospital environment. This transfer of unhealthy bugs in the newborn compromises the immune system, which may drive early gut and non-gut problems in such babies. [1] [3]

A study conducted by the Massachusetts experts showed reduced levels of friendly bacteria in caesarean‐delivered infants. [2]

Breast milk also shapes an Infant’s Microbiome

After birth, more healthy bugs reach the gut via the breast milk. The breast milk, in particular, colostrum, also contains prebiotics to promote the growth of helpful gut bacteria. These gut microbes then develop into mature colonies—and together with their genetic makeup—are referred to as “the microbiome.” They perform an awesome job of shaping an infant’s intestinal health, beginning from the initial years of life and beyond. They boost the digestion and metabolism of food, stimulate the immune system, and facilitate the production of brain chemicals that impact a child’s behavioral and mental function. [3]

Breastfed infants also have a lower risk of necrotizing enterocolitis (NEC). On the contrary, the gut of formula-fed infants harbors more of the unhealthy bugs that cause a number of health problems in later life. [4]

Antibiotic Usage disrupts the gut balance

Another key factor that impacts a child’s microbiome is the use of antibiotics by the mother while the baby is still in the uterus and/or by the child during the early years after birth. As is known, antibiotics disrupt the bacterial economy. In a study published in a pediatric journal, the researchers discovered that children who were exposed to antibiotics at a younger age displayed a stronger vulnerability to inflammatory bowel disease. [5]

Also noted is the increased risk of obesity and compromised immunity in children exposed to antibiotics during the early years of life.

Prematurely delivered infants are prone to imbalance of the gut microbial composition

An important factor that also emphasizes the role of a healthy gut microbiome in infants is the alteration of the gut ecosystem in babies who are born before time. To name a few, these infants are at risk of NEC, sepsis, mental and cognitive disturbances, and attention deficit hyperactivity disorder. The abundance of harmful bugs may account for these complications in preterm babies. But it’s not clear yet if altered gut microbiome or the prematurity per se is responsible for these events. [6]

Diet also shapes the Gut Microbiome

Most parents introduce solid (non‐milk) foods to infants by 6 months of age. Home‐made foods such as non‐digestible carbohydrates, proteins and fibers, primarily fruits and vegetables have a predominant positive effect on the bacterial gut balance. These healthy dietary patterns lower the risk of food allergy in contrast to the processed foods that switch the bacterial balance from good to bad and promote allergies. [7]

Environmental factors can modify a child’s Gut Microbiome

Environmental factors, including where a child was born, family size, and exposure to pets, are also thought to alter the gut microbiome in early years. For instance, infants with older siblings have higher counts of friendly gut bacteria when compared to children without elder siblings. These infants may also have strong defense systems against viruses and allergies like eczema. Similarly, infants living with furred pets like dogs may have higher levels of friendly bugs in the gut. [8] [9]


Several factors affect a child’s microbiome. A know-how of which factors are beneficial and which are harmful can help you manage your child’s health in a more meticulous way.


  1. Rodríguez JM, Murphy K, Stanton C, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microbial Ecology in Health and Disease. 2015;26:10.3402/mehd.v26.26050. doi:10.3402/mehd.v26.26050.
  2. Houghteling PD, Walker WA. Why is initial bacterial colonization of the intestine important to the infant’s and child’s health? Journal of pediatric gastroenterology and nutrition. 2015;60(3):294-307. doi:10.1097/MPG.0000000000000597.
  3. Mueller N, Bakacs E, Combellick J, Grigoryan Z, Dominguez‐Bello M. The infant microbiome development: Mom matters. Trends Mol. Med. 2015; 21: 109–17.
  4. Neu J. The Microbiome and Its Impact on Disease in the Preterm Patient. Current pediatrics reports. 2013;1(4):215-221. doi:10.1007/s40124-013-0031-7
  5. Kronman MP, Zaoutis TE, Haynes K, Feng R, Coffin SE. Antibiotic Exposure and IBD Development Among Children: A Population-Based Cohort Study. Pediatrics. 2012;130(4):e794-e803. doi:10.1542/peds.2011-3886.
  6. Lee YY, Hassan SA, Ismail IH et al. Gut microbiota in early life and its influence on health and disease: A position paper by the Malaysian Working Group on Gastrointestinal Health. J Paediatr Child Health. 2017;53(12):1152-1158. doi: 10.1111/jpc.13640.
  7. Grimshaw KE, Maskell J, Oliver EM et al. Diet and food allergy development during infancy: birth cohort study findings using prospective food diary data. J Allergy Clin Immunol. 2014;133(2):511-9. doi: 10.1016/j.jaci.2013.05.035.
  8. Neu J. The Microbiome and Its Impact on Disease in the Preterm Patient. Current pediatrics reports. 2013;1(4):215-221. doi:10.1007/s40124-013-0031-7.
  9. Laursen MF, Zachariassen G, Bahl MI, et al. Having older siblings is associated with gut microbiota development during early childhood. BMC Microbiology. 2015;15:154. doi:10.1186/s12866-015-0477-6.
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