The Infant Microbiome: 4 Tips To Support Baby Gut Health



What is the infant microbiome?

Our body hosts trillions of beneficial microbes, mostly bacteria, that work with the body to support overall health. These microorganisms are called the “microbiome.” The microbiome is found on the skin, in the mouth, the urogenital tract and the gut.

So far, we have the best understanding of the gut microbiome [1].

How do babies get gut bacteria?

Often, babies get gut bacteria from their birth mother. 

The environment and other members of the family can contribute to the infant microbiome. But with a vaginal birth, the first microbes to colonize your baby’s body come from their birth mother [2]. 

This first transfer of microbes at birth is often called “seeding” [3], [4].

During a vaginal birth, a baby comes in contact with the mom’s gut, vaginal, and skin microbiome. After birth, this mother-child microbial transfer can continue with breastfeeding and skin-to-skin contact. 

Close contact of the baby with other family members (and even your pet!) can also contribute to this passing of microbes.

Babies born by C-section birth pick up more skin bacteria and bacteria found in a hospital environment, in this case, the numbers of protective microbes are often affected [1], [2]. 

Your baby’s first microbes are crucial for their long-life health [2].

How good bacteria help baby gut health

Your baby’s gut microbiome helps your baby’s health by:

  • Keeping the growth of potentially pathogenic bacteria in check [1]
  • Breaking down HMOs, otherwise known as human milk oligosaccharides, which are special sugars found in breastmilk. Gut bacteria then produce short-chain fatty acids (SCFAs), which regulate gut immunity and decrease inflammation [2]
  • Supporting the growth and maturation of a baby’s gut and the immune system [5] 
  • Optimizing your baby’s brain development [1], [2]

The infant microbiome helps to teach a newborn’s immune system how to develop. It teaches how to distinguish the “self” over the environment.

Bacteria that make up the infant gut microbiome train the immune system for tolerance against bacteria that may cause problems or the host [2]. 

If your baby is colonized with an unhealthy balance of bacteria, this can increase the risk of allergies or autoimmune diseases [6], [7]

When it comes to baby brain development, it’s important to consider the gut-brain axis. 

For example, our microbiome is involved in production of [8]:

  • Neurotransmitters that impact mood
  • Short-chain fatty acids (SCFAs) that regulate the nervous system 
  • Compounds that impact immune balance
  • Hormones that balance inflammation [2]

All of which can shape mood, stress response, and behavior [9]–[13]. 

Studies have shown that gut microbiome diversity and microbial composition are associated with a baby’s cognitive development and behavior [14]–[16]. This suggests that during the first years of life, baby gut health has a unique relationship to both gut and brain development. 

The infant microbiome influences early life and development. And it may also program risk for health outcomes for adulthood [2], [17]

4 tips to support infant microbiome development

There are many things you can do to support your baby’s gut microbiome development. For example, consider:

1. Mode of delivery: If it’s an option, choose a vaginal delivery over a C-section birth. If this is not possible, try to avoid a scheduled C-section. 

Going through labor even for a short period of time before a C-section may allow the baby to come into contact with maternal microbes that would have otherwise been transferred in vaginal delivery [18].

2. Pre- and postnatal antibiotic exposure: Antibiotic use during pregnancy may reduce levels of good bacteria to be passed on to a baby [1]. After birth, antibiotic use in newborns before their first year of life has been linked to development of asthma and allergies [2], [6], [7], [17], diabetes, overweight and eczema later in life [2], [20]–[22]. 

If this sounds overwhelming, there are ways to work around the effects of antibiotic use. For example, studies have found that breastfeeding may help with the recovery of the microbiome after antibiotics

3. Diet: Diet and feeding patterns during the first years of life can impact the gut microbiome and baby development [1]. 

If it’s available to you, try to breastfeed for at least the first six months. 

If breastfeeding isn’t possible, seek out a formula that contains HMO prebiotics, which will help to support your baby’s gut health.

4. Probiotics: Probiotics are live microorganisms that can benefit health [23]. If your baby was born by C-section, has used antibiotics, has eczema or digestive troubles (which can be caused by lower levels of beneficial bacteria) you may want to consider using a probiotic specifically formulated for babies. 

Keep in mind that probiotics differ in their health benefits. The right probiotic for your baby will depend on their needs. 

If you want to check your baby’s gut health, you can test your baby’s microbiome. This test will reveal your baby gut type and give personalized recommendations based on your baby’s needs.


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