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Infant microbiome: How decisions in infancy affect health for life

Newborn infants have no microbiota. Help an infant build a healthy microbiome.

Executive Summary

When an infant is born, it has no gut bacteria. The microbial universe in its intestines gets formed, depending on the birth conditions, and its DNA.

Babies born with normal delivery are have healthier microbiome than caesarean–section born babies.

Breastfeeding helps an infant to develop healthy microbiome, and a strong immune system.

Too much focus on hygiene and excessive use of disinfectants may actually harm the gut bacteria of a baby. Let children crawl on floor and eat with dirty hands occasionally.

There are trillions of microorganisms in our intestines. They live in a symbiotic relationship with our body. These organisms manufacture nutrients, such as B–vitamins, vitamin K, and certain amino acids that help us. They, in turn, get their own nutrients from what we eat.

The microbial composition in each of our bodies, called our Microbiota, is unique. That fragile universe, the Microbiome, starts forming only after birth. It is mainly decided by our DNA, age, and food we eat.

To learn more, read this comprehensive article on this website: Microbiome: the other ‘You’.

Disturbance to this delicate balance between various species in microbiota is linked to many medical conditions. For example, digestive system disorders, auto–immune conditions, neuro–psychiatric conditions, cancer, diabetes, heart disease, and obesity.

Since there are no gut organisms present when we are born, it is important that we take certain precautions that help an infant form a healthy microbiome.

Microbiome at birth

When a baby is in the womb, there are no microorganisms in its intestines. However, during birth, the infant gets exposed to the micro–organisms, and the infant’s microbiome starts getting formed.

It seems that the organisms encountered by the baby during delivery in the birth canal take root in the intestines. The baby is exposed to bacterial species that are present in the mother’s vaginal region. That is the start.

The babies who are born with caesarean section have a completely different microbiota than the children born through normal delivery. The normal delivery microbiome is much healthier than the caesarean–section–caused microbiome.

That is a big reason to stay with normal delivery, unless there is a serious medical reason not to.

Vaginal seeding

Some hospitals perform a technique called vaginal seeding. It is used to introduce the mother’s vaginal organisms to the caesarean–section delivered baby. Discuss with your doctor, in case you are likely to have a caesarean baby.

At this time, The American College of Obstetricians and Gynecologists (ACOG) does not recommend vaginal seeding. However, the research is on–going. So keep an eye.

An article published in 2018 in the journal Frontiers in Medicine thinks that the vaginal delivery is more beneficial because caesarean section involves use of antibiotics, which are harmful for gut bacteria.

It also says that C–section babies are born at lesser gestational age (less number of weeks in mother’s womb) and many C–section women are obese and don’t manage breastfeeding properly. This results in C–section babies having worse microbiome than the normal delivery babies.

Breast–milk and breast–feeding

The act of breastfeeding confers a set of good bacteria to the intestines of the baby. The microbiomes of the babies who were fed formula milk were found to be different from those of the breast–fed babies.

And more than the breast milk, it was the breast–feeding act that affected the microbiome more, and for better. The breast–fed babies, in general, had better microbiota.

The infant is likely to face similar germs in its early life that its mother encounters. During breast–feeding, the infant may get exposed to those germs on its mother’s body. It develops immunity to them, as its microbiome gets finely tuned to handle those organisms.

That is why the act of breast–feeding itself seems to help the infant more than just the breast–milk. This was found through working women, who cannot breast–feed during work hours. So, they express breast–milk that the infant gets through other modes of delivery. Such infants are less healthy than the physically breast–fed infants.

In the American Academy of Allergy, Asthma & Immunology Conference in 2015, two studies on infant gut bacteria showed that in the babies, who were not breast-fed, the microbiomes were dominated by certain bacteria called Lachnospiraceae. The breast–fed babies, with low Lachnospiraceae bacteria, were less likely to have pet allergy than babies who were not breast-fed.

The human milk mystery

Breast milk has more than 200 types of complex sugars called Oligosaccharides. The babies cannot digest them. So in the past, a question arose as to why they were in the human breast milk in the first place.

It seems that these oligosaccharides are used as food by the microbiota in the baby’s intestine. They feed certain types of bacteria and suppress the others. The sub–species of bacteria that are fed, generate certain proteins that help to reduce inflammation and increase immunity in the babies.

Thus, breast–feeding helps the baby get organisms on mother’s body and prepare its immune system. Also, the breast–milk has ingredients that help the baby’s microbiome.

Hygiene and infant microbiome

There is a theory that says that our modern sanitary and hygienic practices of using soaps, cleansers, disinfectants, antibiotics, and cleanliness have weakened our immune response by reducing the bacterial exposure that helped us for millennia.

Anecdotally, too, we have heard that children living in poor neighbourhoods, where conditions are often unhygienic, have stronger immunity than their counterparts living in posh, sterile surroundings. They don’t fall sick as often.

The reasoning is the intestines are going to be colonised by some bacteria. If you keep a child in sterile environment, the bacteria, which would have entered and stayed in its intestines, can no more thrive there. So, in their place, some undesirable, and adventitious bacteria arrive and colonise. They are not the regular beneficial lot and may cause harm to the baby.

Perhaps, you should leave your child to crawl on the dirty floor. And, let it eat with those same hands without washing them.

As always, there is a balance to everything. Overload a small baby’s immune system with big microbial contamination, and it will fall sick. Let the baby’s immune system slowly get exposed to microbes around it, and it will become stronger.

Allergies and asthma in infants

In the American Academy of Allergy, Asthma & Immunology Conference in 2015, which was mentioned above, a study showed that the mix of gut bacteria formed during the first 6 months of an infant’s life has a profound effect its immune system, and the risk for allergies and asthma.

The study showed that the infant’s microbiome affected the development of regulatory T–cells. This reduced the allergies.

Actionable tips

  • Choose normal delivery over a C–section delivery.
    Discuss with your obstetrician.
  • Evaluate vaginal seeding option.
    Discuss with your obstetrician, if it is advisable for you.
  • Breastfeed the infant.
    The physical act of breastfeeding is important.
  • Don’t use harsh chemicals, cleansers, and disinfectants in the house.
    Don’t be too paranoid about hygiene.
  • It is OK for a child to be exposed to a bit of non–sterile environment.
    Let babies play a bit in the dirt. Let them crawl on the floor. It is OK if they eat a little bit of food with dirty hands.

First published on: 4th August, 2019

Image credit: PublicDomainPictures from Pixabay


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