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Mom, Baby & Microbiome


We are familiar with the terms bacteria, fungi and viruses but microbiome is the new name on the block. But what is it, and why do we all need to be aware of it, particularly if trying for a baby, are pregnant, or have recently been pregnant?


The microbiome is:


Made up of trillions of bacteria, viruses and fungi living predominantly in our gut but also on our skin and in many other parts of the body, including the reproductive tract

Very individual to a person in the same way that a fingerprint is

Different microbes inhabit different parts of the body and have their own specific functions

The microbiome is responsible for the following functions:


Breaking down food

Producing and absorbing essential nutrients

Regulating hormones

Supporting our immune development

This all suggests how important the microbiome is to our health and wellbeing. It forms our first line of defence against germs that could make us ill and can offer some protection against more serious diseases, including cancer, diabetes, colitis and obesity.


What impacts the development of the microbiome?

The microbiome is dynamic and can be altered by our lifestyle choices.


Approximately 60-70% of our individual microbiome composition remains stable throughout our lifetime

The remaining 30-40% may be significantly affected by the following:

Our diet

Our lifestyle

Medication, in particular antibiotics

The most effective way to influence our microbiome is through diet.


There is extensive research being carried out across the world about the microbiome. Studies have shown that the first 2-3 years of our lives are the most critical for microbiome development and that the process actually starts during pregnancy.


How to aid the development of your baby's microbiome

Pregnancy is a time of significant change to hormones, the immune system and metabolism, all of which can alter or be altered by gut microbiomes.


During the pre-pregnancy, pregnancy and postnatal period, it is essential that these gut microbiomes are regulated to be able to control both mum and baby’s health.


A mom-to-be or new mom can influence her baby’s gut microbiome through her own diet. See our guides on what to eat whilst pregnant and whilst breastfeeding

Illnesses including asthma, allergies, coeliac disease and diabetes in babies and children have all been directly linked to mums with less healthy microbiomes. This is often the result of a poor antenatal diet

Some research has linked poor antenatal microbiomes to complications during pregnancy, including gestational diabetes, preeclampsia and preterm delivery

How does the microbiome transfer from mum to baby?

So, we know that a mom’s diet and lifestyle choices can affect their baby’s gut microbiome. But how does a baby’s microbiome grow?


Microbiomes begin to develop whilst still in utero. The mom’s gut microbiome passes across the placenta into the amniotic fluid. This then transfers to the baby’s gut as they swallow the fluid

During the final weeks of pregnancy, we know that some of the healthy gut microbiome migrates into breast tissue which then transfers to the baby through breast milk

Further colonisation occurs during birth, but the bacteria associated with vaginal birth and caesarean sections differ greatly



Will a C-Section impact the microbiome

The microbiomes of babies born vaginally resemble the microbiome of their mothers more than those born by C-sections

Babies born by C-section have much higher levels of Staphylococci and C-difficile, which are associated with the hospital environment and skin flora

Whereas babies born vaginally have higher levels of good gut bacteria, such as Lactobacillus and Bifidobacterium, colonised in the vagina

Seeding Babies Born via Caesarean Section

As already mentioned, babies born via C-sections have lower levels of good gut bacteria than those born vaginally.


C-section rates in the USA are over 50%, meaning a decline in gut health and general health of babies. In their later lives, asthma, allergies, and immune disorders are increasing in line with C-Section rates which in some countries are approaching 25%.


What does seeding babies mean?

Some research has looked at “seeding babies” born via C-section with vaginal fluids from their mothers to transfer the microbiomes that would replicate a vaginally born baby.


Seeding is a simple process using sterile gauze inserted into the vagina and then wiped across the baby’s face, mouth and skin following birth. This transfer of maternal vaginal bacteria is believed to improve the newborn’s gut colonisation, reducing the risk of asthma, allergies and other immune disorders.


Does seeding babies born via C-section work?

The evidence to support seeding babies is still significantly lacking. There are concerns that seeding could potentially transfer harmful vaginal pathogens such as herpes simplex.


Further studies are currently underway looking at the benefits and risks of seeding for newborns and, until then, local and national policies are unlikely to recommend it.


Probiotic supplements after C-sections

What we do know is that both mothers and babies born via Caesarean Section may benefit from a probiotic supplement to restore gut health balance. This will encourage the growth of good bacteria whilst fighting off some bad bacteria. As with all supplements, a conversation with your healthcare provider is advised.


How to improve your baby's microbiome via skin-to-skin

Immediately following the birth, skin-to-skin between mum and baby is encouraged. There are several known benefits of skin-to-skin:


Regulates mum and baby’s heart rates

Regulates baby’s temperature

Increases the production of the hormone oxytocin, which helps mum and baby bonding

Encourages babies to breastfeed

But, skin-to-skin also allows maternal skin microbes to be transferred to the baby, and the more skin-to-skin that takes place, the greater the transfer. This will help improve your baby’s microbiome diversity.


Antibiotics can affect the microbiome

Pregnant women may be offered antibiotics during pregnancy or labour because of illness. Or because the sacs of water around the baby have ruptured without labour starting, which increases the risk of infection to the unborn baby.


Recent research has highlighted concerns about the overuse of antibiotics leading to antibiotic resistance

More recently, we have discovered that antibiotic use can actually be detrimental to the quality of the microbiome. It can:

Alter metabolic activity

Reduce the diversity and composition of good bacteria

Spread antibiotic-resistant genes increasing the likelihood of more serious illnesses and long-term effects on health

Antibiotics account for approximately 25% of all prescribed medications for babies and young children. It has been suggested that around one-third of these prescriptions are unnecessary.


Research suggests this is directly linked to the increase in antibiotic resistance, the detrimental effect on the microbiome and ultimately, long-term consequences such as obesity, diabetes, allergies, asthma and other immune diseases.


Tips to improve your baby's gut microbiome

To protect your own microbiome and ensure your baby is given the best opportunity for their own health, there are some points to consider:

  • Adopt a balanced diet rich in probiotics if you are thinking of getting pregnant, are pregnant or have recently been pregnant. Consult with me on what to eat when trying to conceive

  • Avoid unnecessary antibiotics

  • Consider vaginal “seeding” if the baby is born via C-section

  • Consider a probiotic for you and your baby if you have had a C-section

  • Exclusively breastfeed for up to 6 months if possible, or consider a probiotic if artificial feeding is introduced

  • Avoid weaning your baby until 6 months of age

  • Skin-to-skin at every opportunity

  • Gentle baby skincare to protect your baby’s skin

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