Microbiome and the effect on a baby’s immune system for life

One of the most exciting areas of research at the moment is on the microbiome!

The human body consists of trillions of human cells as well as trillions of microorganisms. These microorganisms living in and on us include bacteria, fungi, viruses, protozoa, archaea as well as other microbes. These all make up the human biome.

There are about

  • 1 000 species of microbes in our intestines
  • 700 in the mouth
  • 300 – 400 in the vagina
  • 700 on the skin


The trillions of microbes in and on us are essential for human health. The role of bacteria within human health –

  • They help with human digestion
  • They help with metabolism
  • They manufacture vitamins
  • They produce neurochemicals
  • They interact with our hormones
  • They interact with our nervous system
  • They have anti-infective properties

They are integral to our immune system!

Microbes keep our body functioning. Humans give microbes a home and habitat. Human cells + microbes give us a human superorganism. These days we carry fewer microbes than humans have ever before. We have lost 25-40% of our diversity of our microorganisms. But it is this diversity of organisms that protects us. Changes in our microbes lead to obesity, asthma, allergies, immune related disorders, IBS, coeliac disease, some cancers, Parkinsons, MS and even depression. The incidence of coeliac disease has gone up 4 fold since 1950, Autism has gone up 4 fold since 1950, and the obesity national average in 1989 of 14%, has risen to 30%. Organisms are disappearing due to antibacterial substances, the use of antibiotics, a diet of processed foods and the increased caesarean section rate. Prof Martin Blazer – says the “Missing microbes or the disappearing microbiota hypothesis is that our ancient microbiome which protected us against many diseases is degrading, and with that degradation these diseases are being fuelled”.

A persons microbiome is unique as a fingerprint!

To safeguard our health – we need to start looking after our microbes throughout life, but especially through pregnancy and infancy. Microbiome friendly foods include high fibre foods, fermented foods like yogurt, kefir, sauerkraut and kimchi and organic meat. Avoiding processed foods is also important.

A microbiome friendly diet and lifestyle is even important for conception. We need to have Lactobacilli living in a healthy vagina. If there are no lactobacilli, no conception will take place.


What else can we do to safeguard our microbiome and keep it diverse and healthy?

  • Avoid unnecessary antibiotics
  • Benefits of probiotic/prebiotic supplementation
  • Be selective with antibacterial products – we do not want to kill all microorganisms. Only a select few of disease causing ones.
  • Moderate exercise
  • Exposure to natural world

Research shows that there are benefits of having a dog, on the microbiome of children. Early-life exposure to household pets has the capacity to alter risk for overweight and allergic diseases in children, both of which are linked to changes in gut microbiota of infants.


Microbiome and pregnancy

The microbes found in a baby are the same as the microbes found in mother’s gut. We need the microbes there to pass them to the next generation and keep them healthy.

So what does the mother pass on to her baby – the maternal heritage?

Mothers vaginal microbes + Mothers gut microbes + Mothers skin microbes + Mothers

breast milk microbes are all passed to this baby during labour, birth, skin to skin contact and breastfeeding. This occurs only with a natural birth and breastfeeding. In this instance Mother’s microbiome = baby’s microbiome.

Evidence is accumulating on the importance of the prenatal period in determining risk for obesity in childhood and for its role in the establishment and development of the gut microbiome

During pregnancy, the mother’s vaginal microbiota changes and has less diversity of species of bacteria. There is an increase in Lactobacilli (Lactic acid bacteria). This maintains a low pH which limits the bacteria able to live in the vagina. This prevents the pathogens (disease causing microorganisms) from being in the vagina. And so is preparing for birth and breastfeeding. There is also an increase in high energy yielding microbes which supports the growth of mom and foetus during pregnancy as well as giving the newborn high energy yielding microbes at birth which gives baby an energy boost after birth.


Recent research indicates a foetus could be exposed to a small number of bacteria whilst in the womb

  • From amniotic fluid
  • From umbilical cord blood
  • From foetal membranes
  • From the placenta

The vaginal microbiome seeds the baby. During the birth process, the amniotic sac ruptures, and suddenly baby is exposed to a huge load of mother’s vaginal bacteria in the birth canal. The bacteria enter baby’s skin, eyes, ears, nose and mouth. Some bacteria are swallowed. These bacteria are rich in Lactobicillus

As the membranes rupture, bacteria start coming in. And as the baby starts going out, through the birth canal, the baby is acquiring the other bacteria from the vagina. The baby is covered with the bacteria. That is the baby’s first introduction to the world of bacteria, the world we all live in. This is the moment! When the waters break, this marks the start of the main seeding event for founding the infant microbiome. The mother is providing for the baby a natural culture that will naturally inoculate the baby. This is nature in action! Then the birth itself…. Human anatomy means that the baby is likely to come into contact with the mother’s gut microbes during birth (from contact with the mother’s poo). Humans are designed in this way. POO = a good thing! Contact with the mother’s faecal matter transfers key species of bacteria to the baby – one in particular is the Bifidobacterium longum infantis. This is described as the champion coloniser of the infant gut. It quickly colonisers baby ‘s gut (which happen to be fed by special sugars in breast milk…!)


As soon as baby is born, the baby acquires more bacteria

  • From contact with mothers faecal matter
  • From the air
  • From every touch
  • From the mother’s kiss
  • From skin to skin contact
  • (a baby explores with its mouth!!)

Every baby will acquire a different set of microbes.

These micrbiota train the immune system. Baby is born with an immature immune system. The immune system has to learn to tolerate good organisms and has to learn what is friend and what is foe. If this isn’t set up correctly, the baby’s immune system starts to recognise everything environmental as bad. The bacteria in the baby’s gut help train the infant immune system to identify what is friend (to be tolerated) and what is foe (to be attacked). For optimal immune training, the bacteria should arrive in the right order and arrive at the right time. ie in the order of mom’s vaginal microbes as baby passes through the vagina, then mom’s gut microbes (from some poo she passes during the pushing stage of labour), some of mom’s skin microbes when baby is placed skin to skin on mom’s chest and he licks this new environment to explore it, and then goes on to receive some microbes in the breast milk. This optimal immune training gives baby the best possible lifelong health!

The microbiome continues to develop through infancy as the baby grows and develops – whatever the baby touches he puts into his mouth, the baby will acquire more microbes, which all helps with immune training. The microbiome is thought to stabilise between the age of 1 to 3 years.

There is only one chance for immune training, it is a narrow window, and if this doesn’t happen then the immune system will be out of balance, immature and responding haphazardly, potentially for the rest of its life.


Microbiome and caesarean section

Caesars save lives! However, caesars are an abused practice being done when they are not medically indicated. The experience and consequences for the baby is that it is NOT the same for the baby.


How could a caesar impact the infant microbiome?

  • Baby is extracted from mother’s abdomen (rather than emerging from the mother’s vagina)
  • Baby does not pass through the vagina (birth canal) and hence baby will not acquire the “full set” of the mother’s vaginal microbes
  • Baby will not acquire mother’s gut microbes as there won’t be any contact with

her faecal matter

  • Mom is likely to receive a course of IV antibiotics to prevent infection from major surgery. Antibiotics will impact the mother’s skin microbiome, and microbes in her breast milk, which in turn will impact the baby’s microbiome
  • Baby could be exposed to pathogens in theatre.

If it is a caesar with labour, and the amniotic membranes have ruptured prior to surgery, then the baby might still receive some exposure to the mother’s vaginal microbes whilst in the birth canal. Babies born by caesar have an altered microbiome. A vaginal birth baby has mostly anaerobic bacteria such as Lactobacillus and Bifidobacteria….. However, a caesar baby gets more kinds of streptococcus, staphylococcus and bacteria that are aerobic bacteria.


Early microbial exposures associated with caesars could impact baby’s immune training

  • Baby’s microbiome is only founded once, so there is only one chance for optimal immune training
  • Baby’s gut microbes help train the infant immune system, so for optimal immune training, the right gut microbes need to be present in baby’s gut in the narrow window that surrounds birth
  • If you miss this narrow window, there is no second chance
  • Exclusive breastfeeding, good diet and microbiome friendly lifestyle could go some way to help, but not alleviate the problem.


Something else could be impacted by caesars and that is the epigenetic changes during childbirth

  • Epigenetics is the study of changes occurring above the gene
  • Environmental triggers switch genes on or off
  • The hypothesis is that stresses, pressures and hormone releases associated with vaginal birth are environmental triggers that produce epigenetic changes for best lifelong health
  • With a caesar, baby might not be exposed to the same stresses, pressures and hormone releases, so there might be different epigenetic changes.


Babies born by caesar are at increased risk of immune and metabolic disorders. There is

  • Approximately a 20% increased risk of baby developing asthma if he is born by caesarean
  • Approximately a 20% increased risk of developing type 1 diabetes
  • Approximately a 20% increased risk of becoming obese
  • Approximately a 15% increased risk of coeliac disease

What can be done at the time of a caesar to make a difference to the baby’s microbiome correct formation? The use of the Gentle Caesar technique whereby the IV therapy line can be put in mom’s non-dominant hand and the screen lowered at the time of birth. Baby is delivered straight on to mom’s chest with immediate skin to skin contact with her. Support for exclusive breastfeeding as well as the use of evidence based probiotics.

There is fascinating research being done on “Swab seeding”. The preliminary results are showing amazing differences to the baby, if the baby is swab seeded immediately after a caesar. Mom must be HIV free and test negative for Group B Strep. A sterile gauze swab – 8cm x 8cm is wet in sterile saline, folded and fanned out and placed in the mom’s vagina for 60 minutes prior to the caesar. It is fanned out to give maximum exposure of the swab to mom’s vaginal fluid. Just before surgery, the swab is removed and placed in a sterile container. Once baby is born this swab is wiped over baby’s face, mouth and body. And so baby receives mom’s vaginal microbes! It has been found that the babies that were seeded by swab from mom’s vagina, although they were born by caesar, they look more similar to vaginally delivered babies than to caesar delivered babies, which suggests partial restoration of the baby’s microbiome. However, the baby will have no exposure to mom’s gut microbes (the bifidobacteria).


Differences that may be helpful later in life are from

  • Exclusive breastfeeding
  • Evidence based probiotics
  • Microbiome friendly diet once weaned
    • Plenty of fruit and veg
    • Fermented foods and high fibre foods
    • Avoiding processed foods
  • Microbiome friendly lifestyle
    • Avoid unnecessary antibiotics
    • Sensible approach to antibacterial products
    • Exposure to pets and nature

So, a baby born by caesar – has NO mother’s vaginal and gut microbes + mother is given IV antibiotics which leads to an altered microbiome at birth. There is also NO exposure to stressors, pressure and hormones of vaginal birth. NO mother’s vaginal and gut microbes. So, the immune system is not optimally trained, resulting in an increased risk of lifelong health problems for baby!

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