What Impact does the Mode of Delivery, Breastfeeding, Formula-Feeding, Antibiotic Usage, Diet, Stress, and Age Have on the Development and Evolution of the Human Gut Microbiome?

Colonization in the birth canal

Are you ready to embark on a journey through the span of a typical human life, from the perspective of the microscopic hitchhikers in your gut? Our journey starts with childbirth – the logical starting point. Buckle up, you’re in for a wild ride!

The first 24 hours of life are crucial for the development of the gut microbiome, and the mode of delivery – vaginal or Caesarean-section – can impact the long-term health of the child.

Before childbirth, the microbiota is basically sterile. Baby’s first brush with her tiny companions has historically been through the mother’s birth canal, where, like intrepid explorers, pioneering species of bacteria begin to populate her body in a process known as colonization. The bacterial cells that are most abundant in the mother’s vagina are bacteria that produce lactic acids, called Lactobacilli. These are friendly bacteria which crowd out the bad bacteria (pathogens) in the baby’s developing digestive tract.

Breast-feeding, natural birth, and immunity, part 1

The same lactic-acid producing bacteria – Lactobacilli – that dominate in the vagina are also present in the mother’s breast milk,12 along with another beneficial bacteria, called Bifidobacteria. We’ll look at the role of Bifidobacteria in the tile “How microbiotas benefit the body” .

Evolutionary biologist Alanna Collen13 describes the cross-talk between gut, vaginal and breast milk microbes to prime the newborn baby’s immune system after childbirth. She explains here how lactic acid cells – which are normally found in the mother’s gut and vagina – travel from the large intestine to the breast milk:

[Lactic acid cells] are stowaways, travelling inside immune cells called dendritic cells. The dendritic cells are willing participants in the trafficking of the bacteria. Sitting among the dense immune tissue that surrounds the gut, these cells are able to reach out with long arms (dendrites) into the intestine to check what microbes are present. Usually, they are responsible for engulfing pathogens, then waiting for another team of immune cells – the ‘natural killer cells’ – to turn up and destroy them. Extraordinarily, the dendritic cells can also pluck unsuspecting beneficial bacteria from among the crowd to engulf and transport through the blood to the breasts. […]14.

Colonization by C-section

Vaginal delivery provides a “valuable microbial starter pack”, gifting the new-born a generous sprinkling of the founding colonies for her own microbiome as she journeys through the birth canal. Breastfeeding further encourages colonization of the baby’s gut microbiome by beneficial microbes, prevents colonization by bad bacteria, and trains the baby’s developing immune system to distinguish between friend and foe.

So, what happens in the case of births by Caesarean-section? 

By skipping the trip through the birth canal, babies miss out on the bacterial starter pack from their mothers’ vaginal microbiota. These babies are first exposed to environmental microbes outside the birth canal.  

C-section delivery can have a lasting impact on the child’s immunity. They are more prone to developing infections, allergies, and autism.15 While you can match the microbiotas of the child’s gut with that of the mother’s vagina following a natural birth, the microbes of C-section babies cannot be matched with their mothers’. 

When microbiome researcher Rob Knight’s wife had to give birth by emergency C-section in 2012, Knight waited for the medical staff to leave the room, then used a swab to transfer vaginal microbiota from his wife to his daughter, to give his child the opportunity to benefit from her mother’s vaginal microbiota.16

C-sections and immunity

How a baby is delivered has a major impact on the follow-up microbes it receives from its mother’s breast milk. On this point, Alanna Collen notes:

Something about the labour process sounds a klaxon, informing the immune system that it’s time to prepare for the baby to be on the outside of the body, receiving nourishment from breast-milk instead of the placenta. It seems likely that this klaxon comes in the form of the many powerful hormones released during labour. Their release alters which microbes are moved from the gut to the breasts in preparation for the emerging baby.17

C-sections can provide a life-saving alternative where natural births aren’t possible, but they come with potential risks. Bypassing the labor process interferes with the release of beneficial, immune-strengthening microbes into the lactating mother’s breasts.


Hundreds of thousands of years of co-evolution with our microbes didn’t prepare us for the onslaught of changes brought about by our modern lifestyles. Consider, for example, the replacement of breastfeeding with formula feeding. 

We now know that formula feeding may pose health risks for babies. Mostly derived from cow’s milk, modern baby formulas  are supplemented with many essential extras, but they don’t usually contain immune cells and antibodies, oligosaccharides or live bacteria that are found in breast milk.18

Formula-fed babies tend to be more prone to infections, and are at greater risk of developing eczema, asthma, leukemia, type I diabetes, appendicitis, tonsillitis, multiple sclerosis, rheumatoid arthritis, and obesity later in life.19 The risk of obesity correlates with the length of time spent breast-feeding: one study found that the risk of children becoming overweight drops for each extra month of breast-feeding up to the age of nine months. 

In short, babies who are fed formula miss out on the priming of the immune system that happens during breastfeeding. Alanna Collen sums this up perfectly when she says:

The more insight we gather into the importance and the consequences of a natural birth, and extended, exclusive breast-feeding, the more empowered we will be to give both ourselves and our children the best chance of lives of health and happiness.20

The microbiota in early life (0-3 years)

Since the explosion of interest in the human gut microbiome, there has been extensive commentary on the microbiotas of infants up to the age of 3 years and adults. The microbiota of pre-schoolers (3–6 years), primary-school children (6–12 years) children, and teenagers (12–18 years) have been largely overlooked.

The microbiota undergoes most of its development very early in life, and by the age of 3 years, the child’s microbiome is relatively stable and resembles that of an adult – or so it’s been assumed.  Recent studies suggest the microbiome continues to evolve beyond these early years. 

Based on the findings of several studies of the microbiota of pre-school and primary school children (up to the age of 12 years) around the world, it seems that the microbiota continues to develop for at least another decade. As new studies on the subject continue to emerge, so will  opportunities for microbiome-based interventions to promote health among this age group, particularly through diet.21

The hygiene hypothesis and antibiotic usage in early childhood

Some scientists22 speculate that exposing young children to pets and dirt is beneficial for their gut microbiota. However, Martin Blaser begs to differ, claiming that “the microbes in our pets and farm animals are not deeply rooted in our human evolution.”23

Far more important, says Blaser, are changes to the microbiota that occur when young children are prescribed antibiotics too frequently.24

In 2014, Blaser and his team were running more than twenty projects on mice and human subjects to test the effects of antibiotics on resident microbes and their hosts. The results of their experiments on mice uncovered some key findings: early life is “a key window of vulnerability”,25 as young children have periods that are critical for their growth and development; and the loss of friendly gut microbes at this early stage of development drives obesity. We’ll expand on the role of gut microbes in metabolic health in the “Gut microbes and metabolic health” tile.

The mature microbiome: Microbes in adulthood

In tandem with our progress into adulthood, our resident microbes evolve and adapt in response to changes in the environment. By this stage, our tiny companions are decidedly more a product of nurture than nature. As we subject our bodies to dramatic changes – illness, injury, fever, stress and changes to our diet – our microbes shapeshift and reshuffle in response to external stressors. 

Our tiny hitchhikers can’t seem to catch a break. When we injure ourselves, our bodies suffer trauma and inflammation. Studies of critically injured patients26 show that their microbiotas undergo significant changes in the first 72 hours following the trauma. These changes alter the diversity and composition of the microbiota.

Stress, fever and illness can disrupt the microbial balance in the gut, leading to dysbiosis, and laying fertile ground for diseases to flourish. By the time we reach adulthood, diet is by far the factor with the greatest capacity to shift the microbial balance. We’ll explore how dietary changes influence our microbiota in the tile “How to optimize your gut health, part 1: Nutrition”.

The ageing microbiome

As our human cells start showing signs of their collective age, so too do our microbial passengers.27 Many of us have come to associate old age with ill health, but emerging medical research suggests that the top three leading causes of death in 2005–heart disease, cancer and stroke– are not diseases of old age, but rather, diseases of inflammation.28 On this point, Collen says,

What we are now realising is that hearts don’t harden, cells don’t multiply uncontrollably and blood vessels don’t burst just because they are old. […] If there is an effect of advanced age, it is that the modern insults we throw at our bodies have had the necessary time to generate inflammation to the point of catastrophe. If this is the case, a grand old age in the absence of decades of built-up inflammation is a possibility.29

If we look after our microbes, then, we can – in theory – mitigate the extent of damage caused by inflammation.

[12] Collen, Alanna. 10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness (p. 105). HarperCollins Publishers. Kindle Edition.

[13] Ibid.

[14] Ibid.

[15] Collen, Alanna. 10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness (p. 244). HarperCollins Publishers. Kindle Edition.

[16] Ibid, p. 246.

[17] Ibid, p. 254.

[18] Collen, Alanna. 10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness (p. 267). HarperCollins Publishers. Kindle Edition.

[19] Ibid, p. 257.

[20] Ibid, p. 267.

[21] Derrien, et al. (The Gut Microbiota in the First Decade of Life, Trends in Microbiology, December 2019, Vol. 27, No. 12, https://doi.org/10.1016/j.tim.2019.08.001. Retrieved from https://www.sciencedirect.com/science/article/pii/S0966842X19302148#!

[22] For more on the so-called ‘hygiene hypothesis’, see Jack Gilbert, Ph.D., and Rob Knight, Ph.D., with Sandra Blakeslee. Dirt Is Good: The Advantage of Germs for Your Child’s Developing Immune System, (2017)

[23] Martin Blaser, Missing Microbes, Henry Holt & Company, 2014, p. 5.

[24] Ibid., p. 10.

[25] Ibid, p. 12.

[26] See https://pubmed.ncbi.nlm.nih.gov/29766103/ and https://tsaco.bmj.com/content/2/1/e000108

[27] Collen, Alanna. 10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness (p. 266). HarperCollins Publishers. Kindle Edition.

[28] Ibid, p. 308.

[29] Ibid.

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