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?

How your microbiome changes over time.

Colonization in the birth canal

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. Our first exposure to bacteria, fungi, and other crucial microorganisms, has historically been through the mother’s birth canal, where, like intrepid explorers, pioneering species of bacteria begin to populate the baby’s 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, along with another beneficial bacteria, called *Bifidobacteria*.

Evolutionary biologist Alanna Collen describes the cross-talk between gut, vaginal and breast milk microbes to prime the newborn baby’s immune system after childbirth. Lactic acid cells rely on help of dendritic cells to travel from the large intestine to breast milk. The main role of dendritic cells is to engulf pathogens, to wait for immune cells to attack and neutralise them.

However, the same system that is used to neutralise pathogens can also be used to pluck and transport beneficial bacteria and lactic acid cells to where they are needed. In the case of lactic acid cells the journey takes them from the large intestine, through the blood stream, to the breasts.

Microbiome 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 and allergies. 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.

C-sections and immunity

C-sections can have a significant impact on the development of an infant’s immune system. Studies have found that babies born via C-section had lower levels of IgA, an antibody which helps protect against infection, compared to those delivered naturally. This suggests that exposure to maternal microorganisms during delivery is important for establishing a healthy immune system in newborns.

Furthermore, research has also linked C-sections with increased risk of autoimmune diseases such as asthma and type 1 diabetes later in life due to differences in microbial composition at birth. It is thought that this could be because infants born by cesarean section lack exposure to their mother’s vaginal microbiota which helps stimulate the development of regulatory T cells (Treg) – specialized white blood cells involved in controlling inflammation and preventing autoimmunity.

These findings suggest that natural childbirth may be preferable when it comes to setting up a healthy microbiome and developing immunity early on in life, although further research is needed into how best we can support babies born via C-section so they too benefit from optimal gut health throughout their lives.

Formula-feeding for babies - the effect on the microbiome

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.

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. 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.

Interestingly, research has also shown that the composition of infant formulas can affect the development of their microbiome. For example, one study found that babies fed cow’s milk based formulas had higher levels of Firmicutes bacteria than those fed soy-based formulas – this difference was not seen in breastfed infants. These findings suggest that different types of infant formula can influence microbial diversity during early life stages, so it is important to consider these factors when choosing a suitable option for your baby.

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), and teenagers (12–18 years) have been largely overlooked.

Until recently, it was thought that the microbiota undergoes most of its development very early in life, and that by the age of three, the child’s microbiome resembles that of an adult. 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.

The hygiene hypothesis and antibiotic usage in early childhood - how it effects the gut microbiome

Some scientists 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.”*

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

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”*, 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.

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 patients 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.

The aging microbiome - how the microbiome changes over the course of our lives

As our human cells start showing signs of their collective age, so too do our microbial passengers. 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*.

According to Alanna Collen, the processes of heart tissue hardening (heart disease), uncontrollable multiplication of cells (cancers) and sudden bursting of blood vessels (strokes) are not entirely related to the advancement in age. She postulates instead that it is the *”modern insults”* of an unhealthy lifestyle that leads to inflammation, and results in these catastrophes.

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

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