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Home / Learn more about your microbiome

Learn more about your microbiome

by | Jul 5, 2018 | Prevention

Learn more about your microbiome

Background of the microbiome:

As per the World Health Organisation (WHO), non-communicable diseases including cancer, cardiovascular diseases, diabetes, mental disorders and respiratory diseases account for 71% of all deaths globally.

According to a report published by the by the World Economic Forum and the Harvard School of Public Health, non-communicable diseases will cost more than $30 trillion over the next 20 years. It is estimated that the cost of treating these diseases has the potential to bankrupt global healthcare systems by 2030.

Common modifiable risk factors, such as unhealthy diets, physical inactivity, tobacco use, and the harmful use of alcohol, are noted to be strong contributing factors. Research has also found an important link between non-communicable diseases and the diversity of our gut microbiome.

The latest WHO report shows that countries could save more than 8 million lives and more than US$350 billion by scaling up strategies that help prevent non-communicable diseases.



  • Microbiota – a population of microbes, including archaea, bacteria, fungi, protozoa and viruses.
  • Microbiome – the microbial community including their genes and bi-products within a particular ‘habitat’.
  • Epigenetics – the study of how genes are switched on (expressed) or switched off (not expressed) in relation to external factors such as nutrition, exercise, exposure to toxins and stress.

The human body contains around 10 trillion human cells and 100 trillion microorganisms (microbes). These microbes and their genetic material live with us in a symbiotic relationship that is vital to our health. They assist with digestion, metabolism and play an important role in the setting up our immune system.

In general:

  • Microbial imbalances increase our risk of disease, and the health of adults and children is improved when we have a greater diversity of microbes.

The microbiome:

Each part of our body has its own unique diversity of microbes. The genetic elements of the microbes within that part of the body determine health and wellness. The largest and most important is the gut microbiome because of the connection between the gut and immunity and gut and brain. Bacteria within the gut produce neurotransmitters which impact mood and behaviour via the enteric nervous system.

Antibiotics (including the extensive and inappropriate use in humans and animals), antimicrobial substances (cleaning agents and handwashes), caesarean section deliveries, formula feeding, and highly processed diets all disturb the balance of microbes within the microbiome, increasing the risk of disease.

Studies have identified links between imbalances in our gut microbiome and certain diseases, including allergies, ADHD, asthma, autism, auto-immune diseases, certain cancers, coeliac disease, colitis, diabetes, eczema, cardiovascular disease, malnutrition, multiple sclerosis and obesity. These links need further exploration.

The gut microbiome is seeded within the first few years of life. Microbial seeding begins during pregnancy, with vaginal birth and long-term breastfeeding being crucial elements.


During pregnancy, a mother’s gut microbiome decreases in bacterial diversity. This is protective for her baby, who will be born with an immature immune system. In addition, the prevalence of lactobacilli (good bacteria) increases in the mother’s vaginal microbiome. Lactobacilli prevent the growth of harmful bacteria, providing protection for birth, and are also important for breast milk digestion.

As a mother’s microbiome will be passed to her baby during vaginal birth and breastfeeding, it is important that she pays attention to her health during pregnancy. Diet, exercise, stress levels, antibiotic use and antibacterial practices can all negatively impact a mother’s microbiome. Pregnant mothers should be encouraged to avoid processed foods and should try to eat a wide variety of fresh fruit and vegetables.


During vaginal birth, a mother’s vaginal bacteria, rich in lactobacilli are passed to her baby via the birth canal and these enter the baby’s eyes, nose, ears, mouth and skin. The baby is also exposed to her mother’s fecal matter, which transfers important microbial species. Babies born via caesarean section are not exposed to the same microbiota, and the use of intrapartum antibiotics further impact microbiome seeding.

Twenty minutes after birth, the microbiome of a vaginally delivered baby resembles that of their mother’s vagina, while babies delivered via caesarean section have microbial communities that resemble human skin.

Due to an altered microbiome and potential epigenetic changes, babies born by caesarean section are at an increased risk of developing asthma, diabetes type 1, obesity and coeliac disease.  This risk is reduced if the baby is subsequently breastfed.

Skin to skin contact:

Immediate skin to skin contact allows for the transfer of microbes from mother’s skin to her baby. It also regulates the baby’s heartbeat, blood glucose and temperature, promotes cognitive function, improves bonding and increases the likelihood of breastfeeding initiation and continuation.


Breastmilk contains hundreds of beneficial bacteria that colonize the intestine and modify the intestinal microflora to contain less pathogenic (harmful) bacteria.  Breastmilk also contains non-digestible food components (oligosaccharides), which stimulate the growth and maturation of healthy microbes.  The intestinal flora of breastfed infants is dominated by lactobacilli, which decrease the pH of the gut, thereby suppressing the growth of pathogenic bacteria.  Injudicious use of proton pump inhibitors (PPI’s), such as Losec® or Nexiam®, may interfere with this protective process by altering the pH of the gut.

Immune system development:

A newborn baby’s immune system is immature. Gut microbiota train the infant’s immune system to discern between what is harmful and what is not. This is essential in preventing inappropriate inflammatory reactions against the foods we eat and helps us to develop tolerance to allergens. A naive immune system will attack anything and everything, but as a child acquires more bacteria from the air, from touch, from a mother’s kiss, from skin to skin contact, from breastfeeding, from illnesses, from exposure to pets and nature, and from food, the immune system learns to distinguish friend from foe. Getting sick is an integral part of the training of a child’s immune system. Lack of exposure to illness can cause an immune system to become increasingly naive, whereby the body starts to attack its own cells, resulting in auto-immune diseases. A vast majority of diseases, including diabetes, heart disease, cancers and autoimmune diseases can be attributed to disruption in immune response.

Antibiotic era:

External factors, such as the use of antibiotics can alter the community of microbes located in the GI tract. Broad spectrum antibiotics are used to combat pathogenic (harmful) bacteria but will target the normal microbiota as well, thereby altering the diversity of the microbiome.

In addition, overuse and misuse of antibiotics can promote the development of antibiotic-resistant bacteria. Every time a person takes antibiotics, bacteria are killed, but resistant bacteria may be left to grow and multiply.


AFSA Antibiotic Resistance

What we can do to optimize our microbiome:

  1. Eat a diverse range of fresh fruit and vegetables (high fiber foods, yogurt, other fermented foods)
  2. Avoid processed foods
  3. Avoid unnecessary/elective caesarian sections
  4. Allow immediate skin to skin contact post-birth
  5. Support mothers to breastfeed for an extended time
  6. Avoid unnecessary antibiotics
  7. Limit the use of antibacterial substances
  8. Increase exercise
  9. Increase time outdoors and with household pets
  10. Decrease stress levels. Stress increases permeability of the intestines and reduces intestinal immunity, giving viruses and bacteria the opportunity to become pathogenic.


The gestation period and the birthing process are very important for the development of the microbiome of a child. A mother’s microbiome is passed to next generation through vaginal birth and breastfeeding. We need to ensure that microbial seeding occurs completely at birth, ideally through vaginal delivery, that immediate skin to skin contact occurs at birth, and that healthy microbes grow and thrive by supporting their maturation through breastfeeding of a significant duration, and eating a diverse range of foods. Supporting the development of a healthy microbiome is critically important to a child’s life long health, and as the microbiome is heritable, to the health of future generations.


Bloom, D.E., Cafiero, E.T., Jané-Llopis, E., Abrahams-Gessel, S., Bloom, L.R., Fathima, S., Feigl, A.B., Gaziano, T., Mowafi, M., Pandya, A., Prettner, K., Rosenberg, L., Seligman, B., Stein, A., & Weinstein, C. (2011). The Global Economic Burden of Non-communicable Diseases. Geneva: World Economic Forum.

Rodriguez-Castaño GP, Caro-Quintero A, Reyes A, Lizcano F. Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle. Frontiers in Genetics. 2016;7:224. doi:10.3389/fgene.2016.00224.

Ursell LK, Metcalf JL, Parfrey LW, Knight R. Defining the Human Microbiome. Nutrition reviews. 2012;70(Suppl 1):S38-S44. doi:10.1111/j.1753-4887.2012.00493.x.


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