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If Your Gut Could Talk ~ Gut Microbiome, Part 1

If Your Gut Could Talk ~ Gut Microbiome, Part 1

If your gut bacteria could talk, it would make the whole gut health journey a lot easier, right?

Actually, the bacteria of your gut is talking to you via all of your body systems all the time. Bacteria, for better and for worse, can be extremely clever. Your bacteria finds ways and means to communicate with you every day and the more you tune in, the harder it’ll be to ignore it. You’ll notice it saying “eat more of this/less of that!” “I’ve lost some buddies down here, send reinforcements”. If something is amiss, this will be communicated through various symptoms – not just within the digestive system. The gut microbiome is the world the beneficial strains of bacteria, and even yeasts and fungi, have built – and from here, they’ve hooked up communication lines all over the body – the brain, the immune system, the skin, metabolism -  basically everywhere. For this reason, when the gut microbiome is in poor shape, it can impact your whole health. On the flip side, a healthy microbiome can positively influence your overall health. This is why naturopaths follow the 2,000 year old adage that “all disease begins in the gut” – Hippocrates.

What is the human gut microbiome?

The large intestine houses the majority of the microorganisms of the body – the collection of fungi, bacteria, viruses and yeasts. A section of the large intestine called the cecum is where these trillions, yes that’s trillions, of microorganisms take up residence. From this and other key locations – including the skin and mucosal areas like the nasal passages, lungs, and mouth – the microbiome exercises its influence on many areas of health. In fact, the microbiome interacts with almost all human cells.1

What does the gut microbiome do?

The gut microbiome plays a vital part in:

  • Digestion, absorption and assimilation of nutrients
  • The metabolism and production of energy
  • The composition of the gut microbiome (i.e. how much beneficial vs. harmful bacteria) influences the response to treatments such as chemotherapy and immunotherapy2
  • Beneficial bacteria supports immune system regulation, including in autoimmunity2
  • Communicating with the brain through the hormonal and immune systems, as well as signalling the brain by using the vagus nerve 
  • Helps to train and develop the immune system3
  • Gut defence and repair – the microbes of the gut protect the lining of the intestines from damage and harmful pathogens. This is partly done through the fermentation of prebiotic fibre by the microbes that produces short chain fatty acids that the cells lining the gut then use for fuel. 
  • Supports detoxification – of food toxins, cell waste, pollutants, hormones and heavy metals4
  • Supports healthy gut motility (the contractions that help to move the digestive process along) – this helps with regular bowel movements, reducing issues like constipation and excessive gas.5
  • By protecting the gut lining and supporting motility, digestion and absorption of nutrients, a healthy gut microbiome = healthy digestion.

Because the gut microbiome has such far-reaching influences, sometimes it’s easy to forget that the microbiome is also impacting health in areas we don’t associate with ‘gut health’.

External to the gut, the microbiome also has effects on other areas of our health, including: 

  • Regulation of the blood sugar and blood lipid (cholesterol) response1
  • Supporting healthy body composition, i.e. prevents obesity when in balance2
  • Prevention of upper respiratory tract infections & seasonal allergies
  • Through its connection to the skin via the gut-skin-axis, the gut microbiome can protect against eczema, dermatitis and acne – as can the local skin flora
  • Influencing the brain, including mood and mental health, cognition, appetite, sleep
  • Liver and kidney function
  • Healthy vaginal tract – reduced susceptibility to urinary tract infections (UTI)
  • Protection of macromolecules (DNA, proteins, lipids) from oxidative damage.
  • Influencing the mate we choose.6

Where do we get our gut bacteria from?

It was initially thought that the womb was a sterile environment and that exposure to microbes didn’t take place until the baby moved through the birth canal. Recent research shows that microbes are actually present in the amniotic fluid – suggesting that the microbiome of the foetus begins to develop while still in the womb.7 The largest dose of microbes is inherited at birth from the mother as the baby passes through the birth canal in a vaginal labour. Preconception care should ideally always consider the mother’s microbiome – this can be altered right up until birth and even during breastfeeding to optimise the baby’s microbiome. Following from birth, the microbiome can further flourish through the microbes and immune-boosting compounds present in the breast milk.

If dads think they don’t influence their babies’ gut health – they ought to think again! It’s important for fathers-to-be to have healthy semen - negative health outcomes have been identified in children with malnourished fathers – even where the mother was well-nourished. Fathers can also influence their child’s microbiome by being more involved in grooming and feeding.8 In fact, everyone present at the birth has the power to influence the baby’s gut microbiome – the doctors, nurses, midwives, doulas and birth partner.

As babies grow, the environment around them continues to have either a positive or negative impact on the microbiome. Pets, family members, friends, a healthy diet filled with fermented foods and prebiotic fibres can all contribute to a robust microbiome.

Fun facts about the gut microbiome

  • There are 100 TRILLION symbiotic microbes live in and on our bodies
  • The surface area of the gastrointestinal tract is the same size as two tennis courts
  • The human body has more microbes then there are stars in the milky way
  • 5 is the number of times the microbes of the human body can circle the earth if positioned end to end.

Now that you’ve learned about how your gut microbiome is communicating with you all the time, tune in and listen to what it’s telling you. Try making small, positive changes to your diet like adding a side of fermented veggies to your dinner and see what your gut says to you – it’ll likely be “thank you!”

In Part 2, we’ll take an in-depth look at what harms the gut microbiome and how to spot a microbiome that’s out of balance – spoiler alert: your gut will definitely tell you!  


  1. Cani, P.D. Human gut microbiome: hopes, threats and promises. Gut, 2018,67(9).
  2. Valdes, A.M., Walter, J., Segal, E. & Spector, T.D. Role of the gut microbiota in nutrition and health. BMJ, 2018:361.
  3. Zheng, D., Liwinski, T. & Elinav, E. Interaction between microbiota and immunity in health and disease. Cell Research, 2020, 30:492-506.
  4. Kresser Institute. Environmental Toxins, Drug Metabolism and the Microbiome, 2017. Accessed July 2021 from
  5. Quigley, E.M.M. Microflora Modulation of Motility. J Neurogastroenterol Motil, 2011,17(2):140-147.
  6. Rowe, M., Veerus, L., Trosvik, P., Buckling, A. & Pizzari, T. The reproductive microbiome: an emerging driver of sexual selection, sexual conflict, mating systems, and reproductive isolation. Trends in Ecology & Evolution, 2020, 35(3):P220-234.
  7. Stinson, L.F., Boyce, M.C., Payne, MS. & Keelan, J.A. The not-so-sterile womb: evidence that the human fetus is exposed to bacteria prior to birth. Frontiers in Microbiology, 2019.
  8. Gabbianelli, R., Bordoni, L., Morano, S., Calleja-Agjus, J. & Lalor, J.G. Nutri-epigenetics and gut microbiota: how birth care, bonding and breastfeeding can influence and be influenced. Int J Mol Sci, 2020, 21(14):5032.