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How Modern Life Impacts The Gut - Gut microbiome, Part 2

How Modern Life Impacts The Gut - Gut microbiome, Part 2

Modern society has given us so many wonderful things, but healthy gut microbiomes is not one of them.

In Part 1, I discussed what the gut microbiome is, how we acquire it, and why it’s so important to overall health. In Part 2, we will look at the ways that our modern life can be harmful to the healthy balance of the microbiome. Many of the foods, chemicals, medications, lifestyle choices and behaviours that are commonplace in our society are damaging to healthy microflora populations. Sadly, research around the gut microbiome, human health and the impacts of modern life has only recently begun to catch up – well after a lot of the damage has been done. It’s not all bad news – with the information from part 2 and the upcoming part 3, you will be empowered to make better decisions for your gut.

What disrupts the gut microbiome?

It simply can’t be understated how much modern life has harmed the human gut microbiome. As a naturopath, I see my fair share of patients with blatant gut issues – but more and more, I am seeing all manner of body systems and symptoms that are being impacted (even caused) by a damaged gut microbiome.

Antibiotics and other medications

Antibiotics are an important type of medication that can be absolutely necessary. Like anything in life, when they are misused, overused and abused they not only lose their efficacy – they harm the body. Antibiotics do not discriminate - they kill the good bugs with the bad. Some, but not all, strains of probiotic bacteria can be replaced by fermented foods and probiotics – but the populations can take a long time to come back. Add to that, the overuse of antibiotics leads to bacteria becoming resistant.

After a course of antibiotics, the gut is placed in a risky position. What happens in the days and weeks following a course of antibiotics is crucial – are you going to feed the good bugs or the bad? All too often, the bad bacteria are given everything they need to thrive, leading to an imbalance of the gut microbiome known as ‘dysbiosis’.

Other medications can wreak havoc on the gut microbiome, including non-steroidal anti-inflammatory drugs (NSAIDs) and painkillers, the oral contraceptive pill, anti-diabetes drugs, and anti-psychotic drugs.

In Part 1, I discussed the central role the gut microbiome plays in immunity. Antibiotic overuse is also linked to a decrease in immune function as it kills off the beneficial bacteria that make up part of the immune system.

Part of the important work of the gut is to keep potentially harmful pathogens out of the bloodstream. Antibiotic use can impact on the gut’s ability to do its job, damaging what are known as ‘tight junctions’ – little structures that fit into the gaps along the intestinal wall. Tight junctions control what moves in and out of the intestines – essentially the bodyguards of the gut wall.1 When these tight junctions can’t do their job effectively due to damage, all manner of things can move freely between these gaps. This is referred to as intestinal permeability or ‘leaky gut’. Leaky gut is a condition that leaves the body vulnerable to infection, food intolerances, systemic inflammation and toxicity.

Poor diet

Modern agricultural practices and food manufacturing are impacting a great deal on the health of our gut microbiomes. These practices cause a lack of nutrients in soil, rely on heavy pesticide use, and result in foods with practically no nutritional value. Industrial farming practices also reduce microbial diversity in the soil, along with the nutrients that help the microbiome to thrive – this harms the microbiome at every level. How can you avoid these practices? Enjoy foods as close to their natural state as possible, make your local produce market your go-to and buy organic where ever possible. It’s not just fresh produce – grain-fed animals absorb these harmful chemicals and the result is meat that has accumulated toxins and become higher in inflammatory omega-6 fatty acids.2

Commonplace practices such as sterilisation, heating and preserving methods further reduce any microbial activity. When we don’t get naturally occurring microbes and digestive enzymes in the diet anymore, the digestive system suffers too. A sterilised, highly processed diet lacking in nutrients, beneficial bacteria and enzymes that is pro-inflammatory is a recipe for digestive disaster. This harms the microbiome, as well as leading to food, chemical and other environmental sensitivities and gut inflammation developing over time.

Infections and the gut microbiome

Gastrointestinal infections such as gastroenteritis can throw out the balance of good and bad bacteria, causing dysbiosis. Often people who have experienced an infection like this, commonly through food poisoning, present in my clinic as ‘never well since’. Traveller’s diarrhoea and parasites contracted during overseas travel are also common microbiome disruptors. Infections like these create inflammation in the gut that can lead to chronic inflammatory diseases such as gastritis and irritable bowel disease.3

The lungs are connected to the gut microbiome and have a two-way communication stream. The lungs even have their own smaller, less-diverse microbiome. If the gut microbiome is disrupted, it can therefore lead to a greater risk of upper and lower respiratory tract infections.4

Did you know that the mouth is an extension of the gut? If the gut microbiome is disrupted, it can cause an imbalance in the bacteria of the mouth. The reverse is also true, if the mouth microbiome is disrupted, this can lead to infection further down. Probiotic bacteria in the mouth and throat not only help to reduce the risk of infection further down the digestive tract, they also protect the health of the teeth and gums. Gingivitis or gum inflammation can lead to periodontitis – a common inflammatory infection of the gums.5

Other modern factors that disrupt the gut microbiome:

  • Poor oral health and care
  • Toxic chemicals, including glyphosates, food additives (e.g. colours, flavours,
    preservatives, sweeteners), chemicals in cleaning, beauty and personal-care
    products, candles, incense, perfumes are inflammatory and mimic
    chemicals in water supply, plastic packaging.
  • Natural chemicals found in foods: Salicylates,
    amines, histamines, sulphites, high sulphur foods, oxalates, citrates.
  • Urbanisation (western diet, lack of early-life microbial exposure, environmental chemicals and pollutants, antibiotics, etc).6
  • Sanitisation - we’re obsessed with over cleaning! Anti-microbials not only disrupt the microbiome, they also end up in waterways - disrupting aquatic life. Chemical antibacterial soaps, mouth wash, wipes, hand sanitisers, toothpaste, household cleaners are all common culprits. Choose natural, eco-friendly and triclosan-free products.
  • Lack of exercise can effect healthy bowel elimination and lead to an increase in inflammation and toxicity.
  • Over-exercise can increase the ‘leakiness’ of the gut and lead to immune system over activity.
  • Chronic stress and sympathetic nervous system activation. This harms the physical function of the gut, including stomach movement and secretions – leading to a range of issues in the digestive system and beyond. I’ve written a whole article about recalibrating an overactive stress response which you can read
  • Dehydration is an extremely common cause of constipation. Dehydration also reduces the effectiveness of the organs involved in elimination. There is also a difference in the bacteria species found in the microbiota of people with chronic constipation – more harmful bacteria species, such as Bacteroides 7

Modern living has not been good to the gut microbiome and we’re facing the fallout of this now. As research into what helps and harms the gut microbiome catches up, we can begin to see that the choices we make going forward – what cleaning or food products we buy, for example – can be protective, preventative, even restorative to the gut microbiome.  


  1. Feng, Y., Huang, Y., Wang, Y., Song, H., et al. (2019). Antibiotics induced intestinal tight junction barrier dysfunction is associated with microbiota dysbiosis, activated NLRP3 inflammasome and autophagy. PLoS One, 14(6):e0218384.
  2. Kresser Institute. (2019). Why grass-fed trumps grain-fed. Accessed July 2021 from
  3. Discover Magazine. (2021). The gut-lung axis: How your microbiome might be linked to respiratory health. Accessed July 2021 from
  4. Man, S.M. (2018). Inflammasomes in the gastrointestinal tract: infection, cancer and gut microbiota homeostasis. Nature Reviews Gastroenterology & Hepatology, 15:721-737.
  5. Olsen, I. & Yamazaki, K. (2019). Can oral bacteria affect the microbiome of the gut? J Oral Microbiol, 11(1):1586422.
  6. Zuo, T., Kamm, M.A., Colombel, J.F. & Ng, S.C. (2018). Urbanization and the gut microbiota in health and inflammatory bowel disease. Nat Rev Gastroenterol Hepatol, 15(7):440-452.
  7. Zhao, Y. & Yu, Y.B. (2016). Intestinal microbiota and chronic constipation. Springerplus, 5(1):1130.