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The impact fast food has on gut health and how it depletes good gut bacteria

The impact fast food has on gut health and how it depletes good gut bacteria

The impact fast food has on gut health and how it depletes good gut bacteria

Fast food and your Gut Microbiome

Before you start typing ‘fast food near me’ to get your evening fix from UberEats, Deliveroo or Menulog, think about what all this processed and fast food is doing to your gut health.

As convenient as take away food may be, have you considered how it’s affecting your overall health and possibly contributing to the health issues you are dealing with?

If you’re not sure if there’s a direct correlation to the consumption of junk food and your gut microbiome, read on…

Modern life and its effect on our health

It’s no surprise to health professionals that people are experiencing more health issues and that our gut performance is suffering.

Modern life is busy and with this fast pace of life, we have made some sacrifices along the way. We don’t buy healthy produce and cook at home anywhere near as much as we used to. Instead, we often take the cheaper and more convenient options for ready meals, ordering in or eating out.

Why is fast food bad for our gut?

A healthy gut is usually associated with more diverse bacteria residing in our gut. Diversity is achieved through a varied diet, rich in nutrients and based on plants and whole foods.

Processed foods, preservatives, and food additives harm our gut microbiome and overconsumption of fast food can affect the gut microbiome in the following ways:


Fast food is usually high in fat and low in fibre, which can throw off your gut health and microbiome balance. This can reduce the growth of good bacteria that produce beneficial short chain fatty acids like butyrate, known to play a role in reducing inflammation. They are loaded with excess sodium, hidden sugars and unhealthy fats.


Studies show that high-fat diets alter the gut microbiome, in turn, affecting our metabolism. The gut microbiome may be linked to how energy is extracted from our food and how fat is stored. Healthy gut bacteria may increase our metabolism while unhealthy gut bacteria may help store fat.  Quality fats are required in a healthy diet however many unhealthy fats such as trans fats appear in junk or fast food.

Immune system

Fast food not only affects your gut health but has also been found to negatively affect our immune system. What we eat affects our gut microbiome which interacts with our immune cells in our gut.  Eating fast food increases our consumption of fat, salt and sugar which can cause inflammation and poor immune function. 1

What are the worst foods for gut health?

Most of the fast food we order not only lacks the nutrition we need but contains toxins that are harmful to our bodies in many ways.

fast food lowers good gut bacteria


  • Cereal grains (especially refined flour) – for many people, gluten poses a real problem. Going gluten-free lowers inflammation and insulin resistance while helping people lose weight.  All commercial flours and cereals in Australia are fortified with synthetic folic acid, a form of folate that is detrimental to those with the MTHFR gene and associated polymorphisms.
  • Omega-6 industrial seed oils (corn, cottonseed, safflower, soybean, etc.) – a high omega-6 intake from industrial seed oils promotes chronic inflammation. 2
  • Sugar (especially high-fructose corn syrup) – any form of sugar in excess, including refined carbohydrates, poses a risk to your gut health. Sugars and refined starch promote the growth of undesirable bacteria and microbes. It wreaks havoc on your gut and research shows it feeds the bad bugs, creates dysbiosis, and leads to yeast overgrowth (like candida). 3 High levels of sugar in the body that are not immediately burnt as energy convert to fat and are stored in the body, resulting in weight gain.
  • Processed soy (soy milk, soy protein, soy flour, etc.) 4
  • Dairy – for some people, the two proteins in milk (casein and whey) are hard to digest and can lead to food sensitivities. Many people also lack a sufficient quantity of the enzyme lactase to break down the lactose in milk, creating symptoms like gas, bloating, and diarrhea as gut bacteria ferment this sugar instead.
  • Fast foods will affect your gut health. Increasing inflammation and altering the diversity of of beneficial gut bacteria.

Gut-friendly foods

To optimise gut health, follow a simple diet with clean ingredients that are organic, non-GMO, full of healthy fats, and ideally locally grown and sustainably farmed. You’ll feel energized by the richness of a power-packed, phytonutrient-dense way of eating.

Include the following in your diet:

  • Healthy fats 
  • Nuts and seeds 
  • High-fibre, low-glycaemic carbs like leafy greens and cruciferous vegetables
  • Slow carbs, like sweet potatoes and pumpkin 
  • Hypoallergenic proteins (pea, rice, hemp, chia) 
  • Clean and lean proteins like free-range poultry, wild-caught fish, and grass-fed meats

At Advanced Functional Medicine we not only recommend avoiding fast food but taking a number of other steps to heal your gut and maintain a healthy gut microbiome:

1. Take probiotics and eat fermented foods

Research suggests taking probiotics can support a healthy gut microbiome, preventing gut inflammation and other intestinal problems. Many of our patients at Advanced Functional Medicine take a professional-quality probiotic supplement that contains billions of colony-forming units.

Taking a probiotic supplement is a great way to support your microbiome and immune system, whilst feeding your gut foods that are natural sources of probiotics is also extremely beneficial. These probiotic-rich foods help eliminate pathogens like unfavourable bacteria, yeast or parasites.

Some people react to probiotics, this is usually a sign of gut dysbiosis. Stool testing identifies the exact pathogens before clearing these with specific antimicrobial herbs.  We use targeted and specific strains of probiotics to balance your microbiome.

Fermented foods for gut health

“Fermented foods are a natural source of probiotics. Food fermentation dates back over 7,000 years to wine-making in Persia. The Chinese were fermenting cabbage 6,000 years ago. While fermentation initially started as a food preservation method, these ancient civilizations certainly recognized the health benefits.

The type of fermentation that makes most foods rich in probiotics is called lactic acid fermentation. The good bacteria convert sugar molecules in the food into lactic acid, which causes the bacteria to multiply. The lactic acid protects the food from being invaded by pathogenic bacteria.” 5

fermented foods improve gut health

Consuming the following foods regularly may improve gut health:

  • Kefir (pronounced kuh-fear)kefir is a fermented dairy product that may improve lactose digestion, decrease inflammation and boost bone health. Read the labels on store-bought kefir to check for flavouring and added sugar or artificial sweetener. Choose the organic, plain variety of kefir and add your own fresh fruit or raw honey. Or try making your own.
  • Kimchi – kimchi is a popular Korean dish made from fermented cabbage or other vegetables like radishes. Kimchi is low in calories, low in fat but is rich in vitamins, especially vitamin C and beta-carotene, minerals, fibre, phytochemicals and probiotic strains of Lactobacillus plantarum and Lactobacillus brevis.
  • Kombucha – kombucha is a fermented drink made from black or green tea and a specific culture known as a scoby. Scoby stands for ‘symbiotic culture of bacteria and yeasts’. The bacteria and yeasts convert the sugar into ethanol and acetic acid and help to aid digestion. The acetic acid is what gives kombucha its distinctive sour taste.
  • Sauerkraut (pronounced sourcrowt) – sauerkraut is a popular condiment consisting of shredded cabbage fermented by lactic acid bacteria. It is low in calories but contains plenty of fibre, vitamin C and vitamin K.

Again, a number of people do not react well to fermented foods.  Fermented foods feed your gut bacteria, if there is an imbalance of dysbiotic gut bacteria these foods can exacerbate gut-related symptoms such as bloating, gas and adverse changes in the stool.  A stool test and SIBO test are advised with appropriate treatment if this is the case.

2. Eat prebiotic fibre

Prebiotics are the food that probiotics feed on. They are equally important for gut health because they feed the good bacteria in your gut.

Prebiotic foods are harder to digest or absorb. They bypass your small intestine and go straight to your colon, where they feed the good gut bacteria to create healthy, energy-producing short-chain fatty acids.

Prebiotics offer a variety of health benefits, including:

  • reducing fever-related illnesses associated with diarrhea or respiratory events.
  • reducing inflammation in IBD and reducing risk of colon cancer.
  • enhancing mineral absorption.
  • lowering certain risk factors of cardiovascular disease.
  • promoting a sense of fullness, reducing obesity, and promoting weight loss. 6

Prebiotics fall under several categories, including fructans and resistant starch. Each feed different types of gut flora which encourage beneficial bacteria to multiply in the gut.

Excellent choices include:

  • Chicory root (raw)
  • Jerusalem artichoke (raw)
  • Dandelion greens (raw)
  • Chickpeas 
  • Raw garlic, onions, and scallions 7

Prebiotic fibre may also cause bloating, gas and adverse side effects in the digestive system with certain individuals.  These people usually have low stomach acid or other digestive and absorption issues.  Often they have gut dysbiosis, SIBO, hypochloridia (low stomach acid) or a parasitic infection.

3. Eat less sugar and fewer sweeteners

Sugar contributes to inflammation, and inflammation is harmful to the diversity and function of gut bacteria. Research shows that eating a lot of sugar or artificial sweeteners may cause gut dysbiosis, which is an imbalance of gut microbes. 8 Excess sugar also leads to weight gain and result in the downregulation of the immune system.

4. Eat a vegetarian diet and avoid processed meat

You may be able to improve your gut health by eating a vegetarian diet or eating a diet with a high level and diversity of vegetables. Studies 9 have demonstrated a significant difference between the gut microbiomes of vegetarians and those of people who eat processed meats. This is perhaps due to the high levels of prebiotic fibre the vegetarian diet contains.  

Quality grass-fed and organic meats that accompany a high level of vegetables serve most people well as a staple diet.  A vegetarian or vegan diet is beneficial for gut bacteria as long as measures are taken to ensure nutrition and nutrient requirements are met in all areas, such as Vitamin B12, zinc etc.

Following these simple rules can help you steer clear of poor food choices:

  1. Limit eating out as much as possible. Avoid fast food to improve your gut health.
  2. If the ingredient label has any words that you cannot pronounce without a chemistry degree avoid it.
  3. Buy your produce when it is in season (locally if possible).
  4. Grocery shop for your next meal, not for the next two weeks.  Foods should be perishable.  Buy and eat them as fresh as possible.  Look to shop at least 2-3 times per week.
  5. Before you eat, ask yourself the following questions: 
    • Is this food healthy?  
    • Am I really hungry?

So, in summary, avoiding fast food and replacing it with a diet rich in organic, clean food, with probiotics and prebiotics will help you maintain good gut health, contributing to better overall wellbeing and immune function.

When you make the appropriate lifestyle and dietary changes, you can alter the diversity and number of microbes in the gut for the better.

How we can help – Functional Medicine Nutrition advice

At Advanced Functional Medicine, we can help you to eliminate toxic and fast food from your diet, incorporate healthy habits into your life and return your gut to its healthy state.

As part of our treatment model, we provide tailored nutrition advice, guidelines and plans to assist you to achieve your health goals, whether that be for an elite athlete or someone looking to lose weight.

Call us on 1800 11 22 36 to start your journey to wellness or alternatively, complete our Gut health Questionnaire for a comprehensive online health assessment.


The above information is intended to be general, educational advice only, on topics which are of interest to us. It is not intended to represent specific or individual health or medical advice and is not specific to your situation. The below information is educative and is not intended to advertise any service.

Before making any decisions in relation to your health, you should always discuss your individual situation with your own health practitioners to ensure that any advice you have read is right for you.

Jarrod Cooper – ND

Jarrod Cooper – ND

Jarrod Cooper - ND is the founder of Advanced Functional Medicine Australia. He is a Naturopathic Doctor with extensive functional medicine training from leading practitioners in the USA and worldwide.

He is leading the way with advancements of functional medicine, clinically implementing worldwide best practices in Functional Medicine throughout Australia.

Jarrod consults in person from Perth, Western Australia and also online via Telehealth throughout Australia and worldwide.

If you are looking for personalised treatment, we highly recommend contacting Jarrod Cooper’s Advanced Functional Medicine clinic in Australia.

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