Tips to foster a healthy microbiome

tips to foster a healhty microbiome(800 x 500 px)

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In the age of wellness trends and holistic health, one aspect that has captured considerable attention is the microbiome – the bustling community of microorganisms residing within our guts, influencing everything from digestion to mood. As science delves deeper into this microscopic world, a clear narrative emerges: fostering gut health is paramount for overall well-being.

There’s a growing recognition of the profound impact our lifestyle choices have on the diversity and vitality of our gut microbiota. Moreover, the resurgence of age-old practices like incorporating fermented foods into our diets speaks to a wisdom that transcends generations. We have done the research and come up with 10 tips you can use to foster a healthy microbiome – given the evidence of its importance, it should be a cornerstone of healthy living.

      1. Avoid the use of antibiotics unless necessary.

        Antibiotics can disrupt the commensal microbial community, which provides protection against pathogens and therefore increases the risk of colonisation and growth of incoming pathogens.1 These incoming pathogens can contribute to dysbiosis (an imbalance in gut microbiota) and well as increase the risk of infection. Dysbiosis has been linked to the development of obesity by several different mechanisms.2 There are many proven natural remedies to treat certain conditions, which can be discussed with your healthcare provider or if necessary, a functional practitioner. For example, a natural remedy to treat an H.pylori infection is aloe vera juice and liquorice root.3,4

      2. Maintain a healthy circadian rhythm

        All the physiological processes in the human body, including the microbiome, follow a circadian rhythm and respond to cues from the environment, however, in disease states, these responses become disturbed. The modern lifestyle includes the use of artificial lighting, shift work and trans-time zonal travel, all of which have been associated with disturbances in the microbiota. You can maintain a healthy circadian rhythm by keeping a consistent sleep schedule, getting natural light exposure, and exercising consistently.
        5 One tip we have for you is to open your curtains as you wake up so that you get natural light exposure, we know it’s tough but do it for your microscopic guys. The Huberman Lab has a great morning routine that helps maintain a healthy circadian rhythm. This includes getting natural sunlight for at least 10 minutes within the first hour of waking up as well as waking up between 5 and 6 am every morning.

      3.  Limit excessive sugar intake

        Diets high in sucrose result in decreased gut microbiota diversity and an increase in opportunistic pathogens, resulting in a decreased prevalence of specific gut barrier-protective bacteria. A reduction in microbial diversity or altered microbial composition entails various health risks for the host.
        6 Did you know you can retrain your taste buds to become more sensitive to sugar and therefore allow you to reduce your sugar intake? Avoiding sugar is the best practice however, if you do wish to use a sweetener, rather consume raw honey in limited amounts (for those who are not immunocompromised).

      4. Avoid synthetic sweeteners7

        To avoid added sugar, you may be tempted to turn towards non-nutritive sweeteners (NNS), which are substitutes that mimic high-intensity, low-caloric sugar. These alternatives are referenced as synthetic or natural sweeteners which are promoted as healthier alternatives as they are sweeter than sugar and as a result smaller amounts can be used. Some examples of NNS are sucralose, aspartame, monk fruit extract, steviol glycosides, and erythritol. Artificial sweeteners are known to directly affect the composition and function of gut microbiomes such as the ratio of bacterial species and their composition which can lead to dysbiosis.

      5. Eat a diet high in soluble dietary fibre7

        Soluble fibre dissolves in water and forms a gel-like substance in the gut, which slows down digestion and allows for the absorption of nutrients. It is then fermented by the gut bacteria; feeding the beneficial bacteria. Soluble fibre is found in oat bran, barley, nuts, seeds, beans, lentils, peas, and some fruits and vegetables. It is also found in psyllium, a common fibre supplement. Soluble dietary fibres, which include inulin, oligosaccharides, and GOS, increase the abundance of beneficial bacteria species which are associated with various health benefits
        9. An example of a diet high in dietary fibre is the Mediterranean diet (MD), associated with a beneficial microbiome.9 To learn more about the Mediterranean diet, click here. Increasing your fibre intake will not only make your microbiome happy but also improve your internal plumbing.

      6. Include resistance starch in your diet.10

        Resistant starch is defined as starch which escapes digestion and absorption in the small intestine and is fermented in the large intestine of humans, resulting in the production of short-chain fatty acids (SCFA). The fermentation of resistant starch in your large intestine contributes to the reproduction of more good bacteria, boosting your overall gut health.
        11 Some examples of resistant starch are rice or potatoes that have been cooked and cooled. Another example is freezing your bread and then toasting your bread as normal.

      7. Limit alcohol consumption.12

        Chronic alcohol consumption causes intestinal barrier dysfunction and changes in both the quality and quantity of gut microbiota. Although the mechanism is not yet known, alcohol administration affects microbiota qualitatively and quantitatively in both humans and rodents.
        13 Luckily, there is a big non-alcoholic movement going on, providing a range of non-alcoholic beverages and many delicious mocktail recipes.

      8. Incorporate fermented foods into your diet. 14

        Did you know that there are thousands of different types of fermented foods and beverages and that items such as wine, beer and sourdough bread are included on this list? Fermented foods are normally defined as foods or beverages made by controlled microbial growth and enzymatic conversions of major and minor food components.
        14 Nonetheless, some of the most common fermented foods, including sauerkraut, kimchi, kefir, dry fermented sausage, yoghurt, cheese, kombucha, and miso ordinarily contain viable cells in notable quantities ranging between 106 and 109 cells/g or cells/ml. A significant portion of those microbes survive the passage through the human digestive tract. There have been promising results when tested in cells but there is not yet sufficient evidence in human studies to support the health claims being made.14

      9. Limit your consumption of emulsifiers. 15

        Emulsifiers are additives used in food processing to change the flavour and improve the texture, stability, and shelf-life of foods.
        16 Emulsifiers contribute to the increased prevalence of diseases associated with intestinal inflammation, including inflammatory bowel diseases and metabolic syndrome. There are two particular artificial emulsifiers, carboxymethyl cellulose and polysorbate 80, which significantly impact intestinal microbiota by increasing inflammation in the gut. These two emulsifiers irreversibly affected the composition of the microbiota.15 So, be on the lookout for these emulsifiers in the food products you consume and be sure to avoid eating them!

      10. Avoid the consumption of a Western Diet

        A Westernised diet is characterised by a high content of proteins (derived from fatty domesticated and processed meats), saturated fats, refined grains, sugar, alcohol, salt, and corn-derived fructose syrup, with an associated reduced consumption of fruits and vegetables.
        6Western diets have been found to lead to a composition of the microbiota that is associated with different types of disease.9



In the realm of wellness, the microbiome shines as a crucial component of holistic health, influencing our well-being from digestion to mood. Begin nurturing your gut health today by following our 9 tips but make sure to make this part of your lifestyle and not just a passing trend.

So, what is the take away message?

The microbiome trend is one we suggest getting behind as it is essential for holistic well-being. Lifestyle choices significantly impact gut health, emphasizing practices like maintaining a healthy circadian rhythm and adopting fibre-rich diets. By prioritising evidence-backed strategies, we nurture a thriving gut microbiota, unlocking the path to vitality and resilience.

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  1. Lloyd-Price J, Abu-Ali G, Huttenhower C. 2016. The healthy human microbiome. Genome Medicine. Apr 27;8(1). Available here: 
  2. Leong KSW, Derraik JGB, Hofman PL, et al. 2017. Antibiotics, gut microbiome and obesity. Clinical Endocrinology, 88(2), pp.185–200. Available here: 
  3. Panahi Y, Khedmat H, Valizadegan G, et al. 2015. Efficacy and safety of Aloe vera syrup for the treatment of gastroesophageal reflux disease: a pilot randomized positive-controlled trial. Journal of Traditional Chinese Medicine, 35(6), pp.632–636. Available here: 
  4. Hajiaghamohammadi AA, Zargar A, Oveisi S, et al. 2016. To evaluate of the effect of adding licorice to the standard treatment regimen of Helicobacter pylori. The Brazilian Journal of Infectious Diseases, 20(6), pp.534–538. Available here: 
  5. Shanahan F, Ghosh TS, O’Toole PW. 2020. The Healthy Microbiome (What is the definition of a healthy gut microbiome?). Gastroenterology. Nov;160(2). Available here:   
  6. Statovci D, Aguilera M, MacSharry J, et al. 2017. The Impact of Western Diet and Nutrients on the Microbiota and Immune Response at Mucosal Interfaces. Frontiers in Immunology, [online] 8(838). doi:
  7. Chassaing B, Vijay-Kumar M, Gewirtz AT. 2017. How diet can impact gut microbiota to promote or endanger health. Current Opinion in Gastroenterology. Nov;33(6):417–21. Available here:  
  8. Sanyaolu, Adekunle & Okorie, Chuku & Abbasi, et al. 2021. Effect of Artificial Sweeteners on the Gut Microbiome. Science Open Library biomedicine. 4; 179-183. Available here: 
  9. Ferraris C, Elli M, and Tagliabue A. 2020. Gut Microbiota for Health: How Can Diet Maintain A Healthy Gut Microbiota? Nutrients, 12(11), p.3596. Available here:
  10. Krumbeck JA, Maldonado-Gomez MX, Ramer-Tait AE, et al. 2016.  Prebiotics and synbiotics. Current Opinion in Gastroenterology. Mar;32(2):110–9. Available here:  
  11. Raigond P, Ezekiel R and Raigond B. 2014. Resistant starch in food: a review. Journal of the Science of Food and Agriculture, 95(10), pp.1968–1978. Available here: 
  12. Mu Q, Kirby J, Reilly CM, et al. 2017. Leaky Gut As a Danger Signal for Autoimmune Diseases. Frontiers in Immunology. May 23;8. Available here:  
  13. Engen PA, Green SJ, Voigt RM, et al. 2015. The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota. Alcohol Research Current Reviews. 37(2):223-36. Available here: 
  14. Marco ML, Sanders ME, Gänzle M, et al. 2021. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nature Reviews Gastroenterology and Hepatology. 18, 196–208. Available here:  
  15. Naimi S, Viennois E, Gewirtz AT, et al. 2021. Direct impact of commonly used dietary emulsifiers on human gut microbiota. Microbiome. 9, 66. Available here:  
  16. Vo TD, Lynch BS and Roberts A. 2018. Dietary Exposures to common emulsifiers and their impact on the gut microbiota: is there a cause for concern? Comprehensive Reviews in Food Science and Food Safety, 18(1), pp.31–47. Available here: 
  17. Bidell MR, Hobbs ALV, Lodise TP. 2022. Gut microbiome health and dysbiosis: A clinical primer. Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy. Oct 7;42(11):849–57. Available here:  
  18. Thursby E, Juge N. Introduction to the human gut microbiota. 2017. Biochemical Journal. May 16;474(11):1823–36. Available here: 
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Nicola Royce

Nicola Royce

Registered Dietitian, Postgraduate Diploma Diabetes

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