Microbiome Makeover: Simple Steps To Support Your Gut Health

  • Regina Lopes Senior Nursing Assistant, Health and Social Care, The Open University

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Although microbiome and microbiota have been known to researchers for a long time, it is until recent years that more attention has been paid to it as it plays a very important role in human health. It is a field that is currently being extensively researched and scientists are still learning more details about its functions, mechanisms and overall how it impacts health. What it is known for now is that some components of diet have an impact on microbiome makeover, and microbiome plays a crucial role in different aspects of health.

What is the microbiome?1

The term “microbiome” refers to the trillions of microbes and their genetic material living in the human body, their activity and dynamic environment. These microbes are bacteria, fungi, parasites, and viruses. These microbes are mainly found in our gastrointestinal tract (GI tract) or “gut”, which is the digestive system in charge of digesting the food eaten and fluids ingested. Microbes are also found in other parts of the body such as skin and lungs.

For the purpose of this article, the term microbiome will refer to the microbes found in the gut.

What is the difference between microbiome and microbiota?

It is important to differentiate between the terms microbiota and microbiome as sometimes they are used interchangeably but these mean two different things. As aforementioned, microbiome refers to microbes, its genes and activities in the human body. In contrast, the term microbiota refers to the microorganisms themselves (bacteria, fungi, parasites, and viruses).

What is the gut?

Your gastrointestinal tract or “gut” as commonly known, is the part of your body in charge of your digestive system. The gut is composed of the following parts:

  • Mouth
  • Oesophagus
  • Stomach
  • Small intestine
  • Large intestine (colon, rectum, anus)

Digestion is also aided by other organs such as the liver, the pancreas and the gallbladder that produce substances helping to break down the food ingested into nutrients that will be absorbed and then distributed to different parts of the body for different functions.

What is the link between microbiome and gut health?2

In essence, gut health is determined by the microbes living in the gut. There are different types of microbes: some are “healthy” or helpful in keeping our gut health in good balance (“symbiosis”), but others are “pathogenic” meaning that they can create disease (“dysbiosis”). The microbiome affects different aspects of our health including:

  • Digestion (production of amino acids, vitamin k and B vitamins)
  • Immune system (protection against diseases caused by microorganisms)
  • Certain diseases (cardiovascular disease, cancer, diabetes, respiratory)
  • Brain (mood, cognitive function, behaviour, anxiety, depression, Alzheimer’s, Parkinson’s disease, etc.)

The link between the gut and brain is called “the gut-brain axis”. This is a communication in two directions, from gut to brain and brain to gut. This close connection shows how psychological stress can affect the gut, for instance when it is manifested in irritable bowel syndrome (diarrhoea, cramps, bloating). This connection also shows how the gut microbiota can affect the brain (autism, anxiety, depression, mood, cognition and overall mental health).3,4

Maintaining a healthy microbiome in the gut can have a great impact on the overall health.

What simple steps can be taken to support gut health?

Now that scene has been set with information about microbiome, the gut, and the link between them, let us take a look at some simple steps to support gut health.


Diet is what will have the most direct impact on the microbiome and gut health as food and fluids go through the gut to be digested and absorbed.

Taking probiotics

The definition of probiotics is: “Live microorganisms that, when administered in adequately amounts, confer a health benefit to the host.” This means that probiotics are live bacteria found in food or supplements that give a health benefit to the gut. It is required that there is a health benefit documented as the result from the microorganisms in the right dose.  As aforementioned, it is important to keep in mind that certain bacteria, in the correct amounts, are healthy and beneficial to the body, and not necessarily create disease.5

Some foods naturally contain probiotics, other foods have them added, and sometimes they are sold as supplements. Please see FAQ for further information about supplements. The live bacteria are usually: lactobacilli and bifidobacteria, and the strains have to be specified in the labels.

Probiotics can be found in: certain fermented foods that contain the probiotics or that are fermented with probiotics, for instance yoghurts with probiotics, or milk/oat fermented with probiotics.

Probiotics can assist in digestion, immunity, metabolism, decrease diarrhoea provoked by antibiotics, etc.

Eating fermented foods

Fermented foods are the result of a fermentation process using bacteria, yeast or mould. Fermented foods are not probiotics (do not require a documented health benefit) but can contain a mix of microorganisms. Sometimes fermented foods do no longer contain live microorganisms as further processing (pasteurisation, baking) eliminates the bacteria.

Examples of fermented foods that maintain live bacteria but are not probiotics:

  • kombucha
  • kimchi
  • sauerkraut
  • sourdough bread

Taking prebiotics

Prebiotics is the ‘food’ that feeds the probiotics (live microorganisms) found in the gut, particularly lactobacilli and bifidobacteria. The current definition of prebiotic is: “A substrate that is selectively utilised by host microorganisms conferring a health benefit.”

Dietary prebiotics are food that cannot be digested by humans (fibre). Fibre is a type of carbohydrate, and the ones that are considered prebiotics are: inulin, galacto-oligosaccharides, fructo-oligosaccharides, and lactulose.6 These are fibres found in certain foods such as:

  • Asparagus
  • Sugar beet
  • Garlic and onion
  • Soya beans, and beans
  • Chicory
  • Jerusalem artichoke
  • Honey
  • Banana
  • Tomato
  • Rye, and barley
  • Peas
  • Seaweed, and microalgae

Prebiotics can help with cardiometabolic health, nutrient availability, and immunity.

Eating enough dietary fibre

Not all fibres are prebiotics, but dietary fibre plays an important role in gut health by regulating the microbiota.  As a result, dietary fibre has an impact on metabolism of fat and carbohydrates, which may help in the prevention and management of cardiovascular disease, type 2 diabetes, and obesity. However, further research is needed to better understand the mechanisms.7

Fibre is present naturally in the following foods: fruits, vegetables, whole grains, and legumes. It is recommended for a healthy adult, who eats about 2000 (kcals) calories per day, to consume 28 grams of fibre.8


Polyphenols are a type of antioxidant found in certain fruits, vegetables, red wine, coffee, tea. It has been suggested that polyphenols may contribute to microbiome in gut health by promoting growth of healthy bacteria and inhibiting growth of unhealthy bacteria. However, further research is needed.


Keeping hydrated is another way to look after the microbiome and gut health. It has been suggested that drinking enough water has an impact on the gut microbiome.

Besides diet, what other steps can be taken to look after gut health?

Avoid excessive use of medications, in particular antibiotics11

The use of certain medications such as antibiotics, laxatives, metformin (commonly used for type 2 diabetes) and proton pump inhibitors (commonly used for heartburn) have been found to have an association with microbiome makeover.

Particular attention should be given to the use of antibiotics as these directly affect the gut microbiome. Antibiotics reduce the microbiome in the gut, leading to becoming more likely to catch an infection. Also, antibiotic resistance is the result of using too many antibiotics and therefore the body no longer responds to the effect of antibiotics.

Keeping physically active

Physical activity (endurance or strength-training) has also been found to help in diversifying the composition of the gut microbiome.12 No particular amount of exercise is recommended at the moment specifically for gut health, but the World Health Organization recommends about 150 minutes of activity per week.

Frequently asked questions

Should I take probiotic supplements?

Caution should always be practised when considering using supplements of any type as these may not have been through proper rigorous and extensive testing. Before taking any supplement, it is essential to consult with a medical professional whether the supplement in particular is deemed safe and whether the health claims have been recognized. Particular caution should be taken by at-risk individuals when considering taking a probiotic as a supplement. Although these are deemed safe for healthy individuals, for at-risk populations (immunocompromised individuals, premature babies etc.) manufacturers should provide a report of microbiological standards that meet certain criteria.13

After making sure it is safe to take a supplement for an individual condition, it is important to look at the type of supplement as many are not regulated and may be unsafe or may not provide any supplementary benefits compared to eating actual foods containing probiotics.


Microbiome makeover has an important impact on gut health, Looking after your gut health will have an impact on other aspects of your health. To keep your gut healthy, these are the simple steps to follow: looking after your diet, making sure you eat a wide variety of foods including probiotics, fermented foods, prebiotics and fibre. Moreover keeping adequately hydrated, and physically. Finally, being aware of other factors that can affect your gut health (e.g. taking antibiotics).


  1. Berg G, Rybakova D, Fischer D, Cernava T, Vergès MCC, Charles T, et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome [Internet]. 2020 Jun 30 [cited 2024 May 3];8(1):103. Available from: https://doi.org/10.1186/s40168-020-00875-0
  2. Hou K, Wu ZX, Chen XY, Wang JQ, Zhang D, Xiao C, et al. Microbiota in health and diseases. Sig Transduct Target Ther [Internet]. 2022 Apr 23 [cited 2024 May 3];7(1):1–28. Available from: https://www.nature.com/articles/s41392-022-00974-4
  3. Appleton J. The gut-brain axis: influence of microbiota on mood and mental health. Integr Med (Encinitas) [Internet]. 2018 Aug [cited 2024 May 3];17(4):28–32. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469458/
  4. Carabotti M, Scirocco A, Maselli MA, Severi C. The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems. Ann Gastroenterol [Internet]. 2015 [cited 2024 May 3];28(2):203–9. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4367209/
  5. International Scientific Association for Probiotics and Prebiotics. Probiotics [Cited 2024 May 3] Available from: https://isappscience.org/wp-content/uploads/2019/04/Probiotics_0119.pdf
  6. Davani-Davari D, Negahdaripour M, Karimzadeh I, Seifan M, Mohkam M, Masoumi SJ, et al. Prebiotics: definition, types, sources, mechanisms, and clinical applications. Foods [Internet]. 2019 Mar 9 [cited 2024 May 3];8(3):92. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463098/
  7. Cronin P, Joyce SA, O’Toole PW, O’Connor EM. Dietary fibre modulates the gut microbiota. Nutrients [Internet]. 2021 May 13 [cited 2024 May 3];13(5):1655. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8153313/
  8. Sanders ME. Do you know the difference between fibre and prebiotics? A new ISAPP infographic explains - International Scientific Association for Probiotics and Prebiotics (Isapp) [Internet]. 2018 [cited 2024 May 3]. Available from: https://isappscience.org/infographic-fiber-prebiotics/
  9. Wan MLY, Ling KH, El-Nezami H, Wang MF. Influence of functional food components on gut health. Critical Reviews in Food Science and Nutrition [Internet]. 2019 Jul 4 [cited 2024 May 3];59(12):1927–36. Available from: https://www.tandfonline.com/doi/full/10.1080/10408398.2018.1433629
  10. Vanhaecke T, Bretin O, Poirel M, Tap J. Drinking water source and intake are associated with distinct gut microbiota signatures in us and uk populations. J Nutr. 2022 Jan 11;152(1):171–82.
  11. Vich Vila A, Collij V, Sanna S, Sinha T, Imhann F, Bourgonje AR, et al. Impact of commonly used drugs on the composition and metabolic function of the gut microbiota. Nat Commun [Internet]. 2020 Jan 17 [cited 2024 May 3];11:362. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6969170/
  12. Shahar RT, Koren O, Matarasso S, Shochat T, Magzal F, Agmon M. Attributes of physical activity and gut microbiome in adults: a systematic review. Int J Sports Med [Internet]. 2020 Oct [cited 2024 May 3];41(12):801–14. Available from: http://www.thieme-connect.de/DOI/DOI?10.1055/a-1157-9257
  13. Sanders ME, Merenstein DJ, Ouwehand AC, Reid G, Salminen S, Cabana MD, et al. Probiotic use in at-risk populations. Journal of the American Pharmacists Association [Internet]. 2016 Nov [cited 2024 May 3];56(6):680–6. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1544319116307324

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PhD Nutrition Student, University of Plymouth

Registered Nurse with several years of clinical experience as a Clinical Nurse Specialist in Cardiovascular Prevention and Rehabilitation. Strong academic background in Nutrition and Dietetics (BSc and MSc), and currently studying part-time towards a PhD in Nutrition and health. The PhD has reignited her passion for writing to communicate and educate about health concepts to a wider public by translating science into accessible content for a diverse audience. When she is not writing or reading with her cat, she can be found running or doing Pilates.

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