From Probiotics To Fermented Foods: Exploring Ways To Boost Your Microbiome Naturally

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

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Are you aware that a lot of health conditions can be triggered by an unhealthy microbiome? That is why the phrase “a healthy microbiome makes a healthy body” is an undisputed fact. This diverse community of microbes, called the microbiome, residing in your body plays a synergistic role in ensuring your overall wellness. Thus, if you regularly consume foods like kimchi, pickled vegetables, sauerkraut, and so on, you are doing your body a huge favour.

Unfortunately for your microbiome, modern life gives them a hammering. Wonder how? As antibiotics kill the bad bacteria as well as the good ones, so does our love for processed foods. Add that to our innate fear of dirt and a sedentary lifestyle, and you have a recipe for an environment detrimental to your microbiome. This is because these factors result in a lack of diversity. So, what can be done about it? This article explores ways to naturally boost your microbiome. Firstly, how do you know that your microbiome needs a boost? 

Having a resilient microbiome means having a good balance of microbes in your gastrointestinal tract (which is where a large percentage of the microbes in your body reside).1 An unhealthy microbiome can be challenging to recognize. Thus, some signs of an imbalanced microbiome include digestive issues such as constipation, diarrhoea, ulcerative colitis, sleep disturbances, fatigue, hormonal conditions, neurological disorders like chronic migraine, mood disorders, autoimmune diseases, food intolerance, etc. 

Why is microbiome diversity important?

Maintaining the diversity of your microbiome is essential to ensuring that it can carry out the variety of roles it plays in maintaining human health. This diversity is crucial in sustaining the needs of an ideal gut “ecosystem.” When there is a lack of diversity, which can be caused by antibiotics, an unhealthy diet, and so on, the gut will be in a state called dysbiosis. 

Dysbiosis is the disruption of the microbiome and occurs when there is an overgrowth of pathogenic microbes and the loss of health-promoting ones, resulting in decreased diversity in the microbial community. The gut microbial community is impacted by factors including diet, inflammation, pathogenic infections, and antibiotic use. However, diet plays a dominating role in shaping your microbiome and modifying the composition of key populations. A high-fat diet can transform a healthy microbiome into an insidious disease-inducing entity.2

Why do you need to boost your microbiome? 

Here are some reasons why you need to boost your microbiome:

Maintenance of Immune system

The gut has about 70-80% of the immune cells in your body. This implies that there is intricate interplay between your gut microbiome and the immune system.3 Boosting your microbiome enables the suppression of pathogens, pro-inflammatory factors and stimulates the proliferation of immune cells.4

Production of fermentation by-products

The body is typically unable to digest the dietary fibre you eat. However, boosting your microbiome enables the fermentation of this fibre to produce what is called short-chain fatty acids (SCFA) such as acetate, propionate and butyrate.5 These by-products inhibit the growth of pathogens, mucin production and immune-fighting cytokines.4

Strengthening the gut-barrier integrity

Boosting your microbiome decreases permeability and increases tight junctions. This reduces the leakage of endotoxins into the bloodstream and subsequent onset of digestive conditions.

Proper absorption of nutrients

A well-functioning microbiome produces a wide variety of enzymes that help in the breakdown of complex molecules. For instance, some types of bacteria in the gut produce enzymes called proteases that help break down proteins into amino acids. This facilitates their absorption in the small intestine.6

Natural ways to boost your microbiome

One thing that several research has confirmed multitudinously is that diversity is key when it comes to having a well-functioning microbiome. In other words, the more families of bacteria in your gut, the healthier you’re likely to be. Hence, here are some natural ways to boost your microbiome.

Incorporate prebiotics, probiotics and/or synbiotics

Prebiotics are non-digestible dietary fibres that promote the growth of beneficial and specific organisms in the gut. Probiotics are microorganisms that beneficially modulate the composition of the gut microbiome directly.

Synbiotics is a combination of the two (i.e., prebiotics and probiotics). Nutritional supplementation with prebiotics, probiotics, or synbiotics does not only lead to diversity and abundance of gut bacteria but also overcome difficulties in the survival of existing probiotics in the gastrointestinal tract.7

Additionally, dietary interventions aimed at boosting specific challenge-diminished species must be appropriately dosed so that the targeted species do not become too dominant and negatively affect diversity, which will be against the desired effect.8 Foods rich in probiotics include sauerkraut, pickled vegetables like cabbage and cucumber, yoghourt, kombucha, etc.

Consume fermented foods

Fermentation is a process whereby anaerobic biochemical change occurs as a result of enzymatic or microbial action on food. Fermented foods contain a broad range of beneficial bacteria that support immune function, improve metabolic syndrome, intestinal permeability, depression, and anxiety.9

Fermented foods contain microorganisms that enhance the bioavailability of nutrients, enrich the sensory quality of the food, impact bio-preservative effects, degrade toxic components, and reduce anti-nutritive factors. These organisms also produce antioxidant and antimicrobial compounds.10

Regulate your sleep cycle

It has been found in a study that microbiome diversity is positively correlated with sleep efficiency.11 The disruption of sleep cycles induces time-specific changes in the gut microbiome.12 Circadian clock disruption also increases the permeability of the intestinal epithelial barrier, increasing the risk of developing intestinal conditions like leaky gut syndrome. Therefore, maintaining a regular sleep routine boosts and diversifies your microbiome. 

Cut out sugar and processed foods

Regular consumption of processed foods and sugar encourages the growth of bacteria that promote digestive issues and obesity.2 For instance, F. prausnitzii is a beneficial species that is diminished when the microbiota is challenged with a high-fat diet and antibiotics. This bacteria is associated with recovery from diarrhoea.13 

Incorporate intermittent fasting

It might seem strange that we can help our microbiome by not eating. However, a study revealed that intermittent fasting favourably increased the number of anti-inflammatory bacteria Lactobacillus and Bifidobacterium, while the number of pathogenic bacteria decreased.15 

In another study, changes in the microbiome as a result of water-only fasting were associated with a decrease in the population of Fusobacterium, a bacterium that promotes colorectal cancer.14 The results of this study show that water-only fasting could have a profound and long-lasting effect on the gut microbiome and can prompt the development of a more homogenous gut microbial community.14 

Find out if you have any parasitic infections and address them

Certain parasites can affect the gut without causing noticeable symptoms. For instance, the protozoa Giardia intestinalis was found to trigger long-lasting alterations to the commensal microbes in the gut mucosa by damaging the epithelial barrier, leading to a severe immune reaction towards its microbiome.16


What foods help repair the gut microbiome?

Fibres that boost the microbiome are particularly high in whole grains and beans. Also, fermented foods like brined pickles, sauerkraut, kimchi and yoghourt help repair the gut and diversify your microbiome.

How can you tell if you have a healthy microbiome? 

Indicators of a healthy microbiome include absence of pain, bloating and other digestive conditions. Also, regular bowel movement that is pain-free with soft consistency will also give you an idea of how healthy your gut microbiome is.

How long does it take to reset your microbiome? 

This depends mainly on your diet. For some people, the composition of the gut microbiome may return to baseline in a couple of months. But for others, it might take longer than that. 


  • Although you might not be able to restore your microbiome completely, you can definitely make it better
  • Changes to the microbiome are triggered mainly by intake of antibiotics, a diet rich in high fat and processed foods and lack of fibre and fermented foods
  • Therefore, your best bet in boosting your microbiome is making dietary modifications, getting regular exercise, consuming high-fibre foods and incorporating probiotics and prebiotic rich- foods such as almonds, bananas, cabbage, pickled vegetables, yoghourt, etc. 
  • Ensuring you have a well-balanced microbiome is the key to achieving good health and reducing the risk of developing a variety of health conditions both in the gut and the rest of the body


  1. Proctor LM. The Human Microbiome Project in 2011 and Beyond. Cell Host & Microbe [Internet]. 2011 [cited 2024 Apr 16]; 10(4):287–91. Available from:
  2. Brown K, DeCoffe D, Molcan E, Gibson DL. Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients. 2012; 4(8):1095–119.
  3. Wiertsema SP, Van Bergenhenegouwen J, Garssen J, Knippels LMJ. The Interplay between the Gut Microbiome and the Immune System in the Context of Infectious Diseases throughout Life and the Role of Nutrition in Optimising Treatment Strategies. Nutrients [Internet]. 2021 [cited 2024 May 2]; 13(3):886. Available from:
  4. Haapalahti M. Nutrition, gastrointestinal food hypersensitivity and functional gastrointestinal disorders in schoolchildren and adolescents. Kuopio: University of Kuopio; 2005.
  5. Ho JT, Chan GC, Li JC. Systemic effects of gut microbiota and its relationship with disease and modulation. BMC Immunol [Internet]. 2015 [cited 2024 May 2]; 16(1):21. Available from:
  6. Davila A-M, Blachier F, Gotteland M, Andriamihaja M, Benetti P-H, Sanz Y, et al. Intestinal luminal nitrogen metabolism: Role of the gut microbiota and consequences for the host. Pharmacological Research [Internet]. 2013 [cited 2024 May 2]; 68(1):95–107. Available from:
  7. Rioux KP, Madsen KL, Fedorak RN. The Role of Enteric Microflora in Inflammatory Bowel Disease: Human and Animal Studies with Probiotics and Prebiotics. Gastroenterology Clinics of North America [Internet]. 2005 [cited 2024 May 2]; 34(3):465–82. Available from:
  8. Dogra SK, Doré J, Damak S. Gut Microbiota Resilience: Definition, Link to Health and Strategies for Intervention. Front Microbiol [Internet]. 2020 [cited 2024 May 2]; 11:572921. Available from:
  9. Bell V, Ferrão J, Pimentel L, Pintado M, Fernandes T. One Health, Fermented Foods, and Gut Microbiota. Foods [Internet]. 2018 [cited 2024 May 2]; 7(12):195. Available from:
  10. Tamang JP, Watanabe K, Holzapfel WH. Review: Diversity of Microorganisms in Global Fermented Foods and Beverages. Front Microbiol [Internet]. 2016 [cited 2024 May 2]; 7. Available from:
  11. Smith RP, Easson C, Lyle SM, Kapoor R, Donnelly CP, Davidson EJ, et al. Gut microbiome diversity is associated with sleep physiology in humans. PLoS ONE [Internet]. 2019 [cited 2024 May 2]; 14(10):e0222394. Available from:
  12. Voigt RM, Forsyth CB, Green SJ, Mutlu E, Engen P, Vitaterna MH, et al. Circadian Disorganisation Alters Intestinal Microbiota. PLoS ONE [Internet]. 2014 [cited 2024 May 2]; 9(5):e97500. Available from:
  13. Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol [Internet]. 2018 [cited 2024 May 2]; 3(11):1255–65. Available from:
  14. He Y, Yin J, Lei J, Liu F, Zheng H, Wang S, et al. Fasting challenges human gut microbiome resilience and reduces Fusobacterium. Medicine in Microecology [Internet]. 2019 [cited 2024 May 2]; 1–2:100003. Available from:
  15. Khan MN, Khan SI, Rana MI, Ayyaz A, Khan MY, Imran M. Intermittent fasting positively modulates human gut microbial diversity and ameliorates blood lipid profile. Front Microbiol [Internet]. 2022 [cited 2024 May 2]; 13:922727. Available from:
  16. Chen T-L, Chen S, Wu H-W, Lee T-C, Lu Y-Z, Wu L-L, et al. Persistent gut barrier damage and commensal bacterial influx following eradication of Giardia infection in mice. Gut Pathog [Internet]. 2013 [cited 2024 May 3]; 5(1):26. Available from:

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This content is purely informational and isn’t medical guidance. It shouldn’t replace professional medical counsel. Always consult your physician regarding treatment risks and benefits. See our editorial standards for more details.

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Chidubem Chuka Nwosu

Masters of Microbiology, University of Lagos, Nigeria

Chidubem is a research writer and microbiologist with administrative and customer service roles in retail pharmacies. She has years of experience in the pharmaceutical industry as well as remote bilingual translation services for private companies with advanced certification in French.

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