Trust Your Gut: Understanding and Healing Your Microbiome.
We have all heard the phrase ”trust your gut”. And it turns out, it's more than a saying. Your gut is often called your ”second brain” because it is deeply connected to your nervous system and mental health . The butterflies you feel when nervous or the sinking feeling in your stomach when something feels off are signals of this powerful gut-brain axis.
Why Your Gut Matters
Your digestive system is not just about breaking down food. It is home to trillions of bacteria, fungi, viruses and and other organisms that make up your microbiome. When these microbes are in balance, they support digestion, immunity, metabolism and even mood. But when the balance is disrupted, the effects ripple throughout the whole body, showing up not only as digestive issues but also as fatigue, brain fog, skin problems and even anxiety.
What Is the Microbiome?
The microbiome refers to the trillions of microorganisms living in your body, mainly in the large intestine. In fact, we carry around about 40 trillion bacterial cells compared to 30 trillion human cells, making us technically more bacteria than human (Sender et al., 2016).
Most of these microbes live in a symbiotic relationship with us. We provide them with food and shelter and in return, they support our health in many important ways:
Breaking down fibres we cannot digest on our own
Producing short-chain fatty acids (SCFAs), which reduce inflammation, strengthen the gut lining and provide energy for colon cells
Synthesising essential vitamins, such as B1, B9, B12 and vitamin K
Training and regulating the immune system, up to 80% of immune cells are located in the gut
Helping to metabolise bile and supporting detoxification pathways (Valdes et al., 2018)
Think of your microbiome as a garden. If the soil is healthy and diverse, plants thrive. But if the soil is depleted or overrun by weeds, the ecosystem suffers and so do you.
Fascinating Gut Facts
The gut has its own nervous system, called the enteric nervous system, often referred to as the second brain
Your gut produces around 90-95% of the body ’s serotonin , a key neurotransmitter for mood.
People with more diverse gut bacteria tend to have better immune health and a lower risk of chronic disease.
What is Dysbiosis?
Dysbiosis is the imbalance of the gut microbiome and can be caused by:
Loss of beneficial bacteria
Overgrowth of potentially pathogenic bacteria, or
Loss of overall bacterial diversity
Signs and Symptoms of Dysbiosis
Digestive issues like bloating, constipation, diarrhoea or heartburn
Unintentional weight changes
Fatigue & brain fog
Skin issues (acne, eczema, rashes)
Food intolerances & sensitivities
Nutrient deficiencies (like B12, iron, magnesium)
Sugar cravings (Dominguez et al., 2024)
Common Causes of Dysbiosis
Chronic Stress
Stress activates the fight-or-flight response, which shuts down digestion. Blood is diverted away from the gut, stomach acid production decreases and food sits longer in the intestines, creating the perfect environment for harmful bacteria to thrive. Stress hormones, such as cortisol, also alter the gut barrier, increasing the risk of leaky gut (Gao et al., 2022).
Poor Sleep
Lack of sleep disrupts the circadian rhythm, which gut microbes also follow. Studies show that even a few nights of poor sleep can reduce microbial diversity and increase inflammation. Quality sleep allows the gut lining to repair itself and beneficial bacteria to flourish (Sun et al., 2023).
Overuse of Certain Medication
Antibiotics do not discriminate between harmful and beneficial bacteria. Studies have shown that they can have a long-lasting effect on the gut microbiome, potentially impacting gut diversity for up to six months (Palleja et al., 2018). Furthermore, research indicates that even a single course of antibiotics may be associated with an increased risk of depression and anxiety (Lurie et al., 2015; Kohler-Forsberg et al., 2019).
Acid blockers (PPIs) reduce stomach acid, which is not only essential for protein digestion but also for keeping pathogens in check. Reducing stomach acid creates an environment in which unwanted microbes can colonize the upper gut, often contributing to small intestinal bacterial overgrowth (SIBO).
Anti-inflammatories (NSAIDs), common painkillers like ibuprofen, can damage the gut lining, raising the risk of ulcers, bleeding, and increased intestinal permeability, also known as “leaky gut”, all of which fuel dysbiosis (Rogers & Aronoff, 2015).
Low stomach acid
Contrary to popular belief, many digestive issues, such as reflux or bloating, are caused by too little stomach acid rather than too much. Low acid means that food isn't broken down properly, allowing undigested particles to ferment in the intestines, fuelling dysbiosis (Filardo et al., 2022).
Vitamin D deficiency
Vitamin D regulates the immune system and gut barrier integrity. Low levels are linked with reduced microbial diversity and increased inflammation in the gut (Akimbekov et al., 2020). Since most people spend little time in natural sunlight, deficiency is prevalent.
Western Diet (High in Processed Foods & Sugar)
Diets high in refined carbs, sugars, unhealthy fats and additives feed harmful bacteria and yeast, while starving beneficial bacteria of the fibres they need. Over time, this imbalance reduces microbial diversity and promotes inflammation.
Lack of Fibre & Plant Diversity
Beneficial bacteria feed on prebiotic fibres found in plants. Without enough variety, these microbes die off, while less desirable species survive by feeding on mucus from the gut lining itself. This weakens the intestinal barrier and creates inflammation (Desai et al., 2016).
Environmental Toxins
Pesticides, plastic and heavy metals can act as antimicrobial agents, killing good bacteria while encouraging resistant, harmful strains. They also disrupt hormone balance, which indirectly influences gut health (Bhardwaj et al., 2024).
Poor Eating Habits
Eating too quickly, not chewing thoroughly, or eating late at night puts extra strain on digestion. When food isn't broken down mechanically in the mouth, larger particles reach the gut, where they can ferment and fuel dysbiosis.
Excessive Cleanliness & Limited Microbial Exposure
Modern lifestyle often limits exposure to beneficial microbes. Overuse of disinfectants, avoiding soil and keeping homes overly sterile all reduce microbial diversity. Regular contact with natural environment, pets and safe exposure to dirt supports a resilient microbiome and reduces dysbiosis risk.
When we put these pieces together, it is clear that dysbiosis isn't caused by just one thing and it is often the result of modern lifestyle factors stacking up over time. The good news? Each of these causes can be addressed step by step through conscious diet and lifestyle changes.
How to Heal Dysbiosis Naturally
Healing dysbiosis isn't about a quick fix; it is about creating an environment where your gut microbiome can rebalance and thrive. Here is where nutrition and lifestyle become powerful tools.
Remove triggers
Reduce sugar, ultra-processed foods, alcohol and unnecessary medications that feed harmful bacteria.
Eat for Diversity
Add plant diversity by eating a wide variety of vegetables, herbs and plant fibres. Different plant feeds different beneficial bacteria, so variety is the key (Kumar et al., 2025). Aim for at least 30 different plant foods per week, this includes vegetables, fruits, nuts, seeds and herbs. Think ”eat your rainbow”.
Add Fermented Foods
Fermented foods are a natural way to introduce beneficial bacteria into your gut. Foods like sauerkraut, kimchi, kefir, kombucha, miso, tempeh and yogurt are rich in live cultures that can help restore microbial balance. During fermentation, naturally occurring bacteria convert sugars and starches into acids or alcohol, creating a tangy environment that preserves the food and encourages growth of probiotic strains such as Lactobacillus and Bifidobacterium. Regularly including fermented foods in your diet can help increase the diversity of your microbiome, support digestion and strengthen your gut barrier.
Support with Probiotics if Necessary
Specific strains may support balance, depending on your symptoms. For example, Lactobacillus for diarrhoea and Saccharomyces boulardii for post-antibiotic recovery (Parrino, 2006; Remes-Troche et al., 2020).
Nourish with Prebiotics
Prebiotics are a type of fibre that our digestive system can not digest, but our gut microbes thrive on them. When fermented, they produce short-chain fatty acids, like butyrate, that fuel the gut lining, reduce inflammation and support immunity (Yoo et al., 2024). Prebiotic foods include onion, garlic, leeks, asparagus, artichokes, bananas, apples, oats, beans, flaxseeds, almonds and dandelion greens.
Manage Stress, Support Sleep & Activate Vagus Nerve
Stress shuts down digestion, while relaxation techniques, such as deep breathing, meditation, humming or gentle walking activate the vagus nerve and improve gut motility.
Your microbiome follows a circadian rhythm, just like you. Certain bacteria are more active during the day, while others thrive at night. When you don't get enough deep, restorative sleep, this rhythm is disrupted. It can lead to reduced diversity of beneficial bacteria, overgrowth of opportunistic species that fuel inflammation, increased sugar cravings and processed foods and high stress hormone levels. Studies show that even a few nights of poor sleep can alter the microbiome. Consistent, high-quality sleep is one of the simplest but most overlooked tools for long-term gut health (Voigt et al., 2016).
Hydration & Digestion Support
Drink enough water, chew thoroughly and eat slowly! Use lemon water or apple cider vinegar before meals to gently support stomach acid. Additionally, eat bitter herbs and greens, like dandelion root, artichoke leaf, wormwood, yarrow, chamomile, rocket, chicory or endive to stimulate digestive juices.
Lifestyle Factors
Exercise regularly as movement fuels microbial diversity and eat collagen-supporting foods to strengthen the gut lining. Further, regular contact with nature and beneficial microbes is a simple but powerful way to support microbiome diversity. Spend time gardening, play in sand or soil and don't be afraid to get your hands a little dirty! Home-grown fruits and vegetables need to be rinsed lightly instead of scrubbing away every speck of dirt. Lastly, avoid overusing antibacterial soaps and hand sanitizers and clean your home with natural non-antibacterial products. These exposures introduce a wide variety of microbes that strengthen your immune system, improve microbial diversity and support long-term gut health.
Early-Life Exposure Matters
Children who play outdoors and interact with pets develop more resilient microbiomes, which can reduce the risk of allergies, autoimmune conditions and digestive issues later in life (Zhang et al., 2024).
Testing options for dysbiosis
While symptoms can give clues, functional tests provide deeper insight into what is really going on in your gut. Here are some of the most useful ones:
Organic acid test (OAT)
What it shows: By measuring metabolites in urine, this test can reveal yeast/fungal overgrowth, bacterial imbalance and nutrient deficiencies.
Why it matters: It helps identify hidden microbial activity that stool tests may miss and shows how imbalances affect your body's chemistry.
Comprehensive digestive stool analysis
What it shows: Levels of beneficial vs. harmful bacteria, parasites, yeast, inflammation markers, digestive enzymes and short-chain fatty acids.
Why it matters: It provides a detailed map of your microbiome and digestive function, so you can target therapies precisely (e.g., probiotics, enzymes or antimicrobials)
Hydrogen & methane breath test (SIBO test)
What it shows: It measures gasses produced by bacteria in the small intestine afte drinking a sugar solution (usually lactulose or glucose).
Why it matters: It helps diagnose SIBO, a common but often missed cause of bloating, constipation and IBS-like symptoms.
These tests are not about finding something wrong, but about creating a road map. They show where the imbalances are, so that nutrition, lifestyle and targeted support can be personalised rather than guessing.
Key Takeaways
Gut health affects more than just digestion, it influences mood, immunity and metabolism.
Dysbiosis is an imbalance in gut microbes that can cause a wide range of symptoms. Healing goes beyond probiotics, it requires nutrition, lifestyle, stress management and sometimes testing.
Think of your microbiome as a garden. When you nourish it with variety, fiber and care, it fluorishes and so does your overall health.
Funtional tests like OAT, stool analysis and breath test can guide targeted healing.
References
Akimbekov, N. S., Digel, I., Sherekhan, D. K., Lutfor, A. B. & Razzaque, M. S. (2020). Vitamin D and the Host-Gut Microbiome: A Brief Overview. Acta Histochemica et Cytochemica. 53(3):33-42. https://doi.org/10.1267/ahc.2011
Bhardwaj, G., Riadi, Y., Afzal, M., Bansal, P., Kaur, H., Deorari, M., Tonk, R. K., Almalki, W. H., Kazmi, I., Alzarea, S. I., Kukreti, N., Thangavelu, L. & Saleem, S. (2024). The hidden threat: Environmental toxins and their effects on gut microbiota. Pathology - Research and Practice. 255:155173. https://doi.org/10.1016/j.prp.2024.155173
Desai, M. S., Seekatz, A. M., Koropatkin, N. M., Kamada, N., Hickey, C. A., Wolter, M., Pudlo, N. A., Kitamoto, S., Terrapon, N., Muller, A., Young, V. B., Henrissat, B., Wilmes, P., Stappenbeck, T. S., Nunez, G. & Matens, E. C. (2016). A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility. Cell. 167(5):1339-1353. https://doi.org/10.1016/j.cell.2016.10.043
Dominguez, A. M. C., Salazar, D. J. R., Stefanolo, J. P., Serrano, M. C. C., Casas, I. C. & Pena, J. R. Z. (2025). Intestinal Dysbiosis: Exploring Definition, Associated Symptoms, and Perspectives for a Comprehensive Understanding - a Scoping Review. Probiotics and Antimicrobial Proteins. 17:440-449. https://doi.org/10.1007/s12602-024-10353-w
Filardo, S., Scalese, G., Virili, C., Pontone, S., Di Pietro, M., Covelli, A., Bedetti, G., Marinelli, P., Bruno, G., Stramazzo, I., Centanni, M., Sessa, R. & Severi, C. (2022). The Potential Role of Hypochlorhydria in the Development of Duodenal Dysbiosis: A preliminary Report. Frontiers in Cellular and Infection Microbiology. 12:854904. https://doi.org/10.3389/fcimb.2022.854904
Gao, F., Guo, R., Ma, Q., Li, Y., Wang, W., Fan, Y., Ju, Y., Zhao, B., Gao, Y., Qian, L., Yang, Z., He, X., Liu, Y., Peng, Y., Chen, C., Chen, Y., Gao, C., Zhu, F. & Ma, X. (2022). Stressful events induce long-term gut microbiota dysbiosis and associated post-traumatic stress symptoms in healthcare workers fighting against COVID-19. Journal of Affective Disorders. 303:187-195. https://doi.org/10.1016/j.jad.2022.02.024
Kohler-Forsberg, O., Petersen, L. & Gasse, C. (2019). A Nationwide Study in Denmark of the Association Between Treated Infections and the Subsequent Risk of Treated Mental Disorders in Children and Adolescents. JAMA Psychiatry. 76(3):271-279. https://doi.org/10.1001/jamapsychiatry.2018.3428
Kumar, S., Mukherjee, R., Gaur, P., Leal, E., Lyu, X., Ahmad, S., Puri, P., Chang, C. M., Raj, V. S. & Pandey, R. P. (2025). Unveiling roles of beneficial gut bacteria and optimal diets for health. Frontiers Microbiology. 16. https://doi.org/10.3389/fmicb.2025.1527755
Lurie, I., Yang, Y. X., Haynes, K., Mamtani, R. & Boursi, B. (2015). Antibiotics Exposure and the Risk for Depression, Anxiety, or Psychosis: A Nested Case-Control Study. Journal of Clinical Psychiatry. 76(11):1522-1528. https://doi.org/10.4088/JCP.15m09961
Palleja, A., Mikkelsen, K. H., Forslund, S. K., Kashani, A., Alllin, K. H., Nielsen, T., Hansen, T. H., Liang, S., Feng, Q., Zhang, C., Pyl, P. T., Coelho, L. P., Yang, H., Wang, J., Typas, A., Nielsen, M. F., Nielsen, H. B., Bork, P., Wang, J., Vilsboll,T., Hansen, T., Knop, F. K., Arumugam, M. & Pedersen, O. (2018). Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology. 3:1255-1265. https://doi.org/10.1038/s41564-018-0257-9
Parrino, T. A. (2006). Review: Saccharomyces boulardii reduces risk for antibiotic-associated diarrhea. ACP Journal Club Archives. 144(2). https://doi.org/10.7326/ACPJC-2006-144-2-045
Prichett, L. M., Yolken, R. H., Wu, L., Severance, E. G. & Kumra, T. (2022). Relationship between antibiotic exposure and subsequent mental health disorders in a primary care health system. Brain, Behaviour, & Immunity-Health. 21:100430. https://doi.org/10.1016/j.bbih.2022.100430
Remes-Troche, J. M., Coss-Adame, E. & Ortiz, R. S. (2020). Lactobacillus acidophilus LB: a useful pharmabiotic for the treatment of digestive disorders. Therapeutic Advances in Gastroenterology. https://doi.org/10.1177/17562848209711201
Rogers, M. A. M. & Aronoff, D. M. (2015). The Influence of Nonsteroidal Anti-Inflammatory Drugs on the Gut Microbiome. Clinical Microbiology and Infection. 22(2):178.e1-178.e9. https://doi.org/10.1016/j.cmi.2015.10.003
Sender, R., Fuchs, S. & Milo, R. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biology. 14(8):e1002533. https://doi.org/10.1371/journal.pbio.1002533
Sun, J., Fang, D. Wang, Z. & Liu, Y. (2023). Sleep Dprivation and Gut Microbiota Dysbiosis: Current Understandings and Implications. International Journal of Molecular Sciences. 24(11):9603. https://doi.org/10.3390/ijms24119603
Valdes, A. .M., Walter, J., Segal, E. & Spector, T. D. (2018). Role of the gut microbiota in nutrition and health. BMJ. 361. https://doi.org/10.1136/bmj.k2179
Voigt, R. M., Forsyth, C. B., Green, S. J., Engen, P. A. & Keshavarzian, A. (2016). Circadian Rhythm and the Gut Microbiome. International Review of Neurobiology. 131:193-205. https://doi.org/10.1016/bs.irn.2016.07.002
Yoo, S., Jung, S. C., Kwak, K. & Kim, J. S. (2024). The Role of Prebiotics in Modulating Gut Microbiota: Implications for Human Health. International Journal of Molecular Science. 25(9):4834. https://doi.org/10.3390/ijms25094834
Zhang, L., Agrawal, M., Ng, S. C. & Jess, T. (2024). Early life exposures and the microbiome: implications for inflammatory bowel disease prevention. Gut. 73(3):541-549. https://doi.org/10.1136/gutjnl-2023-330002
Comments