Your gut is home to trillions of microorganisms. Many of them are beneficial or commensal bacteria, and they play an important role in digestion, nutrient absorption, immunity and overall health.
A healthy gut microbiome is balanced and diverse, packed with beneficial bacteria such as Bifidobacterium, Lactobacillus and others that support your body in functioning at its best. When that balance is disrupted, normal digestive and immune processes can be affected, and a range of symptoms may develop.
Gut dysbiosis is the name given to this kind of imbalance. It happens when potentially harmful bacteria become overrepresented, creating an imbalance between beneficial and disruptive bacteria that can undermine how well your gut functions. A 2022 overview in the journal Microorganisms links dysbiosis with a wide range of digestive and wider health problems, although most of this research shows association rather than proven cause.
Dysbiosis is generally considered multifactorial, meaning several things contribute at once: lifestyle, diet, genetics, previous infections and, in some cases, certain medications including antibiotics and NSAID’s such as Naproxen.
What are the symptoms of an unhealthy gut?
The symptoms of gut dysbiosis vary from person to person. Some people experience common digestive issues such as bloating, diarrhoea, constipation, indigestion and stomach discomfort, whereas others notice chronic fatigue, weight changes, mood changes or disturbed sleep.
Gut imbalances may also show up in your skin. The gut and the skin communicate in both directions along the gut-skin axis, and a 2025 review in Gut Microbes describes how an imbalance on one side may contribute to problems on the other. The links found so far are associations rather than proven causes.
Some people with gut symptoms also notice that they tolerate certain foods less well than before, although this can have a range of possible explanations and should not be assumed to be caused by dysbiosis alone.
What causes a gut imbalance?
Research points to several factors that may contribute to gut dysbiosis.
Medication: Antibiotics fight infection effectively, but they can also deplete beneficial gut bacteria along the way. Prolonged or frequent antibiotic use is a recognised contributor to dysbiosis; a 2023 review, mostly in children, found changes that can persist for up to two years after treatment. If you have recently finished a course, our guide to how to help your gut recover after antibiotics covers what helps. Other medicines that may affect the balance of the gut include NSAIDs like Naproxen and Proton Pump Inhibitors such as Omeprazole, which research suggests can reduce the bacterial richness of the gut microbiome.
Diet: A Western-style diet, high in processed foods, sugars and saturated fats but low in fibre, has been associated with a reduction in the diversity and number of beneficial gut bacteria. Researchers argue it can also increase inflammation throughout the body, raising the risk of chronic conditions over time.
Excessive alcohol intake: Research indicates that frequent consumption of alcohol can damage the gut lining and alter the composition of the gut microbiota, making the environment more hospitable to harmful microbes.
Chronic stress: High levels of stress hormones such as cortisol have been associated with negative effects on gut balance and the strength of the gut barrier, potentially reducing the number of beneficial bacteria.
Lifestyle: A lack of physical activity has been associated with changes to the composition and activity of the gut microbiome, and reviews of exercise research link regular movement with a more diverse mix of gut bacteria.
Gastrointestinal infections: A bout of gastroenteritis can alter the make-up of the gut microbiota, sometimes for the long term. In some people this develops into post infectious IBS, where IBS symptoms begin after the infection itself has cleared, reported in roughly 5 to 32% of cases.
Sleep quality: Poor sleep quality and lack of sleep may disrupt the gut microbiome, according to a 2020 review of sleep and circadian rhythm research, and the relationship appears to run in both directions.
Environmental factors: Exposure to pollutants and certain chemicals may also adversely affect gut bacteria, according to a 2019 review of toxicology research, although the evidence in humans is still limited.
Intestinal parasites: Parasites like Giardia lamblia, Blastocystis hominis, and Entamoeba histolytica can compete with commensal bacteria for nutrients and space. This competition has been shown to reduce populations of beneficial bacteria such as Lactobacillus and Bifidobacterium. Over time, that shift may disrupt the normal balance of the microbiome.
Testing for intestinal parasites may be appropriate in some cases, particularly where symptoms suggest infection.
How is gut dysbiosis tested and identified?
Understanding the state of your gut microbiome starts with the full picture: your medical history, your current symptoms, your diet and lifestyle habits, and any medication you have taken, particularly antibiotics.
A gut microbiome health test in the form of a stool sample can provide detailed, personalised information about the composition and diversity of the bacteria within your gut. Our reports are designed to help you understand which bacteria you carry and in what proportions. They are not a clinical diagnosis. If you are new to testing, our guide explains what a gut microbiome test is, how they work, and what they can help you to identify. There is no agreed optimal gut microbiome profile, so no test can tell you that your gut is right or wrong. What it can show is the composition and relative abundance of your gut bacteria, patterns worth considering alongside symptoms, diet, lifestyle, and medical history.
In certain circumstances, a healthcare professional may also arrange a blood test to check for inflammation, and nutrient deficiencies are worth exploring too, as these can be linked to gut health issues.
Breath tests and microbiome tests provide different types of information: breath testing is used mainly to assess small intestinal bacterial overgrowth, whereas a microbiome test gives broader information about bacterial composition.
How we measure gut diversity using the Shannon Index
One of the core metrics we use when interpreting gut microbiome results is the Shannon Index, which measures microbial diversity by looking at both the number of bacterial species present and how evenly they are distributed across the sample.
In simple terms, a higher score reflects a more varied and balanced microbiome, while a lower score may suggest reduced diversity or overrepresentation of certain bacterial groups. Research has linked lower microbial diversity with less favourable gut health patterns, although the Shannon Index should never be interpreted on its own.
In our reports, the Shannon Index, which can be found on the very first page of our sample report, is used alongside the wider bacterial breakdown to help place an individual result into context. It is not a diagnostic result, but one part of the broader picture. Where diversity appears low or suboptimal, this may help inform the dietary and prebiotic recommendations included in the report.
How do you fix a gut imbalance?
There is no single treatment pathway for gut dysbiosis. That said, a range of diet and lifestyle modifications are broadly supported by evidence as the first step towards restoring the balance and function of the gut microbiome. The general principle is to feed beneficial bacteria whilst reducing the conditions that allow less favourable microbial patterns to thrive.
Knowing which bacteria you have within your gut, and which foods may support them, makes those changes targeted rather than guesswork. A gut microbiome test for gut dysbiosis can show whether the balance of bacteria in your gut has shifted.
The dietary changes with the best evidence behind them are reducing sugar intake, increasing daily fibre to the NHS-recommended 30g, and including fermented foods that contain live cultures. In a 2021 trial at Stanford University, 36 healthy adults ate either more fibre or more fermented foods for 17 weeks; the fermented-food group showed a steady rise in gut bacterial diversity and a fall in markers of inflammation.
Understanding what foods are good for your gut health and why, will help you to make better dietary choices long-term.
Increased physical activity, maintaining an adequate sleeping pattern and implementing effective stress management techniques are also supported by research as contributing positively to gut microbiome balance.
Learn more about how to improve your gut health naturally with dietary and lifestyle changes.
In some cases, a healthcare professional may suggest more targeted support, such as supplements containing live bacterial cultures. The evidence here is mixed, so make that decision with a qualified healthcare professional rather than on your own.
Can a gut imbalance lead to other conditions?
Poor gut health has been linked to a range of chronic conditions. Most of this research is associative: it shows that dysbiosis and these conditions occur together, not that one causes the other. A 2025 review in the Journal of Internal Medicine reached the same overall picture across the human lifespan, linking disruptions of the gut microbiota with a range of inflammatory and metabolic conditions while noting that cause and effect remain hard to separate.
Autoimmune disorders: Imbalances in gut bacteria have been associated with conditions including rheumatoid arthritis, type 1 diabetes, and multiple sclerosis, though the mechanisms involved are still being studied.
Digestive conditions: Dysbiosis and increased gut permeability, sometimes referred to as leaky gut, are associated with irritable bowel syndrome, inflammatory bowel disease, and gastro-oesophageal reflux disease. A 2019 systematic review of 24 studies found that people with IBS tended to carry a measurably different mix of gut bacteria from people without it, though whether that is cause or consequence is not yet clear.
Metabolic disorders: An imbalanced microbiome has been associated with an increased risk of obesity, metabolic syndrome, and type 2 diabetes. A well-known 2006 study, largely in mice, suggested that an imbalanced microbiome may harvest more energy from food, but in people this relationship has proved complex and is not yet fully understood.
Mental health: The gut-brain axis is a bidirectional communication pathway between the brain and the gut, mapped in detail by a major 2019 review. Research suggests that microbiome imbalances may contribute to mental health issues including anxiety and depression via this pathway, though this is an emerging field and causation has not been established. If low mood or anxiety is affecting your life, speak to your GP, or refer yourself to NHS talking therapies in England.
Immune function: The beneficial bacteria within our gut play a role in educating our immune system. Dysbiosis may weaken immune responses, which could increase susceptibility to infections and illness.
Can a gut imbalance go away on its own?
Sometimes, yes. The gut microbiome is resilient, and mild imbalances can correct themselves without treatment or deliberate changes. When symptoms appear and persist, that may be a sign your gut would benefit from support, starting with the diet and lifestyle changes described above.
When should you see a GP?
Persistent gut symptoms deserve a proper medical assessment, and some symptoms should always be checked promptly, whatever you think the cause is. See your GP without delay if you notice blood in your stool, unexplained weight loss, a change in your normal bowel habit lasting more than three weeks, difficulty swallowing, persistent vomiting, or ongoing abdominal pain. The same applies if you develop new digestive symptoms for the first time over the age of 50, if you have been told you have iron-deficiency anaemia, or if bowel or ovarian cancer runs in your family. These symptoms usually turn out to have less serious explanations, but they need to be ruled out by a doctor, not put down to a gut imbalance.
A home gut microbiome test is not a substitute for seeing a GP and cannot rule out any of the conditions above. If your symptoms are severe, persistent or getting worse, speak to your doctor first.
For most people, supporting the gut comes back to the same foundations: more fibre, fermented foods with live cultures, regular movement, decent sleep and less alcohol. This guide is for information only and does not replace medical advice from your GP or pharmacist.
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Related Feel Gut guide: https://feelgut.co.uk/blogs/gut-health/proton-pump-inhibitors-and-the-gut-microbiome
