What Is Gut Dysbiosis?
Your gut is home to trillions of microorganisms, including bacteria, viruses and fungi. Together, these make up your gut microbiome.
Many of these microorganisms play an important role in keeping you healthy. They help digest food, produce beneficial substances, support your immune system and protect against harmful bacteria.
A healthy gut contains a wide variety of microorganisms that work together to support normal digestion and overall health.
However, sometimes the balance of these microorganisms becomes disrupted. This is known as gut dysbiosis.
Gut dysbiosis can occur when:
- Beneficial bacteria decrease: There are fewer of the bacteria that help keep your gut healthy.
- Potentially harmful bacteria increase: Certain bacteria grow in greater numbers and may disrupt normal gut function.
- The variety of gut bacteria decreases: Having fewer types of microorganisms may affect how well your gut microbiome functions.
These changes can influence digestion, nutrient production and the way your immune system works.
For example, some beneficial gut bacteria help break down dietary fibre and produce substances that nourish and protect the lining of your intestines.
When these bacteria become less abundant, some of these important functions may be affected.
Research has linked gut dysbiosis with digestive conditions such as irritable bowel syndrome (IBS), as well as ymptoms including bloating, abdominal pain, diarrhoea and constipation.
What Are the Signs and Symptoms of Gut Dysbiosis?
Gut dysbiosis can be associated with a wide range of symptoms, although these vary from person to person.
Most commonly, symptoms affect the digestive system. However, research suggests that changes in the gut microbiome may also be associated with problems affecting other parts of the body.
Digestive Symptoms
The most commonly reported digestive symptoms associated with gut dysbiosis include:
- Bloating: An uncomfortable feeling of fullness, pressure or swelling in your abdomen.
- Excessive gas and flatulence: Increased intestinal gas, sometimes accompanied by abdominal discomfort.
- Abdominal pain and cramping: Pain or discomfort that may occur after eating or around bowel movements.
- Diarrhoea: Frequent, loose or watery stools.
- Constipation: Difficulty passing stools or having bowel movements less frequently than usual.
- Alternating diarrhoea and constipation: Switching between loose stools and difficulty passing stools.
- Nausea: Feeling sick, sometimes accompanied by bloating or abdominal discomfort.
- Feeling excessively full after eating: Becoming uncomfortably full, even after a relatively small meal.
Can Gut Dysbiosis cause SIBO?
Gut dysbiosis has also been associated with digestive conditions such as small intestinal bacterial overgrowth (SIBO). This condition is linked to an overgrowth of bacteria in the small intestine and is linked with bloating, gas, and irregular bowel movements.
Do Gut Dysbiosis and SIBO Cause the Same Symptoms?
Gut dysbiosis and SIBO can be associated with similar digestive symptoms, including:
Abdominal bloating and distension
Excessive gas and flatulence
Abdominal pain or discomfort
Diarrhoea
Constipation or changes in bowel habits
Feeling uncomfortable or excessively full after eating
Skin Problems
Your gut and skin are connected through what researchers call the gut–skin axis.
Studies have found differences in gut bacteria among people with certain skin conditions, including:
- Eczema
- Psoriasis
- Rosacea
Fatigue, Mood Changes and Brain Fog
Your gut and brain communicate with each other through what is known as the gut–brain axis.
Changes in gut bacteria may be linked to:
- Persistent tiredness or fatigue
- Anxiety
- Low mood or depression
- Brain fog or difficulty concentrating
- Migraines
Nutrient Deficiencies and Poor Absorption
In some cases, particularly when there is an overgrowth of bacteria in the small intestine, the body may have difficulty absorbing certain nutrients from food.
This can sometimes contribute to:
- Vitamin B12 deficiency: Which may cause tiredness, weakness or neurological symptoms.
- Poor fat absorption: Which may result in greasy, fatty or difficult-to-flush stools.
- Other nutritional deficiencies: Which may develop if the body is unable to absorb nutrients properly.
- Unexplained weight loss: Which can occur in more significant cases of malabsorption.
What Causes Gut Dysbiosis?
Several factors can contribute to gut dysbiosis by disrupting the balance of microorganisms living in the intestines. Some of the most important include antibiotic use, a diet low in fibre, gastrointestinal infections, certain medications, chronic stress and excessive alcohol consumption.
Other factors, such as poor sleep and age-related changes in gut function, may also influence the composition of the gut microbiome.
1. Antibiotic Use
Antibiotics are one of the most well-established causes of disruption to the gut microbiome.
Although antibiotics are essential for treating bacterial infections, they can also affect the beneficial bacteria naturally present in the intestines.
Research has shown that antibiotic treatment can:
Reduce the diversity of bacteria in the gut.
Decrease populations of beneficial microorganisms, including certain Bifidobacterium species and butyrate-producing bacteria.
Allow potentially harmful or antibiotic-resistant bacteria to become more abundant.
Alter the production of microbial metabolites that are important for intestinal health.
Increase susceptibility to certain intestinal infections, including Clostridioides difficile.
2. A Diet Low in Fibre and Plant Diversity
Diet is one of the most important factors influencing the composition and function of the gut microbiome.
A diet consistently low in fibre may reduce the availability of nutrients needed by certain beneficial gut bacteria.
Dietary patterns that may adversely affect the gut microbiome include:
Eating insufficient vegetables, fruits, legumes and wholegrains.
Consuming a limited variety of plant-based foods.
Following diets high in saturated fat and low in fibre.
Frequently eating highly processed foods instead of fibre-rich alternatives.
Following long-term restrictive diets that unnecessarily exclude numerous food groups.
Eating a varied diet containing different sources of fibre can help support a more diverse community of gut microorganisms.
3. Gastrointestinal Infections and Food Poisoning
Gastrointestinal infections can cause significant disruption to the intestinal environment and the microorganisms living within it.
Bacterial, viral and parasitic infections may lead to inflammation, changes in intestinal motility, alterations in the intestinal lining and shifts in the composition of the gut microbiome.
Examples of gastrointestinal pathogens include:
Campylobacter
Salmonella
Shigella
Certain pathogenic strains of Escherichia coli (E. coli)
Giardia duodenalis
Norovirus
In some people, digestive symptoms continue long after the original infection has resolved.
This can occur in a condition known as post-infectious irritable bowel syndrome (PI-IBS), which may develop following an episode of gastroenteritis or food poisoning.
4. Certain Medications
Proton Pump Inhibitors (PPIs)
Medicines such as omeprazole and lansoprazole reduce stomach acid production.
Stomach acid helps limit the number of microorganisms entering the intestines from the mouth and stomach.
Long-term acid suppression may therefore alter the intestinal microbial environment and influence the composition of the gut microbiome.
Other Medications
Studies have also reported changes in gut microbiome composition associated with:
Metformin: Commonly prescribed for type 2 diabetes.
Non-steroidal anti-inflammatory drugs (NSAIDs): Such as ibuprofen.
Opioid painkillers: Which can also affect intestinal motility.
Certain antipsychotic medications: Which have been associated with changes in gut microbial populations.
These findings do not mean that everyone taking these medications will develop gut dysbiosis. Medications should not be stopped or changed without advice from the prescribing clinician.
5. Chronic Psychological Stress
The gut and brain communicate through a complex network known as the gut–brain axis.
This communication involves the nervous system, stress hormones, immune system and intestinal microorganisms.
Prolonged psychological stress may influence the intestinal environment through changes in:
Gastrointestinal motility.
Digestive secretions.
Immune activity.
Gut–brain signalling.
Research has also identified associations between psychological stress and changes in the abundance of certain gut bacterial groups.
Although stress does not necessarily cause gut dysbiosis, it may contribute to changes in digestive function and the gut microbial environment.
6. Excessive Alcohol Consumption
Excessive or prolonged alcohol consumption can disrupt the intestinal environment and alter gut microbial populations.
Research suggests that alcohol-related changes may include:
Reduced microbial diversity.
Changes in beneficial bacterial populations.
An increased abundance of certain potentially inflammatory microorganisms.
Alterations in microbial metabolism.
Changes in intestinal barrier function.
These effects may contribute to inflammatory processes affecting the intestines and liver.
7. Poor Sleep and Disrupted Circadian Rhythms
Insufficient sleep, irregular sleep patterns and disruption of the body’s internal clock have been investigated as possible contributors to changes in gut microbial composition.
The body’s circadian rhythm helps regulate many physiological processes, including digestive function.
Although research is still developing, maintaining regular sleep patterns may help support overall gut health.
8. Ageing and Changes in Gut Function
The gut microbiome naturally changes throughout life.
Infants develop their microbiome during early childhood, while its composition continues to change throughout adulthood and older age.
Age-related factors that may influence the microbiome include:
Changes in dietary intake and nutritional status.
Reduced physical activity.
Greater exposure to medications.
Changes in gastrointestinal motility.
Alterations in immune function.
An increased prevalence of chronic illness.
How Do You Test for Gut Dysbiosis?
There are several types of tests that may help investigate aspects of the gut microbiome and digestive function.
Comprehensive Stool Testing
Comprehensive stool tests can measure selected bacteria, fungi and other microorganisms present in the digestive tract. These tests are useful as they can highlight if there is an overgrowth of bad bacteria or low levels of good bacteria as well as overgrowth of yeast or parasites.
They can also detect intestinal inflammation and markers of digestion and absorption.
Pancreatic elastase: A marker used to assess pancreatic enzyme production.
Calprotectin: A marker that can help identify intestinal inflammation.
SIBO Breath Testing
If your main symptoms include bloating, excessive gas, abdominal discomfort, diarrhoea or constipation, your clinician may consider whether small intestinal bacterial overgrowth (SIBO) or intestinal methanogen overgrowth (IMO) could be contributing to your symptoms.
A SIBO breath test measures gases such as hydrogen and methane after you drink a test solution, usually glucose or lactulose.
How Is Gut Dysbiosis Treated?
Treatment for gut dysbiosis focuses on identifying factors that may have disrupted the gut microbiome and taking steps to support a healthier balance of intestinal microorganisms.
Treatment may involve a combination of dietary changes, probiotics, prebiotics anti-inflammatory supplements depending on the specific cause.
1. Dietary Changes
Diet plays an important role in supporting a healthy gut microbiome.
Eating a varied, balanced diet that includes a wide range of plant-based foods can help encourage the growth of beneficial gut bacteria.
Helpful dietary changes may include:
Increasing fibre intake: Foods such as vegetables, fruits, wholegrains, beans and lentils provide nourishment for beneficial gut bacteria.
Eating a greater variety of plant foods: Different types of bacteria thrive on different types of fibre, making dietary variety important.
Including fermented foods: Foods such as live yoghurt, kefir and sauerkraut may help support microbial diversity.
Reducing highly processed foods: Limiting foods high in saturated fat and low in fibre may support a healthier gut environment.
However, increasing fibre too quickly can worsen bloating, gas and abdominal discomfort, particularly in people with IBS or SIBO. Therefore it is best to work with a specialist to design the best diet for you.
2. Probiotics and Prebiotics
Probiotics
Probiotics are live microorganisms that, when taken in adequate amounts, may provide health benefits such as lactobacillus or bifidobacterium.
Certain probiotic strains have been studied for their potential to improve specific digestive symptoms and support gut function.
However, not all probiotics work in the same way, and taking a probiotic does not necessarily correct gut dysbiosis.
Their effectiveness depends on the particular strain, dose and condition being treated.
Prebiotics
Prebiotics are substances, often specific types of dietary fibre, that are used by beneficial microorganisms in the gut.
They may help support the growth or activity of beneficial bacteria.
However, some prebiotics can increase gas and bloating, particularly in people with IBS or SIBO other digestive sensitivities.
3. Identifying and Addressing Underlying Causes
An important part of managing gut dysbiosis is understanding why the gut microbiome may have become disrupted.
Possible contributing factors include:
Previous gastrointestinal infections or food poisoning.
Antibiotic use.
A diet low in fibre or lacking variety.
Certain medications, including proton pump inhibitors (PPIs).
Digestive conditions such as SIBO.
Changes in intestinal movement, also known as gut motility.
Identifying these factors can help guide a more individualised approach to improving digestive health.
Where an underlying medical condition is suspected, appropriate investigation and treatment may be necessary.
4. Supporting Gut Health Through Lifestyle Changes
Lifestyle factors can also influence the gut microbiome and digestive function.
Helpful measures may include:
Getting adequate sleep: Maintaining a regular sleep schedule supports the body’s natural circadian rhythms.
Managing stress: Stress-management techniques may help support gut–brain communication and digestive function.
Exercising regularly: Physical activity can support general health and normal intestinal function.
Limiting excessive alcohol consumption: Reducing alcohol intake may help protect the intestinal environment.
5. Getting help and Support
Because everyone’s gut microbiome is different, there is no universal approach to managing gut dysbiosis.
A personalised consultation can help identify factors that may be contributing to your digestive symptoms and develop a practical plan to support your gut health.
During a consultation, we will
Review your symptoms, diet and medical history.
Consider whether further investigations or tests are appropriate.
Identify dietary factors that may be contributing to digestive discomfort.
Help you make gradual dietary changes to support microbial diversity and gut function.
Consider targeted probiotic or prebiotic supplements where appropriate.
Identify potential nutritional deficiencies and help you address them.
Monitor your progress and adjust your nutritional plan as needed.
- Recommend supplements where appropriate
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Book a Consultation with a Gut Health specialist
We offer consultations at our sister clinic ibs-solutions.co.uk and a range of specialist digestive health tests to help investigate possible underlying causes, including SIBO and gut Microbiome tests.
References
The information on this page is supported by peer-reviewed scientific research, including the following studies:
- Wastyk HC, et al. (2021). Gut-microbiota-targeted diets modulate human immune status. Cell, 184(16), 4137–4153.
Research investigating how high-fibre and fermented-food diets influence gut microbiome composition and immune function.
Read study on PubMed - Su GL, et al. (2020). AGA Clinical Practice Guidelines on the Role of Probiotics in the Management of Gastrointestinal Disorders. Gastroenterology, 159(2), 697–705.
Clinical guidance evaluating the evidence for probiotics in different gastrointestinal conditions.
Read study on PubMed - Porcari S, et al. (2025). International consensus statement on microbiome testing in clinical practice. The Lancet Gastroenterology & Hepatology, 10(2), 154–167.
An international expert consensus examining the potential uses and current limitations of microbiome testing in clinical practice.
Read study on PubMed