Intestinal dysbiosis

Intestinal dysbiosis refers to changes in the composition or function of the microorganisms that inhabit the gut. It may be associated with diseases, infections, medication or changes in diet, although it does not currently constitute, in itself, a clinical diagnosis defined by universally accepted criteria.

What is gut dysbiosis?

The digestive system is home to bacteria, viruses, fungi and other microorganisms that make up the gut microbiota. This community plays a part in the breakdown of certain food components, produces substances that interact with the body and contributes to the functioning of the intestinal barrier and the immune system.

The term ‘dysbiosis’ is used when changes are detected in the diversity of the microbiota, in the proportion of certain microorganisms, or in the functions they perform.

However, there is no single microbiota that is considered normal for everyone. Its composition varies with age, diet, environment, medication, bowel function and numerous individual factors.

For this reason, finding differences compared with a reference group does not in itself prove that a disease exists, nor that these differences are the cause of any symptoms. Establishing causal links between the microbiota and disease remains one of the main challenges facing research.

Is it a disease?

Dysbiosis is primarily regarded as a biological condition or an abnormality associated with various clinical conditions. Numerous studies have identified distinct microbiota profiles in people with digestive, inflammatory and metabolic diseases, as well as conditions affecting other systems. However, an association does not automatically allow us to determine whether the microbial imbalance causes the disease, arises as a consequence of it, or whether the two situations influence one another.

The microbiota can also change as a result of diet, medication, bowel movements, an infection or the progression of a disease itself.

For this reason, the term ‘intestinal dysbiosis’ should not be used as an automatic explanation for any digestive or general symptom. The clinical priority is to determine whether there is a recognised disease or disorder that explains the symptoms.

Why the microbiota may change

The gut microbiota is dynamic and can change temporarily throughout a person’s life. Antibiotics can cause significant changes because they act on both the bacteria responsible for an infection and other gut microorganisms. The extent and duration of these changes depend on the drug, the dose, the duration of treatment and individual characteristics.

Gastrointestinal infections, other medicines, bowel preparation for a colonoscopy, certain surgical procedures and some inflammatory, metabolic or liver diseases can also have an influence.

Diet plays a significant role, although it cannot be reduced to the idea that a single food ‘damages’ or ‘cures’ the microbiota. What is usually of greater importance is the overall dietary pattern, its variety and its content of different types of fibre.

Rest, physical activity and other lifestyle factors are also linked to the microbiota. However, it is not yet possible to accurately quantify the effect of each factor, nor to translate all these findings into routine personalised treatments.

What symptoms can it cause?

Dysbiosis does not have a specific set of symptoms that would allow it to be recognised or diagnosed. Abdominal bloating, flatulence, pain, diarrhoea or constipation may co-occur with alterations in the microbiota, but they also feature in numerous digestive problems.

These include irritable bowel syndrome, coeliac disease, food intolerances, infections, inflammatory bowel disease, small intestinal bacterial overgrowth and various bowel motility disorders.

Fatigue, difficulty concentrating, bad breath or the sensation of being unable to tolerate many foods are even less specific. They should not be attributed to the microbiota without first assessing other possible causes.

Therefore, whilst these symptoms may warrant a medical assessment, they do not, on their own, confirm the presence of dysbiosis.

When to seek medical advice

The presence of blood in the stools, anaemia, fever, unintentional weight loss or persistent diarrhoea requires medical assessment. Severe or progressive pain, repeated vomiting, night-time diarrhoea and recent, persistent changes in bowel habits should also be investigated.

These symptoms do not necessarily indicate a serious illness, but they should not be attributed solely to an ‘imbalance in the gut flora’. In people who are immunocompromised, elderly or who have recently taken antibiotics, severe or persistent diarrhoea may require more urgent assessment.

How it is assessed

There is currently no single test that can confirm gut dysbiosis, demonstrate that it is causing the symptoms, or automatically select a treatment.

The assessment begins with the patient’s medical history. The doctor analyses the nature of the symptoms, their duration, diet, medication, history of infections and the presence of any warning signs.

Depending on the case, blood or stool tests, tests to rule out coeliac disease, inflammation tests, breath tests, endoscopy or colonoscopy may be requested. These investigations do not diagnose general dysbiosis. Their purpose is to identify specific conditions that may be causing the symptoms or secondarily altering the microbiota.

Stool microbiota analysis

Microbiota analyses examine the microorganisms or their genetic material in a stool sample. These techniques are valuable in research and can describe certain characteristics of the microbial community. However, a faecal sample primarily represents the contents of the colon and does not fully reflect all the microorganisms present in the mucosa or other parts of the digestive tract.

Results may also vary depending on sample collection and storage, the sequencing technique, data processing, the database used and the reference population.

The international consensus published in 2025 notes that the clinical utility of these tests remains limited in many settings and that their performance and interpretation require standardised procedures and professionals with multidisciplinary skills. It also warns against the direct-to-consumer availability of tests whose clinical value has not been demonstrated.

The difference between dysbiosis, SIBO and intestinal infection

Intestinal dysbiosis is not the same as small intestinal bacterial overgrowth, known as SIBO. SIBO refers to an excessive or abnormal presence of microorganisms in the small intestine and is investigated in specific clinical situations, usually through breath tests.

Dysbiosis is a broader concept. It can refer to changes in different parts of the gut and there is no equivalent clinical test that allows it to be confirmed in general terms.

Nor should it be confused with a gastrointestinal infection. In an infection, there is a pathogenic microorganism or an identifiable infectious process. In dysbiosis, changes are observed in a complex microbial community, without there necessarily being an infection.

What is the treatment for gut dysbiosis?

There is no one-size-fits-all treatment that can correct any form of gut dysbiosis.

When a specific condition alters the microbiota, the primary aim is to diagnose and treat that condition. It may be necessary to address an infection, an inflammatory process, a functional disorder, a confirmed intolerance or the adverse effect of a medicine.

The phrase ‘restoring balance’ sounds simple, but there is no ideal microbial profile that can be replicated in exactly the same way in every person. Therapeutic decisions must be based on the identified clinical problem and not solely on the abundance of certain bacteria listed in a report.

Diet and the microbiota

A varied diet, regularly including vegetables, fruit, pulses, nuts and whole grains, provides different types of fibre that can be utilised by gut microorganisms.

However, rapidly increasing fibre intake can worsen flatulence, bloating, pain or diarrhoea in some people. The amount and type should be tailored to the individual’s tolerance and the specific digestive problem.

Fermented foods, such as certain yoghurts and kefirs, can form part of a balanced diet when well tolerated. They should not be presented as a treatment capable of correcting any disturbance in the microbiota on its own.

Nor is it recommended to generally eliminate gluten, dairy products, carbohydrates or other food groups without clinical justification. Highly restrictive diets can lead to an unbalanced diet and increase the risk of nutritional deficiencies.

When symptoms necessitate numerous dietary changes, it may be helpful to seek the advice of a dietitian-nutritionist with clinical experience.

Probiotics and prebiotics

Probiotics are live microorganisms which, when taken in an appropriate amount, can be beneficial in certain situations.

Their effects depend on the strain, the dose, the formulation and the condition being treated. Not all probiotics are equivalent, nor is every product suitable for ‘restoring the gut flora’.

Prebiotics are substances that certain microorganisms can utilise. Some may promote beneficial microbial functions, but they can also cause flatulence or bloating in sensitive individuals.

Synbiotics combine probiotics and prebiotics. Postbiotics contain inactivated microorganisms, parts of them, or substances they have produced.

The use of these products should be assessed based on the available evidence for each formulation and clinical situation. A supplement should not be chosen solely on the basis of advertising or a commercial stool analysis.

Faecal microbiota transplantation

Faecal microbiota transplantation involves administering microbiota from a carefully selected donor who has undergone health screening.

Its best-established indication is recurrent Clostridioides difficile infection in certain patients. The 2024 guidelines from the American Gastroenterological Association recommend microbiota-based therapies in selected scenarios involving this infection, but do not recommend them as standard treatment for irritable bowel syndrome or inflammatory bowel disease outside of clinical trials.

It should not be used as a general treatment to ‘restore the microbiota’, alleviate fatigue, lose weight or treat digestive symptoms without a precise diagnosis.

Procedures carried out outside a controlled healthcare setting may transmit infections and lead to complications.

In which conditions is the microbiota important?

Research into the microbiota is being carried out in relation to inflammatory bowel disease, irritable bowel syndrome, obesity, diabetes, liver diseases, certain cancers and various neurological disorders.

Significant associations have been identified in several of these conditions. However, it is not always clear whether changes in the microbiota are a cause, a consequence or a marker of the disease. Research is leading to the development of new treatments and potential biomarkers, but many of these applications are not yet part of standard clinical practice.

Therefore, the fact that the microbiota is involved in a disease does not mean that a commercial faecal test can diagnose it or that a supplement can treat it.

Which healthcare professionals can help

Primary care practitioners can carry out an initial assessment of digestive symptoms and request initial tests where necessary. A gastroenterologist is consulted when symptoms persist, there are warning signs, a specific condition is suspected, or specialised tests are required.

A dietitian-nutritionist with clinical experience can help improve dietary variety, adjust fibre intake and avoid unnecessary restrictions.

Where there is an inflammatory, infectious, metabolic or immune-related condition, treatment must focus on that condition and may require the involvement of various specialists.

Living with symptoms attributed to dysbiosis

Persistent digestive discomfort can affect eating, work, rest and social life. The lack of an immediate explanation can lead to tests, diets and treatments of uncertain benefit.

The safest approach is to identify the main symptoms, check for any warning signs and look for recognisable diseases or clinical disorders.

Maintaining a varied diet, avoiding the unnecessary use of antibiotics, taking regular exercise and ensuring adequate rest are sensible measures for general and digestive health. They do not guarantee the presence or disappearance of a specific microbiota profile.

The microbiota can change over time, but its evolution cannot be measured solely by the disappearance of a symptom or by the isolated quantity of a particular bacterium. An individualised assessment allows us to look after our gut health without automatically attributing any discomfort to dysbiosis.