The Microbiome and Aspergillosis: What It Means

Couple preparing a balanced meal with vegetables, beans and wholegrain bread — A varied, balanced diet supports general health, but it does not replace treatment for aspergillosis.

Originally published: 13 August 2020 | Last reviewed: 18 September 2026 | Next review: September 2028

The word microbiome is used more and more in healthcare. It can sound as though it explains everything—from gut symptoms and immunity to asthma, infection and mood. The reality is more interesting, but also more uncertain.

Research is showing that the communities of microbes living in and on our bodies can influence inflammation and immune responses. This may be relevant to aspergillosis. However, microbiome research has not shown that aspergillosis is caused by an “unhealthy microbiome”, or that diets, probiotics or supplements can replace established treatment.

What is the microbiome?

The microbiome is the community of microscopic organisms that live in and on the body. It includes bacteria, fungi and viruses. Large numbers live in the gut, but microbes are also found in the mouth, nose, skin and airways.

For many years, doctors assumed that healthy lungs were sterile. We now know that the airways can contain small amounts of microbial material, although the lungs are very different from the gut: they have far fewer organisms and are constantly being cleared by coughing, mucus movement and immune defences.

What does this have to do with aspergillosis?

We breathe in fungal spores every day. Most people do not develop aspergillosis because their airways and immune system deal with these exposures effectively. In some people, however, the balance between the fungus, the lungs and the immune response changes.

This balance can be affected by many things, including underlying lung disease, damaged airways, mucus clearance, immune-suppressing treatment, severe asthma, previous infections and the medicines needed to treat them. The microbiome may be one part of this wider picture.

For example, researchers are studying whether changes in the bacteria and fungi found in the gut or airways can influence inflammation, allergy and susceptibility to infection. This may help us understand conditions such as ABPA, bronchiectasis and invasive aspergillosis more clearly in future.

Colonisation, infection and inflammation

It is useful to separate three ideas that can become confused:

Colonisation means that a microbe is present but is not necessarily causing disease or requiring treatment.
Infection means that a microbe is causing damage or illness and needs clinical assessment and, often, treatment.
Inflammation is the body’s immune response. It can be helpful, but it can also cause symptoms and damage when it is too strong or prolonged.

A sputum result showing a bacterium or fungus does not, on its own, tell clinicians which of these is happening. They consider the result alongside your symptoms, scans, lung function, blood tests and changes over time.

Does diet affect the microbiome?

Diet influences the microbes in the gut, and a varied, balanced diet with plenty of plant foods and fibre is generally good for overall health. This is sensible advice for most people, including those living with aspergillosis.

But it is important not to overstate what this means. There is currently no special “aspergillosis microbiome diet”, and there is no good evidence that changing your diet can clear Aspergillus from the lungs, prevent an ABPA flare-up, or replace antifungal treatment.

If poor appetite, weight loss, diarrhoea, reflux or medication side effects are affecting what you can eat, speak to your clinical team or ask whether a referral to a dietitian would help.

What about antibiotics, antifungals and probiotics?

Antibiotics can alter the bacteria in the gut and airways, but they are sometimes essential for treating a bacterial infection or exacerbation. Antifungal medicines are also important treatments for many forms of aspergillosis. Do not stop, delay or change prescribed medication because of concerns about the microbiome without discussing it with your clinical team.

Probiotics and supplements are often marketed as ways to “repair” the microbiome. The evidence is mixed, products vary widely, and they are not proven treatments for aspergillosis. They may not be suitable for everyone—particularly people who are severely unwell or immunocompromised—so check with a clinician or pharmacist before starting one.

What can you do now?

You do not need to try to perfect your microbiome. The most useful approach is to support your general health while continuing the treatment plan agreed with your clinicians.

Eat as varied and balanced a diet as you can manage.
Keep hydrated and seek help if medication affects appetite or digestion.
Use antibiotics and antifungals exactly as prescribed.
Continue inhalers, airway-clearance techniques and other respiratory treatments.
Discuss persistent changes in cough, sputum, breathlessness, bowel symptoms or weight with your healthcare team.
Be cautious about claims that a supplement, test or restrictive diet can “reset” the microbiome or cure a chronic condition.

What might research bring in future?

Microbiome research may eventually help clinicians understand why people respond differently to infections and treatments, identify patterns linked with inflammation, or develop more personalised care. For now, much of the research is early-stage and does not yet change routine treatment for aspergillosis.

It is a promising area of science—but it is not a reason to blame yourself, your diet or your body for having aspergillosis.