Gut Health & Wellbeing
The gut microbiome and IBD: what parents need to know
Learn how the gut microbiome is connected to IBD, how diet and probiotics may influence gut health, and what parents need to know about supporting children with Crohn’s disease or ulcerative colitis.
If your child has Crohn’s disease or ulcerative colitis, you may have heard about the gut microbiome and its possible role in intestinal inflammation.
Researchers are increasingly interested in how the bacteria and other microorganisms living in the digestive tract interact with the immune system, the intestinal lining and the development of inflammatory bowel disease (IBD).
You may also have come across advice about probiotics, fermented foods, prebiotics or supplements designed to improve gut health.
But what is the gut microbiome, how is it connected to IBD, and can changing it help your child feel better?
Understanding what researchers currently know — and what remains uncertain — can help you make informed decisions without feeling that you need to fix your child's gut microbiome yourself.
🔬 What is the gut microbiome?
The gut microbiome is the community of microorganisms living in the digestive tract, particularly the large intestine. It includes bacteria, viruses, fungi and other microscopic organisms, along with their genetic material and the substances they produce.
Every person's gut microbiome is different. It develops from early life and continues to change in response to factors such as diet, medication, illness, age and the environment.
A healthy gut microbiome supports several important functions:
Digestion: Gut microbes help break down certain components of food that the body cannot digest on its own.
Nutrient production: Some microbes produce substances such as short-chain fatty acids, which help support the intestinal lining.
Immune function: Gut microbes interact with the immune system and help it respond to microorganisms and other substances.
Protection: The normal gut microbiome helps limit the growth of some harmful microorganisms.
Intestinal barrier health: Microbial products help support the lining that separates the contents of the intestine from the body's underlying tissues.
The microbiome is not simply a collection of good and bad bacteria. Different microorganisms have different functions, and their effects depend on the wider environment in which they live.
🧩 How is the gut microbiome connected to IBD?
Crohn’s disease and ulcerative colitis are complex conditions involving interactions between the immune system, genetic susceptibility and environmental factors. The gut microbiome is thought to be an important part of this picture.
Studies have found differences in the composition and activity of gut microorganisms in many people with IBD compared with people without the condition.
One commonly observed pattern is dysbiosis, a term used to describe an alteration in the microbial community that may affect its normal functions.
Research has identified several differences in people with IBD, including:
Reduced diversity of certain gut microorganisms.
Changes in the abundance of particular bacterial species.
Differences in the substances produced by gut microbes.
Alterations in the interaction between microbes, the intestinal lining and the immune system.
However, these patterns are not identical in everyone with IBD. There is no single microbiome profile that applies to every child with Crohn’s disease or ulcerative colitis.
Researchers are also investigating whether these microbial changes contribute to inflammation, occur because of inflammation, or involve both processes.
When the intestine becomes inflamed, the environment in which microorganisms live changes. This may allow some microbes to thrive while others become less abundant. These changes could, in turn, affect the intestinal barrier and immune responses.
A 2025 international meta-analysis of paediatric IBD studies found differences in gut microbial communities in children with Crohn’s disease and ulcerative colitis. The findings also suggested associations between microbial patterns, disease activity and treatment response.
You can read the 2025 paediatric IBD microbiome study on PubMed.
The research is promising, but scientists have not yet established a single microbial imbalance that explains IBD or can be corrected to cure the disease.
🧒 Does an unhealthy gut microbiome cause IBD?
Not on its own, based on current evidence.
It is tempting to think that if researchers find differences in the gut microbiome in people with IBD, restoring the microbiome to a healthier state should resolve the condition.
Unfortunately, the relationship is more complicated.
IBD develops through a combination of factors, and the microbiome is only one part of that process. Genetic susceptibility, immune responses, environmental influences and the integrity of the intestinal lining are also important.
Some microbial changes may contribute to inflammation, while others may be consequences of the disease or its treatment.
This distinction matters because there is currently no proven method of restoring a particular microbiome profile that reliably cures Crohn’s disease or ulcerative colitis.
It is also important to understand that your child's IBD is not your fault. You did not cause the condition by feeding them the wrong foods or failing to give them probiotics.
🥗 Can diet improve the gut microbiome?
Diet can influence the gut microbiome, but there is no single diet that produces the same effects in every person.
Gut microbes use components of food, including certain types of fibre, to produce substances that can support intestinal health.
For example, some bacteria ferment fibre to produce short-chain fatty acids, including butyrate. These substances help nourish cells in the intestinal lining and play a role in regulating immune activity.
A varied diet can provide different nutrients and food components that support a range of gut microorganisms.
Depending on your child's needs and tolerance, useful foods may include:
Fruits and vegetables: Provide fibre and a variety of plant compounds.
Whole grains: Offer different types of fibre that gut microbes can use.
Legumes: Beans, lentils and chickpeas provide fibre and other nutrients.
Nuts and seeds: Supply fibre and healthy fats, where suitable for your child's age and tolerance.
A variety of protein sources: Help meet the nutritional needs of a growing child.
However, children with IBD may not tolerate all these foods equally, particularly during a flare. Some may need adjustments to fibre intake or food texture, depending on their symptoms and whether they have intestinal narrowing.
There is no need to force your child to eat foods that make them uncomfortable or to introduce a restrictive diet in the hope of changing their microbiome.
The aim is to provide adequate nutrition while working within your child's individual needs.
🌾 What are prebiotics?
Prebiotics are substances, often particular types of fibre, that certain microorganisms in the gut can use selectively. They help support the activity of particular microbes.
Some foods contain naturally occurring prebiotic fibres, including:
Onions and garlic.
Asparagus.
Oats.
Legumes.
Bananas.
Some whole grains.
Prebiotics are not the same as probiotics. Prebiotics provide substances that microbes can use, whereas probiotics are live microorganisms that may provide a health benefit when consumed in adequate amounts.
Although prebiotics are an interesting area of gut health research, evidence is insufficient to recommend prebiotic supplements as a reliable way to induce remission in children with IBD.
Some prebiotic fibres can also increase gas, bloating or abdominal discomfort. If your child has symptoms after eating particular foods, an IBD dietitian can help you work out whether adjustments are appropriate.
🦠 Do probiotics help children with IBD?
Probiotics are live microorganisms that may provide health benefits when taken in adequate amounts. They are available in supplements and some fermented foods.
However, probiotics are not all the same. Different strains can have different effects, and research involving one strain or formulation cannot automatically be applied to another.
Evidence for probiotics in IBD is mixed and depends on the condition being treated.
Crohn’s disease
Current evidence does not support routinely using probiotics to induce or maintain remission in Crohn’s disease.
Ulcerative colitis
Some studies suggest that particular probiotic formulations may have a role as an additional treatment in selected cases of ulcerative colitis. However, the evidence varies, and probiotics are not a universal treatment for the condition.
Evidence in children is more limited than in adults, and probiotics should not replace prescribed medication.
For a detailed overview, see the US National Institutes of Health fact sheet on probiotics.
If you are considering a probiotic supplement for your child, discuss it with their gastroenterologist, particularly if they are taking immunosuppressive medication or have a severely weakened immune system.
🧫 Which probiotic strains have been studied for ulcerative colitis?
Research has investigated specific probiotic strains and combinations for ulcerative colitis, including:
Eight-strain probiotic formulation (formerly known as VSL#3): Contains a combination of Lactobacillus, Bifidobacterium and Streptococcus thermophilus strains. Some studies suggest potential benefits as an additional treatment for UC.
Escherichia coli Nissle 1917: Studied mainly for maintaining remission in ulcerative colitis, with most evidence coming from adults.
Other Lactobacillus and Bifidobacterium strains: Some have been investigated for their potential effects on intestinal inflammation, but results vary between strains and formulations.
Evidence in children remains limited, and no probiotic is established as a routine treatment for paediatric UC. The exact strains matter, as different products cannot be assumed to have the same effects.
For more information, see the ESPGHAN position paper on probiotics and prebiotics in children.
🥛 What about fermented foods?
Fermented foods such as yoghurt containing live cultures, kefir, sauerkraut and certain fermented soy products are often discussed in relation to gut health.
Some contain live microorganisms, while others may contain microbial products that remain after fermentation. Their composition varies according to how they are made and processed.
These foods may be included in a balanced diet if your child tolerates them. However, there is not enough evidence to say that eating fermented foods will reliably restore the gut microbiome or induce IBD remission.
Some fermented foods may also contain lactose, substantial amounts of salt or other ingredients that do not suit every child.
Think of them as optional foods rather than a treatment your child needs to consume to keep their IBD under control.
💊 How do medications affect the gut microbiome?
Medications can influence the gut microbiome, but their effects vary.
Antibiotics, for example, can alter the balance of gut microorganisms because they affect susceptible bacteria, including some that normally live in the digestive tract.
Other medicines may also influence microbial composition, directly or indirectly. At the same time, treating intestinal inflammation can change the gut environment and may allow microbial communities to shift.
This does not mean that medications used to treat IBD are harmful or should be avoided. Controlling inflammation is important for protecting your child's bowel, growth and overall health.
If your child needs antibiotics for an infection, follow the prescribing clinician's advice. Do not stop or avoid a necessary treatment because of concerns about the microbiome.
🧪 Can a stool microbiome test tell you what your child needs?
Commercial stool microbiome tests are sometimes promoted as a way to identify bacterial imbalances and recommend personalised diets or supplements.
However, these tests generally cannot establish what is causing a child's IBD symptoms or determine which supplement will bring the disease into remission.
There are several limitations:
The gut microbiome varies naturally between individuals.
Results can change with diet, medication, illness and other factors.
Different laboratories may use different methods and reference ranges.
There is no universally accepted healthy microbiome profile for every child.
Many commercial reports offer dietary or supplement recommendations that have not been validated in clinical trials.
A stool microbiome test is also different from faecal calprotectin testing. Faecal calprotectin is used by healthcare professionals to help assess intestinal inflammation, whereas commercial microbiome tests describe microorganisms in a sample.
If you are considering testing, discuss it with your child's gastroenterologist before spending money on a commercial service.
🔬 What about faecal microbiota transplantation?
Faecal microbiota transplantation (FMT) involves transferring processed stool from a carefully screened donor into a recipient's digestive tract to change the recipient's microbial community.
FMT has an established role in treating certain cases of recurrent Clostridioides difficile infection. Researchers are also investigating its potential for IBD, particularly ulcerative colitis.
However, the evidence for IBD remains limited, and the treatment is not recommended for routine use in children with IBD outside appropriate specialist settings or clinical trials.
FMT can carry risks, including the transmission of infectious organisms. Donor screening and medical supervision are essential.
It should not be attempted at home or through unregulated services.
🌱 What can parents realistically do to support gut health?
You do not need to overhaul your child's diet or purchase multiple supplements to support their gut health.
Practical steps include:
Offer variety where tolerated. Include a range of foods that provide fibre, protein, vitamins, minerals and sufficient energy.
Prioritise growth and nutrition. Children with IBD need enough food to support development, particularly during periods of active disease.
Avoid unnecessary restrictions. Removing multiple food groups can lead to nutritional deficiencies and make eating more stressful.
Follow your child's treatment plan. Controlling inflammation is essential, and diet alone cannot reliably manage active IBD.
Discuss supplements with the treating team. Probiotics, prebiotics and other products should be considered in light of the evidence and your child's individual circumstances.
Seek help from an IBD dietitian. A dietitian can help you support nutrition without making meals unnecessarily complicated.
Sleep, physical activity and avoiding smoking exposure are also important for overall health. However, none of these steps guarantees a particular microbiome profile or prevents every flare.
❤️ What should parents take away from the research?
The gut microbiome is an important and rapidly developing area of IBD research. Scientists are learning more about how microorganisms interact with the intestinal lining, immune system, diet and treatments.
Although researchers have identified differences in the microbiomes of many people with Crohn’s disease and ulcerative colitis, there is still much to learn about which changes contribute to disease and which occur because of inflammation.
For now, there is no single food, probiotic or supplement that can reliably restore the microbiome and cure IBD.
A varied, nutritionally adequate diet can support your child's general health, but you do not need to chase a perfect gut microbiome. Working with your child's gastroenterologist and IBD dietitian is the best way to explore nutrition and complementary approaches safely.
Your child does not need to fix their gut microbiome to deserve to feel better. Effective treatment, appropriate nutritional support and individualised care remain central to managing IBD.
📚 Further reading
Crohn’s & Colitis Foundation — Resources about IBD, nutrition and treatment.
Gut Microbiome and IBD — Crohn’s & Colitis Australia — An overview of the gut microbiome and its relationship with IBD.
International paediatric IBD microbiome study (2025) — Research examining microbial patterns in children with Crohn’s disease and ulcerative colitis.
National Institutes of Health: Probiotics for health professionals — An evidence-based overview of probiotics and their potential health effects.
This article is for general information and education. It is not a substitute for medical advice from your child’s doctor, paediatric gastroenterologist or IBD team.
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