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Functional disorders and the gut: What does research show?

By Published 9 min read

Stomach pain, bloating, fatigue or aching muscles, without blood tests or scans being able to show why. That is how many people with a functional disorder live.

It does not mean the symptoms are imagined. The Danish public health portal sundhed.dk says that a functional disorder is regarded as an illness on an equal footing with other illnesses, and that it can be understood as a condition in which the brain and the body are overloaded and do not work together normally [1].

The stomach is often involved, which is why gut bacteria are so often mentioned as a possible explanation. Here is what the research actually shows.

What does the term cover?

In Denmark, "functional disorder" (funktionel lidelse) is used for an illness with physical symptoms that make everyday life hard, and that cannot be explained by another known disease [1]. Lægehåndbogen, the Danish doctors' handbook on sundhed.dk, describes four groups of symptoms [2]:

  • Stomach and gut: stomach pain, frequent loose stools, bloating, nausea, acid reflux and heartburn
  • Heart and lungs: palpitations, pressure in the chest and breathlessness without exertion
  • Muscles and joints: pain that moves around, and altered sensation
  • General symptoms: fatigue, headache, dizziness and difficulty concentrating

To get the diagnosis, you need at least three symptoms from at least one of the groups. They must have lasted at least three months, and other diseases must be ruled out [2]. If your symptoms come from one or two organ systems, it is called a single-organ disorder. If they come from more, it is called the multi-organ type [3].

When it is only the gut

Gut specialists have their own names for the functional disorders of the gut. Since 2016, the international Rome criteria have called them disorders of gut-brain interaction [4]. They include:

  • IBS (irritable bowel syndrome)
  • functional dyspepsia, which sundhed.dk calls "mavekatar"
  • functional bloating
  • functional diarrhoea and chronic constipation

The criteria were updated in May 2026 with Rome V, which among other things made the requirements for an IBS diagnosis less strict [5]. In the Danish diagnosis codes, "functional disorder, gastrointestinal" exists as a subtype of functional disorder [6]. So these are two ways of describing the same area.

How many people have it?

In a Danish population study, doctors interviewed 1,590 randomly selected adults. About one in ten met the criteria for a functional disorder. Only 2 percent had the severe multi-organ type, and about 4 percent had the type with symptoms from the stomach and gut [3].

The disorders overlap a lot. Irritable bowel, widespread pain and chronic fatigue rarely appeared alone: most people who had one of them also had at least one of the others [3].

Nor is it necessarily lifelong. When researchers followed 5,738 Danes for five years, about half of those who had a functional disorder no longer met the criteria at follow-up [7].

Looking at the gut alone, the numbers are even higher. In a Danish questionnaire study, 10.5 percent had symptoms of IBS and 7.7 percent of functional dyspepsia [8]. In an international study of 73,076 adults, 40 percent of those who answered online met the criteria for at least one functional gut disorder. Among those interviewed face to face, it was 21 percent [9].

What happens in the body?

The causes are not fully mapped, but researchers have found some mechanisms.

A more sensitive gut. In five groups with a total of 1,144 patients with IBS or functional dyspepsia, researchers used a small balloon to measure how much stretching the stomach or gut could take before it hurt or felt uncomfortable. The more sensitive it was, the worse the symptoms. The link held even after taking anxiety and depression into account [10].

A stomach infection can be the trigger. A meta-analysis of 45 studies found that about 10 percent had IBS a year after a gut infection. The risk was a little over four times higher than in people who had not had an infection [11].

Both findings come from observational studies. They show associations, not the whole explanation.

Do gut bacteria play a part?

Possibly, but it has not been shown.

In IBS, gut bacteria are on average a little different from those of healthy people. A review of 24 studies found, for example, fewer Bifidobacterium and Faecalibacterium. But over 40 percent of the studies did not report whether patients and healthy people were comparable, and the authors themselves write that it is unknown whether the bacteria are a result of IBS or a cause [12].

The best test of whether bacteria are the cause is to give patients a new gut flora with a faecal transplant:

  • In a Danish trial, 52 patients with IBS got capsules with stool from healthy donors or dummy capsules. The transplant changed the gut flora, but after three months the placebo group was doing best [13].
  • A 2026 meta-analysis of 13 trials with 693 patients found no certain effect, and the certainty of the evidence was very low [14].
  • The 2026 Danish IBS guideline concludes that faecal transplantation has no effect on IBS symptoms [15].

In fibromyalgia, one study found differences in the gut bacteria of 77 women with fibromyalgia compared with 79 people without it [16]. When researchers transferred stool from patients to germ-free mice, the mice developed pain [17]. That is interesting, but these are animal experiments, and it has not been shown in humans.

For functional disorders as a whole, we have not found a single study of gut bacteria or probiotics.

Do probiotics help?

There are no trials showing that probiotics treat functional disorders. The trials are about the individual diagnoses, and the results are weak:

  • IBS: The 2026 Danish guideline says that some strains may have an effect on specific IBS symptoms, but that the evidence is low to very low. It recommends no particular products, because those sold in Denmark may differ from those that were tested [15]. Read more in the article on probiotics and IBS.
  • Functional dyspepsia: The British guideline does not recommend probiotics and says the evidence is even less clear than in IBS [18]. In dyspepsia trials, about 44 percent improve on placebo, so a good experience with a product says little [19].
  • Fibromyalgia: In the largest trial we found, 110 patients got either a multi-strain probiotic or placebo for twelve weeks. There was no difference in gut symptoms or in anything else that was measured [20]. A review of trials in fibromyalgia and chronic fatigue called the evidence limited [21].
  • Children with stomach pain: The European and North American paediatric gastroenterology societies recommend hypnotherapy and cognitive therapy. Probiotics may be suggested, but the only strain named is Lactobacillus rhamnosus GG, and only for IBS [22].

What has better evidence?

For functional disorders as a whole, the best-studied treatments are therapy and low-dose medicine:

  • In a Danish trial of 138 patients with the severe multi-organ type, 53 percent were better after ten weeks of low-dose imipramine, against 25 percent on placebo. Side effects were more common with imipramine, though [23].
  • sundhed.dk names graded activity training and cognitive behavioural therapy as treatment [1].
  • Not everything works: a Danish trial of mindfulness found no difference in the main outcome compared with an enhanced version of usual care [24].

For the gut, the guidelines point to things other than probiotics:

  • Psyllium (psyllium husk): In a 2026 meta-analysis of 30 trials, more people with IBS improved on fibre supplements than on placebo, and psyllium stood out [25].
  • Dietary advice and a low-FODMAP diet: The Danish guideline recommends standard dietary advice first, and a low-FODMAP diet with help from a dietitian as the next step [15].
  • Cognitive behavioural therapy and hypnotherapy are both judged to have an effect on IBS [15]. The Danish guideline notes, however, that psychological treatment for IBS is not currently offered within gastroenterology in Denmark [15].
  • For functional dyspepsia, a test for the stomach ulcer bacterium Helicobacter pylori, with treatment if it is found, is one of the best-documented treatments [18][26].

Several Danish regions have clinics for functional disorders that your doctor can refer you to, for example at Aarhus University Hospital [29].

A disputed boundary

Whether chronic fatigue syndrome (ME/CFS) belongs under functional disorders is disputed in Denmark. In December 2025, the Danish Health Authority described a high level of conflict between the parties, and wrote that it wants to put an end to the misconception that a functional disorder is a purely psychosomatic condition [27]. We do not take sides in that debate here.

When should you see a doctor?

A functional disorder can only be diagnosed once other diseases have been ruled out [2]. See a doctor if you have gut problems and one or more of these alarm symptoms [15]:

  • Weight loss you cannot explain
  • Pain or bowel movements that wake you at night
  • Blood in your stool
  • Fever
  • Anaemia

If you have pain in the upper stomach, also see a doctor if you vomit repeatedly or there is blood in your vomit [28]. The same applies if a close relative has bowel cancer or inflammatory bowel disease [15].

The bottom line

  • A functional disorder is a recognised illness with real symptoms, not something you imagine.
  • About one in ten Danish adults meet the criteria, but only 2 percent have the severe form, and about half no longer meet the criteria five years later.
  • The gut is more sensitive in people with functional gut disorders, and a stomach infection can set it off.
  • Gut bacteria are a little different in IBS and fibromyalgia, but nobody has shown that they are the cause.
  • No trials show that probiotics treat functional disorders. In IBS, the evidence is low to very low.
  • Psyllium, dietary advice, cognitive therapy and hypnotherapy have better evidence.

Sources

  1. Sundhed.dk. Funktionel lidelse. Patienthåndbogen. Updated 2025. sundhed.dk
  2. Rosendal M. Funktionel lidelse. Lægehåndbogen, sundhed.dk. Updated 2025. sundhed.dk
  3. Petersen MW et al. Irritable bowel, chronic widespread pain, chronic fatigue and related syndromes are prevalent and highly overlapping in the general population: DanFunD. Sci Rep. 2020. PMID 32094442
  4. Drossman DA. Functional Gastrointestinal Disorders: History, Pathophysiology, Clinical Features and Rome IV. Gastroenterology. 2016. PMID 27144617
  5. Krause A et al. Rome V Criteria for Adults: What's New and Why? United European Gastroenterol J. 2026. PMID 42857891
  6. Dansk Pædiatrisk Selskab. Recidiverende mavesmerter hos børn. Clinical guideline. 2022. paediatri.dk
  7. Schovsbo SU et al. Fluctuation of functional somatic disorders in a population-based cohort. The DanFunD study. PLoS One. 2024. PMID 39413108
  8. Rasmussen S et al. Overlap of symptoms of gastroesophageal reflux disease, dyspepsia and irritable bowel syndrome in the general population. Scand J Gastroenterol. 2015. PMID 25525975
  9. Sperber AD et al. Worldwide Prevalence and Burden of Functional Gastrointestinal Disorders, Results of Rome Foundation Global Study. Gastroenterology. 2021. PMID 32294476
  10. Simrén M et al. Visceral hypersensitivity is associated with GI symptom severity in functional GI disorders: consistent findings from five different patient cohorts. Gut. 2018. PMID 28104632
  11. Klem F et al. Prevalence, Risk Factors, and Outcomes of Irritable Bowel Syndrome After Infectious Enteritis: A Systematic Review and Meta-analysis. Gastroenterology. 2017. PMID 28069350
  12. Pittayanon R et al. Gut Microbiota in Patients With Irritable Bowel Syndrome: A Systematic Review. Gastroenterology. 2019. PMID 30940523
  13. Halkjær SI et al. Faecal microbiota transplantation alters gut microbiota in patients with irritable bowel syndrome: results from a randomised, double-blind placebo-controlled study. Gut. 2018. PMID 29980607
  14. Aumpan N et al. Fecal Microbiota Transplantation for Symptom Improvement in Patients With Irritable Bowel Syndrome: Systematic Review and Meta-Analysis of Randomized Controlled Trials. Gastroenterology. 2026. PMID 42162772
  15. Dansk Selskab for Gastroenterologi og Hepatologi. Colon irritabile: Diagnostik og behandling. National guideline. 2026. dsgh.dk
  16. Minerbi A et al. Altered microbiome composition in individuals with fibromyalgia. Pain. 2019. PMID 31219947
  17. Cai W et al. The gut microbiota promotes pain in fibromyalgia. Neuron. 2025. PMID 40280127
  18. Black CJ et al. British Society of Gastroenterology guidelines on the management of functional dyspepsia. Gut. 2022. PMID 35798375
  19. Huang X et al. Meta-Analysis: Placebo Response and Its Determinants in Functional Dyspepsia. Am J Gastroenterol. 2021. PMID 34404084
  20. Calandre EP et al. The Probiotic VSL#3 Does Not Seem to Be Efficacious for the Treatment of Gastrointestinal Symptomatology of Patients with Fibromyalgia: A Randomized, Double-Blind, Placebo-Controlled Clinical Trial. Pharmaceuticals (Basel). 2021. PMID 34681287
  21. Roman P et al. Are probiotic treatments useful on fibromyalgia syndrome or chronic fatigue syndrome patients? A systematic review. Benef Microbes. 2018. PMID 29695180
  22. Groen J et al. ESPGHAN/NASPGHAN guidelines for treatment of irritable bowel syndrome and functional abdominal pain-not otherwise specified in children aged 4-18 years. J Pediatr Gastroenterol Nutr. 2025. PMID 40444524
  23. Agger JL et al. Imipramine versus placebo for multiple functional somatic syndromes (STreSS-3): a double-blind, randomised study. Lancet Psychiatry. 2017. PMID 28408193
  24. Fjorback LO et al. Mindfulness therapy for somatization disorder and functional somatic syndromes: randomized trial with one-year follow-up. J Psychosom Res. 2013. PMID 23272986
  25. Staudacher HM et al. Fiber Supplementation in Irritable Bowel Syndrome: A Systematic Review and Meta-Analysis of Randomized Controlled Trials. Gastroenterology. 2026. PMID 42600900
  26. Ford AC et al. Efficacy of Helicobacter pylori eradication therapy for functional dyspepsia: updated systematic review and meta-analysis. Gut. 2022. PMID 35022266
  27. Sundhedsstyrelsen. Opfølgning på vidensafdækningerne om ME/CFS. Presentation at a theme meeting for the parliamentary health spokespeople, 11 December 2025. Published by ME Foreningen after a freedom of information request. me-foreningen.dk
  28. Sundhed.dk. Mavekatar (funktionel dyspepsi). Patienthåndbogen. Updated 2023. sundhed.dk
  29. Aarhus Universitetshospital. Funktionelle Lidelser. The department's page for patients. auh.dk

This article is general information and not medical advice.