Dysbiosis

Also called microbial imbalance, gut dysbiosis.

Dr Chad OkayFounder, Suna Health

3 min read. Updated .

Dysbiosis means an imbalance in the gut microbiome. Most often it refers to lower diversity, a loss of beneficial species, or an overgrowth of unhelpful ones. The term is used in research and clinical writing, but there is no agreed clinical threshold. Many gut conditions are associated with dysbiosis, but cause and effect are still being worked out.

Why the term is hard to pin down

There is no single definition of dysbiosis that all researchers agree on. Reviews of the concept note that no consensus conference has agreed a definition of dysbiosis, so it is best thought of as a description rather than a diagnosis. It captures the observation that a microbiome looks different from a typical healthy one, but the boundary between healthy variation and pathological imbalance is blurry.

What dysbiosis usually looks like

  • Lower microbial diversity than expected for someone of similar age and lifestyle.
  • Loss of keystone beneficial species, especially Faecalibacterium prausnitzii and Akkermansia muciniphila, which produce anti-inflammatory compounds.
  • Overgrowth of pro-inflammatory species, often within Proteobacteria.
  • Reduced production of short-chain fatty acids like butyrate, which fuel the colon lining.

Common triggers

  • Antibiotics. A single course can shift composition for months. Repeated courses change baseline diversity for years.
  • Ultra-processed diets low in fibre and high in emulsifiers and certain sweeteners.
  • Chronic stress, which alters gut motility and local immune signalling.
  • Long-term proton pump inhibitor use, which reduces stomach acid and changes which bacteria can travel through to the colon.
  • Medical interventions like chemotherapy, gut surgery, or repeated bowel preparation.

Conditions linked with dysbiosis

Associations exist between dysbiosis and IBS, IBD, colorectal cancer, type 2 diabetes, obesity, atopic conditions like eczema and asthma, and some mental-health conditions. The relationship is bidirectional in most cases. Disease changes the microbiome; the microbiome influences disease. Research has not yet established that correcting dysbiosis cures any of these conditions, and microbiome-based testing and treatment are not yet validated for routine clinical use.

How to spot it without a stool test

There is no symptom that is specific to dysbiosis. Common patterns include daily bloating, irregular bowel movements, food cravings (especially for sugar), low energy that does not respond to sleep, and frequent minor illness. None of these are diagnostic on their own. Three or four together, alongside known triggers, suggest the gut is worth attention.

When it needs a doctor, not a stool test

Dysbiosis is a description, not a diagnosis. Blood in the stool, weight going down on its own, unexplained anaemia, or a change in bowel habit that has not settled each deserve a doctor at any age, and UK guidance offers a simple home stool test (FIT) for an unexplained change with no minimum duration. Anything that wakes you at night, brings fevers, or keeps building should never wait for a consumer test result.

Common questions

Can a stool test diagnose dysbiosis?
Stool sequencing tests show what's in your microbiome but cannot tell you with certainty that you have dysbiosis or what to do about it. Results vary day to day with diet. Most clinicians treat consumer microbiome tests as informational rather than diagnostic.
How long does it take to fix dysbiosis?
Composition starts shifting within 24 to 48 hours of dietary change. Larger compositional changes build over weeks of sustained dietary change, though composition also reverts quickly once the change stops.
Is dysbiosis the same as SIBO?
No. Dysbiosis describes an imbalance in the colonic microbiome. SIBO refers specifically to bacterial overgrowth in the small intestine, where bacteria are not meant to live in high numbers. The two can co-exist.
Do antibiotics always cause dysbiosis?
Yes, in the short term. A single seven-day course typically reduces diversity for two to four weeks before recovery begins. Some species can remain reduced for months afterwards. Repeat courses are the bigger concern. Saccharomyces boulardii taken alongside antibiotics has good evidence for reducing antibiotic-associated diarrhoea.

Sources

Written by Dr Chad Okay. Contributor: Dr Parisah Hussain, MBChB, BSc (Hons), DRCOG, MRCGP. Last updated 17 September 2026. From Digests.

Digests explains how the body works in general, everyday terms. It is not medical advice. It is not a substitute for someone who can examine you and knows your history, and we do not tell you what dose of any medicine to take.

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