Overview
The gut microbiome is the vast community of trillions of bacteria, viruses, and fungi that live in the digestive tract. A healthy, diverse microbiome supports digestion, immunity, metabolism, and even mental health. Disruption of this balance (dysbiosis) has been linked to many conditions, from IBS to obesity and depression.
How common is it?
Dysbiosis is common but difficult to define precisely because the 'ideal' microbiome varies widely between healthy individuals. Changes in the microbiome are associated with antibiotic use, poor diet, illness, and stress.
Causes and risk factors
The modern lifestyle, including antibiotic use, highly processed diets low in fibre, and high in sugar, stress, lack of sleep, and reduced early-life microbial exposure, all reduce microbiome diversity.
Common risk factors
- Antibiotic use (kills beneficial bacteria as well as harmful ones)
- Diet low in fibre and high in processed foods and sugar
- Chronic stress and poor sleep
- Lack of early-life microbial exposure (C-section birth, formula feeding)
- Proton pump inhibitor use
- Smoking and excess alcohol
- Chronic illness and some medications
Symptoms
- Bloating, gas, and abdominal discomfort
- Diarrhoea or constipation (or alternating between both)
- Fatigue
- Food intolerances
- Recurrent infections
- Mood changes, anxiety, or depression
- Skin conditions worsening
When to see a doctor
See a doctor if gut symptoms are persistent, significantly affecting your quality of life, or if you have blood in stools, unexplained weight loss, or symptoms that began after a course of antibiotics.
Diagnosis
There is no single validated clinical test for dysbiosis. Diagnosis of related conditions (IBS, SIBO, C. difficile infection) uses stool tests, breath tests, and colonoscopy. Commercial stool microbiome tests are available but have limited clinical validity currently.
Treatments
Dietary intervention
Increasing dietary fibre from diverse plant sources (30 different plants per week is a research-based target) is the most evidence-based way to improve microbiome diversity.
Probiotics
Live beneficial bacteria found in fermented foods (yoghurt, kefir, sauerkraut, kimchi, miso) or supplements. Specific probiotic strains have evidence for specific conditions (e.g. Lactobacillus for antibiotic-associated diarrhoea).
Faecal microbiota transplant (FMT)
Transfer of stool from a healthy donor into the gut of a patient. Highly effective (90%+) for recurrent Clostridioides difficile infection. Under investigation for other conditions.
Self-care and lifestyle
- Eat at least 30 different plant foods per week for microbiome diversity
- Eat fermented foods daily: yoghurt, kefir, kimchi, sauerkraut
- Minimise unnecessary antibiotic use and take probiotics during any antibiotic course
- Reduce ultra-processed food consumption and increase fibre
Prevention
A diverse, plant-rich diet, minimising antibiotic use, managing stress, and adequate sleep all support a healthy microbiome.