saudigastro.com/patients/gut-microbiome-and-food
Category
Common
Red flags
4
This article is educational and does not replace your doctor's advice. Seek urgent care for any red-flag symptoms.
What is it?
The gut microbiome is the community of trillions of bacteria, along with viruses, fungi and other microbes, that lives mainly in the colon. We live in partnership with it. These microbes ferment fibre that we cannot digest into short-chain fatty acids, which feed the cells of the colon lining, they help to train the immune system, and they make some vitamins. Each person has a unique mix, shaped by birth, early feeding, diet, medicines (especially antibiotics), age and where they live. Three terms are often confused. Probiotics are live microbes that, in adequate amounts, may give a health benefit. Prebiotics are food components, mostly fibres, that feed helpful microbes. Fermented foods, such as yoghurt, laban and pickled vegetables, are made with microbes but do not always contain strains that have been proven to help health.
How common is it?
Everyone has a gut microbiome. Interest in it is high because differences in the microbiome have been linked with many conditions, including inflammatory bowel disease, irritable bowel syndrome, obesity, diabetes and liver disease. It is important to know that most of these links come from observational studies and do not prove that the microbiome is the cause, or that changing it will treat the disease.
Why does it happen?
Diet is one of the strongest everyday influences on the microbiome. Plant fibre, from vegetables, fruit, legumes and whole grains, feeds beneficial microbes and supports diversity. A diet high in refined sugar, fat and heavily processed food is associated with less favourable microbial patterns, although studies so far are mostly observational. Antibiotics can reduce diversity for weeks to months and are sometimes followed by diarrhoea; they remain essential when needed. Other influences include stress, sleep, travel, smoking and infections.
Symptoms
- Gas and bloating when fibre or fermentable foods are increased too quickly
- Loose stools or diarrhoea during or after antibiotics
- Constipation or irregular bowel habit on a low-fibre diet
- Symptoms of irritable bowel syndrome (cramps, bloating, altered stools)
Red flags — seek urgent medical care
Watery diarrhoea several times a day after antibiotics, with fever or belly pain
May be a Clostridioides difficile infection. See your doctor urgently or go to the hospital; do not take anti-diarrhoea medicines first.
Blood in the stool, black stools, or unexplained weight loss
Not explained by the microbiome. Needs urgent medical assessment and possible tests.
Fever, chills or feeling very unwell after starting a probiotic, especially if you have a weak immune system, a central venous line or a serious illness
Probiotics have, rarely, caused bloodstream infections in vulnerable people. Stop the product and get medical help the same day.
Persistent diarrhoea for more than a few weeks, or diarrhoea that wakes you at night
Needs tests for inflammation, infection or malabsorption; see your doctor.
How is it diagnosed?
There is no routine test of the microbiome that is recommended for patients. Commercial stool tests that report your bacteria and give diet or supplement advice are not validated for use in making decisions about your treatment, and their results can vary between samples. If you have symptoms, your doctor uses standard tests (blood tests, stool tests for infection or inflammation, and endoscopy when needed) to look for specific diseases.
What the latest science says
The American Gastroenterological Association guideline on probiotics (Su et al., Gastroenterology, 2020) suggests probiotics for certain uses only, such as preventing necrotising enterocolitis in preterm babies and managing pouchitis, and suggests against routine probiotic use in Crohn’s disease, ulcerative colitis and for treating Clostridioides difficile infection outside of trials. Evidence in irritable bowel syndrome is limited and strain-specific. For the diet, the World Health Organization (2023) recommends at least 25 g of fibre daily for adults, and large cohort studies link higher fibre and whole-grain intake with lower risk of heart disease, diabetes and bowel cancer. A small randomised trial from Stanford (Wastyk et al., Cell, 2021) found that adding fermented foods for ten weeks increased microbial diversity and reduced some inflammation markers, but it was small and short, so firm advice cannot be based on it. Observational studies link ultra-processed foods with bowel inflammation and other diseases, but they cannot prove cause.
Outlook — what to expect
The microbiome responds to long-term eating patterns more than to single foods or short courses of supplements. A steadily plant-rich, high-fibre diet is good for the gut and the rest of the body whatever the microbiome does. Research is moving fast, and personalised advice based on the microbiome is not yet ready for everyday care.
Treatment
Habits & Lifestyle
Small, steady habits do more than short "gut resets".
- Aim for variety: many different plant foods across the week (vegetables, fruit, legumes, nuts, seeds, whole grains, herbs) rather than a few in large amounts.
- Use antibiotics only when your doctor prescribes them, and finish the course as directed.
- Stay active, sleep well and manage stress; these all influence gut function.
- Wash your hands and handle food safely to prevent gut infections, especially when travelling.
Diet
The best-supported way to nourish your gut microbes is a food-first, fibre-rich pattern.
- Work towards about 25 to 30 g of fibre a day by adding one extra portion of vegetables, legumes or whole grains at a time, and drink enough fluid.
- Choose whole-wheat or jareesh and brown rice more often, and include foul, lentils, chickpeas and hummus.
- Include fermented foods you enjoy, such as plain laban or yoghurt without added sugar, as part of the diet. Evidence of benefit is promising but not firm.
- Limit ultra-processed foods such as sugary drinks, packaged snacks, processed meats and sweets.
- If you have irritable bowel syndrome, a low-FODMAP diet (a diet that temporarily reduces certain fermentable carbohydrates) should be done with a dietitian, as it is not meant to be permanent.
Medications
Probiotic, prebiotic and "gut health" supplements are not regulated like medicines, and their quality varies.
- Probiotics are not needed by healthy people. If you choose to try one, pick a product with the strain name and amount stated on the label, use it for a defined trial period, and stop if there is no benefit.
- Talk to your doctor before using probiotics if you have a weak immune system, are very ill, have a central line, or are pregnant.
- Antibiotics treat infections only. They should not be taken for viral illnesses, and some diarrhoea after antibiotics needs assessment.
- Faecal microbiota transplantation is a medical treatment used mainly for repeated Clostridioides difficile infection under specialist care; it is not a self-help option.
Procedures & Surgery
There are few procedures related to the microbiome in everyday care.
- Stool tests for infections such as C. difficile are routine when diarrhoea follows antibiotics.
- Colonoscopy or endoscopy is done for warning signs, not to assess the microbiome.
- Faecal microbiota transplantation is delivered by colonoscopy, enema or capsule in specialist centres for selected infections.
Living with the condition
- Be wary of products that promise to "rebalance" or "repair" your gut; no product has been proven to do this for healthy people.
- Make changes one at a time and give each a few weeks, so you can tell what helps.
- Keep a symptom diary and bring it to your visit.
In the Saudi context
Traditional Saudi foods already contain gut-friendly ingredients: jareesh and harees (whole or cracked wheat), foul and other legumes, dates (which provide fibre), laban, and vegetables in salads and stews. Dates are healthy in modest amounts, about two to three at iftar, but are rich in sugar, so people with diabetes should count them in their plan. Commercial laban or ayran drinks may contain a lot of salt or added sugar, so check the label. Fibre and fluid intake often drop in the heat and during Ramadan; plan fibre-rich foods at suhoor, such as oats, foul and whole-grain bread, and drink water between iftar and suhoor.
Questions to ask your doctor
Save this list or print it before your appointment — doctors appreciate prepared patients.
- Would a probiotic help my specific condition, and which strain has evidence?
- Are my symptoms related to my diet, my antibiotics or something else?
- How much fibre should I aim for, given my condition?
- Is a low-FODMAP diet right for me, and can I see a dietitian?
- Are stool microbiome tests worth doing?
Trusted resources
Was this guide helpful?
Status: Approved for publication by SGA; individual clinician review is ongoing · Published 24/04/2026
For general education only; it does not replace your doctor’s advice. Individual clinician review of this guide is ongoing. SGA clinician? Review this guide