SIBO and Histamine Intolerance and How They May Be Connected

SIBO and histamine intolerance are often mentioned together, and the link makes sense on paper. Small intestinal bacterial overgrowth (SIBO) means there are more bacteria than usual in the small intestine, the part of the gut where DAO, the enzyme that breaks down histamine from food, is made. Some gut bacteria can produce histamine, and inflammation in the small intestine may reduce DAO. But direct research on how often SIBO causes or worsens histamine intolerance is limited, and both conditions are frequently over-diagnosed online. This guide explains the possible connection, how SIBO is diagnosed and treated by doctors, and what to do if you suspect both.

What SIBO is

The small intestine normally contains relatively few bacteria compared with the large intestine. Several things keep it that way: stomach acid, the regular “sweeping” movements of the gut, the valve between the small and large intestine, and the immune system. When these defences are weakened, bacteria can build up in the small intestine. They ferment food, producing gas and sometimes interfering with digestion and absorption.

Common symptoms include bloating, abdominal discomfort, wind, diarrhoea and sometimes constipation. In more severe cases, SIBO can cause weight loss and deficiencies of nutrients such as vitamin B12. The American College of Gastroenterology’s clinical guideline on SIBO, published in 2020, lists conditions that raise the risk, including previous abdominal surgery, slow gut movement, some causes of reduced stomach acid, and certain chronic illnesses. It also recognises a related condition in which methane-producing organisms overgrow, often linked with constipation.

How SIBO may affect histamine

Bacteria that make histamine

Some bacteria can convert the amino acid histidine, found in protein foods, into histamine using an enzyme called histidine decarboxylase. Examples include certain strains of Morganella, Klebsiella and some lactic acid bacteria. A 2020 review of histamine intolerance in Biomolecules discusses the gut microbiota as one possible source of histamine. In theory, an overgrowth of histamine-producing bacteria in the small intestine could add to the histamine load. Whether this happens in SIBO, and how much it matters, has not been well studied in people.

Effects on DAO

DAO is made by cells lining the small intestine. Conditions that inflame or damage this lining, such as coeliac disease and inflammatory bowel disease, are known to be associated with lower DAO activity. It is plausible that SIBO could reduce DAO in a similar way, especially when it causes inflammation, but this has not been firmly established.

Overlapping symptoms

Even where there is no direct causal link, SIBO and histamine intolerance share symptoms such as bloating, abdominal pain and diarrhoea. In a 2019 study in Intestinal Research of people with low DAO activity and digestive complaints, 92% reported bloating, 71% diarrhoea and 68% abdominal pain, all of which are also typical of SIBO. This overlap means one can easily be mistaken for the other, or both may be present together.

Methane overgrowth and constipation

Not all overgrowth looks the same. When methane-producing organisms, which are archaea rather than bacteria, build up in the gut, the main symptom is often constipation and bloating rather than diarrhoea. The ACG guideline calls this intestinal methanogen overgrowth and treats it as a related but separate condition. Constipation itself can worsen bloating and discomfort, and it slows the passage of food, so it is worth addressing whatever the role of histamine.

What the evidence does and does not show

• It is plausible. Bacteria can make histamine, and gut inflammation can reduce DAO.
• It is not well studied. There are few studies directly measuring histamine or DAO in people with SIBO, and no trials showing that treating SIBO cures histamine intolerance.
• Claims online often go further. Statements that SIBO is “the hidden cause” of most histamine intolerance, or that symptoms disappear within months of treatment, are not supported by research.

The practical message is that SIBO is worth considering in people with histamine-type symptoms and significant digestive problems, especially when there are risk factors, but it should be diagnosed and treated by a doctor rather than assumed.

Signs that SIBO might be worth investigating

None of these prove SIBO, but together they may be a reason to discuss testing with your doctor:

• Bloating, wind or diarrhoea that persists despite a carefully followed low histamine diet.
• Bloating soon after meals, across many different foods, not just high histamine ones.
• Risk factors such as previous abdominal surgery, known slow gut movement, long-term use of acid-reducing medicines, diabetes with gut symptoms, or a diagnosis of IBS.
• Symptoms that started after a bout of gastroenteritis.
• Signs of poor absorption, such as unexplained weight loss, fatty or pale stools, or low vitamin B12 or iron.

Weight loss, blood in the stool, anaemia or night-time symptoms are warning signs that need prompt medical assessment for other causes, whatever the role of SIBO.

Medicines and conditions that may raise SIBO risk

Some medicines and conditions are linked with a higher chance of SIBO, mainly because they reduce stomach acid or slow the movement of the gut. Long-term use of proton pump inhibitors for acid reflux, opioid painkillers, and conditions such as diabetes with nerve damage to the gut, scleroderma, previous bowel surgery and some thyroid problems are among those discussed. Do not stop any of these medicines on your own. If you think a medicine may be playing a part, your doctor can review whether it is still needed, whether the dose can be changed or whether there is an alternative.

How SIBO is diagnosed

The most common test is a breath test. After fasting and a special diet the day before, you drink a sugar solution, usually glucose or lactulose, and breathe into tubes at intervals over a couple of hours. The samples are tested for hydrogen and methane, gases produced when bacteria ferment the sugar. An early rise suggests bacteria in the small intestine. The ACG guideline describes breath testing as a simple and non-invasive option, while noting that results need careful interpretation and that false positives and false negatives occur.

Breath tests are best arranged through a doctor or gastroenterologist, who can interpret the results alongside your symptoms and history. Home kits sold online vary in quality, and a positive result on its own does not always mean SIBO is the cause of your symptoms. Other tests, such as blood tests for coeliac disease, iron and vitamin B12, may also be needed.

Preparing for a breath test

Breath tests need some preparation, and the exact instructions come from the clinic doing the test. Typically you will be asked to avoid antibiotics for several weeks beforehand, to stop some laxatives and other medicines for a short time if your doctor agrees, to eat a simple low-fibre diet the day before, and to fast overnight. Smoking and exercise are usually not allowed during the test. Following the instructions carefully reduces the chance of a misleading result. Tell the clinic about all the medicines you take, and do not stop any prescribed medicine without checking with your doctor.

How doctors treat SIBO

Treatment depends on the type of overgrowth, the underlying cause and your overall health, and it should be guided by a doctor.

• Antibiotics. The ACG guideline supports antibiotics for symptomatic SIBO, and rifaximin, an antibiotic that stays mainly in the gut, is commonly used. Methane-predominant overgrowth may be treated differently. Your doctor will decide which antibiotic, if any, suits you.
• Treating the underlying cause. Where possible, doctors address what allowed the overgrowth, such as reviewing medicines, managing diabetes or treating slow gut movement. Without this, SIBO often returns.
• Diet. Some doctors and dietitians use temporary dietary changes to reduce symptoms. These should be short and supervised, because combining restrictive diets can lead to nutritional problems.
• Correcting deficiencies. Vitamin B12, iron and other nutrients may need to be replaced.

Herbal antimicrobial products are widely promoted online for SIBO. A few small studies have looked at them, but the evidence is limited, product quality varies, and some herbs interact with medicines. Talk to your doctor before using them. The ACG guideline also found insufficient evidence to recommend for or against probiotics for treating SIBO.

Eating when you have both

If you have histamine intolerance and SIBO, or suspect both, the diet can become very restrictive very quickly. A low histamine diet removes aged, fermented and stored foods. Diets used for SIBO symptoms, such as a low FODMAP diet, remove foods that bacteria ferment easily, such as onions, garlic, beans and some fruits. Combining the two cuts out a lot.

A few principles keep this manageable:

• Work with a registered dietitian if you need to combine diets.
• Keep the most restrictive phase short and reintroduce foods as soon as you can.
• Base meals on foods that fit both diets, such as rice, oats, potatoes, quinoa, carrots, courgette, cucumber, peppers, fresh chicken, fresh beef, very fresh or frozen-at-sea white fish, blueberries and firm bananas.
• Use garlic-infused oil and fresh herbs for flavour instead of onion and garlic.
• Eat fresh food and freeze leftovers on the day of cooking to keep histamine low.

Our histamine intolerance food list and elimination diet plan cover the histamine side in detail, and our guide to histamine intolerance and bloating discusses how the two diets overlap.

A day of eating that fits both diets

Here is an example of meals that are low in histamine and gentle for a gut prone to fermentation. Breakfast could be porridge made with oats and lactose-free milk, topped with blueberries and a few pumpkin seeds. Lunch could be rice with freshly cooked chicken, carrots and courgette, dressed with olive oil, salt and fresh herbs. A snack could be rice cakes or a firm banana. Dinner could be very fresh or frozen-at-sea white fish or beef with potatoes and green beans, flavoured with garlic-infused oil. Drinks could be water and peppermint or ginger tea. This is a short-term example rather than a long-term plan, and a dietitian can help you widen it safely.

Common claims about SIBO and histamine, checked

• “SIBO is the root cause of most histamine intolerance.” There is no evidence for this. Histamine intolerance has several proposed causes, including genetic differences in DAO, gut inflammation, medicines and diet.
• “Everyone with bloating should be tested for SIBO.” Bloating is very common and usually has simpler explanations. Testing is most useful when there are risk factors or persistent symptoms.
• “A positive home breath test confirms SIBO.” Breath tests can give false positives, particularly with lactulose, and need interpretation by a doctor.
• “Herbal protocols are as good as antibiotics.” The evidence is limited to a few small studies.
• “Histamine symptoms disappear after SIBO treatment.” Some people improve, but this is not guaranteed and has not been studied properly.

Probiotics, SIBO and histamine

Probiotics are often suggested both for SIBO and for histamine intolerance, but the evidence is weak in both cases. Some probiotic strains are thought to produce histamine, while others may not. The ACG guideline found insufficient evidence to recommend for or against probiotics for SIBO, and adding more bacteria when there is already an overgrowth is not always helpful. If you are considering a probiotic, discuss it with your doctor. Our probiotics guide looks at what is known about different strains.

After treatment

If SIBO is treated successfully, some people notice their digestive symptoms and histamine-type symptoms improve. Others find that histamine symptoms continue, which suggests other causes are involved. Either way, it is worth reviewing your diet after treatment and reintroducing foods gradually, rather than staying on a restricted diet out of habit. Keeping a histamine food diary before and after treatment helps you and your doctor judge what changed.

SIBO can come back, especially if the underlying cause is still present. Recurring symptoms are a reason to go back to your doctor rather than to repeat treatments on your own.

Living with both conditions

Managing two overlapping gut conditions can be tiring, especially when food choices are limited and symptoms come and go. A few things help. Keep a simple list of meals you know you tolerate so you are not deciding from scratch every day. Batch cook and freeze portions on the day you cook them, so fresh, safe food is always available. Plan ahead for eating out and travel. Look after sleep and stress, because both affect gut symptoms and histamine tolerance. And keep in contact with your doctor or dietitian, so that restrictions are reviewed and loosened as soon as possible rather than becoming permanent. Feeling anxious about food is common in this situation, and it is worth mentioning to your doctor if it starts to affect your life.

Other gut conditions to consider

SIBO is only one of several gut conditions that can overlap with histamine intolerance. Coeliac disease, inflammatory bowel disease, irritable bowel syndrome, lactose intolerance and bile acid problems can all cause similar symptoms. Our guides to histamine and IBS and histamine intolerance and gut health discuss these overlaps. Coeliac disease needs testing while you are still eating gluten, so do not cut out gluten before talking to your doctor.

When to see a doctor

Call emergency services straight away if you or someone else has swelling of the lips, tongue or throat, difficulty breathing or wheezing, a hoarse voice, feeling faint or collapse. These are signs of anaphylaxis, which needs an adrenaline (epinephrine) injection and urgent care.

See your doctor if you have ongoing bloating, diarrhoea or abdominal pain, unexplained weight loss, blood in your stool, anaemia, night sweats or symptoms that wake you at night. These need investigation for causes beyond SIBO and histamine intolerance. Talk to your doctor before taking antibiotics or herbal antimicrobial products, and before starting a combined restrictive diet, especially if you are pregnant, underweight or have other health conditions. Some medicines can affect DAO, as our guide to medications that may block DAO explains, but never stop a prescribed medicine without advice.

Questions about SIBO and histamine

Can SIBO cause histamine intolerance?

It is possible. Some gut bacteria make histamine, and inflammation in the small intestine may reduce DAO. Research directly linking the two in people is limited, so SIBO should be diagnosed properly rather than assumed.

How is SIBO tested?

Usually with a glucose or lactulose breath test that measures hydrogen and methane. Results should be interpreted by a doctor alongside your symptoms, because false positives and false negatives occur.

Will treating SIBO cure my histamine intolerance?

Some people find their histamine symptoms improve after SIBO treatment, but there is no research showing that this happens reliably. If symptoms continue, other causes are likely to be involved.

Can I follow a low histamine and low FODMAP diet together?

Yes, but the combination is very restrictive. Work with a dietitian, keep the strict phase short and reintroduce foods as soon as possible.

Are herbal antimicrobials as good as antibiotics for SIBO?

A few small studies suggest herbal products may help some people, but the evidence is limited and product quality varies. Some herbs interact with medicines. Discuss them with your doctor first.

Should I take probiotics for SIBO?

The ACG guideline found insufficient evidence to recommend for or against probiotics for SIBO. Some strains may produce histamine. Ask your doctor before starting one.

Medical disclaimer: This content is for informational purposes only and does not constitute medical advice. Always consult a qualified healthcare provider before starting any supplement regimen.