A Functional Medicine Approach to Small Intestine Bacterial Overgrowth

Small Intestine Bloating

In this article we look at the health of the small intestine with a particular focus on Small Intestine Bacterial Overgrowth or SIBO for short.

Our Nutritionists and Functional Medicine Practitioners regularly see SIBO and help to support clients with SIBO. The truth is though, SIBO is often just a symptom or a reaction to something. Whether it’s chronic or acute stress, an infection, antibiotic use, poor bowel motility, reduced acid and enzyme production, a misfiring vagus nerve, there are lots of potential underlying factors. This is why a Functional Medicine style approach, delivered correctly can work well in overcoming SIBO and the symptoms of IBS associated to SIBO.

In this article, we look at, the role of the small intestine, what is SIBO, how it’s diagnosed, what might cause SIBO in the first place and treatment considerations


Why a healthy small intestine is important

Most of your nutrient absorption takes place in the 3 main sections of the small intestine. In the first part of the small intestine, the duodenum, it still should have a fairly acidic environment which helps with the absorption of many minerals, certain water soluble vitamins such as many of the B vitamins and vitamin C and fat soluble vitamins, such as A, D, & E, thus poor HCl in the stomach can still have negative effects on the absorption of nutrients further down the chain. The large majority of your fat is absorbed in this part of the small intestine along with some carbohydrate absorption as well.

Proteins and carbohydrate digestion and absorption continue in the jejunum, and then in the final phase in the ileum it finishes the job of digesting many nutrients including B12 and dietary cholesterol.

It’s all about balance

In the majority of people, bacteria is found at its highest levels in the colon/large intestine. It is possible however for these bacteria to overgrow in the small intestine where there is meant to be comparatively much less bacteria.

When bacteria beings to overgrow in the small intestine, this is one of the primary causes of Irritable Bowel Syndrome (IBS), with one study suggesting that 84% of those with IBS had excessive fermentation and gas production, an indicator or SIBO. The same group of individuals when treated for SIBO saw a dramatic improvement in there IBS symptoms, suggesting that the SIBO was a driving force behind their symptoms.

Whilst the SIBO can be seen as a possible cause of IBS, it still begs the question, what causes SIBO. More on this further down!

The challenge you may have is that the excessive amounts of bacteria in the small intestine or the particular balance of bacteria in that region of the digestive tract leads to bacteria fermenting dietary carbohydrates such as sugars, starches and fibre.

In the right areas of the digestive tract (the colon), this fermentation process can be extremely beneficial, helping to reduce intestinal inflammation, reduce the risk of colon cancer and so forth. If you have SIBO then this fermentation occurs much higher up the digestive tract, in an area the digestive system was not designed for such levels of fermentation.

Unfortunately, this can lead to bloating, distention, excessive gas, increased intra-abdominal pressure and increased risk of reflux and heartburn etc. People often find themselves becoming more and more intolerant to foods, in particular a lot of very healthy, higher fibre foods. This can be very frustrating when you feel you are making good food choices and your digestive symptoms seem to get worse.

Unfortunately excesses of bacteria in the small intestine also have the capacity to interfere with the acids and enzymes that our body produces to help breakdown food. As a result, our overall digestion and absorption of nutrients can become effected. This can be another contributing factor to IBS symptoms and the side effects noted from SIBO.

It is not uncommon for those with SIBO to also have dominance of bacteria that when overgrown are more likely to cause symptoms. These opportunistic bacteria can often contribute to certain types of bacteria toxins being produced in the gut. These toxins, known as endotoxin or Lipopolysaccharides (LPS) have been shown to be very pro-inflammatory and can lead to damage to the gut wall, increased intestinal permeability, IBS type symptoms as well as more systemic symptoms and conditions, such as autoimmune diseases, cognitive impairment, arthritic conditions etc.

What are the classic symptoms of SIBO?

Common symptoms of SIBO

  • Bloating and gas, especially within 1-2 hours of eating
  • Bloating that steadily gets worse through the day
  • Intolerance to fibrous foods – beans, lentils, chickpeas, onions, garlic, broccoli, cauliflower, cabbage, kale etc
  • Abdominal discomfort
  • Changeable stools – can be loose stools or constipation, depending on the types of bacteria present and the gases being produced
  • Intolerance to foods that contain lactose – cow’s milk, cheeses, yoghurt etc

Less common symptoms of SIBO

  • Weight loss or inability to gain weight
  • Arthritic pains
  • Anaemia – B12, iron insufficiencies
  • Nerve pain – possibly because of low B12
  • Fatigue and muscle pain
  • High fat content in the stool – floating, greasy or pale stools
  • Acne and rosacea

As well as symptoms there are also associations with specific conditions and SIBO. As a result, I may suspect SIBO if an individual also presents with even just mild symptoms of SIBO plus any of the following:

  • Chronic fatigue / fibromyalgia
  • Restless legs syndrome
  • Gallstones
  • Interstitial Cystitis
  • Hypothyroid
  • Fatty liver
  • Acne rosacea
  • Anxiety

It should be noted that these are associations and do not always mean there is a direct cause. In fact, in my experience with SIBO, it is the SIBO that is a symptom of another dysfunction elsewhere. I believe this is why SIBO has such significant recurrence rates and its response to antimicrobial treatment alone can be very hit and miss. Often individuals need to be supported on a number of levels to get long-term success with addressing SIBO.

How is SIBO Diagnosed?

The current diagnosis of SIBO typically relies on lactulose or glucose breath test. There are benefits and negatives for both, with lactulose arguably the more reliable substrate to use if you are not able to run both.

There is also something called a small intestine aspirate, which is performed during an endoscopy and may be something to speak with your gastroenterologist about.

SIBO breath testing looks at levels of hydrogen and methane that have been absorbed into circulation following the fermentation of the substrate such as glucose or lactulose and then exhaled.

The breath test is designed to help understand the amount of fermentation in the first 100mins or so of the test.

Whilst the breath test does not tell you exactly what bacteria are overgrown in the small intestine the most common are E.coli, klebsiella, proteus, aeromonas for hydrogen production and the archaea methnobrevibacter smithii in methane positive test results. Although high levels of methane at the start of the test and throughout is more an indication of general intestine methane overgrowth (IMO) and may not be small intestine specific.

Ultimately there are some significant caveats when it comes to interpreting SIBO test results.

Stool Testing

Stool testing is not accurate for diagnosing SIBO, however you can pick up on some markers that may indirectly indicate that SIBO is present. In this respect, stool testing is probably best used to determine potential factors that are contributing to the cause of SIBO.

  • Chronically low SIgA levels often resultant from chronic stress/frustration, chronic infections etc.
  • Elevated fat in the stool is a sign of SIBO presence and also a sign of poor pancreatic enzyme or bile acid production/function. Note: destruction of bile acids and digestive enzymes can occur from bacterial overgrowth.
  • Increased faecal zonulin – A sign of intestinal permeability, perhaps resulting from excessive levels of gram negative bacteria producing endotoxins (LPS).
  • Increased or reduced Short Chain Fatty Acids (SCFAs). Low levels especially butyrate is associated with slowed bowel motility and increased levels are a possible sign of SIBO as they are a product of bacterial fermentation. Having said that when someone adopts a therapeutic diet to try and treat SIBO, over time this can have negative effects on the levels of SCFAs and lead to imbalances in the colon. Hence following diets like low FODMAP and Specific Carbohydrate Diets don’t come without their drawbacks, not to mention their restrictive nature.
  • As well as these, it is crucial to look for other imbalances in the gut that might be contributing to the development of SIBO such as infections, general microbiome imbalances etc.

What are the far-reaching causes of SIBO?

SIBO has a significant number of potential underlying factors that contribute both to the initial development and the ongoing occurrence of SIBO.

We have natural mechanisms that help to prevent SIBO, these include the following:

  • The production of hydrochloric acid and bile acid. These are the acids that help us to breakdown proteins and fats.
  • Proper motility through the digestive tract, reliant on optimal functioning of the migrating motor complex (MMC), vagus nerve stimulation (brain-gut connection) and the interstitial cells of Cajal (cells located within the muscle layers of the gut wall that communicate between our nervous system and the smooth muscle of the gut).
  • A valve between the small intestine and large intestine known as the ileocecal valve that helps to prevent backflow of bacteria.
  • Secretory immunoglobulin’s such as Secretory IgA that help to maintain bacterial balance and prevent opportunistic overgrowths and chronic infections.

Four main treatment areas to consider with SIBO include:

Impaired motility

  • Autoimmunity and dysfunctional Migrating Motor Complex – often due to food poisoning, gastroenteritis etc
  • Traumatic Brain Injury
  • Hypothyroid
  • Chronic infections
  • Diabetes – neuropathy of the vagus nerve
  • Mould Toxicity
  • Ehlers-Danlos Syndrome or other connective tissue conditions
  • Scleroderma

Impaired Digestion

  • Hypochlorhydria – low stomach acid
  • Poor bile flow – low bile acid
  • Pancreatic enzyme insufficiency
  • Poor brush boarder enzyme function – enzymes that sit in the lining of the gut to help with the final breakdown of food before it is absorbed
  • Secretory IgA deficiency – An antibody found at the mucosal layer
  • Chronic stress
  • Imbalanced bacteria

Impaired flow through intestines

  • Abdominal surgery resulting in adhesions
  • Endometriosis
  • Ehlers-Danlos Syndrome or other connective tissue conditions
  • Ileocecal value dysfunction
  • Anatomical Abnormalities


  • Opiates / Narcotics
  • Antispasmodics
  • Tricyclic antidepressants
  • Proton Pump Inhibitors (PPIs – antacids)
  • Cholestyramine

As you can see from just this list there is a huge array of potential underlying factors that should be consider while addressing the overgrowth and following treatment to prevent the reoccurrence. This should not overwhelm you however as many can be ruled out based upon your history and others can be ruled out with further investigation.

Unfortunately, with SIBO the reoccurrence rates are very high, with around two thirds of people relapsing with SIBO following antimicrobial therapy. This means the antimicrobial treatment is just the starting point and determining the true underlying cause of the SIBO is where long-term success will be found.

Treatment considerations for Small Intestine Bacterial Overgrowths

  1. Treat the SIBO – Most people see this as the only goal. If this is the only focus relapse is highly likely.
  2. Treat the cause – Motility, structural, digestive.
  3. Restore the microbiome – Appropriate balance of microbes.

The approach should encompass mind and body. A starting point as always is to look at one’s foundations, so assessing sleep, stress/relaxation, nutrition, movement etc. In some people working on the basics can be enough and further complexities/imbalances need not be investigated. If a resolution does not occur, then further investigation into SIBO and other imbalances may be warranted.

Here are a few areas you can work on immediately:


Specific diets have been shown to help with the symptoms of SIBO, however if used they should remain short term protocols for therapeutic benefit. The issue with many restricted diets that help with the symptoms of SIBO is that over time they can cause problems of their own, such as an imbalanced colon, constipation, nutrient insufficiencies etc.

Some of the most successful short-term therapeutic diets for SIBO include:

  • Low FODMAP
  • Specific Carbohydrate Diet (SCD)
  • A combination of the above

It is also worthwhile supporting the body to help with digestion. This might include bitter foods prior to a meal to help stimulate acids and enzymes. Bitter foods might include rocket, dandelion, chicory, apple cider vinegar, radish etc.

I like to create as much variety still even within the limitations of the above diet to provide a spread of nutrients and also to prevent any developing allergies/sensitivities resulting from over exposure to any one single food while the gut is inflamed.

In many cases I allow my clients to play around with the restrictions set out with the therapeutic diets. Changing diet alone is not going to resolve SIBO, it is going to help manage symptoms only. For that reason, challenging yourself with foods and seeing if you respond better to those foods over time is a good indication of improvement within the small intestine.

We also need to be particularly careful that we are not creating anxiety around foods when embarking on a therapeutic diet that restricts certain foods. It is important to note that it is not the food that is at fault. Food is NOT the enemy!! Often our thoughts around food can have more of an impact on how we respond to those foods than any reaction itself. If anxiety has developed around food or certain situations that trigger off digestive symptoms, then I may work alongside a hypnotherapist to add in gut targeted hypnotherapy.

Meal timing is one of the most important factors when developing a nutrition strategy for someone with SIBO. Avoiding high frequency of meals is typically best. I would take someone to 2-4 meals per day without any snacking, at least 4 hours between eating and the very least a 12 hour fast every day from the last meal of the day to the first.

As well as focusing on what you eat and when you eat, how you eat is also important, thus, the promotion of mindful eating is important.


One of the most important areas of consideration is the management of stress. This may mean looking at the following areas:

  • Investigating the impact of both past and present stressors / traumas
  • Reviewing one’s schedule and prioritisation of time
  • Reviewing your current exercise demands and marrying up an appropriate exercise intensity to your capacity to recover
  • Optimising sleep health and sleep hygiene
  • Consider the inclusion of meditation / mindfulness practice

Hands on Therapy

I have seen many people improve their digestive health through the support of a good osteopath or physical therapist. This can include visceral mobilisation and massage as well as addressing musculoskeletal imbalances.

Other possible therapies that can help include acupuncture, diaphragmatic breathing, restorative forms of yoga, homeopathy, cranial sacral therapy. A lot of these are also focused on the management of stress and ultimately the balance of your autonomic nervous system (fight or flight vs rest & digest).

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