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The approach for small intestine bacterial overgrowth: treatment is threefold: 1) correct the underlying cause; 2) provide nutritional support, if necessary; and 3) treat the overgrowth (Dukowitcz, 2007)

Correct The Underlying Cause

Firstly we need to consider what has previously been mentioned in our article “Small intestine bacterial overgrowth: Causes” – there are several endogenous defence mechanisms which prevent bacterial overgrowth. As a reminder they include: secretion of gastric acid, intestinal motility, a properly functioning ileocecal valve, production of secretory immunoglobulins (sIgA) on the surface of the gastrointestinal mucous membrane and the bacteriostatic properties of pancreatic juice and bile.

So first things first, start here. An experienced clinician alongside functional lab testing will help decide which, if any of these, need attention.

Chronic stress cannot be emphasised enough as a key factor in the onset of SIBO due to it’s impact on the immune system, thyroid and gut microbiome, among others.

Provide Nutritional Support

Nutritional support, particularly in those patients with weight loss or vitamin and mineral deficiencies, is an important component of SIBO treatment. Supplementation and maintenance of vitamin B12  and fat-soluble vitamins are often key components of treatment. Lactase and fructase deficiency may develop due to inflammation of the small bowel brush border, and thus dietary restrictions are often advocated, such as limiting fructose and lactose when appropriate (Dukowitcz, 2007).

Frustratingly some of the nutrients essential for digestive and immune health, are the same nutrients that are at risk of deficiency, such as vitamin A and D.

Vitamin A – found in organ meats, sweet potato, pumpkin, carrot, cantaloupe, mango, spinach, broccoli, kale & butternut squash.

Vitamin D – as many are aware supplementing with Vitamin D is frequently recommended. Food sources however include fatty fish such as salmon and sardines, mushrooms, beef liver, cheese, and egg yolks.

Treat The Overgrowth


The key treatment option here is the use of antimicrobials or a course of antibiotics. For those wishing to go the more ‘natural’ route there are many options to consider. These include oregano oil and berberine. among many others. I recommend working with a qualified practitioner if considering this approach.

Do check out my webinar on SIBO for more details. Available via my shop.


Probiotics offer a wide a variety of benefits via several mechanisms including:

  1. competition with pathogens
  2. production of bacteriocins
  3. inhibition of bacterial translocation
  4. enhancement of mucosal barrier function
  5. down regulation of inflammatory responses
  6. metabolic effects
  7. modulation of gut motor and sensory responses and signalling between luminal bacteria,  the intestinal epithelium, and the immune system

(Chen, 2014)

In SIBO it is also beneficial to use probiotics that are responsible for decreasing the pH in the intestinal lumen, inhibiting bacterial adhesion to enterocytes and increasing the production of nitrogen oxide. Probiotics such as Lactobacillus, Streptococcus thermophilus and Bifidobacteria reduce gas production.

Research also demonstrates that prebiotic compounds may also be beneficial as they nourish the desirable bacterial strains, thus helping to fight SIBO.

Saccharomyces Boulardii

S. Boulardii is a yeast strand of probiotic. S. Boulradii functions include:

  • Regulation of immune responses, either acting as an immune stimulant or by reducing pro-inflammatory responses.
  • An increase in secretory IgA levels (remember this is an endogenous protective mechanism and can be lowered via things like stress)
  • Enhancing the integrity of the tight junction between enterocytes, thus preserving intestinal integrity and function (prevention of leaky gut)
  • Directly or indirectly interfering with intestinal pathogens – for example S.Boulardii can directly inhibit the growth of pathogens (such as Candida albicans)

(McFarland, 2010)

Biofilm Disruptor

microbial populations embedded in complex, self-produced polymeric matrices, adherent to each other, and surfaces or interfaces. An important reason to study these multispecies biofilms is that sessile cells often have a radical different physiology than planktonic cells, among others resulting in enhanced antimicrobial resistance, virulence and other functions, often related to quorum sensing

Biofilm is just what the name implies: a sticky film made by living, microscopic critters. Why do they make it? To ensure their survival. But there is more to biofilm than just that. It turns out that biofilm makes fighting an infection pretty tricky. That is why we recommend a Biofilm disruptor as part of a treatment protocol for SIBO.

there is evidence showing that mucosal bacteria growing in biofilms on surfaces lining the gut differ from luminal populations, and that due to their proximity to the epithelial surface, these organisms may be important in modulating the host’s immune system and contributing to some chronic inflammatory diseases.

Could biofilms play a key role in those who suffer from chronic gastrointestinal symptoms?


For those who are methane producers this supplement (called Atrantil) may be beneficial. See the script of a podcast between Chris Kresser and Dr. Kenneth Brown here.

It can be bought here.


One of the dietary approaches that can be beneficial in the short term to reduce symptoms and thus improve quality of life is the FODMAP diet. This falls in alignment with ‘treatment number 3 – treat the overgrowth’. The video (click here),  mentioned in article on causes of SIBO, helps shed light on the FODMAP approach.

A great resource if considering following a FODMAP approach is the Monersh University App. For more details please visit their website: click here.

Other dieatary approaches used by practitioners include the Specific Carb Diet and the GAPS diet.

It is important to note recent research has raised concerns about the long term use of a FODMAP protocol, again making it important to consult with an experienced clinician to ensure you minimise the impact of these concerns. Some may find they only react to specific FODMAPs and thus don’t need to follow the complete programme.

FODMAPs do not cause the underlying FGID, but represent an opportunity for reducing symptoms

Others suggest that a FODMAP diet should not be followed, at least not strictly. The idea here is that by starving the bacteria of food encourages them to go in to hibernation and thus reducing the likelihood of a successful protocol. When the individual goes back to a more varied diet, symptoms often come back due to the overgrowth returning. It’s like putting fuel on to a fire that was still smouldering.

Key Points re: FODMAP Approach

If following a FODMAP diet these are some useful recommendations/insights to be aware of:

  • In order to ensure symptoms are well-controlled, a strict trial of the low FODMAP diet is warranted for the first 6–8 weeks.
  • While some may not experience benefit, it  does provide good relief of symptoms in about 75% of patients.
  • Liberalising FODMAP restriction to the level of adequate symptom control should be exercised to make use of the potential health benefits of higher FODMAP intake on the gut microbiota.

Small Intestine Bacterial Overgrowth: Treatment Conclusions

As you can see there are many things to consider when treating SIBO, and even once it has been confirmed via testing, it may take some time to resolve.

We recommend you read our article on restoring health to the digestive system for additional recommendations.