SIBO: Prebiotics & Small Intestinal Bacterial Overgrowth

SIBO small intestinal bacterial overgrowth treatment gut health and disease fix your gut

The use of prebiotics and probiotics in small intestinal bacterial overgrowth, or SIBO for short, has been generally considered a bad idea. The thinking does make sense. If you have an overgrowth of bacteria in the small intestine then why would you want to add more with probiotics or feed them with prebiotics.

There is research pointing at the benefits of certain probiotics, one of which we have covered here. Recently I have come across a very promising case study where lactulose was used to effectively treat a 48 year old man with confirmed small intestinal bacterial overgrowth.

Investigations Into IBS

I very much appreciated the work that went into this patient’s diagnosis. This person had a long history of chronic diarrhea and intermittent abdominal pain. Many times IBS will be the first diagnosis. This time they dug a bit deeper into the symptoms including

  • Stool analysis for pathogens
  • Colonoscopy with biopsy
  • Iron studies
  • B12 and B9 studies
  • Thyroid function tests
  • Hormonal investigations into the cause of diarrhea
  • 24 hour fecal fat investigations

Each and everyone of these investigations came back with no abnormalities and within the reference ranges. The only notable exception was extensive diverticulosis of the small intestines.

SIBO Diagnosis

Further investigations included a small intestinal aspirate and a microbiological analysis in the first part of the small intestine. They counted 1012 colony forming units per millilitre of bacteria in the aspirate confirming a small intestinal bacterial overgrowth. While a healthy small intestine is not sterile anything over the cut off range of 105 CFU/ml is considered an overgrowth.

Ok, so after 27 years of unexplained chronic bowel problems and numerous different investigations we finally have a solid idea on why. Small intestinal bacterial overgrowth consisting of aerobes and facultative anaerobes, including Streptococcus spp and coliforms.

Interventions for SIBO

The patient was prescribed a  triple therapy of two antibiotics and clavulanic acid for four weeks. His symptoms didn’t improve and a repeat aspirate found the same levels (1012 CFU/ml) of bacteria in the small intestine. The antibiotic treatment was a failure.

The second intervention involved a prebiotic called lactuloseHere we see something very novel. In this particular case study the patient was then treated with the prebiotic lactulose. I can almost hear the outcry. Won’t you feed the bad bacteria?

This is the million dollar question. If we can treat certain bacterial overgrowths in the small and the large intestine with prebiotics then the era of bombing our microbiome with antibiotics may end. At least we can minimise their use, relying on less damaging antimicrobial herbs, and prebiotics in synergy.

Back to the case study.

10 grams of lactulose was consumed twice daily for four weeks. This is a heroic dose to start on. Anyone that has explored using prebiotics knows you start with a low dose and very gradually increase it until you hit the therapeutic range.

Why lactulose? The theory proposed in this paper, and one that I have been considering for years now, is the effects of short chain fatty acid, or SCFA, production from our beneficial fermenters on the pathobionts in the gastrointestinal tract. Does the supplementation of a prebiotic and the increase in SCFA, resulting in the acidifying of the gastrointestinal tract, impair certain pathogens growth? Here the evidence is both sparse and possibly misleading. Some in vitro investigations show that certain, less than friendly, bugs can consume different prebiotics (2). Is this a true representation of what actually happens in the gut? I’m not so sure.

Results of Lactulose on SIBO

Here we see a complete turn around in long term chronic symptoms. After only 3 days of lactulose treatment the patient experienced complete resolution of diarrhea and abdominal pain.

A third aspirate was taken and the bacterial count had lowered to 107 CFU/ml. This is a drop from 1012 CFU/ml which is a whopping 1,000,000 bacterial CFU per millilitre.

Seeing as this in not quite within the reference range for a healthy bacterial count in the small bowel they increased the lactulose dose to 20 gram twice daily which had no further reduction on the bacterial count. After the treatment time frame the lactulose was stopped. During this time the patient’s symptoms came back. They tested the small intestines bacterial count and found that it had increased to 1011 CFU/ml. Again they administered lactulose and the bacterial count dropped back to 107 CFU/ml. Taking the lactulose daily resulted in symptom resolution for this particular patient.

One Root Cause of SIBO

In this case study we can see one possible root cause for SIBO. Stasis due to the diverticulosis could have been leading to a higher count of bacteria in the small intestine. While SIBO is a large and nebulous condition with a range of possible root causes the lack of movement in the small intestine, discussed here, is one to investigate.

Here the lactulose is both reducing the bacterial count in the small intestine and improving motility which may have been lacking. I am fascinated by the reduction in bacterial counts here. Is it due to short chain fatty acid production? More human trials are needed here.

Final Thoughts

Here I think it is important to mention a few key things. Everyone is unique. Every disease or illness manifests differently in each individual. When a clinical trial finds that an intervention, let’s say probiotics, has a significant beneficial effect it is very rarely 100% of the people that improve.

Today we have covered a case study in which SIBO was effectively treated with the prebiotic lactulose. This is encouraging and supports the theory that prebiotics are selective in what bacteria they feed. More research is definitely needed here. Future articles will explore the selective feeding of different prebiotics and the effect of short chain fatty acid synthesis on the gut microbiome and gastrointestinal tract environment. And as always, there are cases where prebiotics like lactulose wouldn’t be recommended for SIBO patients. 

If you have had any experiences with prebiotics and gut issues share your thoughts below

References and Resources

  1. Culture-proven small intestinal bacterial overgrowth as a cause of irritable bowel syndrome: response to lactulose but not broadspectrum antibiotics
  2. In vitro fermentation of lactulose by human gut bacteria.
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  1. Hello Todd,
    Thank you for another very informative article!

    I have Blastocystis (hopefully “had” as I did an antibiotic treatment with Bactrim – sulfamethoxazole and trimethoprim a few weeks ago but haven’t retested since) and am treating now the SIBO. The dr told me it was a methane dominant SIBO (although I didn’t have issues with constipation, on the contrary). I started taking the Candibactin products: BR with berberine and AR with oregano and thyme essential oils. However, I feel that they are strong and would like to protect my flora so I was wondering if you think pro- and prebiotics are a good idea for SIBO? If so during the treatment or only after?
    I read your article about lactulose, might give it a try. I am also taking s boulardii (the Biocodex one). And do you think I need a biofilm disruptor as well? I consume ACV and coconut oil on a daily basis…
    Oh, and what do you think about Diatomaceous earth?

    Sorry for the long comment and looking forward to your opinion on this!


    1. Hi,I’ve also a long history where they found Blastocystis..Got an antibiotic treatment with bactrim…no effect. Than with paromomcyn…than the Blastocystis wasn’t found anymore. But my symptoms where still there!
      Did a kind of dysbiose test and found Entreobacter cloacea, wich was a little too much that could work pathogen…Also a SiBo breath test: outcome was a very high level of methan ( and very low hydrogen)…but most of the time a high level of methan is associated with constipation, but I’ve more loose stools. Following right now a herb ‘treatment’ with Neem and Allicinmax- also Oregano, but I took this for three days and became really bad. So now no oregano..But trying following also a diett (Fast tact diett)..Looks like my symptoms becoming less. Wondering if there is a relation between Blastocystis, entreobactrer cloacea and Sibo (methan) without obstipation? you know more about this Todd? Kind regards from Norway.

  2. Hey Roxana,

    The answers very much depend on you and your circumstances.

    The biocodex boulardii probiotic would be good. Another great probiotic for methane dominant SIBO is the biogaia probiotic drops (lactobacillus reuterii DSM 17938). The lozenges from the same brand have a particular FODMAP that may aggravate SIBO so that version may be best avoided.

    Lactulose as a prebiotic would possibly be indicated but it would depend on what sugar you used for your breathe test. If you used lactulose (the most common sugar) and it picked up SIBO then it would be contraindicated as a prebiotic (as it would end up feeding the bacteria that are overgrowing in your small intestine).

    Keep us posted on how you go!


    1. Oh sorry. Diatomaceous earth…I don’t use this particular supplement for gut infections. Others clinicians are big fans. I think that in gut focused work there are better studied herbs and supplements that get most people better more reliably. I’m definitely keeping my mind open here though 🙂

  3. Hi Todd, I am currently being treated with antibiotics for Sibo and am overwhelmed and confused on the use of probiotics. CDiff is always a concern when taking any antibiotics, also all good bacteria being killed with antibiotics isn’t great in the long run either and I am really trying to understand which probiotics will help my overall immune system, prevent CDiff after antibiotic use, and help prevent Sibo from returning, they all seem to be contradictory can you please help me figure out which probiotic will help me and not make Sibo symptoms worse or return? Thank you!

    1. Hey Hayley.

      Thanks for taking the time to leave a comment!

      It would very much depend on the type of SIBO you are treating as well as the antibiotic you are using.

      For antibiotic associated diarrhoea (and c. diff prophylactic treatment) L. rhamnosus LGG and/or S. boulardii biocodex strain are evidence based strains that show good success.

      I haven’t seen SIBO worsen from selective probiotic use. I often recommend LGG/Bb12 for hydrogen dominant SIBO and L. reuteri DSM17938 for methane dominant. Others would depend on symptoms.


    2. Hi Todd,
      I have a lot of digestive issues and have found no solution. I have been told that my gut bacteria is stopping my detox pathways. One said I had staph and another said I had steph and then yet another said I had candida. I am not breaking down my sulfur and I get sick when I eat phenolics and if I take ox bile and fibers. I can’t really eat much of anything but I do know I started getting sick after I started taking a lot of probiotics with prebiotics. Went on fodmap worked for a little then I couldn’t eat any fruit or vegetables. Ate only meat for about 4 years and started to add more fruits and vegetables in did ok for a little and then antibiotics and steroids. I can’t seem to find anything to help. Any information is ou could share to help would be great

  4. This is a great case study. I might reframe it as “a patient with incurable SIBO, due to diverticulitis in the small intestine.” I guess the bad bacteria hide out in those pouches and then repopulate the small intestine when the conditions are right.

    I have had a similar experience with lactulose treating colonic dysbiosis. It gives me worse gas, but shifts gas from H2S to hydrogen. Then when you stop the lactulose most of the gas goes away. It definitely seems to create a different ecology in the colon, probably because it changes the pH during treatment and bad things die off in low pH.

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