3 Medications That Can Cause SIBO (Small Intestinal Bacterial Overgrowth)

Jan 15, 2022 | Digestive System, Addiction & Recovery, Chronic Fatigue | 0 comments

Which Medications Cause SIBO?

Small Intestinal Bacterial Overgrowth (SIBO), is a form of gut dysbiosis resulting from excessive bacteria growth in the small intestine. [1] Whilst at least some bacteria are present in the small intestines in healthy individuals, a balance is required for optimal digestive function. Human intestinal microbiota create a complex polymicrobial ecology, and we ideally want the right strains, in the right places, in the right numbers!

In an average person, the concentration of the bacteria in the small intestine rarely exceeds 1000 organisms/ml. The small intestine is not a sterile environment, but bacteria levels are significantly lower in number when compared to the large intestine. [2]

In cases of SIBO, an interruption or failure of certain crucial biological functions can lead to the intestinal flora growing to higher volumes than normal. If the bacteria strains begin to proliferate and colonise the small intestine in large numbers, this is the start of SIBO. Sometimes, SIBO can simply be the overgrowth of the wrong species of bacteria. Some bacteria strains are beneficial to our health and aid digestion, but others can cause pronounced health issues if allowed to gain dominion. As with many things, the right balance is the key.

SIBO symptoms can manifest in a wide variety of ways, including brain fog, depression, muscle aches, bloating, abdominal pains, constipation and/or diarrhoea. Over extended periods, SIBO can also lead to malabsorption and nutritional deficiencies. [3]

What causes SIBO? Whilst there are many factors that can contribute to SIBO developing, one of the most common causes of SIBO is the use of certain medications. There are many medications that can disrupt the intestinal microbiome, and individuals using these medications are sometimes unkowingly intaking some of the biggest risk factors for SIBO development.

In this article, we will take a look at three of the medications most often associated with SIBO onset.

1. Proton Pump Inhibitors

Proton pump inhibitors (PPIs) have been shown in research to be a causal factor in SIBO development. Proton Pump Inhibitors are drugs commonly prescribed for individuals experiencing issues with acid reflux, as they are effective at reducing gastric acid secretion. Gastric acid secretions are vital in preventing bacterial buildup, as these secretions naturally help supress levels of bacteria. As PPIs interfere with these secretions, it is perhaps no surprise that several scientific reviews have found that patients treated with PPIs often develop gut dysbiosis and SIBO at a much higher rate than average. [4]

Proton Pump Inhibitors Are Some Of The Most Commonly Prescribed Medications
Proton Pump Inhibitors Are Some Of The Most Commonly Prescribed Medications

One prospective study of 47 outpatients treated with Omeprazole (a commonly prescribed PPI) found that bacterial overgrowth was present in 53% of the patients who received it. Concerningly, the study noted that Omeprazole usage at 20mg per day significantly increased bacterial colonization of the duodenum in the outpatients they monitored. [5]

Proton Pump Inhibitors can play an important role in helping certain medical situations. In the management of painful stomach ulcers, such medications can be very helpful and provide much relief to patients. However, problems can arise when these medications are prescribed to an individual that is simply suffering from intermittent heartburn or mild acid-reflux issues, without displaying signs of an underlying condition that warrants PPI usage.

There is data to suggest that PPIs might be being overprescribed in many such scenearios. For example, Omeprazole is a very commonly prescribed medication, ranking as the eighth most commonly prescribed medication in the United States (2019), and the second most frequently prescribed medication in the Netherlands (2009). [6] [7]

In cases of regular but mild heartburn, it can serve the practitioner and patient well to first discuss and try non-medication interventions such as analysing the patient’s diet, the times they are eating, and their stress levels. Such situations may require more time and effort from both patient and practitioner, but can be a safe way to provide long lasting beneficial treatment outcomes.

One of the most common scenarios that PPI medications are prescribed is alongside anti-inflammatory medications (NSAIDs). This is done to mitigate the well known gastrointestinal impact that NSAIDs have. The practice of prescribing both medications at once is very common, but research suggests that this may be an oversimplified interpretation of the intended use of Proton Pump Inhibitors, and could even potentially be harmful to the patient. Recent evidence has emerged that indicates that the gastrointestinal irritation and stomach related side effects associated with NSAIDs can actually be made worse for some patients when they are combined with PPIs. [8]

A 2018 study concluded that “The coprescription of PPIs and NSAIDs has benefited patients at risk of upper-GI ulcers and bleeding. However, this common prescribing practice may have potentially deleterious effects on small-bowel mucosa, possibly through a combination of gut dysbiosis and increased intestinal permeability.” This damage to the the small bowel mucosa harms on of our natural defences against pathogenic and harmful bacteria, and can set the stage for SIBO to develop.

Not all PPIs have the same level of impact on the intestinal microbiome, so it is worth talking to your doctor if you are on any of these medications and are seeking to switch to an alternative.

2. Opioid And Opiate Painkillers

Opioid And Opiate painkillers are the most commonly prescribed medications for treating pain, and many people experiencing digestive issues or abdominal pain may find themselves taking such medication for some much needed relief. Codeine, Tramadol, and Oxycodone are some of the most commonly taken examples of such medications.

Opioid And Opiate Painkillers Do Huge Damage To The Intestinal Microbiome
Opioid And Opiate Painkillers Do Huge Damage To The Intestinal Microbiome

There is a very dense concentration of opioid receptors in the gastrointestinal tract. There are three types of opioid receptors, mu, delta, and kappa. Activation of these receptors, particularly mu receptors, inhibits gastric emptying, reduces mucosal secretions, and increases fluid reabsorption. [9] Gastric emptying plays a key role in ensuring that undigested food matter doesn’t stay too long where it shouldn’t. The bacteria in the small intestine however, are delighted when everything slows down, as this allow them to gorge and feast on the partially digested food matter. It is easy to see how this can serve as a precursor for SIBO development, as it is essentially serving up a buffet in the small intestine.

Constipation is a well known side effect from these drugs, and it has been found that they cause a slowed intestinal transit time for food. [10] Opiates also inhibit intestinal secretions via an action on the enteric nervous system as well as in the central nervous system. [11] This side effect of opioid painkillers is particularly unhelpful for those who already have SIBO. A study in 2015 found that reduced small bowel transit specifically predisposes individuals to the development of SIBO. [12]

Opioids disrupt the normal digestive processes, and this in turn often leads to the development of chronic gastrointestinal issues. Research has found that ‘a persistent decrease in gastrointestinal motility induced by opioids is a primary cause of gut microbial dysbiosis’. [13] There exists a vicious cycle whereby opioids are prescribed to patients that present IBS symptom profiles. Opioid medications are often used to manage abdominal pain and cramping, and to prevent dihorrea/loose stools. Though well intentioned, this practice could ultimately be making the situation worse in the long term, and could lead to changes in the intestinal microbiota – potentially triggering SIBO development.

It is also worth considering the 2020 study in which mice with colitis were given the common opioid drug hydromorphone. Post-analysis of their gut microbiota revealed high abundance in the bacterial communities associated with ‘virulence, antibiotic resistance, toxin production, and inflammatory properties’. [14]

Opioid and opiate painkillers are extremely damaging to the intestines, disrupting the microbiome and damaging the intestinal lining leading to inflammation. [15]

Important: Opioid medications can result in physical addiction. If you are currently taking opioid painkillers regularly, stopping suddenly can be dangerous. If you are planning to stop taking painkillers, it is advised that you speak to your doctor about ways you can safely reduce your dosage over time.

3. Broad Spectrum Antibiotics

Although it may initially seem like antibiotics would be helpful in preventing SIBO, some medications in this category can actually contribute to SIBO onset. This is because of the drastic effect that broad spectrum antibiotics have on the intestinal microbiota. Certain antibiotics can kill off beneficial bacteria strains as well as pathogenic ones, in an indiscriminate offensive on any bacteria that gets in the way.

This can lead to unpredictable and vast reductions in intestinal flora, and this unbalanced state, pathogenic bacteria strains can start to get a foothold. [16] Individuals may be prescribed antibiotics for an infections such as gum, sinus, or ear infections. In these cases, both the doctor and the patient may simply focus on how effective a particular antibiotic drug is at treating the ailment in question. Often however, there can be hidden collateral damage in the gastrointestinal tract.

Broad Spectrum Antibiotics Can Cause SIBO By Disrupting The Normal Intestinal Flora
Broad Spectrum Antibiotics Can Cause SIBO By Disrupting The Normal Intestinal Flora

A 2018 study found that antibiotics disrupted the microbiota significantly. “Alterations in microbial communities lead to changes in functional structures based on the metabolites produced in the gut, and these environmental changes result in various bacterial infections and chronic enteric inflammatory diseases.” [17] The study went on to state that “understanding the pathogenesis caused by antibiotics would be a crucial key to the treatment of antibiotic-associated diseases by mitigating changes in the intestinal environment and restoring it to its original state.”

Common features of post-antibiotic dysbiosis include a loss of taxonomic and functional microbiome diversity, combined with reduced colonisation resistance against invading pathogens, which harbours the danger of antimicrobial resistance. [18] These disruptions to the microbiota can lead to cases of SIBO developing, and can be difficult to restore.

To attempt to reduce the impact of antibiotics on the intestinal microbiome, individuals taking these types of medications are often recommended to increase intake of probiotics. This could be in the form of fermented foods such as yoghurt with active cultures, kimchi, kefir, or sauerkraut. Probiotic supplements can also provide a source of beneficial bacteria cultures to replenish depleted numbers.

Because of their detrimental effects on the microbiome, broad spectrum antibiotics are not recommended for treating SIBO. There are however, some more specialised antibiotics that practitioners have used successfully to treat SIBO – The rifamycin antibiotic ‘Rifixamin‘ being a prominent example.

Important: Antibiotics have no beneficial impact in treating viral infections, and are only useful in cases when it is known or strongly suspected that a bacterial strain is causing the issue. Therefore this situation can sadly arise out of misdiagnosis, as antibiotics are sometimes prescribed to patients with viral pneumonia, bronchitis, or viral upper respiratory infections. Antibiotics will not help to treat such conditions, but instead could cause long term harm to a patients intestinal microbiome. Indeed, a 2016 report by the Centers for Disease Control and Prevention estimated that at least 30% of antibiotics prescribed in US outpatient settings are unnecessary. [19]


Individuals who have been taking any of these medications for extended periods of time can often end up with a diagnosis of SIBO later down the line.

Understanding how these medications affect the small intestine is essential in the treatment of SIBO, as these risk factors will need to be approached carefully by your healthcare provider. SIBO treatments can only be effective once the causal factors contributing to it’s development have been dealt with.

If you have been on any of these medications for long periods of time and are suffering from SIBO symptoms such as abdominal pains, regular bowel and intestinal disfunction, or bloating, it could be a good idea to ask your doctor about SIBO.


1. Achufusi TGO, Sharma A, Zamora EA, Manocha D. Small Intestinal Bacterial Overgrowth: Comprehensive Review of Diagnosis, Prevention, and Treatment Methods. Cureus. 2020 Jun 27;12(6):e8860. doi: 10.7759/cureus.8860. PMID: 32754400; PMCID: PMC7386065.

2. Sorathia SJ, Rivas JM. Small Intestinal Bacterial Overgrowth. [Updated 2021 Jul 18]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2021 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK546634/

3. Bures J, Cyrany J, Kohoutova D, Förstl M, Rejchrt S, Kvetina J, Vorisek V, Kopacova M. Small intestinal bacterial overgrowth syndrome. World J Gastroenterol. 2010 Jun 28;16(24):2978-90. doi: 10.3748/wjg.v16.i24.2978. PMID: 20572300; PMCID: PMC2890937.

4. Lo WK, Chan WW. Proton pump inhibitor use and the risk of small intestinal bacterial overgrowth: a meta-analysis. Clin Gastroenterol Hepatol. 2013 May;11(5):483-90. doi: 10.1016/j.cgh.2012.12.011. Epub 2012 Dec 24. PMID: 23270866.

5. Lewis SJ, Franco S, Young G, O’Keefe SJ. Altered bowel function and duodenal bacterial overgrowth in patients treated with omeprazole. Aliment Pharmacol Ther. 1996 Aug;10(4):557-61. doi: 10.1046/j.1365-2036.1996.d01-506.x. PMID: 8853759.

6. https://clincalc.com/DrugStats/Top300Drugs.aspx

7. http://www.sfk.nl/pdf-documenten/data-en-feiten/data-en-feiten-2009

8. Gwee KA, Goh V, Lima G, Setia S. Coprescribing proton-pump inhibitors with nonsteroidal anti-inflammatory drugs: risks versus benefits. J Pain Res. 2018 Feb 14;11:361-374. doi: 10.2147/JPR.S156938. PMID: 29491719; PMCID: PMC5817415.

9. Swegle JM, Logemann C. Management of common opioid-induced adverse effects. Am Fam Physician. 2006 Oct 15;74(8):1347-54. PMID: 17087429.

10. Patel D, Callaway J, Vaezi M. Opioid-Induced Foregut Dysfunction. Am J Gastroenterol. 2019 Nov;114(11):1716-1725. doi: 10.14309/ajg.0000000000000354. PMID: 31464739.

11. Bueno L, Fioramonti J. Action of opiates on gastrointestinal function. Baillieres Clin Gastroenterol. 1988 Jan;2(1):123-39. doi: 10.1016/0950-3528(88)90024-3. PMID: 2838107.

12. Roland BC, Ciarleglio MM, Clarke JO, Semler JR, Tomakin E, Mullin GE, Pasricha PJ. Small Intestinal Transit Time Is Delayed in Small Intestinal Bacterial Overgrowth. J Clin Gastroenterol. 2015 Aug;49(7):571-6. doi: 10.1097/MCG.0000000000000257. PMID: 25319735.

13. Akbarali HI, Dewey WL. Gastrointestinal motility, dysbiosis and opioid-induced tolerance: is there a link? Nat Rev Gastroenterol Hepatol. 2019 Jun;16(6):323-324. doi: 10.1038/s41575-019-0150-x. PMID: 31024090; PMCID: PMC7045338.

14. Sharma U, Olson RK, Erhart FN, Zhang L, Meng J, Segura B, Banerjee S, Sharma M, Saluja AK, Ramakrishnan S, Abreu MT, Roy S. Prescription Opioids induce Gut Dysbiosis and Exacerbate Colitis in a Murine Model of Inflammatory Bowel Disease. J Crohns Colitis. 2020 Jul 9;14(6):801-817. doi: 10.1093/ecco-jcc/jjz188. PMID: 31773170; PMCID: PMC7346895.

15. Jalodia, R., Abu, Y.F., Oppenheimer, M.R. et al. Opioid Use, Gut Dysbiosis, Inflammation, and the Nervous System. J Neuroimmune Pharmacol (2022). https://doi.org/10.1007/s11481-021-10046-z

16. Zhang S, Chen DC. Facing a new challenge: the adverse effects of antibiotics on gut microbiota and host immunity. Chin Med J (Engl). 2019 May 20;132(10):1135-1138. doi: 10.1097/CM9.0000000000000245. PMID: 30973451; PMCID: PMC6511407.

17. Yoon MY, Yoon SS. Disruption of the Gut Ecosystem by Antibiotics. Yonsei Med J. 2018 Jan;59(1):4-12. doi: 10.3349/ymj.2018.59.1.4. PMID: 29214770; PMCID: PMC5725362.

18. Lange K, Buerger M, Stallmach A, Bruns T. Effects of Antibiotics on Gut Microbiota. Dig Dis. 2016;34(3):260-8. doi: 10.1159/000443360. Epub 2016 Mar 30. PMID: 27028893.

19. https://www.cdc.gov/media/releases/2016/p0503-unnecessary-prescriptions.html

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Written by Keymer Health

January 15, 2022

3 Common SIBO Risk Factors And How To Avoid Them

3 Common SIBO Risk Factors And How To Avoid Them

Small Intestinal Bacterial Overgrowth (SIBO) is a form of gut dysbiosis that has been increasingly common in the Western world in the past couple of decades. What could be the cause of such a meteoric rise? this article, we will look at three of the most common factors that contribute to SIBO, and give an overview of how and why these factors can put an individual at risk.

Related Articles

3 Common SIBO Risk Factors And How To Avoid Them

3 Common SIBO Risk Factors And How To Avoid Them

Small Intestinal Bacterial Overgrowth (SIBO) is a form of gut dysbiosis that has been increasingly common in the Western world in the past couple of decades. What could be the cause of such a meteoric rise? this article, we will look at three of the most common factors that contribute to SIBO, and give an overview of how and why these factors can put an individual at risk.

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