Quick answer: Some infections and medications can affect the gut barrier by disturbing the microbiome, increasing inflammation or loosening tight junctions. Examples include bacterial infections like H. pylori and C. difficile, parasites like Giardia, and medications such as antibiotics, NSAIDs, PPIs and steroids. Never stop a prescribed medication on your own; work with your provider instead.
Key takeaways
Food-borne bacteria, C. difficile, yeast overgrowth, viruses and parasites can all inflame the gut and disturb the microbiome.
Antibiotics, NSAIDs, acid-reducing medications and some others can affect the gut lining or microbiome.
The article stresses not stopping any prescribed medication, and instead talking with your doctor if you have gut symptoms.
Work with your provider first
The first step is always to work with your healthcare provider to treat infections and review medications. Background: introduction to leaky gut.
Bacterial infections
Salmonella and Campylobacter are food-borne infections that increase gut inflammation, and C. difficile causes severe diarrhea, with antibiotic use a major risk factor. H. pylori infects the stomach and causes inflammation and ulcers, and E. coli (some strains) can cause severe infections.
Other infections
Other infections include candida overgrowth when the microbiome is disrupted, cytomegalovirus (CMV), and parasites such as Giardia, Cryptosporidium and Blastocystis.
Medications
I am not suggesting that you stop these medications. If you take any of them and have gut symptoms, talk with your doctor.
Antibiotics
Antibiotics are absolutely warranted when needed, but they can also disrupt beneficial gut bacteria. Supporting gut health after a course is a good idea.
NSAIDs
Regular use of drugs such as ibuprofen can damage the gut lining and weaken its barrier function.
Proton pump inhibitors (PPIs)
Reducing stomach acid can affect digestion and the microbiome.
Steroids and immunosuppressants
These can increase infection risk and affect the gut.
Caffeine
Moderate caffeine is safe for most people, but large amounts can loosen stools and raise stress hormones.
Microbes, medications and healthy aging
Older adults often take more medications, and the microbiome tends to lose diversity with age. Thoughtful medication use helps protect gut health over time. See microbial diversity.
When to see a naturopathic doctor
It may be time to see a naturopathic doctor if you have ongoing bloating, gas, diarrhea or constipation, or food reactions that seem to be multiplying. The same is true if you have fatigue, skin flares or joint aches alongside gut symptoms, or if you want a personalized gut plan instead of guessing.
See a medical provider promptly for blood in your stool, black stools, unexplained weight loss, persistent vomiting, severe abdominal pain, fever, or trouble swallowing.
What the research shows
Antibiotics change gut bacteria, but healthy guts tend to recover. In a 2018 study by Palleja and colleagues, 12 healthy young men took a 4-day course of three strong antibiotics. Helpful groups such as Bifidobacterium and butyrate producers fell sharply and less helpful bacteria bloomed, but most of the gut community returned close to normal within about 6 weeks. Nine common species were still missing in most of the men after 6 months. These were healthy young men and a very strong antibiotic mix, so effects may differ with other medicines.
Acid-reducing medicines have also been studied. A 2013 meta-analysis by Lo and Chan pooled 11 studies with 3,134 adults and found that people taking proton pump inhibitors (PPIs) had about 2.3 times the odds of small intestinal bacterial overgrowth (SIBO). The link was seen only when SIBO was measured with the more accurate method of sampling fluid from the small intestine, not with breath tests. These were observational studies, and anyone on PPIs should talk with their prescriber before making changes.
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Questions to bring to your clinician
These questions can help you get the most out of your next visit.
Could any of my past infections or current medications be affecting my gut health?
Could any medications I take be affecting my gut lining?
Should I talk with my prescribing doctor before making any changes?
How can I support my gut after a past infection or course of antibiotics?
Frequently asked questions
Do antibiotics cause leaky gut?
They can disrupt the microbiome. Use them when needed and support your gut afterward.
Should I stop my PPI?
Not on your own. Talk with your doctor about whether you still need it.
Can H. pylori affect the gut lining?
Yes. It causes stomach inflammation and can lead to ulcers.
Is coffee bad for the gut?
Moderate coffee is fine for most people.
Sources
- Palleja A, Mikkelsen KH, Forslund SK, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol 2018. PMID: 30349083. https://pubmed.ncbi.nlm.nih.gov/30349083/
- Lo WK, Chan WW. Proton pump inhibitor use and the risk of small intestinal bacterial overgrowth: a meta-analysis. Clin Gastroenterol Hepatol 2013. PMID: 23270866. https://pubmed.ncbi.nlm.nih.gov/23270866/
- Kusters JG, van Vliet AH, Kuipers EJ. Pathogenesis of Helicobacter pylori infection. Clin Microbiol Rev 2006. PMID: 16847081. https://pmc.ncbi.nlm.nih.gov/articles/PMC1539101/
- Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 2011. PMID: 20847294. https://pmc.ncbi.nlm.nih.gov/articles/PMC3063582/
- Bjarnason I, et al. Mechanisms of Damage to the Gastrointestinal Tract From Nonsteroidal Anti-Inflammatory Drugs. Gastroenterology 2018. PMID: 29221664. https://pubmed.ncbi.nlm.nih.gov/29221664/
- Imhann F, et al. Proton pump inhibitors affect the gut microbiome. Gut 2016. PMID: 26657899. https://pmc.ncbi.nlm.nih.gov/articles/PMC4853569/
- MedlinePlus: Helicobacter Pylori Infections
- MedlinePlus: Antibiotics
This article is for educational purposes only and is not medical advice. It does not replace an individual evaluation. Talk with your healthcare provider before starting supplements or changing medications, especially if you are pregnant, nursing, or managing a health condition.
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