Know How Antibiotics Can Mess With Your Gut And Cause Acidity!

Introduction

Antibiotics used to treat bacterial infections have saved millions of lives over the centuries. However, their action is usually not selective and in the process of killing harmful bacteria, they also affect some healthy flora crucial for your gut. By disrupting the balance of gut microbiota, antibiotics can also cause reflux of food and acid into the oesophagus causing symptoms such as heartburn.   

In this blog, we’ll discuss how antibiotics can affect your gut and cause acid reflux. With this, you can learn how to keep a balanced gut flora after antibiotic treatment and fix acidity issues.   

Antibiotics and Acid Reflux

The gut, particularly the intestines contain several microorganisms, including bacteria (both good and bad) that help in the digestion process.   

Antibiotics that are used to treat bacterial infections in the body, unfortunately, cannot differentiate between the good and bad bacteria present in the gut and produce negative results such as¹: 

• Kill the good bacteria in the gut   
• Create an imbalance in the intestinal ecosystem and an overgrowth of harmful bacteria  
• Increase pressure within the stomach   
• Affect digestion and gastric motility 
• The use of antibiotics can lead to heartburn in some cases. While not a frequent occurrence, certain antibiotics which disrupt the natural balance of gut bacteria, might result in gastrointestinal issues, including heartburn. Moreover, some antibiotics like tetracyclines or macrolides can irritate the gastric lining. In response, the glands in the stomach secrete more acid. This acid can lead to greater reflux of food and acid into the oesophagus, causing heartburn. 

Here are the Digestive Side Effects of Some Antibiotics

• Nausea and vomiting 
• Acid reflux 
• Heartburn 
• Gas and bloating 
• Abnormal Cramping   
• Diarrhoea   
• Loss of appetite

Effects of Antibiotics on an Infant’s Gut

The microbial population of an infant’s gut has a significant impact on the child’s overall health. Decreased gut microbiome diversity can be associated with an increased risk of allergic and autoimmune diseases. Antibiotic treatment in infants has been found to reduce both the number as well as species of gut bacteria. Gut microbiota may take weeks to months to recover, and in some cases, certain species may not fully return without intervention². 

Restoring Gut Health After Taking Antibiotics

Rebuilding gut bacteria is crucial to minimise the negative effects of using antibiotics. You can speed up the process of healing the gut with antibiotics in several ways: 

1. Prebiotics   

Prebiotics are the nutrients in certain food items that act as a “food source” for gut microbes. They induce the growth or activity of beneficial bacteria such as Bifidobacteria and Lactobacilli, thereby improving gut health. Examples include carbohydrates such as fructo-oligosaccharides (FOS) and galacto-oligosaccharides³. 

2. Probiotic Supplements 

Probiotics contain live bacteria and yeasts that are vital for gut health. Depending on the type of microbial strain utilized, probiotics can have variable beneficial properties⁴. You should take them as suggested by your doctor as the ideal dose depends on the specific condition being treated (e.g.,  vs. IBS). 

3. Fermented Foods   

Fermented foods are naturally rich in probiotics. They are an excellent approach to proper gut health post-antibiotic use. Ideally, fermented foods such as yoghurt, kimchi, kefir, sauerkraut, should be a part of a regular diet⁵.  

4. Fruits and Vegetables   

Fruits and veggies are naturally rich in prebiotics (also important for gut microbiome). Bananas, sweet potatoes, and other tubers are fresh and readily available sources of prebiotics. 

5. Exercise   

Exercise is not only important for helping you to stay in shape but is also crucial in improving the condition of your gut wall. It promotes the growth of bacteria and enriches the diversity of the microbiome. It protects your system from colon cancer and gastrointestinal disorders⁶.   

6. Stress Management 

Stress releases certain hormones in your body that in turn have an impact on the nature of your microbiome damaging the diversity. Gut-brain axis is bi-directional and the altered gut microbiome can affect regulation of certain neurotransmitters thus intensifying the stress⁷.  

Antibiotics kill good bacteria in gut, this is linked to development of obesity, asthma and irritable bowel syndrome. Hence antibiotics must be cautiously and only used when absolutely necessary. 

Managing Acid Reflux After Consuming Antibiotics

Lifestyle changes such as quitting smoking, avoiding alcohol, proper diet and regular exercise can help deal with symptoms of heartburn. However, if these are persistent, some medications may be prescribed by doctors to help relieve acid reflux. These include: 

• Antacids, which help neutralise stomach acid. Antacids may provide quick relief, but they cannot heal an oesophagus damaged by stomach acid. 
• H2-receptor antagonists (H2RAs) can decrease stomach acid. It does not act as quickly as antacids but may provide longer relief. 
• Proton pump inhibitors, such as omeprazole can reduce stomach acid. All the PPIs have similar efficacy, however, Omeprazole due to its better safety and highest affordability is the most used PPI globally⁸. 

Persistent heartburn (>2 days/week) may indicate GERD (Gastroesophageal Reflux Disease). Always consult your doctor if you have persistent digestive symptoms after antibiotic treatment as they will recommend the right medication and dosage based on your health condition.  

When Does Good Bacteria Return After Taking Antibiotics? 

It has been found that most gut bacteria will resume levels prior to that of taking the antibiotics course in about two months. However, one should make a note the full diversity and original composition may not completely return⁹. 

Conclusion

Antibiotics can disrupt the balance of gut flora, potentially leading to acidity issues or other digestive discomforts. It’s important to restore the gut microbiome after antibiotic treatment. This can be achieved through dietary changes, such as consuming prebiotic and probiotic-rich foods or supplements, and lifestyle modification, such as regular exercise and stress management. If you experience persistent or severe digestive issues after taking antibiotics, it’s crucial to consult with a healthcare professional for guidance and appropriate treatment. 

References

1. Lathakumari RH, Vajravelu LK, Satheesan A, Ravi S, Thulukanam J. Antibiotics and the gut microbiome: understanding the impact on human health. Medicine in Microecology. 2024 Apr 8:100106. https://www.sciencedirect.com/science/article/pii/S2590097824000090#:~:text=Abstract,protect%20human%20health%20throughout%20life. 

2. Tanaka M, Nakayama J. Development of the gut microbiota in infancy and its impact on health in later life. Allergology International. 2017;66(4):515-22. https://www.sciencedirect.com/science/article/pii/S1323893017301119#:~:text=Perturbation%20by%20antibiotics&text=The%20use%20of%20antibiotics%20in,selects%20for%20drug%2Dresistant%20bacteria. 

3. Davani-Davari D, Negahdaripour M, Karimzadeh I, Seifan M, Mohkam M, Masoumi SJ, Berenjian A, Ghasemi Y. Prebiotics: Definition, Types, Sources, Mechanisms, and Clinical Applications. Foods. 2019 Mar 9;8(3):92. https://pmc.ncbi.nlm.nih.gov/articles/PMC6463098/ 

4. Gul S, Durante-Mangoni E. Unraveling the Puzzle: Health Benefits of Probiotics-A Comprehensive Review. J Clin Med. 2024 Mar 1;13(5):1436. https://pubmed.ncbi.nlm.nih.gov/38592298/ 

5. Soemarie YB, Milanda T, Barliana MI. Fermented Foods as Probiotics: A Review. J Adv Pharm Technol Res. 2021 Oct-Dec;12(4):335-339.https://pmc.ncbi.nlm.nih.gov/articles/PMC8588917/ 

6. Monda V, Villano I, Messina A, Valenzano A, Esposito T, Moscatelli F, Viggiano A, Cibelli G, Chieffi S, Monda M, Messina G. Exercise Modifies the Gut Microbiota with Positive Health Effects. Oxid Med Cell Longev. 2017;2017:3831972. https://pmc.ncbi.nlm.nih.gov/articles/PMC5357536/ 

7. Santos J, Maran PL, Rodríguez-Urrutia A. Stress, microbiota, and the gut–brain axis in mental and digestive health. Medicina Clínica. 2025 Jan 16. https://www.sciencedirect.com/science/article/abs/pii/S0025775324007723 

8. Treatment for GER & GERD: NIH (Internet) https://www.niddk.nih.gov/health-information/digestive-diseases/acid-reflux-ger-gerd-adults/treatment 

9. Anthony WE, Wang B, Sukhum KV, D’Souza AW, Hink T, Cass C, Seiler S, Reske KA, Coon C, Dubberke ER, Burnham CA. Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults. Cell reports. 2022 Apr 12;39(2).  https://www.sciencedirect.com/science/article/pii/S2211124722004016#:~:text=We%20observe%20an%20acute%20decrease,an%20increased%20antibiotic%20resistance%20burden. 

Disclaimer: The information provided here is for educational/awareness purposes only and is not intended to be a substitute for medical treatment by a healthcare professional and should not be relied upon to diagnose or treat any medical condition. The reader should consult a registered medical practitioner to determine the appropriateness of the information and before consuming any medication. PharmEasy does not provide any guarantee or warranty (express or implied) regarding the accuracy, adequacy, completeness, legality, reliability or usefulness of the information; and disclaims any liability arising thereof. 

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