Rachel Sanford

It’s no secret that antibiotics destroy your gut. But sometimes they’re necessary. They do a great job of killing bad bacteria…but they also kill the good guys. So once you’re done with a course of antibiotics your gut is like a scorched battlefield. If you don’t rebuild it the right way, you leave room for bad bacteria to take over, which leads to brain fog, fatigue, food cravings, leaky gut, and chronic inflammation. The good news is that you can bounce back stronger than before – if you know what to do. Here are the most effective ways you can rebuild your gut after taking antibiotics.  

1. Take s. boulardii during your course Saccharomyces boulardii is a probiotic yeast. Unlike certain other yeasts, this one is beneficial, especially if you’re taking antibiotics. Studies show it can help relieve diarrhea and mitigate negative microbiome changes from antibiotics [1]. Take this one daily when you’re on antibiotics as well as a few weeks after you stop. 

2. Introduce probiotics 

Once you’ve finished your antibiotics, it’s important to quickly start rebuilding with good bacteria aka probiotics. When you choose a probiotic, find one that has strong studies behind it like Omni-Biotic AB-10. It’s a specific blend of probiotics that helps restore and maintain bacterial diversity in your gut. You can also incorporate fermented foods with naturally-occurring probiotics like raw sheep yogurt or sauerkraut. Just be cautious because fermented foods can cause major reactions in people who are histamine-sensitive. Learn more about histamine on The Human Upgrade episode #811. 

3. Feed the good guys with prebiotics 

If you want the good guys to survive, you have to feed them what they like. They love prebiotics.  You can get prebiotics from many foods like artichokes, asparagus, leeks and honey [2]. You can also take prebiotic fiber as a supplement. Look for acacia fiber, larch arabinogalactan, or partially hydrolyzed guar gum. Your gut bacteria also love polyphenols which are antioxidants that you can get from coffee and deeply colored vegetables [3].  

4. Follow an anti-inflammatory diet 

Your diet plays a huge role in your gut health. Sometimes what you think is helping your gut is actually destroying it. Lectins are anti-nutrients that shred your gut lining [4]. You can find them in grains, legumes, and nuts. Oxalates are another type of anti-nutrient. They’re compounds that bind to minerals in your body and form razor sharp crystals that can irritate your tissues and interrupt your gut microbiome [5]. Most of the foods that are highest in oxalates are what people consider “superfoods” – spinach, beets, sweet potatoes, raspberries, almonds, kale, and chocolate (you can find high-oxalate food lists online). Cut these high-toxin foods to make it easier for your gut to recover after antibiotics. You can learn more about following a low-toxin diet in The Bulletproof Diet. Download a free copy of the diet roadmap here. 

5. Take specific postbiotics – Prebiotics are food for your gut bacteria, and postbiotics are essentially “bacterial poop”. They’re beneficial compounds that certain bacteria make that benefit your gut health. One of the most impactful ones is butyrate. Studies show it can alleviate issues from antibiotic use [6]. If you’re healthy your gut bacteria make butyrate. But most people don’t make enough. You can also take it as a supplement. I like the butyrate from BodyBio. 

6. Support your gut lining 

Certain antibiotics can thin the protective mucus layer in your gut and weaken the cells that make up your gut lining [7]. Studies show collagen protein supports these cells and strengthens your intestinal barrier [8]. Take up to 20 grams per day and make sure it’s from grass-fed cows. Another thing you can do to support your gut lining is take l-glutamine which is an amino acid. Studies show it’s an important nutrient for your gut cells and taking it can improve gut barrier function [9]. Soluble fibers and prebiotics, which you read about earlier, also help support your gut lining [10]. 

7. Do intermittent fasting 

Intermittent fasting means going a specific amount of time (usually ~12-18 hours) without food. When you give your gut a break, it can rest and repair. Plus, studies show intermittent fasting positively impacts the diversity and abundance of good bacteria in your gut [11]. Just be sure not to overdo it, especially if you’re under a lot of stress or you’re a woman. If you’re new to fasting and don’t know where to start, check out the free fasting challenge at fastwithdave.com.  

Rebuilding your gut after antibiotics is a journey, but with the right steps—probiotics, prebiotics, postbiotics, and mindful habits—you can restore balance and feel your best. Start with one or two strategies from this guide, listen to your body, and consult a functional health practitioner if you need personalized support.  

For more information on how to support your microbiome, check out Human Upgrade podcast episodes:

#1088: “Biohacking Benefits of Omni-Biotic” and

#1037 – “How to Heal Your Gut: Exploring the Latest Bacterial Science and New Treatments” 

Or watch the full episode on YouTube:

 

 

References 

1. Kabbani TA, Pallav K, Dowd SE, Villafuerte-Galvez J, Vanga RR, Castillo NE, Hansen J, Dennis M, Leffler DA, Kelly CP. Prospective randomized controlled study on the effects of Saccharomyces boulardii CNCM I-745 and amoxicillin-clavulanate or the combination on the gut microbiota of healthy volunteers. Gut Microbes. 2017 Jan 2;8(1):17-32. doi: 10.1080/19490976.2016.1267890. Epub 2016 Dec 14. PMID: 27973989; PMCID: PMC5341914. 

1. 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. doi: 10.3390/foods8030092. PMID: 30857316; PMCID: PMC6463098. 

1. Nazzaro F, Fratianni F, De Feo V, Battistelli A, Da Cruz AG, Coppola R. Polyphenols, the new frontiers of prebiotics. Adv Food Nutr Res. 2020;94:35-89. doi: 10.1016/bs.afnr.2020.06.002. Epub 2020 Jul 7. PMID: 32892838. 

1. Vojdani A. Lectins, agglutinins, and their roles in autoimmune reactivities. Altern Ther Health Med. 2015;21 Suppl 1:46-51. PMID: 25599185. 

1. Hanstock S, Ferreira D, Adomat H, Eltit F, Wang Q, Othman D, Nelson B, Chew B, Miller A, Lunken G, Lange D. A mouse model for the study of diet-induced changes in intestinal microbiome composition on renal calcium oxalate crystal formation. Urolithiasis. 2024 Dec 12;53(1):4. doi: 10.1007/s00240-024-01672-2. PMID: 39666019. 

1. Canani RB, Costanzo MD, Leone L, Pedata M, Meli R, Calignano A. Potential beneficial effects of butyrate in intestinal and extraintestinal diseases. World J Gastroenterol. 2011 Mar 28;17(12):1519-28. doi: 10.3748/wjg.v17.i12.1519. PMID: 21472114; PMCID: PMC3070119. 

1. Ramirez J, Guarner F, Bustos Fernandez L, Maruy A, Sdepanian VL, Cohen H. Antibiotics as Major Disruptors of Gut Microbiota. Front Cell Infect Microbiol. 2020 Nov 24;10:572912. doi: 10.3389/fcimb.2020.572912. PMID: 33330122; PMCID: PMC7732679. 

1. Song W, Chen Q, Wang Y, Han Y, Zhang H, Li B. Identification and Structure-Activity Relationship of Intestinal Epithelial Barrier Function Protective Collagen Peptides from Alaska Pollock Skin. Mar Drugs. 2019 Jul 31;17(8):450. doi: 10.3390/md17080450. PMID: 31370332; PMCID: PMC6723256. 

1. Achamrah N, Déchelotte P, Coëffier M. Glutamine and the regulation of intestinal permeability: from bench to bedside. Curr Opin Clin Nutr Metab Care. 2017 Jan;20(1):86-91. doi: 10.1097/MCO.0000000000000339. PMID: 27749689. 

1. De Santis S, Cavalcanti E, Mastronardi M, Jirillo E, Chieppa M. Nutritional Keys for Intestinal Barrier Modulation. Front Immunol. 2015 Dec 7;6:612. doi: 10.3389/fimmu.2015.00612. PMID: 26697008; PMCID: PMC4670985. 

1. Pérez-Gerdel T, Camargo M, Alvarado M, Ramírez JD. Impact of Intermittent Fasting on the Gut Microbiota: A Systematic Review. Adv Biol (Weinh). 2023 Aug;7(8):e2200337. doi: 10.1002/adbi.202200337. Epub 2023 Mar 22. PMID: 36950759.