rebuilding the gut after antibiotics
Until antibiotics were introduced around World War II, infections were common and often a cause of death. For that reason, they are one of the most significant innovations ever in the field of medicine. While most aspects of antibiotics are positive, they do come with side effects. Antibiotics affect the microbiome, often wiping out the “good” bacteria needed for a healthy gut. A healthy microbiome is essential for efficient digestion and nutrient absorption, with gut dysbiosis playing a role in many inflammatory conditions.
Types of antibiotics:
Bacteriostatics stop bacteria from growing and dividing, relying on your immune system to clear the infection.
These include:
Macrolides (Azithromycin, Clarithromycin, Erythromycin)
Tetracyclines (Doxycycline, Minocycline)
Sulfonamides (Sulfamethoxazole (often with trimethoprim))
Chloramphenicol
Clindamycin
Linezolid
Bactericidal antibiotics kill bacteria directly, damaging bacterial cell walls, membranes and DNA.
These include:
Beta-lactams (Penicillins, Cephalosporins, Carbapenems, Monobactams)
Fluoroquinolones (Ciprofloxacin, Levofloxacin, Moxifloxacin)
Aminoglycosides (Gentamicin, Tobramycin, Amikacin)
Metronidazole
Vancomycin
Daptomycin
Rifamycin
Antibiotics don’t just act on the infection site- they also reach the intestinal tract, sinuses, skin, and lungs, where they can disrupt the balance of beneficial bacteria. The degree of disruption depends on spectrum (broad vs. narrow); absorption and metabolism (whether much reaches the gut); duration of use, and finally whether it’s bactericidal or bacteriostatic.
Severe disruption:
Clindamycin: One of the most microbiome-damaging; can reduce microbiome diversity for four months and is associated with C. difficile colitis.
Very high disruption:
Vancomycin (oral): Used to treat C. diff but also wipes out most Gram+ commensals.
High disruption:
Broad-spectrum β-lactams (amoxicillin, Augmentin, cefdinir, ceftriaxone): Kill many Gram+ and Gram– gut bacteria; can cause diarrhea, yeast overgrowth, or long-term dysbiosis.
Fluoroquinolones (ciprofloxacin, levofloxacin): Strongly reduce microbial diversity for up to a year; linked to C. difficile and gut inflammation.
Moderate disruption:
Macrolides (azithromycin, clarithromycin): Affect both gut and sinus microbiota; may persist for weeks; can select for resistant species.
Tetracyclines (doxycycline, minocycline): Broad activity but partially bacteriostatic; can alter gut and skin flora; sometimes linked to yeast overgrowth.
Sulfonamides + Trimethoprim (Bactrim): Inhibit folate metabolism in many gut species; usually transient effect if short course.
Anaerobe-targeted disruption:
Metronidazole: Wipes out anaerobic gut flora but spares some aerobes; diversity rebounds slowly.
Minimal gut effect:
Aminoglycosides (gentamicin, tobramycin): Poorly absorbed orally; mostly act systemically or topically.
Narrow-spectrum β-lactams (penicillin V, dicloxacillin): Spare much of the gut flora; microbiome often rebounds quickly.
Positive gut effect:
Rifaxamin is unusual in that it is used specifically to treat a broad spectrum of bacteria in the gut, attacking bad bacteria and sparing good bacteria. It is often used to treat Small Intestinal Bacterial Overgrowth (SIBO) and other conditions associated with IBS. It is not systemic and its mechanisms are local to the gut.
Shorter, more targeted courses of antibiotics can limit effects on the microbiome.
So how do you rebuild after a course of antibiotics? Be aware that it may take weeks to months to get your gut back on track. Antibiotics can throw off the delicate balance of bacteria, resulting in too much “bad” bacteria and not enough “good” bacteria. A good way to find out exactly where you stand is a microbiome test such as Thorne Gut Health or Viome Gut Intelligence Test. If you know which strains are too high, you can take herbs to help decrease them, i.e. garlic or berberine. (There are too many bacterias to get specific here…I will sometimes do an online search once I get my results.) You may also pick specific probiotics to replenish what you are low on.
For the immediate post-antibiotic phase, the focus is on repopulating, reducing inflammation, and supporting the gut lining.
Probiotics (start during or right after antibiotics) Take 2-3 hours away from antibiotic doses for at least 4-8 weeks.
Anti-inflammatory, gut-soothing diet with bone broth, cooked vegetables, olive oil, fish, berries, prebiotic foods (as tolerated). Avoid refined sugar, alcohol, processed foods, and excess dairy- they feed yeast and inflammatory bacteria. You may also want to avoid irritants such as gluten and/or dairy until bloating subsides.
Gut-lining support helps repair intestinal permeability (“leaky gut”) after antibiotics. This can include L-glutamine (3–5 g twice daily on empty stomach); zinc carnosine (37.5–75 mg daily); aloe vera extract or deglycyrrhizinated licorice (DGL); collagen or bone broth (rich in glycine and proline).
After about 3-4 weeks, the rebuilding & balance phase can begin, prioritizing feeding good bacteria and restoring microbial diversity.
Add prebiotics (fiber for the microbiome) slowly after the gut feels calmer. These may include inulin, acacia fiber, or resistant starch (from green bananas, cooled rice/potatoes); and fermented foods (if tolerated): sauerkraut juice, kefir, kimchi, miso, yogurt. (If histamine or MCAS-prone, introduce fermented foods carefully if at all; start with prebiotic fibers first.)
Support motility & detox with magnesium glycinate or citrate.
From month two onward, look toward stabilizing the gut for long-term health.
Rotate probiotic strains every 2-3 months.
Eat a wide variety of plants (20-30 types weekly).
Maintain adequate sleep and stress reduction, both directly affect gut flora.
Avoid unnecessary repeat antibiotic courses.
Products to soothe the GI tract:
SPMs (Specialized Pro-Resolving Mediators) resolve inflammation in the intestinal barrier.
Vitamin D limits inflammatory pathogens and promotes immune tolerance.
Specific amino acids (L-proline, L-threonine, L-serine, L-cysteine) rebuild the mucosal layer.
L-Glutamine can support gut barrier function.
Immunoglobulins bind pathogenic microbes and their toxins.
Mastic gum helps relieve stomach pain and heartburn.
Bismuth works as an antacid and can help kill bacteria that cause stomach problems.
Slippery elm soothes heartburn, constipation and stomach discomfort.
Marshmallow root forms a mucus-like substance that coats the intestinal barrier.
Zinc carnosine can help heal GI damage from too much acid.
Product Examples: Gastro D (D’Adamo); GI Relief (Thorne); GI Revive (Designs for Health); GI Stress (Gaia); Ultra GI Replenish (Metagenics); GI Response (Innate Response); Mega IgG2000 (Microbiome Labs)
Prebiotic supplements:
Prebiotic Plus (Thorne)
Florassist Prebiotic Chewable (Life Extension)
Poly Prebiotic (Pure)
Probiotic Supplements:
There are multiple strains of probiotics that serve various purposes in the microbiome. Probiotics help colonize the GI tract and improve intestinal transit. They also improve gut barrier reinforcement, bile salt metabolism, enzyme activity and neutralization of toxins. Strain-specific probiotics may help with the endocrine and nervous system and immunomodulation.
Probiotic foods and supplements are best rotated to encourage diversity in the microbiome. General recommendations are to take 1-25 billion colony-forming units (CFUs) daily. (Most probiotic yogurts contain 1 billion CFUs per serving.) Purchase only products with “active, live cultures.”
Probiotic GI (Pure)
Ultra Flora Spectrum (Metagenics)
VSL#3
MegaSpore Probiotic (Microbiome Labs)
Gummies are available for kids, including Kid’s Probiotic (Nordic Naturals) and MegaSpore Biotic Gummies (Microbiome Labs)
Healing from antibiotics can take anywhere from weeks to months, so be patient! Even after your gut is “healed” it is always a good idea to provide a little TLC to keep it as healthy as possible in the long term.
*Information in this handout is for informational purposes only. Supplements should be discussed with a physician and started slowly.
