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Supporting Your Gut Health During and After Antibiotic Treatment

Writer: Jaime Heer, FNTP, RWSJaime Heer, FNTP, RWS

Antibiotics are sometimes an essential tool for fighting bacterial infections, but it's true that they can disrupt the delicate balance of your gut microbiome. While antibiotics kill harmful bacteria, they can also wipe out beneficial bacteria that play a crucial role in digestion, immune function, and overall health.


If you’ve been prescribed antibiotics, don’t panic! There are steps you can take to minimize the damage to your gut health and help your microbiome recover more quickly. Keep reading for my go-to Microbiome Restoration Blueprint:


1. Support Your Gut with the Right Probiotics

When you take antibiotics, it’s important to repopulate your gut with beneficial bacteria so that the opportunistic bacteria, aka "bad bacteria," don't get the opportunity to overgrow and crowd out the "good bacteria." But it's important to know that not all probiotics are created equal, and some are going to be much more effective than others at supporting your gut during and after antibiotic treatment.


Here are the probiotics that I recommend when helping clients restore their microbiome:


Microbiome Labs HU58: HU58 is a single-strain probiotic with a concentrated dose of Bacillus subtilis HU58. This particular strain is especially beneficial for supporting digestive function and over-all gastrointestinal health.

  • Take 1 capsule with breakfast & 1 capsule w/ dinner. (2-3 hours AWAY from antibiotics.)


Restoreflora: another powerful probiotic that specifically targets the restoration of your gut’s microbiome with probiotic strains Saccharomyces boulardii, Bacillus subtilis HU58, and Bacillus clausii SC109. This supplement is designed to support the growth of healthy gut bacteria, promote gut health, and reduce the risk of antibiotic-associated side effects like yeast overgrowth or digestive upset.

  • Take 1 capsule with breakfast & 1 capsule w/ dinner. (2-3 hours AWAY from antibiotics.)





How to Take:

  • Take your probiotics at least 2 hours away from your antibiotic dose to maximize their effectiveness.

  • Continue taking these probiotics for 4 weeks after finishing your antibiotic course to ensure your gut flora is restored.


After finishing antibiotic treatment + 4 weeks additional of HU58 & RestoreFlora, switch to:


Megaspore: this is a spore-based, broad-spectrum probiotic that helps to recondition the gut by promoting microbial diversity and maintaining key beneficial gut bacteria. It is able to survive the harsh environment of upper digestive tract so that it can successfully reach your large intestine and colonize your gut.

  • Follow dosing instructions on bottle until you reach 2 capsules/day with largest meal of the day.

  • Take for 3 months after antibiotic treatment and then switch to a probiotic rotating schedule using alternating probiotics w/ a variety of strains such as Terraflora Daily Care & ProbioMed 50.


*Pro Tip: For long-term gut health, it's important to change your probiotics every month or so. This helps ensure that your gut receives a diverse range of strains, rather than just the same ones repeatedly.


MegaMucosa: this is designed to rebuild a healthy mucosal barrier using serum-derived immunoglobulins, amino acids, and bioflavonoids. Especially beneficial for support your gut immune system and intestinal lining & to combat any damage done during your antibiotic treatment.

  • Following dosing instructions on the bottle until you reach 3 capsules upon waking & 3 capsules before bedtime.

  • Take for 1 month - 3 months following antibiotic treatment.




2. Incorporate Fermented, Prebiotic and Polyphenol-Rich Foods

Prebiotics and polyphenols are essential for feeding your healthy gut bacteria and supporting the regrowth of a healthy microbiome. Prebiotics are non-digestible fibers found in plant foods that promote the growth of beneficial bacteria, while polyphenols—found in plant-based foods—have anti-inflammatory properties and can help nourish gut bacteria to keep them happy and thriving.


Fermented Foods:

Fermented foods are rich in probiotics that support a healthy gut microbiome by introducing beneficial bacteria.


  • Kimchi: Fermented Korean cabbage with a variety of beneficial bacteria.

  • Sauerkraut: Fermented cabbage that helps boost healthy gut bacteria.

  • Kefir: A fermented dairy drink rich in probiotics, which can support gut health.

  • Miso: Fermented soybean paste with beneficial probiotics that can help balance gut bacteria.

  • Tempeh: A fermented soy product that’s high in protein and gut-friendly probiotics.


Prebiotic-Rich Foods:

  • Garlic: A powerful prebiotic that promotes the growth of beneficial gut bacteria.

  • Onions: Contain a type of prebiotic fiber called inulin, which supports gut bacteria.

  • Leeks: A great source of prebiotics to help support your microbiome.

  • Vegetables: Rich in fiber that feeds your healthy gut bacteria.

  • Bananas (unripe): High in resistant starch, which acts as a prebiotic.


Polyphenol-Rich Foods:

  • Berries (blueberries, strawberries, raspberries): Packed with polyphenols that support gut health and reduce inflammation.

  • Green Tea: Rich in polyphenols that support a healthy gut microbiome.

  • Olives and Olive Oil: Polyphenols in olives support gut health and act as natural anti-inflammatory agents.

  • Nuts (almonds, walnuts): Full of polyphenols to nourish the gut and reduce oxidative stress


© Better Belly Nutrition
© Better Belly Nutrition

3. Incorporate Gut-Healing Foods & Nutrients:

In addition to probiotics, prebiotics, and polyphenol-rich foods, it's important to focus on healing your gut lining, which can sometimes be compromised by antibiotics, especailly in the case of a weakened or over-stimulated immune system. The following gut-healing foods and supplements can help reduce damage to your intestinal lining and promote the healing process:

  • Bone Broth:

  • Wild caught fish

  • Pasture-raised eggs

  • Grass-fed beef liver

  • Coconut oil

  • Coconut yogurt

  • Aloe vera

  • Ghee

  • Turmeric & ginger

  • Slippery elm

  • Sweet potatoes


Supplements:

  • Megamucosa - 1 tsp upon waking and before bed for 30-90 days.

  • GI Revive - 1 tsp upon waking and before bed for 30-90 days.

  • Mt. Capras Colostrum - Take 2-4 capsules twice daily, on empty stomach for 90 days.

    • Use this code at checkout for $10 off your first order from Mt. Capra's: REFSUN8EB6WZ5


4. Maintain a Healthy Lifestyle for Gut Health

In addition to dietary changes and supplements, maintaining a healthy lifestyle is key to supporting your gut during antibiotic use:

  • Rest and Sleep: Adequate sleep helps support immune function and promotes gut healing. Aim for 7-9 hours of sleep each night.

  • Manage Stress: Chronic stress will absolutely affect your gut health, so practice stress management techniques like yoga, meditation, or deep breathing exercises.

  • Exercise: Regular physical activity helps support gut motility, improve digestion, and promote a healthy microbiome. Be sure to move everyday! Even better if you can get outside to get exposure to beneficial microbes + fresh oxygen and Vitamin D.


While antibiotics are necessary for treating infections, they can take a toll on your gut health. By supporting your microbiome with the right probiotics, prebiotic and polyphenol-rich foods, plus gut-healing nutrients, you can help minimize the impact of antibiotics on your gut and speed up recovery. Remember, a healthy gut is crucial for overall well-being, and with the right approach, you can protect your microbiome and heal your gut after antibiotic use.


Purchase your Antibiotic Recovery Supplement Bundle via my Fullscript Dispensary for 15% off by clicking the button below:





Disclaimer: Always consult with your healthcare provider before starting any new supplements or making significant changes to your diet, especially during or after antibiotic treatment.

 
 

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Jaime Heer, FNTP, RWP

Based in Santa Barbara, CA

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