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How to Restore Gut Health After Antibiotics

Updated: Mar 8, 2023

We know how the overuse of antibiotics can compromise our overall health (if you haven’t read our last post, read it HERE). Obviously, avoiding antibiotics altogether is the easiest way to ensure antibiotics don’t disrupt your essential and beneficial gut microbiome.

However, a severe infection can make taking them unavoidable and you will need to take steps to proactively restore your gut health and combat the effects of the antibiotics.

Here are 11 ways to support and restore your gut health during and after antibiotics.

1. Take Probiotics

Taking probiotics can decrease the risk of invasion by opportunistic pathogens as well as reducing antibiotic-associated symptoms like diarrhea.

Saccharomyces Boulardii (S. Boulardii), for example, is a beneficial yeast that can help stop the spread of Candida specifically after a round of antibiotics. Candida is usually present in small amounts in most people, but it can take over and cause problems if given the chance. S. Boulardii has also been found to preserve and restore the intestinal barrier, protecting from ‘leaky gut’. Most importantly, because it’s a yeast and not a bacteria, antibiotics don’t affect it at all. It’s a fabulous choice for many infections like H. Pylori as well.

Use High-Quality Probiotics with Antibiotics

Probiotics work to restore your gut health by re-establishing the good bacteria. Of course, it will never replace what you have built since birth, but it is helpful none the less. If you are taking antibiotics, I recommend taking 50-100 billion CFUs during or immediately after a cycle of antibiotics.

If you have SIBO, use a soil-based probiotic like ProbioSpore by Designs for Health or ProFlora 4R by Biocidin.

When taking probiotics with antibiotics, it is important to wait at least two-three hours after consuming the antibiotics to take the probiotics. You should begin taking the probiotics the day that you begin antibiotics (or even before), and continue for at least a couple of weeks after the antibiotic course is through.

Research shows that those who supplement with probiotics while taking antibiotics had a 60% reduced risk of having their gut microbiomes overrun with opportunistic microbes common after antibiotic use.

2. Consume Probiotic-Rich Foods during and after antibiotic treatment as well. There are many probiotic food sources, including whole raw dairy, cultured coconut yogurts, kimchi, kefir, pickles, olives, and my ultimate favorite sauerkraut. Did you know that sauerkraut has TRILLIONS of probiotics in just 1 tbsp!

Take note: while kombucha can be excellent for someone with a diverse gut microbiome, this beverage might cause issues after a round of antibiotics. Kombucha is made with a lot of sugar that pathogenic bacteria love. In an empty gut microbiome, those sugars might entice bacteria to take over the gut microbiome. So, if you drink kombucha – you only need a little and if you feel super bloated after intake, stop drinking it!

3. Boost Prebiotics

Another strategy to restore your healthy gut flora after antibiotics is to make sure you feed it well with foods that they love. The only way to grow probiotics in the gut is to nourish them. This means eating foods that contain high levels of prebiotics.

Prebiotics are food for bacteria in our large intestine because they aren’t digested ‘further up’ in our small intestines. Prebiotic foods are usually high in fiber and plant polyphenols.

So, try to consume your prebiotics daily.

  • Chicory root

  • Asparagus

  • Jerusalem artichoke

  • Garlic

  • Onions and leeks

  • Dandelion greens

  • Bananas (a little green is best)

  • Apples (with skin)

  • Ground flaxseed

  • Jicama root

  • Apple cider vinegar

  • Dandelion greens (cooked)

  • Oats (GMO and gluten free)

  • Seaweeds

4. Eat a Diversity of Gut Healing Foods

A diverse, fiber-rich diet is your best bet for increasing the diversity of probiotics that antibiotics can threaten. The most fiber rich sources will come from fruits and veggies. If you’re someone who gets stuck on one or two veggies – it’s time to branch out. Even if you didn’t like it years ago – try it again! Utilizing food as medicine isn’t always about taste.

Note: raw veggies can be very difficult to break down for many people. If you struggle with bloating, gas, abdominal cramping and so forth, you will want to cook your veggies even the slightest to ensure proper digestion.

Highest fiber rich foods:

  • Berries (raspberries and blackberries are the highest)

  • Artichoke hearts

  • Chia, flax, hemp, sesame

  • Almonds/walnuts

  • Avocados

  • Beans and hummus: navy, garbanzo, lima, black beans, kidney, lentils, pinto

  • Squash (acorn is highest)

  • Peas / split peas

  • Leafy greens: collards, Swiss chard, turnip greens

  • Cruciferous: broccoli, cauliflower, Brussels

  • Sweet potatoes

  • Apples

  • Pears

  • Jicama

  • Guava

  • Quinoa

  • Oats

Healthy fats are essential to gut healing, especially omega-3s:

  • Fish

  • Shellfish

  • Walnuts

  • Ground flaxseed

  • Chia

  • Hemp

  • Avocado and avocado oil

  • Olives and extra virgin olive oil

  • Coconut oil, yogurt, milk and flakes

  • Grass-fed butter or ghee

  • Whole, raw dairy

  • Whole, pasture-raised eggs

  • Cod liver oil

Quality Proteins are essential to gut healing:

Protein helps to repair and rebuild your body, keep the immune system strong, support digestion, transport nutrition and heal the gut. One particular amino acid from protein foods called L-glutamine is very good at rejuvenating your gut lining. It’s found in both animal and plant foods, although animal sources have much higher amounts. L-glutamine is the main nutrient and energy source for the cells that line the intestinal tract and promotes good mucosal integrity.

Glutamine rich foods include:

  • Fish

  • Shellfish

  • Red cabbage

  • Whole fat dairy

  • Whole eggs

  • Nuts and seeds (almonds, walnuts, pistachios, pumpkin seeds, chia)

  • Dark leafy greens (parsley, spinach)

  • Red kidney beans

  • Seaweeds

  • Grass-fed, pasture-raised meats (beef, poultry, lamb)


Zinc is the wound healer! Beef, lamb, pork, fish and shellfish (oysters, crab), poultry, pumpkin seeds, hemp seeds, lentils, black beans, chickpeas, whole eggs, whole dairy and kefir, mushrooms, leafy greens (spinach), avocado.

Vitamin C is an immune booster and healer! Bell peppers, kiwi, guava, oranges, strawberries, papaya, broccoli, parsley, pineapple, brussels sprouts, cauliflower, mango, lemon, grapefruit, honeydew, peas, tomatoes, rose hips, acerola cherries, chili peppers, blackcurrants, cantaloupe, red cabbage.

Vitamin D is essential! Mushrooms, fish and shellfish, whole eggs, beef, organ meats, sunlight (without sunscreen and sunglasses).

Antioxidants! Dark chocolate/cocoa, pecans, blueberries, strawberries, artichokes, goji berries, raspberries, cranberries, acai berry, baby kale (cooked), red cabbage, beets, spinach, purple and red grapes, cinnamon, oregano, basil, peppermint, turmeric, pomegranate, cauliflower, walnuts, pistachios, almonds, red kidney and black beans.

5. Bone Broth

Bone broth is an excellent source of collagen and elastin. These two peptides help give our epithelial cells structure. They help clog up larger holes around the gut lining that leaves our bodies susceptible to pathogens. For optimal gut-health benefits, use bones from pasture-raised animals. They (hopefully) won’t carry any pesticides or heavy metals used in factory farming. Also, make sure the packaging states “antibiotic-free” meat.

6. Limit Your Intake of Sugars and Artificial Sweeteners

Sugars will feed opportunistic bacteria and in turn, through the amazing gut-brain connection through the vagus nerve … make you crave them. If you are craving high sugar foods, take a step back and be mindful. Take control. Interestingly enough, some evidence has also shown that artificial sweeteners like aspartame increase blood sugar by stimulating the growth of unhealthy bacteria like Enterobacteriaceae in the gut microbiome.

7. Breastfeed for at Least Six Months

Breastfeeding is very important for the development of the gut microbiome. Children who are breastfed for at least six months have more beneficial Bifidobacteria than those who are bottle-fed. If you struggle with breastfeeding, it’s important to know that skin-to-skin contact with your baby can be just as beneficial. There is a lot of support out there as well – you’re not alone.

8. Reduce Stress

Studies have found that stress triggers a fight-or-flight response that releases hormones in various parts of your body, which in turn affects your microbiome, reducing diversity. To compound the situation, that altered gut microbial population then affects the regulation of neurotransmitters, intensifying stress further. Try to cut out unnecessary stressors and make time to love yourself up.

9. Exercise

Exercise changes the make-up of your microbiome. In fact, studies have found that exercise is able to enrich diversity in your microbiome, improving the balance of specific families of bacteria. Exercise stimulates the growth of bacteria which can improve the integrity of your gut barrier and protect against gastrointestinal disorders and colon cancer.

10. Add Gut Repairing Supplements to Your Routine

Collagen does more than just improve your hair, skin, and nails. It also plays a role in restoring gut health. This is because collagen makes up the villi of your small intestine. Your villi are like tiny little fingers that grab nutrients and move them into your bloodstream. They vastly increase the surface area of your gut, making it easier for your body to absorb nutrients. Taking a collagen or bone broth powder or supplement can help restore your gut lining, nurture your villi, and ward off leaky gut.

There are also great gut healing mixes like Leaky Gut Revive, GI Revive, IgGI Shield. They help combat the root cause of leaky gut by fortifying your gut and keeping your microflora in balance. Using it in conjunction with collagen will provide a one-two punch of protection against harm to your gut from antibiotics.

11. Get Your Gut Tested

The best way to fight off a bacterial infection post-antibiotics is to get educated on your personal gut microbiome. Consider trying GI Map Testing by Diagnostic Solutions. This test uses a DNA sequencing to isolate the bacteria in your sample. Based on the abundance of each species, the testing can give you a detailed report on the expected ratios of each species in your gut microbiome – good and bad – along with the overall health of your gut – ability to digest your foods, detox capacity, gluten issues, inflammation, etc.

This knowledge is important because each species has different dietary preferences. Knowing which gut bacteria are causing you discomfort can tell you which foods you should remove your diet to prevent an overgrowth.


Advocate for yourself. Before you fill an antibiotic prescription, make sure your doctor has confirmed the need with a lab test. Because so many antibiotics are overprescribed, you want to ensure it’s a necessity before subjecting your fragile microbiome to any drug’s nuking effects. Keep in mind, there are natural and effective ways for many issues like ear infections and acne.

Spread out the probiotic doses. Because antibiotics indiscriminately destroy any and all bacteria as they make their way through your body, wait at least three hours after taking antibiotics before you take your probiotic dose. This gives the probiotics more time to settle in and set up shop in your gut.

Choose antibiotic-free foods. Many farmers use antibiotics to fatten up their livestock, so you could be unwittingly ingesting antibiotics and damaging your microbiome if you eat tainted foods. Choose organic and antibiotic-free meat, dairy, fish, and eggs whenever possible and invest in a high-quality water filter to filter out unnecessary contaminants.

Focus on prebiotics. Feed those babies! Prebiotics are indigestible fibers that feed your good gut bacteria and help them thrive so they can get to work supporting your health. If you are someone who doesn’t like prebiotic rich foods than consider prebiotic supplement (like Phytobiome by Designs for Health) but try your best to focus on a diet high in whole, plant-based foods.

Live a gut-healthy life. Nourishing your gut goes well beyond just taking probiotics while taking antibiotics. Making daily choices to stay away from microbial depleters like antibacterial cleansers and antimicrobial personal care products, being active, keeping your stress levels in check, and spending plenty of time outdoors will all help you create a gut environment conducive to a healthy probiotic population that is the key to long-term and vibrant health.

Check out our blog post Natural Antimicrobials for potential alternatives before accepting an antibiotic prescription. Consider getting a second opinion if you believe there are other viable options available. If you absolutely need antibiotics, consider your recovery plan. A lot of this process will involve dietary changes. And always eat like your gut depends on it, because it does.


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