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How to Restore Gut Health After Antibiotics

Updated: Mar 8

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.