6 Ways to Restore Healthy Gut Flora Easily

I have successfully treated my family with herbs, rather than pharmaceuticals, for many years. However, there are those occasional times when we just felt antibiotics were called for. That is when we get serious with our fermented foods. If you need to learn how to restore healthy gut flora, read on for six ways fermented foods can help.

Antibiotics are both a curse and a blessing. When you need them because everything else you’ve tried isn’t working, they are a blessing.  They can take a life-threatening infection and turn it around quickly.  It’s hard to argue with a $15 prescription when the alternative is suffering and maybe even death.

Recently a family member had to take antibiotics for seven days due to cellulitis.  The infection was painful and immobilizing and came with the risk of blood clots.  The prescription for antibiotics seemed a no-brainer.  It worked, and by the end of the antibiotic period, the infection was gone.  We thought we’d be smart and increase probiotic foods during the antibiotics, hoping that there would be no residual effects.  No luck.

Antibiotics clean out your system of all bacteria, indiscriminately.  While antibiotics are meant to kill off the bad bacteria, they also kill off the good bacteria in your body and throw your microbiome out of balance.  It’s common for these unpleasant symptoms to follow antibiotic use:  Bad breath, constipation or diarrhea, nausea, poor digestion, yeast infections, weak immune function, mood disorders, anxiety, sleep disorders, eczema, hormonal imbalance, and even leaky gut syndrome.  Sometimes it seems like the curse of antibiotic use outweighs the blessing.

While the after-effects of antibiotic use can last for months, there are things you can do to repair the damage and restore healthy gut flora quickly.  Try these strategies to re-establish a healthy microbiome after antibiotic use.  These are the same steps we are taking to restore my family member’s healthy gut flora.

How to Restore Healthy Gut Flora–6 Easy Ways

Eat bone broth.

Bone broth contains glutamine which reduces inflammation in the body and repairs the epithelial lining of the gut.  Grab my bone broth recipe here.  Bone broth works hand in hand with fermented food to heal gut damage caused by antibiotic use so that a healthy microbiome can be re-established.

Add milk or water kefir to your morning routine.

Kefir is one of the best sources of the good bacteria.  Kefir has more beneficial bacteria than yogurt.  Even children can be persuaded to drink a cold glass of kefir in the morning. Drink four to six ounces of kefir a day to repopulate the gut.

Add fermented vegetables to your lunch and dinner menu.

Fermented vegetables work harder than probiotic capsules to encourage healthy populations of good bacteria.  Plus fermented vegetables contain naturally occurring inulin, an insoluble starch that the good bacteria feed on.

Vary the flavors, colors, and textures with fermented vegetables to eliminate boredom.  Add ginger, peppers, herbs, and spices to fermented vegetables to improve the flavor.  Pickles, sauerkraut, fermented carrots and beets provide different levels of good bacteria than kefir and can help speed up the return to a healthy microbiome.

Ferment your condiments.

Ferment condiments like ketchup, mustard, relish, and chutney to increase the probiotic benefit.  When someone’s stomach is nauseated and their digestion is subpar, their appetite may be impaired. By adding some fermentation to their usual condiments, it can speed the return to healthy digestion, and perk up a sluggish appetite.

Increase the prebiotics in the diet.

Increase the inulin, oligosaccharides, pectin, beta glucan, and other prebiotics in the diet. Prebiotics, like inulin, are indigestible fibers which the gut bacteria use as an energy source.  Usually, their food comes from the food that we eat. But if the diet is subpar, they might not have the prebiotics necessary to thrive in our guts.

Foods rich in these indigestible fibers are onions, garlic, leeks, asparagus, under-ripe bananas, jicama, yacon, sunchokes, dark chocolate, dandelion, and chicory – both greens and roots.  Grains that are high in beta-glucan, another of the prebiotics, include whole wheat, whole oats, barley, flax, and chia seed.  Fruit that is high in pectin includes cranberries, apples, and lemons.  Many inulin rich herbs have starchy roots.  Besides dandelion and chicory, other roots that contain inulin include elecampane, burdock, marshmallow, and echinacea.

You can increase these prebiotics in your diet simply by adding more onions and garlic to sauces and stock.  Serve asparagus, sunchokes, and jicama as vegetables, add flax and chia seed to your morning oatmeal, and drink herbal tea that includes burdock or echinacea. Choose pectin-rich fruit for snacks.

Include some of these prebiotic-rich foods in your ferment recipes.

Drink kombucha at least once a day.

Kombucha supports the liver in processing toxins in the body.  Besides adding beneficial bacteria to the gut, kombucha will help the body clear out the residual effects of antibiotic use and restore a healthy microbiome.

“Antibiotics” means “against life,” while “probiotics” means “for life.”  The more prebiotics and healthy bacteria you add to your diet after antibiotic use the sooner you will have life restored to your microbiome.  Now you have a plan.


If you are not accustomed to making your own fermented foods, experts agree that sauerkraut is the easiest one to start with. Follow this basic sauerkraut recipe and use the Fermentools starter kit for a successful ferment.


Chris is a teacher, author, gardener, and herbalist with 30+ years’ of growing herbs and formulating herbal remedies, skin care products, soaps, and candles. She teaches workshops and writes extensively about gardening, crafts, scratch cooking, fermentation, medicinal herbs, and traditional skills on her blog at JoybileeFarm.com.






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