How to Restore Gut Flora After Antibiotics

05/09/2018 | 8 min. read

Dr. David Williams

Dr. David Williams

how to restore gut flora after antibiotics

By now, practically everyone is aware that while antibiotics can be lifesavers, they also have a downside.  Antibiotics kill bacteria; however, the killing is indiscriminate. Beneficial forms of bacteria, that reside in the intestinal tract and are essential for health, are destroyed alongside pathogenic forms. The result is very damaging to your gut and overall health. Thankfully, there are a lot of ways to restore gut flora after antibiotics.

Antibiotics and Gut Flora

Research has now shown that antibiotic use can permanently transform the natural balance of bacterial strains and have long-lasting detrimental health effects. The use of antibiotics early in life has been shown to eradicate essential bacteria that help immune cells mature. Since antibiotics have become the most common prescription drugs given to children, we've seen an increase in diseases of the immune system and those like obesity that are related to metabolism. A weeklong course of antibiotics can dramatically change the gut's microbiome for a year or longer, and antibiotic-resistant genes can remain practically forever. Antibiotic-resistant strains can persist due to a lack of "selective pressure" that would normally come from higher numbers of beneficial strains.

Most people aren't aware that this imbalance or dysbiosis in the gut can be directly responsible for many serious and chronic health problems. These include conditions like:

  • Clostridium difficile (C. diff.) infections
  • Crohn's disease
  • ulcerative colitis
  • colon cancer
  • lactose intolerance
  • acid reflux
  • vitamin deficiencies
  • metabolic disorders which result in weight gain and obesity
  • allergies
  • bladder/urinary tract infections
  • vaginal infections
  • high cholesterol
  • asthma
  • yeast infections
  • high blood pressure
  • neurological disorders
  • cognitive, behavioral and mood disorders
  • depression
  • impaired respiratory function
  • type 1 and type 2 diabetes
  • colon and rectal cancer
  • cardiovascular disease and death

Commonly Recognized Signs of Gut Bacteria Imbalance

You may not realize that the source of your issues is due to a gut bacteria imbalance caused by the use of antibiotics. Here are some signs that your healthy gut flora has been damaged:

  • upset stomach
  • abdominal cramping
  • excess gas
  • bloating
  • diarrhea
  • constipation
  • indigestion
  • yeast infection
  • chronic bad breath

The good news is there are ways to help speed up the process of restoring gut flora after antibiotics. Below, I will explain some of the most important ones.

Tips on Restoring Gut Flora After Antibiotics

1. Probiotics are the underlying key to restoring the gut microbiome following antibiotic use.

Probiotics are beneficial forms of bacteria that are naturally found in fermented foods. They need to be ingested daily to reestablish the beneficial bacterial growth in the gastrointestinal tract that has been destroyed by antibiotics. This can be accomplished with live fermented foods and probiotic supplements.

After antibiotic use, it's vital to gradually introduce various fermented foods into your diet. Don't stick with one particular food; try to alternate and experiment. Variety is the key to having a healthy gut and immune system. Each type of fermented food contains its own unique strains of bacteria that will help "seed" and start to balance your own gut garden. Here are some fermented foods you might choose to add to your diet:

  • yogurt
  • buttermilk
  • whey
  • kefir
  • borscht
  • sauerkraut
  • kimchi
  • miso
  • natto
  • kombucha

Probiotics in the form of supplements also need to be taken regularly following antibiotic use. They provide constant replenishment of beneficial bacteria. It has been suggested that for every week of antibiotic usage, a probiotic supplement needs to be taken for at least a month. 

Personally, I feel probiotics need to be taken daily for a lifetime. Antibiotics aren't the only drugs that disrupt and destroy the microbiome; common medications like antacids and over-the-counter and prescription pain medicine disrupt gut bacteria.

Probiotic supplements don't replace fermented foods following antibiotics. They provide the daily "insurance" for the days you can’t ingest those foods, as well as a consistent, steady supply of beneficial bacteria, which is necessary to restore and maintain the microbiome. Here are some of strains of bacteria to look for in a quality probiotic:

  1. Bifidobacterium lactis
  2. Bifidobacterium longum
  3. Bifidobacterium bifidum
  4. Lactobacillus rhamnosus
  5. Lactobacillus acidophilus
  6. Lactobacillus plantarum
  7. Lactobacillus fermentum
  8. Lactobacillus salivarius
  9. Bacillus coagulans
  10. Bacillus clausii
  11. Bacillus subtilis
  12. Saccharomyces boulardi
  13. Saccharomyces cerevisiae

2. For the bacteria to become reestablished in the gut following antibiotics, they must be "fed” with fiber-rich foods.

Beneficial bacteria in the gut feed on undigestible fiber. These are the compounds and fibers that your body can't digest but feed beneficial bacteria. Bacteria break these fibers down through the process of fermentation.  By-products of this fermentation process include various vitamins and compounds that support our immune systems and essential fatty acids that provide fuel for the cells that make up the intestinal wall.

Here are some fiber-rich foods to include in your diet for better gut health:

  • asparagus
  • artichokes
  • squash
  • zucchini
  • mushrooms
  • kale
  • onions
  • garlic
  • leeks
  • beans
  • legumes
  • nuts
  • seeds
  • sweet potatoes
  • green bananas
  • whole fruits

Here are some tips regarding changing your diet to a more fiber-rich selection:

  1. When picking fruits and vegetables, try to find those that are grown locally. Locally grown fruits and vegetables have soil bacteria and organisms that are native to your specific climate and environment. They are part of your personal ecosystem and can make your system more compatible with local pollens or allergens.
  2. If your intestinal tract is especially sensitive, you may have to go easy on the high-fiber foods until some healing takes place. Bone broth is a natural probiotic and loaded with healing collagen. Baked fruits and vegetables are easier to handle than raw ones. Baking apples helps release the pectin, which soothes the intestinal tract. Baked sweet potatoes are another great option, particularly when you add a little virgin coconut oil. Coconut oil is a great source of medium chain fatty acids (MCFAs).
  3. Of all the apples, Granny Smith apples have the highest levels of phenolics, proanthocyanidins and dietary fiber. And as a bonus, unlike other apples, Granny Smith apples specifically encourage the growth of specific strains of bacteria that are predominant in the guts of lean individuals.
  4. The extra intestinal gas formed when beneficial bacteria break down dietary fiber through fermentation is one of the most common complaints when first starting probiotics. The excess gas can be especially pronounced after a round of antibiotics, when the entire pH of the gut has changed. Understand that gas is normal and a sign the beneficial bacteria are working. Typically, after two to four weeks, the pH will normalize and things will calm down. It's perfectly okay to skip taking the probiotic for a day or two and let the bacterial activity proceed more slowly if you need to.

3. You may have to rebuild the proactive mucus lining of the gut after long-term antibiotic use.

If someone has taken antibiotics for an extended period, the protective mucus lining of the gut often has been damaged. When this happens, it becomes difficult for beneficial bacteria to establish a foothold in the intestines. Therefore, many people who consume probiotic supplements and foods after using antibiotics come to the conclusion that "they don't work."

The destruction of the protective mucus exposes the intestinal wall to the effects of harmful bacteria, yeasts like Candida albicans, fungi and other pathogens. This results in reduced amounts of Immunoglobin A (IgA) in the mucus intestinal barrier. IgA is the primary protective antibody in the gut.  Symptoms of low IgA levels include inflammation of the gastrointestinal tract resulting in problems like ulcerative colitis and Crohn's disease, food allergies, depression, diabetes, rheumatoid arthritis, thyroid issues, dermatitis, etc.

There are several ways to help rebuild the protective mucus barrier and increase IgA levels, giving beneficial bacteria a more stable platform to colonize. Here are a few tips:

  1. Numerous probiotics have been shown to increase IgA levels. Some of these include: reuteri, L. casei, B. bifidum, B. lactis and L. helveticus. I’m sure future research will reveal others. This is just one reason why taking a quality probiotic supplement is so important after using antibiotics.
  2. A special yeast probiotic called Saccharomyces boulardii has been shown to displace harmful yeasts like Candida, and it sets the stage for repair by increasing IgA levels. If your probiotic supplement doesn't already contain this beneficial yeast, it can be purchased as a stand-alone supplement. In addition to a quality daily probiotic supplement, I would suggest starting with one capsule a day of this yeast taken between meals. After a few days, increase it to two capsules and gradually work up to 3 or 4 capsules a day between meals. Normally, it will only need to be taken for a month to six weeks.
  3. If you have a juicer, cabbage juice can also help repair a damaged gut wall. It contains protective mucin-like compounds and loads of lactic-acid-producing beneficial bacteria. Anywhere from a cup to a quart a day can work wonders.
  4. The amino acid L-glutamine acts as strong anti-inflammatory compound and promotes the growth and restoration of the intestinal lining. I suggest 5 grams of powder daily when trying to restore normalcy after antibiotic use. Glutamine is one of the primary nutrients needed to maintain an intact intestinal barrier. It's at the top of the list when it comes to nutrients used to heal leaky gut syndrome. Glutamine supplementation increases IgA production in the gut.

BONUS TIP: Drinking chlorinated water also destroys beneficial bacteria in the gut. After all, chlorine and other chemicals are added to drinking water to eliminate bacteria. If your drinking water is chlorinated, you're fighting an uphill battle in trying to maintain the good bacteria in your gut. If you're not fortunate enough to have your own uncontaminated deep-water well or pristine spring you have a few options. You can filter or distill your water. You can also let a pitcher sit uncovered overnight to help break down the chlorine, or, even better, add two teaspoons of powdered vitamin c to chlorinated water to help neutralize it.

Antibiotics are wonderful tools and they save lives by fighting off serious infections. Unfortunately, they have been overused without any regard for the effect they have on our microbiome. As we learn more about the complexity of the human microbiome, we're starting to learn the severe health consequences of disrupting it. Obviously there may be times when you need antibiotics, but hopefully, by following these suggestions, you can minimize their long-term side-effects. Even if you haven't taken antibiotics recently, these tips are still relevant if you want to make a lifestyle change to support your gut health. 

Dr. David Williams

Meet Dr. David Williams

For more than 25 years, Dr. David Williams has traveled the world researching alternative therapies for our most common health problems—therapies that are inexpensive and easy to use, and therapies that treat the root cause of a problem rather than just its symptoms.

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