How to Keep Good Bacteria While on Antibiotics Naturally

How to Keep Good Bacteria While on Antibiotics Naturally

If you’ve done any reading on the human digestive system, you’re familiar with the term “normal flora.” These are the good bacteria that help us break down and digest our food. In fact, the human body typically has about ten times more bacterial cells than it does human body cells, and the majority of those are in our gut. So being on antibiotics for an extended period of time, which Lyme’s sufferers often do, can destroy that normal flora and cause digestive problems. Here are some foods you can eat to restore that normal flora and protect your digestive system while you stay on your course of antibiotics.

Yogurt and other Probiotics

You’ve seen the commercials for the yogurts that help re-establish healthy bacteria into your gut. But yogurt isn’t the only source of probiotics. You can also find them in tempeh and delicious Japanese miso.. These substances help to regrow healthy gut bacteria by serving as a live combatant against unhealthy bacteria, competing for food sources, and digesting unhealthy bacteria directly.


Fermented proteins and grains are an excellent source of gut-friendly bacteria, and this tea has become so popular it’s no longer hard to find. Any health food store will have kombucha tea in stock, and while the taste takes some getting used to, it’s very good for your digestive system. Many doctors suggest drinking kombucha concurrent to or after an antibiotics cycle to help restore the healthy gut bacteria.

Bananas and other Prebiotics

Bananas are often hailed as an easily-digested fruit. Excellent as an energy source for runners, who tend to have constant digestive problems, these fruits are also good sources of prebiotics, which are indigestible carbohydrates that provide inulin, lactitol, and other flora-friendly nutrients that help you regrow gut bacteria. Other sources of prebiotics include artichokes and garlic.

Whole Grains

While fiber is often pointed to as a problem for those with intestinal problems, it is also a prebiotic. Be careful to check the label of your grain before buying; it should say “whole grain,” not “whole wheat,” which may be more processed. These sources keep things moving within your digestive tract without losing too much normal flora, and also provide the same substances as bananas and other prebiotics.


This sweet substance can replace sugar as a sweetener, especially since sugar is one of the causes of loss of gut flora. Using honey as a natural sweetener adds another layer of flavor to your food, but it also helps restore natural flora as a source of prebiotics. Add some to your probiotic yogurt and double your protection in addition to enjoying a healthy, delicious snack.


Kefir is what’s known as a synbiotic, which contains both of the above substances. These substances, pre- and probiotics, work in tandem to create the optimal balance of normal flora in your digestive tract. Many companies attempt to add synbiotics to their packaged food, but the best sources are always natural.

Homemade Broths

These meat broths, especially those using bone, are high in the normal flora stored in bone marrow of the animal used. By creating your own meat or bone broth, you retain the helpful bacteria that taking antibiotics can destroy. And since broth is cooked slowly at a low temperature, it doesn’t cook out or kill off the pre- and pro-biotic properties of the bone marrow.

While all of the above foods are healthy and delicious additions to a healthy, balanced diet, they’re especially helpful to those people who are on antibiotics, whether it’s a long-term dependency or simply a single cycle. Natural remedies can be used in tandem with antibiotic cycles to help the body respond better to treatment and reduce the harm and side effects caused by antibiotics. Adding these items to your diet will help you reduce disease and discomfort by creating a balanced, healthy environment in your digestive tract.

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4 Responses to How to Keep Good Bacteria While on Antibiotics Naturally

  1. Don Mau says:

    Hi Paisley;
    I’m glad to see you are suggesting a meat broth. Such a good source of protein. These lyme pateints who turn into vegetarians aren’t helping themselves.

    There is a good article here talking about how probiotics don’t make it through stomach acid. Only 2-4%.


  2. Marie says:

    I have found that Ther-Biotic Complete by Klaire Labs to be extremely effective. The probiotics can survive and grow in the GI tract despite heavy antibiotics. I had almost no good bacteria in my gut and after a few months of Ther-Biotic (while on many antibiotics) I now have a healthy flora count.

    • Jenna Smith says:

      Thanks for the recommendation! I have used Therelac ( in the past which uses 5 strains but delivers 40 billion CFU per capsule versus Ther-Biotic ( which delivers 12 strains but only 25 billion CFU per capsule. Either product is a great choice for those of us using antibiotics to recover from Lyme disease.

      NOTE: Remember to purge your body of parasites ( a hiding place for Borrelia) and take a strong biofilm busting protocol while on any Borrelia-killing treatment to prevent the chronic nature of the disease.


    • Paisley says:

      Thanks for the insight Marie, I will have to try that!

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