Skip to content

6 minute read.

Maintaining proper balance of healthy gut flora – the complex community of microorganisms that live in the digestive tracts – is a crucial, yet widely overlooked component of human health. While the inception of antibiotics has lengthened lifespans, our excessive and often unnecessary use of these medications account for adverse, long-term health consequences. “Antibiotic” literally translates as “against life,” and their objective is to eliminate the “bad” bacteria that is responsible for your illness. However, antibiotics are not selective as to which bacteria they annihilate, and as a result they also kill the “good” bacteria. This is important because these beneficial bacteria support your immune system, protect you from disease and infection, help you digest and process food, aid in nutrient absorption and eliminate waste. We now know that at least 70% of our immune system resides within our gut. Unfortunately, after a course of antibiotics the natural balance between beneficial and pathogenic (disease causing) bacteria is compromised. So what can you do to repair and restore this imbalance following a course of antibiotics? Consider the following recommendations:

1) Dietary Considerations:

Avoid sugar and other simple carbohydrates. This is a good general rule but is especially important when recovering from an infection and following a course of antibiotics. Pathogenic, or “bad” bacteria love sugar. By avoiding dietary sugars and simple carbs (which are foods that easily turn into sugar), you essentially starve the bad bacteria.  

Incorporate fermented foods. By consuming fermented foods you are exposed to a greater diversity of beneficial bacteria. This diversity is key in maintaining a healthy immune system. Historically, prior to refrigeration, humans consumed large amounts of bacteria in the form of fermented and cultured foods. Consider experimenting with a variety of different ferments such as kefir, sauerkraut, kombucha, kimchi, beet kvass and other fermented vegetables or fruits. If you are new to eating ferments, consume smaller amounts to begin with. Two fork-fills per day is adequate.

Notice that beer, though fermented, did not make the list. Not only is beer is full of carbohydrates, it also reduces your gut motility – contractions of that mix and propel contents in the gastrointestinal tract.  A reduction in gut motility, combined with plentiful carbohydrates, can lead to an overpopulation and imbalance of gut bacteria.

Consume bone broths. Bone broths and other sources of glycine, like gelatin and aloe vera juice aid in repairing and maintaining the integrity of the gut lining.

2) Probiotics:

The friendly microbes in our intestines have been termed ‘probiotics’ and they comprise the beneficial types of bacteria and yeast found in the normal microflora of our gut. Probiotics are also found in certain foods and as dietary supplements. There are hundreds of different types of probiotics, from lactobacilli (for example, Lactobacillus acidophilus and Lactobacillus GG), bifidobacteria (such as Bifidobacterium bifidus) and some yeasts (Saccharomyces boulardii). During and following a course of antibiotics, it is imperative to take a high-strength probiotic. Considering that antibiotics are indiscriminate to the bacterial microbes they address, it may seem counterintuitive to take probiotics during a course of antibiotics. However, there are many randomized, placebo-controlled trials that have demonstrated the effectiveness in taking a high potency, professional grade, probiotic during a course of antibiotics. The reason being is that it helps to maintain the balance of gut flora, reduce side effects and prevent the growth of ‘bad’ bacteria during and after the therapy. Moreover, Dr. Nigel Plummer, a doctor in microbial physiology and a leading authority on probiotics, has found that there is clear evidence that the use of probiotics around an antibiotic decreases the level of antibiotic resistance! Antibiotic resistance is the ability of a bacteria to evolve to the point where they resist the effects of the medication previously used to treat them, and thus reduces or eliminates the effectiveness of antibiotics. Antibiotic resistance is accelerated by the misuse and overuse of antibiotics.

For short term antibiotic usage, start taking the probiotics (with food) when you first begin your course of  antibiotics (spaced at different times in the day). Recommended dosing is, 25 billion bacteria per day, continuing for a total of  30 days. Look for probiotic products that are supported by clinical data for effectiveness in humans, and found in peer-reviewed published studies. Be aware that literature published by the manufacturer can be suspect for promoting their products. See below for our recommended protocol and suggested probiotic products.

3) Prebiotics:

In simple terms, prebiotics are a source of food for probiotics, and thus are an important part of any regimen to protect or rebuild a healthy microbiome. Prebiotics are generally soluble fibers. Dietary fiber can be split into two categories – soluble fiber which is fermented by gut bacteria, and insoluble fiber which is not fermentable and acts as roughage. During and after antibiotic use, focus on getting plenty of soluble fiber found in starchy tubers, squash, Jicama, Jerusalem artichoke and peeled fruits. Allium vegetables such as garlic, onion, leeks, chives, and scallions are great choices. Add them to food raw for the best source of prebiotics. By providing our microbiome with a food source, we can encourage the healthier members of microbiota to grow and in the process make us healthier.

4) Support Your Liver:

Antibiotics can also take a toll on your liver, particularly if you’re on them for an extended period of time. Our liver has over 500 different jobs it performs. Not only is the liver responsible for metabolizing and detoxifying medications, it also acts as the clean-up crew to the thousands of microbes that have expired as a results of the antibiotics.  Milk thistle is a great supplement for supporting liver health, and can be taken in a pill or as a tea (420mg/day in divided doses). Eating beets and carrots can stimulate and support overall liver function. Glutathione, a compound that supports liver detoxification, can be found in avocados and leafy greens. Consider incorporating these foods, as they are also beneficial prebiotics. Also, don’t forget to drink plenty of water, as it will help flush out unwanted toxins.

Consider this: bacteria take residence in our bodies from the day we are born and remain with us throughout our lives. The gut bacteria is established in the first 2-3 years of life and play important roles in nutrition, digestion, metabolism, immune function and protection. Our gut protects us, so let’s protect our gut! If you find yourself in a situation where antibiotics are indicated, consider the following protocol to help support your overall health.


This protocol assumes that you are resting, avoiding alcohol, drinking lots of clear liquids and eating a clean diet, per the above recommendations.

During your course of antibiotics:

  1. Take HMF Forte (Syerol) or HLC Intensive (Pharmax) 1 cap 2x/day during your antibiotic course. Take this probiotic at a different time of day from your antibiotic.
  2. Incorporate 2 servings of prebiotic foods per day. Eat organic if possible.
  3. Eat good quality raw unpasteurized kraut or vegetable ferments – 2 fork fulls/day.

After your course of antibiotics:

  1. Take 1 HMF Replenish or HLC High Potency cap for a minimum of 30 days.
  2. Continue the 2 servings of prebiotic foods per day. Eat organic if possible.
  3. Take Milk Thistle 420mg/day in divided doses, 20 minutes away from food to help detoxify and support your liver.