How to help your gut biome after taking antibiotics.

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A few months ago I had a root canal that triggered an infection in my gums/jaw. Not a fun time, but after a number of days of pain I reluctantly gave in to taking antibiotics that my dentist prescribed.

I’m not a fan of taking antibiotics because I know that in addition to killing off any infection-causing microorganisms, it also can kill off the good bacteria in your gut.

It can take time for your good gut bacteria to recover after a round of antibiotics due to how much of the good bacteria can be harmed. “Broad-spectrum antibiotics can affect the abundances of 30% of the bacteria in the gut community, causing rapid and significant drops in taxonomic richness, diversity and evenness.” (Source)

There is also research that shows that even 2 years after antibiotics there is still a disruption in your gut.(Source)

Getting your gut back to health can take some time, especially if you’re not doing anything to help it. So to aid my own recovery, I’ve found 5 ways to really help your gut biome recover after taking antibiotics.

Take Probiotics

This may seem like an obvious one, but there are a few things to know about taking probiotics after a round of antibiotics. First, you should take a month of probiotics for every week of antibiotics you were on. This means a long stretch for anyone on a longer cycle of probiotics. Second, a multi-strain probiotic is more potent than a single or double strain. Since there is a large amount of strains of bacteria in your gut, the more strains you add will help the healing process.

Its been found that taking probiotics during rounds of antibiotics also reduce or prevent Antibiotic-associated Diarrhea, which can be caused by the altering of your gut’s microbial balance (source). In studies, it showed that taking probiotics reduced the risk of diarrhea by 50%.

If you’re taking probiotics during the antibiotic course, its best to take them a few hours apart – since antibiotics will remove the probiotics themselves. So taking the probiotics a few hours after the antibiotic is the best way.

I take HMF Forte by Genestra for my probiotic supplement. It contains 10 Billion CFU, is gluten-free, vegan, non-GMO and fairly priced. I focused on this brand because it contains Bifidobacterium animalis subsp. lactis which has been shown to counteract the effects of gluten when you’re gluten intolerant. You can read more on my gluten intolerance and how I’m healing my gut after going gluten free.

Eat Fermented Foods

Along with the probiotics, getting natural bacterial into your system is also important. The best way to do this is by eating fermented foods.

Fermented foods are foods produced by the action of microbes, and include yogurt, kefir, kimchi, sauerkraut, and kombucha.

These foods contain good bacteria like Lactobacillus, Lactococcus, Leuconostoc, and a large number of other fun-sounding and gut-helping organisms.

The benefit of eating fermented foods alongside taking probiotics is the increase in other strains of good bacteria. While probiotics can have lots of good strains of bacteria, they may not cover all the strains your gut needs, so increasing the intake of fermented foods can help this.

Increase Prebiotic Foods

You most likely have heard of probiotics – most Yogurt commercials push this – but prebiotics are just as important. Think of prebiotics as fuel for the bacteria in probiotics.

Prebiotics are a type of soluble fiber that the human body actually cannoy digest, but the bacteria in our gut can, and need it for food.

The two most predominant prebiotcs – those with the most research and understanding behind them – are inulin and oligofructose with inulin being the most abundant and found in a large number of plants.

With the increase of processed foods, there has been a decrease in people eating inulin-rich foods. When you are taking probiotics, its important to provide this food to help your gut biome thrive.

Natural prebiotics can be found in:
Raw chicory root
Raw onion
Raw leeks
Dandelion root
Whole wheat flour

Eliminate Foods that Reduce Antibiotic Effectiveness

So if you need to take antibiotics, you need to make sure they work efficiently, so your body can get back to normal faster. If a round of antibiotics doesn’t work, you may need to take a second round which hurts your gut biome even more.

Certain foods are known to reduce the effects of medications and antibiotics, and should be avoided during the time you’re taking the medication.

Grapefruit is a known fruit that reacts with a large number of medications in a negative way. Studies have shown that grapefruit (and potentially other citrus fruits) can hinder medication by inhibiting drug transporters(source).

Foods that are supplemented with calcium have also been seen to promote antibiotic resistance. This includes foods like calcium-fortified orange juice, which should be avoided (source).

Thankfully, other studies have shown that naturally-occurring calcium – like that in yogurt – doesn’t have the same negative effect.

Remove Sugar From Your Diet

When you take antibiotics, your gut microflora essentially get taken out. When that happens, there’s a greater chance for fungi to overtake your gut. Normally the good bacteria keep the fungi at bay, but if they are partially removed, fungi like candida albicans could flourish and cause more issues(source).

If fungi (and especially yeast) overtake your gut, you could suffer from ailments like diarrhea, infections, tiredness, joint pains and more.

Fungus like Candida thrive on sugars and bad/simple carbohydrates like white bread and pasta. These carbohydrates get turned into sugars by your body, giving more food to the fungi. If your gut’s bacteria is lowered and hurting due to antibiotics, then adding sugars will make the yeast take over.

So during and after any antibiotics, keep away from sugars and simple carbs to allow your system to not get overrun!


When you have to take antibiotics, know that your gut is going to suffer, but at least there are things you can do to help it get back to normal faster.

  • Take probiotic suppliments during and after (and hopefully you’re already taking them!)
  • Focus on eating naturally occurring probiotic foods like yogurt, komboucha, sauerkraut
  • Power up your good bacteria with prebiotic foods
  • Avoid calcium-enriched foods as well as citric fruits while taking antibiotics to make them work faster.
  • Avoid sugars and simple carbohydrates while your gut heals, so you maintain the bacteria/yeast balance.

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