Digestive Health

Totally Nuke the Side Effects of Antibiotics your Doctor Dismisses

By Kim Crawford, M.D. Last updated: May 8, 2019
side effects of antibiotics

What are the Inevitable Side Effects of Antibiotics?

Antibiotics can be life-saving and sometimes irreplaceable therapy for bacterial infections. However, there are appropriate and inappropriate uses of antibiotics. The side effects of antibiotics being covered here are so prevalent that you will get them. To clarify, these don’t include allergic reactions, rashes, or antibiotic resistance. In this article, I’ll discuss side effects that cause damage to the lining of your gut and disrupt your GI microbiome. These changes could spell disaster for your health from one “round” of oral antibiotics, let alone a gut-killing course of IV antibiotics. The more your gut is “on the verge” of going rogue, the worse the damage that a course of antibiotics will produce. In fact, the overuse of antibiotics has led to an epidemic of leaky gut.

Overuse of Antibiotics

I both admire and appreciate the work of Louis Pasteur. I recognize that antibiotics have a firm place in not just allopathic but all medical circles. However, I’d like to express- there is some glaring antibiotic overuse which has been studied. To point out, overuse isn’t just happening in the United States. Worldwide, the over-prescribing of antibiotics is leading to “superbugs.” Luckily, research on phages will likely culminate in viral phages to then attack the superbugs. In the meantime, do your part; please stop asking for antibiotics when you have a cold.

antibiotics side effectsYour doctor shouldn’t prescribe them (antibiotics), but he/she usually doesn’t take the time to explain why. If he does, he knows you might “leave him.” Indeed, that’s a problem right there.

We also have women reporting urinary burning who get treated with both an antibiotic for a possible urinary tract infection as well as a vaginal anti-fungal for a possible yeast infection. This type of “shotgun medicine” is atrocious.

Again, it’s your health, so you must do your part. It’s more expensive to go see your doctor but please have an exam, get the right “cultures” and so on. If you have recurrent urinary infections, find out if you need bioidentical hormones (if menopausal) or cessation of birth control pills (if pre-menopausal).

If E. Coli has been the infecting bacteria, rather than chronic, suppressive, GI-toxic daily antibiotics, see if d-mannose is appropriate. Stop taking oral antibiotics for acne; it’s outdated dermatology care. Further, If you have allergies with recurrent sinus infections, ask if a colloidal silver spray is appropriate. Check out the benefits of oregano oil and essential oils as natural antibiotics as well.

The Importance of a Healthy GI Tract

The gut AKA the human intestinal tract is populated by more than 100 trillion microorganisms; including over 1000 species of known bacteria. That’s a lot of bugs! These microorganisms in our GI tracts are a huge part of our personal genetic code. In fact, they are in our genetics 150x more than the genes in the entire human genome. This bacterial DNA controls much of our immunity, regulates digestion and even produces vitamins and other nutrients. In addition, they are an enormous influence on our metabolism, mood, immune system, brain health and, of course, gut health. In addition, 70-75% of the body’s lymphocytes set up housekeeping in gut-associated lymphoid tissue. Therefore, when your gut is not well, you’re not well.

What happens to a Population Taking too Many Antibiotics?

Antibiotics can damage your gut microbiome; those 100 trillion bugs we just discussed. Antibiotics not only eradicate the infecting bug, they are like an atomic bomb in your gut wiping out your good, health-promoting bacteria. They also ding the gut lining. 

We doctors give out too many prescriptions for antibiotics when colds (viruses!) and even most sinus infections and cases of bronchitis will get better without them. This is well documented. Patients come to see doctors, asking for antibiotics and everything else they see on television. We’re all a bit culpable here unless you see a doctor like me where antibiotics are a rare thing. We also know the cases of C. difficile colonic infections (serious!) are preceded by antibiotic use—typically for an upper respiratory infection.

So, how bad is the problem in our guts after taking antibiotics? Significantly, studies have shown that a one-week course of antibiotics can adversely affect your microbiome for up to a year. The malfunctioning microbiome studied in cases of long-term antibiotic use leads to issues such as food allergies, leaky gut, autoimmune disease, depressed immunity, fatigue, higher stress levels, skin issues, behavioral problems, mitochondrial dysfunction, and obesity. I’ll give you the solutions in a bit. But first, when should you take antibiotics?

When do I Need Antibiotics?

If you are admitted to the hospital with a fever and IV antibiotics are suggested, generally speaking, these antibiotics are being appropriately prescribed. If you have symptoms of a urinary tract infection and there are white cells and bacteria in the clean-catch UA (urine analysis), a 3-day course of antibiotics is appropriate; unless you have already identified that E. Coli is the culprit (it’s the most common one) and wish to try d-mannose. If you have a temperature over 100.5-101 degrees and are coughing up or blowing out discolored mucus, you need either an antibiotic or one of the alternatives discussed above; administered by a knowledgeable professional. It’s not wise to “experiment” with anti-bacterials other than antibiotics if you are immuno-compromised.

When don’t I Need Antibiotics?

If you have a cold, it is a virus. You don’t kill viruses with antibiotics. Further, if you have burning when you urinate and it’s a vaginal yeast infection, that’s treated with anti-fungal cream, not antibiotics. Lastly, if you are seeing a Dermatologist or other doctor who is giving you antibiotics for acne or rosacea, know there are much better therapies that won’t hurt your gut for these skin conditions. To emphasize, that’s just for starters.

Is Leaky Gut A Side Effects of Antibiotics?

side effects of antibioticsLeaky gut is something that I believe is rampant and untreated in most Americans. We have so many reasons to have leaky guts, and most of us with a leaky gut don’t show GI symptoms.

Antibiotics will eventually “get you.”

It’s all reversible, but your microbiome and gut lining takes a beating with every “round” of antibiotics you take.

What To Do Before Taking Antibiotics

Clean up your diet

Do eat an anti-inflammatory diet, a nutritional ketosis diet or a Paleo diet for optimal health. Ramp up your soluble and insoluble fiber intake, focusing on vegetables, raw nuts, and sprouted seeds. Eat prebiotic fiber so that the good bacteria you’ll re-introduce will have something to munch.  Foods rich in prebiotics include Jerusalem artichoke, onions, garlic, and jicama. Fermented foods such as sauerkraut, fermented carrots and beets are also high in prebiotic fiber.

Dietary Dont’s

Don’t eat GMO foods, gluten, grain-fed meats, farmed fish, sugary or processed foods, artificial sweeteners (other than stevia), non-organic fruits and vegetables unless they have a “shell” such as an avocado. In addition, water doused with fluoride or chlorine wreak havoc on your gut. Bathing in contaminated water absorbs through your skin and eventually does indeed harm your gut.


Cardiovascular exercise is great for your GI health so get moving!

Open your windows

When I was in medical training, we were taught to tell patients to “keep the windows closed” due to pollution and pollen. Now we know that indoor air quality is worse than outdoor air unless you have high-quality stand-alone filters throughout your home. Now, my advice is to “air out” whenever weather permits. Recent studies show increasing out-to-indoor airflow can improve the diversity and health of the microbes in your home, which then benefit you.

Kiss your dog

To my knowledge, the health benefits of planting a kiss on your dog’s nose haven’t been studied. Notably, studies have shown that children with pets have healthier microbiomes than children who don’t. Why not take it one step farther and give that dog of yours’ a kiss, especially after you’ve brushed his teeth? I have four rescue collies with clean teeth and clean breath who get lots of kisses. It’s just for my microbiome, right?

Get dirty

From hand-washing your dishes to building sand-castles on the beach to digging in the garden, exposure to bacteria can augment your microbiome.

Take probiotics

Choose a potency count (colony forming units) of 30-50 billion CFU’s per day—taken in two doses. Make sure they are refrigerated. Get yourself multiple species of bacteria, as high diversity tends to be associated with a healthier gut. Products containing species of Bifidobacteria and Lactobacillus are usually appropriate. Make sure that they have a GMP sticker, a non-GMO sticker, and a gluten-free sticker or label. Many probiotics have GMO cornstarch as a filler so beware of taking toxins. I also suggest everyone take a form of nutritional yeast called saccharomyces boulardii. In fact, you can get a prescription for this prescribed as Florastor.

Miscellaneous Toxin Avoidance

Various toxins such as heavy metals, mold toxins, dust mites, solvents and indoor chemicals can harm your gut. Keep your environment as toxin-free as possible.

What to do After Taking Antibiotics – A Prepped Gut

If you have prepared and done the above prior to taking antibiotics you are well ahead of the game. You don’t need to do much more than the above, especially if your course of antibiotics was short—for instance, 3 days for a urinary tract infection or a week to 10 days for bronchitis. Study everything above and realize it’s about returning your gut to perfect health so that you can return to perfect health. Here are the tweaks you need to make. Remember, your GI lining is re-born in 8 weeks with intensive repair work, so that’s the basis for my recommendations.

Diet: Eat as clean as you can, following one of the healthy diets you are already on. Add more fermented veggies and assiduously avoid gluten and sugar for 8 weeks.

Probiotics: Double up on your regular dose for 8 weeks. Make sure you are taking these 2x per day if you haven’t been.

Other Supplements: Add 2 tsps/10 grams of l-glutamine to your morning reds/greens drink or smoothie.

What to do After Taking Antibiotics – An Unprepped Gut

If you haven’t prepped your gut at all, assuming the worst case scenario; your eating plan isn’t all-that-healthy, you might have toxin exposure, and you’re not taking probiotics. Here’s what you need to do to restore your microbiome to health again. These practices also need to happen for 8 weeks (minimum) to completely restore your gut health; whether it’s 3 days for a UTI or a month of IV antibiotics.


Please choose one of the diet plans mentioned above and add fermented foods to lunch and dinner for 8 weeks. Consume no sugar, dairy, grains, eggs, beans or nightshade vegetables (eggplant, tomatoes, peppers), caffeine or alcohol for 8 weeks if you have any GI symptoms such as bloating, gas, heartburn, diarrhea or constipation. If you don’t have symptoms, limit your caffeine to your morning cup of coffee and limit your alcohol to 1-2 drinks or gluten-free beer (Omission beer), dry wine or vodka. Otherwise just “eat clean” and avoid gluten, sugar and processed foods. (Note: Due to the toxins in my home, not only did I develop leaky gut but so did my husband who is now on week 7 and actually enjoying his super clean diet).

Other: Please use a non-fluoride toothpaste to brush your teeth. If you don’t have a filter for your shower, please purchase one. Review the behavioral tips above and be conscious about doing them as well. Further, if you can afford an IQ-Air indoor filter, get one for your bedroom.


For your probiotic regimen, take a higher dose of your basic probiotic for long courses of antibiotics and wait until GI symptoms are gone to get these started. To follow, add sporulating probiotics to your regimen; these are all of the bacillus species and refrigeration is not necessary. In addition to your gut-healing regimen, add a collagen powder to your morning drink or have bone broth twice daily. Add other gut-healing herbals which are listed in our GI rejuv product. If you prefer to find these at your health food store, make sure you purchase non-GMO, gluten-free and GMP certified supplements. Finally, to give your gut a rest, take digestive enzymes prior to meals.

If you’re going to do this, you might as well do it all at once, right? I bet you’ll think twice before asking your doctor for antibiotics. Wink.

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1 Comment

  1. This is so comprehensive-I always thought just eating yogurt would do it, obviously NOT! THANKS for always providing great advice.

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