How Antibiotics Negatively Affect Your Gut

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Antibiotics are powerful medications that can be used to effectively treat a variety of conditions. However, reckless use can cause significant damage to the gut resulting in microbial imbalance and widespread dysfunction.

To protect the gut and overall health it is essential that people be aware of the undesirable impact of antibiotics, societies increased exposure to antibiotics, and effective methods of limiting or reversing antibiotic damage.

The Impact of Antibiotics

Antibiotics have facilitated greater health and wellness by allowing the medical community to resolve conditions and disease that were previously difficult to treat. The benefits of antibiotics are not in question. However, the rampant and unnecessary usage of antibiotics causes significant gut dysfunction, which can cascade into a variety of serious conditions.

Using antibiotics when they aren’t necessary typically hinders health more than helping it. Antibiotics block critical processes resulting in bacterial death and/or ceasing microbial multiplication. This action effectively destroys harmful bacteria but eliminates beneficial strains as well. However, the scope of damage caused by antibiotics depends on various factors including the type of medication, length of treatment, and how often it is used.

The gut is a carefully balanced ecosystem of many different strains of “good” and “bad” bacteria – learn even more about the gut here. When antibiotics are introduced, they indiscriminately destroy both helpful and harmful bacteria. This action effectively eliminates infectious and potentially harmful bacteria, but also decimates healthy bacteria.

The bacterial disruption caused by antibiotics results in microbial imbalance, or dysbiosis. This can leave the gut vulnerable to infection and fungal overgrowth. Therefore, it is important to use antibiotics only when necessary.

Taking a Look at the Damage

Some studies suggest that even a single course of antibiotics is enough to permanently alter gut flora. Therefore, even if a patient uses the minimal antibiotics they risk damaging their gut. Other research has found that certain antibiotic treatments can reduce bacteria diversity, which limits gut function. Furthermore, prolonged use of antibiotics can result in significant damage to the microbiome that may not be restored for years or may remain permanently impaired.

A 2011 article published in Nature, written by Martin Blaser, states that there are significant long-term issues associated with reckless antibiotic use. His work suggests that influencing gut microbes with antibiotics may promote the transference of potentially deadly organisms thereby increasing the risk of mortality via infectious disease.

Other research has shown that proper gut bacteria balance is a necessary part of maintaining a healthy immune response. Imbalanced gut flora, caused by antibiotics or otherwise, is a leading contributor to autoimmune dysfunction. When antibiotics disrupt microbial balance in gut, the intestinal lining weakens leading to leaky gut syndrome. This condition allows particulates such as toxins and partially digested food to enter the bloodstream and trigger autoimmune reactions.

Continuous activation of the immune system results in widespread inflammation that can lead to the development of serious autoimmune disorders including Crohn’s disease, fibromyalgia, chronic fatigue syndrome, Hashimoto’s thyroiditis and other. Some believe that the development of leaky gut, promoted by antibiotic use, is a prerequisite of autoimmune dysfunction.

Increased Exposure to Antibiotics

A primary issue with antibiotics is rampant and unnecessary usage. Antibiotics are continuing to be prescribed for non-bacteria related conditions including viruses such as the common cold and the flu. Unfortunately, it appears that antibiotic usage is increasing.

In 2014, an article published by BMC Medicine stated that widespread usage of prescription antibiotics doubled between the years of 2000 and 2010. The same study found that almost 50 percent of the antibiotics prescribed for home use are not necessary for treating the patient’s condition.

The food we consume may also contribute to greater uptake of antibiotics. Many products, unless specifically labeled and certified as organic, are likely treated with courses of antibiotics to combat animal-borne illness caused by overcrowding and irresponsible farming. Ingesting foods containing antibiotics can influence the balance of flora in the gut resulting in dysbiosis. Because of the rampant prevalence of antibiotics, it is important to take the appropriate measures to combat microbial imbalances.

Protecting the Gut with Probiotics

Probiotics are perhaps one of the best ways to limit the destructive effects of antibiotics. Probiotics are strains of live bacteria that help recolonize and establish healthy bacteria that help balance gut flora. Utilizing a probiotic supports the restoration of good bacteria that may have been killed during antibiotic treatments. Maintaining a healthy gut balance with the aid of a probiotic supports the many systems and functions associated with the gut. Of these, immunity is perhaps the most affected.

Probiotics should be taken at least two hours after antibiotic treatments because the lingering effects may destroy the colony-building bacteria in the probiotic supplement. Ideally, a multi-strain probiotic is used to ensure proper gut biodiversity. Each week of antibiotic treatment, should be followed with a full month of probiotic supplementation. Those who have undergone extended courses of antibiotics should almost always implement this strategy to lessen the elimination of healthy bacteria and support gut restoration.

We recommend HoltraCeuticals’ Ultrabiotics.

Defend Yourself from Antibiotic Damage

Antibiotics have been one of the most impactful developments of modern medicine. This is because they effectively combat numerous diseases and conditions that were previously difficult to resolve. However, it is important to use antibiotics only when necessary as even mild courses of treatment can have long-lasting effects on gut health.

Keeping the gut functioning at its best is essential to overall health and wellness. Incorporating probiotics into antibiotic treatments can significantly limit the lasting damage of antibiotics. If antibiotics are necessary, be sure to use them sparingly while supporting the gut with probiotics to help maintain gut health and overall wellness.


1. How Antibiotics Wreak Havoc on Your Gut. Amy Myers MD.

2. The high price of antibiotic use: can our guts ever fully recover? Chris Kresser.

3. How To Restore Gut Flora After Antibiotics. Holistic Primary Care.

About Holtorf Medical Group

The Holtorf Medical Group specializes in optimizing quality of life and being medical detectives to uncover the underlying cause of symptoms, rather than just prescribing medications to cover-up the symptoms. We are experts in natural, prescription bioidentical hormone replacement and optimization, complex endocrine dysfunction, fibromyalgia, chronic fatigue syndrome and Lyme disease.

We’ve dedicated our practice to providing you the best in evidenced-based, integrative medicine that’s not only safe and effective, but provides measurable results.