5 Anti-Thyroid Side Effects Of Antibiotics You Need To Know

anti-thyroid side effects of antibiotics

Drugs are not always the answer, especially when it comes to a compromised immune system in people with hypothyroidism and Hashimoto’s.

Antibiotics have been used for decades as a medication that kills or slows the growth of bacteria. This class of drugs is among the most frequently prescribed medications today. They are useful in the treatment of infections, pneumonia, allergies and skin problems.

Thousands of children, adults and animals are being treated with antibiotics every year and they are successfully curing different diseases. Whether it is just a gut trickling episode of infective diarrhea or a life-threatening infection antibiotics are considered as the go to magic-pills.

However, it doesn’t mean that antibiotics come without side effects. Recent studies revealed that the side effects and long-term consequences of antibiotic use are much worse than it was previously thought.

Furthermore, antibiotics could be doing significant black magic to your thyroid especially if you are already taking thyroid medication.

In fact, there are 5 anti-thyroid side effects of antibiotics that are seldom taken into consideration by both – patients and doctors:

1. Use of antibiotics changes gut micro-flora and can make you more hypothyroid

There are two major types of antibiotics based on the area of action broad and narrow spectrum. For example, Erythromycin the most widely used antibiotic of all, is a broad-spectrum antibiotic that doesnt work against any specific pathogen. It tries to kill them all and also eradicates the friendly flora of our intestines. Narrow spectrum antibiotics such as Vancomycin target a specific family of bacteria.

Studies show that not only overuse or an unjustified use of antibiotics disrupt the gut flora and cause disbyosis. But also even a single course of antibiotics creates an imbalance between friendly and not-so-friendly micro flora that can affect thyroid hormone pathway and how your body uses and utilizes thyroid medication.

There are two types of thyroid hormones in our body, inactive form T4 and active T3. Every cell of your body needs thyroid hormones for normal function, however they are able to use the T3 form only. A conversion of T4 to T3 peripherally, a major part of which occurs in the liver, muscles, brain and the thyroid gland itself, ensures that you get an adequate supply of T3 to your cells.

In addition, up to 20% of T4 to T3 conversion happens in your digestive tract but only in the presence of specific good gut bacteria. This process requires an enzyme named sulfatase and this is exactly where intestinal bacterias come into the picture. There is no other source of this enzyme except those micro-friends that are considered as enemies by antibiotics which wipe them out.

Reduced levels of T3 precipitates a state of hypothyroidism and this can happen despite abundant reserves of T4 and iodine in the body. Further harm is caused by suppression of the Hypothalamus-Pituitary-Adrenal or HPA axis through surplus of T4 that is not converted into T3.

HPA axis operates via a classical feedback system. Positive feedback to hypothalamus secretes Thyroid Releasing Hormone (TRH) which in turn stimulates the anterior part of the pituitary gland to produce Thyroid Stimulating Hormone (TSH).

Having an excess of T4 peripherally sends a negative feedback suppressing thyroid hormone synthesis and aggravating the already created hypothyroid state. This clearly translates into unresolved hypothyroid symptoms because no amount of thyroid medication can help you if the inherent mechanism operated with the help of gut bacterias is dysfunctional in the first place.

2. Antibiotics can affect efficacy and potency of thyroid drugs

There are two polar types of interactions between drug compounds, synergism and antagonism. While synergism means enhancing the effect of a particular drug, antagonistic drugs reduce the efficacy and potency of each other.

Two commonly prescribed antibiotic drugs such as Ciprofloxacin and Rifampicin are known to change the efficacy of thyroid medication. Here is how:

  • Ciprofloxacin which is prescribed for acute diarrhea has an antagonistic effect on thyroid medications and reduces efficacy of thyroid drugs making patients more hypothyroid.

  • Rifampicin which is an anti-tubercular drug increases the effect of thyroid drugs and yields synergistic output that can result in hyperthyroid symptoms.

Both of these medications thus, create an imbalance between circulating T4 and T3 levels affecting the HPA axis.

3. Some antibiotics reduce absorption of thyroid medication

Another and more direct mechanism that affects thyroid medication is the presence of fluoride which is an element that is found in our teeth, bones and toothpastes as well as in antibiotics of fluoroquinolones or quinolones family.

A chemical fluoride is used as a stabilizer for medications, however it actually de-stabilizes thyroid hormone balance in our body in two ways:

  • By directly reducing absorption of medications prescribed for hypothyroidism and Hashimotos disease

  • By competing with iodine which is a building block that is necessary for thyroid hormone production

Taking quinolone antibiotics along with Levothyroxine may lead to reduced absorption of thyroid drugs and cause noticeable changes in TSH.

4. Autoimmune diseases, allergies and many other health issues are predictable consequences of antibiotics

antibiotics consequences for thyroid

Intestinal walls of your digestive system have a protective barrier called epithelium. While this epithelium is chiefly concerned with the absorption of food and drugs into bloodstream, it is not the sole purpose.

It creates a boundary between gut and the abdominal cavity, preventing the communication between what is inside and outside gut. When that protection is breached, an exaggerated exposure to those alien colonies occurs and this guarantees an immune response within the body.

This is what exactly happens with the use of antibiotics. Some of these drugs are very aggressive and have the ability to damage the intestinal epithelial cells and unleash those bacterias which are supposed to be contained in a protected space. This phenomena is called increased intestinal permeability and is proposed to be one of major causes of autoimmune disease including Hashimoto’s thyroiditis.

These triggers an immune mediated reaction and leads to the production of auto-antibodies, a major step-up in the progression of Hashimotos disease and many other autoimmune conditions.

In addition, when the normal bacterial biofilms of the intestinal lining becomes disrupted by antibiotic use and there are not enough good gut bacteria, it compromises the development of T regulatory cells of the immune system.

Shifts in the immune system and immuno-suppression create a whole new set of troubles, leading to more infections, allergies, autoimmune diseases and intake of more antibiotics to fight them. This is a vicious cycle indeed.

5. Antibiotic resistance can trigger and worsen Hashimoto’s and hypothyroidism

Antibiotic resistance

The modern era of antibiotics started with the discovery of penicillin by Alexander Fleming in 1928. However, the first cases of antibiotic resistant bacteria were identified soon after in the United Kingdom in 1962 and in the United States in 1968.

Since then pharmaceutical companies have developed and introduced many new antibiotics to solve the resistance problem. However, despite these efforts persistent bacterial infections still remain a big threat especially for people with a compromised immune system.

Antibiotic resistance occurs when bacteria become “resistant” to the therapeutic doses of antibiotics and continue to multiply because medication has lost its ability to control and kill bacterial growth effectively. This happens due to overuse and misuse of antibiotics but also because of negative side effects of antibiotics to the gut flora as already mentioned earlier in this article.

Today, a whopping 80% of the antibiotics sold in the US are used in farm animals mainly to prevent infections and promote growth. As a result even if you are not taking antibiotics you still can develop antibiotics resistance through the food supply.

In people with Hashimoto’s and hypothyroidism antibiotic resistance can be a trigger and a contributing factor that worsens the disease. It opens the door to a host of infections linked to thyroid disease that your immune system is unable to fight effectively. Some of them include H pylori, E. coli, Epstein-Barr Virus (EBV), Yersinia enterocolitica and Borrelia burgdorferi to just name a few.

The problem is that in conventional medicine all these infections are treated with even more antibiotics. For example, a treatment for H pylori involves not only one antibiotic but a triple and quadruple therapy when 3 or 4 antibiotics are used to erradicate this bacteria. Antibiotic resistance and weak immune system make this approach ineffective.

However, there are natural substances that are often even more effective than antibiotics. Often natural compounds for H pylori remain the only option for people who have already developed an antibiotic resistance.

Antibiotics and thyroid

7 Steps To Avoid Negative Antibiotic Impact On Your Thyroid

1. Use antibiotics responsibly. They are designed to fight infections and are absolutely useless for a common cold and flu.

2. Check if antibiotics contain fluoride as one of ingredients and are on the list of fluoroquinolones or quinolones family that is well-known to reduce absorption of thyroid medication.


3. Ask for a less aggressive type of antibiotics that cause less damage to your intestinal walls.

4. Repair your gut damage and restore flora after antibiotic use.

Doctors prescribe antibiotics but they fail to take measures to repair damage that these drugs cause to your gut flora. As a result, the gut flora of most patients treated with antibiotics never fully recover.

Constipation, indigestion and bloating are very common symptoms of severe dysbiosis and a weak immune system that is unable to fight infections. Unfortunately, probiotics alone are only bandaids and do not fully replenish the gut flora with all good bacteria. It is important not only to re-populate the intestines with beneficial bacteria but also restore the variety of species.

5. Watch for antibiotics in your food, especially animal products like dairy, eggs, fish and meats.

6. Get tested for persistent infections if you continue to struggle with low grade inflammation, Hashimoto’s and hypothyroidism symptoms that just don’t go away.

7. Consider a natural alternative to antibiotics.

As you see antibiotics are not always the best available solution, especially when it comes to a compromised immune system in people with hypothyroidism and Hashimoto’s and those who already developed antibiotic resistance.

The good news is that there are powerful natural herbal alternatives available that use different mechanisms of action. As such, plant antibiotic choices can help with many common alignments without further contributing to resistance issues and help to recover from the damage caused by antibiotic use.

Look into available natural alternatives to antibiotics and other drugs and use them whenever possible.

P.S. Learn about a life-changing holistic treatment for hypothyroidism and Hashimoto’s disease in our free online Hypothyroidism Seminar: The Right And Wrong Ways To Heal

Thyroid Hormone Pathways


Ciprofloxacin and Rifampin Have Opposite Effects on Levothyroxine Absorption. Goldberg, A. et. al. Thyroid, October, 2013

Cohen, S. Thyroid Healthy. 2014

The Antibiotic Resistance Crisis: Part 1: Causes and Threats. Ventola CL. Pharmacy and Therapeutics. 2015;40(4):277-283.

About Marina Gutner, PhD
