Antibiotics and Your Microbiome

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The Pure TheraPro Team

The Pure TheraPro Education Team is comprised of researchers from diverse backgrounds including nutrition, functional medicine, fitness, supplement formulation & food science. All articles have been reviewed for content, accuracy, and compliance by a holistic integrative nutritionist certified by an accredited institution.
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Each year, approximately 269 million antibiotic prescriptions are dispensed via outpatient pharmacies in the United States. Most of these prescriptions are unnecessary as they are for bronchitis, the common cold or a viral sore throat—symptoms that don’t respond to antibiotics. It is estimated that 47 million unnecessary antibiotic prescriptions are written each year from doctor offices and ER departments.

Antibiotics are one of the most commonly prescribed pharmaceuticals in nursing homes. It is estimated that 50-70% of nursing home residents received at least one course of antibiotics within a given year, and up to 75% of these prescriptions were wrongly prescribed. Either they were not needed, were the wrong type of antibiotic, wrong dose or wrong duration of treatment, and these errors cause patients a variety of side effects—C. diff, antibiotic resistant infections, chronic yeast infections, poor immune function and allergic reactions. These are statistics straight from the CDC website

Research is demonstrating the vast impact antibiotics play on our immune system and gut microbiome. It is now believed that even one round of antibiotic can reduce your microbiome by 90%.

Your microbiome is a community of bacteria that play a role in disease response as well as homeostasis. Your sickness and wellness are determined greatly by how prolific and diverse your microbiome.

The gut microbiome consists of up to 100 trillion bacteria and other microorganisms and are responsible for fighting pathogens, breaking down food, regulating immune function, synthesizing vitamins and even metabolizing drugs. Any disruption in your gut microbiome has the propensity to cause disease.

Your microbiome is your defense against pathogens trying to invade your system, and these good bacteria work together in a militant fashion, complete with artillery to get the job done and keep you healthy. They may use their own biowarfare, or antimicrobial compounds, to kill bad bacteria. They help train your immune system to work optimally and help build a stronger intestinal mucosa to guard against pathogens. They’ve also been known to utilize crowd control devices in your gut to literally throw the bad bacteria and invaders out of your sacred house.

Your microbiome is an intricate system that when functioning properly, provides you with incredible health benefits—mental clarity, positivity, a strong immune system, glowing skin and shiny hair, optimal digestion and nutrient absorption and more.

Antibiotics, however, throw a wrench into this system and can create an imbalance which can be affected for a few weeks or even years! Without their protection, your system is at risk of pathogenic invaders as well as gut issues, such as C. diff, SIBO, Leaky Gut Syndrome and nutrient malabsorption.

Studies of humans at all ages show that antibiotics affect the gut microbiome and immune function. A retrospective analysis of more than 333,000 children in the US Military Health System (MHS) database demonstrated that children who took antibiotics in the first 2 years of life were associated with a 26% heightened risk of obesity. Multiple rounds of antibiotics increased these risks. 

A 2016 study on infants given antibiotic treatment found alterations in gut microbiota as well as weakened immune functions for years. 

Antibiotics have also been linked to asthma in children, as well as gut issues, such as inflammatory bowel disease, according to similar research. 

Antibiotics affect the microbiome of adults. A Stanford screening of 900,000 stool samples of healthy men and women who had taken the antibiotic, Ciprofloxacin, found that although the gut microbiome returned to normal within a month, certain strains of bacteria remained low or even didn’t return at all.

The antibiotic, Clindamycin, also demonstrated negative effects on the gut microbiome. Like Ciprofloxacin, Clindamycin is a broad-spectrum antibiotic. Studies showed its microbiome disturbance may cause the pathogenic bacteria, Clostidium difficile (C. diff) to colonize and overgrow, leading to chronic gut issues, such as colitis.

Disturbance of the gut microbiome by antibiotic usage has also been associated with autoimmune disease and inflammatory syndromes. These associations have established that antibiotic use early in life impacts immune function as an adult. 

The effects that antibiotics have on the microbiome depend on:

  • The type of antibiotics
  • Duration of treatment
  • Whether more than one antibiotic was used for treatment
  • Dosage

Broad spectrum antibiotics have been shown to have a greater impact on long-term microbiome disruption, and are linked to causing allergies and antibiotic resistance.



Here is a list of the most common broad-spectrum antibiotics:








Animal studies have shown a relationship between microbiome disruption caused by antibiotic treatment and immune response. Mice given antibiotic treatment had an increased incidence of type-1 diabetes. Their T-cell count was also lower, meaning poor immune function. Psoriasis was also higher among neonatal mice given antibiotics compared to the control group.

Animal studies have also shown the link between gut bacteria and lung protection against respiratory illnesses such as flu virus infections. Gut bacteria signal the mucosal lining of the lung as a protective mechanism. According to the researchers, immune cells signaled the response within two days, while the virus simultaneously was multiplying in the lining of the lungs. Antibiotic-treated mice had five times more virus in their lungs two days after infection compared to mice that were not treated with antibiotics. The immune response of the antibiotic-treated mice was greater, as well, leading to more damage, more severe symptoms and worse outcomes.  

80% of the mice with healthy gut microbiomes survived when infected with the flu; only one-third of the mice treated with antibiotics survived the flu infection. 

Short-term effects of antibiotic use may result in chronic diarrhea, digestive issues and yeast overgrowth caused by the impact to the gut microbiome.

Saccharomyces Boulardii, a beneficial yeast, can help manage these symptoms and is antibiotic resistant, meaning it may be taken at the same time as a course of antibiotics. Saccharomyces Boulardii has also demonstrated positive effects on immune function, according to research.

If you’ve recently had a round of antibiotics and would like to help replenish your gut microbiome to support immune function and digestive health, here are some tips:



If you’re currently taking antibiotics, consider supplementing with Saccharomyces Boulardii. It may be taken at the same time as antibiotics. Sacc B is a transient beneficial yeast, meaning that it will not take residence in your gut. You will also need to take probiotics, which do “shack up” in your digestive tract, in order to replenish your gut microbiome.

If you’re currently taking antibiotics, you can still take probiotics—just be sure to take them at least three hours away from the time you took your antibiotics to help ensure their survival.

Not all probiotics are the same! Look for ones that survive stomach acid and are absorbed via the small intestine for greater bioavailability. Also, check labels for fillers, excipients, flow agents, etc which may irritate the gut lining and also interfere with optimal absorption. Steer clear of magnesium stearate and stearic acid.



The Western diet does not promote optimum gut microflora. Look for fiber-rich foods and those which naturally are considered prebiotics, which help feed good bacteria. These foods are naturally high in fiber as well as plant polyphenols, which help support the proliferation of good bacteria strains. So, stock up on fresh organic fruits, nuts, seeds, whole grains, vegetables and legumes.


Exercise reduces stress levels, which can impact your microbiome and reduce their diversity. Your microbiome also plays a role in regulating hormones and neurotransmitters, important for many bodily functions from sleep, metabolism, immune function and mood stability. In addition, exercise helps support healthy gut mucosa, the barrier that protects your digestive tract, according to research. 


Although antibiotics, when used properly, can be life-saving pharmaceuticals, it’s important to always weigh the risks vs the benefits and fully understand the systemic consequences of taking them.