Do Antibiotics Impact the Microbiome?

In one of the scariest times we will always remember, the era of COVID-19, the way we view our immunity and how we work with our physicians when we experience not just viruses but bacterial infections, is forever changed – likely for the better. Lessons are learned through hardship, especially shared hardship.

Antibiotics save lives. And we all have Dr. Alexander Fleming to thank; he discovered penicillin in 1928, the first antibiotic which opened the doors to this emergent paradigm shift of treating infectious bacterial agents. Currently, the world of antibiotics is broad, and host to many classifications. The main classes are beta-lactam antibiotics (e.g., penicillin and cephalosporin), fluoroquinolones, tetracycline, macrolides, and aminoglycosides. There are more than 100 antibiotics in use today.

The most common ailments for which antibiotics are prescribed include ear infections, sinus infections, strep throat, urinary tract infections, bronchitis and upper respiratory tract infections.

According to Dr. Clinton Osborn on, antibiotics work in three ways:

1. “Inhibiting the bacteria from producing protein. Note that proteins are essential building blocks for bacterial development.
2. “Inhibiting further production of bacteria. Bacterial inhibition happens when the antibiotic stops bacterial reproduction.
3. “Directly attacking the bacteria and destroying its cell walls.”

However, there are bacteria that cannot be vanquished by antibiotic warriors. These are typically known as antibiotic-resistant bacteria. According to Dr. Osborn, the most common antibiotic-resistant bacteria are Clostridium difficile, which typically affects the large and small intestines; and methicillin-resistant Staphylococcus aureus (MRSA), which is “an opportunistic pathogen, and [...] prevalent on the skin.”

Antibiotic Resistance

There are also increasing cases (and understanding) of other antibiotic resistance. It’s important to note here that humans don’t become antibiotic resistant—bacteria do.

In a scientific review, researchers point out, “Human pathogens have repeatedly acquired the genetic capacity to survive antibiotic treatment owing to heavy selective pressures resulting from widespread antibiotic use. The incidence of antibiotic-resistant infections is rising sharply, while the rate of discovery of new antibiotics is slowing. In 2015, antibiotic-resistant pathogens were estimated to cause over 50,000 deaths a year in Europe and the USA. The toll is projected to rise to 10 million deaths per year worldwide by 2050. These figures suggest we are reaching the end of the antibiotic era.”

Animals may also have a key role in the spread of antibiotic resistance, because drug-resistant bacteria is capable of transferring from animals to human via food supply. Even the water or fertilizer used to grow food crops can be contaminated with these bacteria, eventually making their way to the human gut and restarting the cycle. Since using antibiotics in any way can result in resistance, even those who have never been prescribed these drugs before are at risk due to environmental factors.

According to the World Health Organization (WHO), antibiotic misuse/overuse is responsible for accelerating antibiotic resistance. You can take several steps to reduce the impact and limit the spread of resistance. To help control the spread of antibiotic resistance, the WHO recommends:
• Only using antibiotics when prescribed by your doctor.
• Never sharing or using leftover antibiotics.
• Preparing food hygienically, following the WHO Five Keys to Safer Food (keep clean, separate raw and cooked, cook thoroughly, keep food at safe temperatures, use safe water and raw materials) and choose foods that have been produced without the use of antibiotics for growth promotion or disease prevention in healthy animals.

You can also help reduce risk of infections by regularly washing your hands, avoiding close contact with individuals who are ill, and keeping vaccinations up to date.

Antibiotics & The Microbiome

Authors of the aforementioned scientific review investigating the impact of antibiotic therapy on the microbiome write, “Antibiotics shape the ecology of the gut microbiome in profound ways, causing lasting changes to developing and mature microbiotas.” A dysbiotic microbiome may not perform vital functions such as nutrient supply, vitamin production, and protection from pathogens.”

There have been several studies looking at the impact of specific antibiotics on composition of the microbiome. One study showed that amoxicillin consumption
caused significant shifts in microbiome composition. This alteration lasted approximately 30 days on average and were observed for more than 2 months in some of the treated individuals. Another study of individuals taking ciprofloxacin also showed significant changes that lasted for several weeks.

Antibiotics & AAD

One of the key side effects of antibiotic therapy commonly experienced is antibiotic-associated diarrhea (AAD), which is also a consequence of dysbiosis. In fact, more than a third of people who take antibiotics develop AAD. Authors of a scientific paper write, “Although the diarrhea may be the result of increased gastrointestinal (GI) motility in some cases, a disruption of the GI flora that normally acts as a barrier to infection and aids in the digestion of carbohydrates is a far more common cause.”

Researchers in one study explain that incidence of antibiotic-associated diarrhea (AAD) often occur in healthcare settings, usually caused by Clostridium difficile. AAD typically occurs in up to 35% of patients taking antibiotics.

One meta-analysis of pooled data from 63 randomized controlled human trials (with a total of 11,811 participants) to identify the relative risk of AAD among individuals who received probiotics during antibiotic treatment compared with those who received no probiotics or were given a placebo.1 The studies encompassed a variety of antibiotics, taken alone or in combination, and several probiotics, including Lactobacillus, Bifidobacterium, Saccharomyces, and some combinations. The researchers found that overall, the “pooled evidence suggests that probiotics are associated with a reduction in AAD.”

A similar meta-analysis looked at probiotics’ impact on AAD in children and adults. The study of 31 RCTs found a pooled relative risk of 0.43 for development of ADD in those taking probiotics along with antibiotics to combat C. difficile infection.

A more recent systematic review assessed the impacts of probiotics used for addressing AAD in an outpatient setting; 17 studies with 3,631 participants were reviewed. According to the researchers, pooled results found that AAD was present in 8% of the probiotic group compared to 17.7% in the control group, and the species-specific results were similar regarding the probiotic strains L. rhamnosus GG and S. boulardii. The results suggest that probiotic use may be beneficial in reducing risk of AAD among outpatients.


As mentioned earlier, antibiotics can save your life, and likely already have. This course of medical action should be used more sparingly and appropriately, which will assist your body in more effective utilization of the antibiotic. Taking probiotics during the time you take antibiotics will help dramatically reduce experiencing AAD. And continuing to take probiotics will also help your friendly flora populations to flourish, allowing them to crowd out any pathogenic bacteria that necessitates the need for the antibiotics in the first place!

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