Antibiotics and the Microbiome: Restoring Gut Flora After Antibiotics

June 6, 2023

Antibiotics have rapid effects on microbiome composition and health. Effects that can be detrimental to host health, especially with over exposure, which is increasingly common. We cannot always avoid antibiotics and should not when we need them, they are after all life saving drugs. However, we can take measures to lessen the harmful effects they have on our microbiomes.

If you are interested in learning more about how antibiotics affect the microbiome and how those effects can be prevented, we will cover those topics in the following sections:

  • How do antibiotics work?
  • The misuses and abuses of antibiotics
  • Effects of antibiotics on gut flora
  • Antibiotic resistance: the emergence of superbugs
  • How to restore gut flora after antibiotics
  • Stool banking: a future protocol for antibiotic use?

First, let’s cover how antibiotics work to fight bacterial infection.

How do antibiotics work?

The use of antibiotics began with the discovery of penicillin in the 1920’s. Since then many more antibiotics have been discovered and used to cure bacteria caused infections that were once a death sentence. Antibiotics enter the human body and specifically target and kill bacteria, leaving human cells untouched. They are able to do so by targeting specific traits that exist in bacterial cells and not human cells.

For example penicillin blocks bacteria from creating a cell wall, which they need to survive - human cells do not have cell walls. There are other types of antibiotics that affect other mechanisms necessary for bacterial life.

Though for all the good antibiotics have done for human health, they are not without their consequences. This is because antibiotics don’t just affect the bad, pathogenic bacteria but also the good bacteria that are crucial to our health.

The misuses and abuses of antibiotics

The problem with antibiotics is not entirely the antibiotics themselves. They are life saving drugs and many of us owe our lives to their discovery, but the over consumption of them is leading to their ineffectiveness. Some of the ways antibiotics are misused are easily avoidable. Below we outline two of the most common ways antibiotics are abused.

Antibiotics aren’t effective on viral infections

Many of the inappropriate prescriptions of antibiotics have been targeted at viral infections. Illnesses caused by viruses cannot be treated by antibiotics. This is because viruses are structured differently than bacteria and do not replicate in the same way. So, antibiotics don’t end up killing the viruses that are making you sick but just cause unnecessary harm to your microbiome.

Avoiding antibiotics in foods

Taking antibiotics is not the only way we are exposed to them, antibiotics and antibiotic resistant bacteria can also enter into our system through foods. Many animals are fed antibiotics to promote growth and by consuming meat products from these animals we may be putting are self at larger risk of antibiotic resistance.

Effects of antibiotics on gut flora

Antibiotics are one the greatest discoveries of modern medicine. They have transformed human health, making once deadly ailments and infections easily treatable but everything good has its cost and antibiotics are no exception. Along with killing bad bacteria that cause infection and illness, antibiotics also can end up killing a whole host of helpful bacteria.

Though antibiotics are prescribed to kill off pathogenic bacteria, they are not targeted drugs. Meaning they cannot just target what is causing infection but instead any bacteria in their path regardless if they are good or bad. So, though they can be life saving when it comes to certain infections, they can be dangerous to your health when they are overprescribed where they are not necessary.

Interrupting microbiome development

Unfortunately many of the people receiving high and unnecessary doses of antibiotics are young children, who are still in the midst of microbiome development. This period of microbiome development is critical to the normal colonization of bacteria in the body and disruptions in it can lead to long-term consequences. Early interruptions to the microbiome by antibiotics has been linked to higher risks of obesity, asthma and allergies.

The onset of dysbiosis by antibiotics

In the direct aftermath of taking antibiotics it is not uncommon to experience dysbiosis. A broad-spectrum antibiotic can affect the microbiome, causing notable decreases in bacterial diversity - a key aspect of microbiome health. After taking antibiotic it can take months, if not years for the gut microbiome to recover from the intervention. And there is evidence to suggest that some may never fully recover from the use of antibiotics.

A state of dysbiosis, which can be onset by antibiotics use, has been associated with a number of health conditions. These conditions include, but are not limited to Crohn’s, Ulcerative Colitis, Autism and Obesity.

Antibiotic resistance: the emergence of superbugs

With over exposure to antibiotics came the emergence of superbugs. Superbugs are bacterial pathogens that have developed a genetic resistance to certain antibiotics. Unfortunately, antibiotic resistant superbugs are on the rise while the discovery of new antibiotics is on the decline.

What are superbugs

Superbugs are a classification of bacteria that have developed antibiotic resistance. This is a natural process that has been exasperated and played out quicker due to the over prescription and abuse of antibiotic drugs. For example, antibiotic resistant bacterial strains of M. tuberculosis, the bacteria that causes TB, are on the rise. The once deadly, made very treatable disease may soon return as a major threat to human health.

How does antibiotic resistance develop?

Bacteria can evolve into “superbugs” in a couple of ways. The first way is through genetic mutations that cause them to become resistant to certain antibiotics. Another and the most effective way in which superbugs evolve is through gene transfer. Bacteria are capable of engaging in gene transfer, whereby they can pass along genetic information to one another.

Gene exchange among bacteria has increased the speed at which bacteria has been able to evolve mechanisms to become antibiotic resistant. One such mechanisms is known as a biological pump, in which enzymes degrade antibiotics and wash them out before they take effect.

How does overuse cause resistance?

Yes, bacteria evolves naturally to become resistant to threats to their survival but by overusing antibiotics this evolution happens a lot faster. When we use antibiotics at the frequency we have been using them, the bacteria is forced to evolve at a quicker rate to survive; which it can do quite effectively.

How to restore gut flora after antibiotics?

If we can’t avoid antibiotics, the next best thing we can do is try to restore our microbiome after them and know how to stay healthy while taking antibiotics. Diet can help ensure that your microbiome has the resources necessary to repopulate properly by providing nutrients that promote gut health and microbe diversity.

Diets to jumpstart your microbiome post antibiotics

Eating foods that promote microbiome health and diversity is important at all times but it is especially crucial when you are recovering from antibiotics. For that, natural probiotics (found in foods) and prebiotics are key. Though it is always important not to overdo one food group. A healthy system thrives off a diverse and balanced diet, so make extra sure fibre and fermented foods are a part of that balance in the aftermath of antibiotics.

Stool banking: a future protocol for antibiotic use?

It has been suggested that banking one’s own stool before the use of heavy antibiotics may be a way to help minimize the detrimental effects of antibiotics on the microbiome. By banking one’s own stool and implanting it post antibiotics, the natural population of microbes in the gut will recover more effectively and quicker.

Autologous FMTs more effective post antibiotics compared probiotics

In a study out of the Weizmann Institute of Science in Israel participants were given a round of antibiotics and then either given a probiotic mixture, an autologous FMT or were placed in a controlled group and given nothing. Those who were given the probiotic, had a gut that was colonized by the bacteria from the mixture for up to six months, rather than a replenishment of their original gut microbes. Those who were given aFMT, that is a fecal transplant using their own pre antibiotic stool, saw the fastest rate of microbial recovery. Though the study was inarguably very small and therefore limited in scope, the results are of interest to those trying to find ways to prevent the dismal effects of antibiotics on the microbiome.