Long-Term Effects of Antibiotics: 5 Ways to Boost Healthy Bacteria

Antibiotics are one of the most important and influential medical creations, but overuse has lead to antimicrobial resistant “superbugs”. Posing a concern to human, animal, and environmental health.

They kill off harmful bacteria but as a result they also destroy helpful bacteria. When it comes to IBD and IBS, antibiotics may be required to fight off infection, but misuse could further worsen related symptoms.

What do antibiotics treat?

The term antibiotics means:

“ …any chemical substance produced by a microorganism which has the capacity to inhibit the growth of bacteria and other microorganisms or to destroy them.” [1]

Antibiotics work against bacteria but not viruses:

  • Bacteria are living organisms existing as single cells. In some cases they’re beneficial but some are harmful, causing illness and invading the body, interfering with normal body processes.
  • Viruses aren’t alive. They grow and reproduce only after they invade living cells. Your immune system can fight some before they cause illness, but others may need to run their course in your body [2].

Doctors who are more liberal with antibiotics may recommended them when they’re not certain if an illness is caused by a bacteria or virus.

Common side effects of antibiotics

The purpose of antibiotics is to fight bacterial infections, but certain people experience negative side effects.

Short term side effects include stomach upset, diarrhea, loss of appetite, fungal infections or oral thrush [3]. Severe symptoms include allergic reactions (difficulty breathing, swelling in the throat or mouth, severe watery or bloody diarrhea, and yeast infections.

Contact your doctor if you have side effects after taking antibiotics. In order to prevent misuse, your physician may keep you on the antibiotic and manage the side effects, adjust the dose, or put you on a different antibiotic.

If you experience an allergic reaction such as skin rash, or anaphylaxis (shortness of breath, severe nausea or vomiting, dizziness, fast heart rate, and swelling of the face, lips, or tongue) immediately call your emergency line for medical assistance.


What is antibiotic overuse?

Antibiotic overuse is when antibiotics are used when they aren’t needed. As a result of antibiotic overuse, antimicrobial resistance has been on the rise. This causes a serious global threat of concern to human, animal, and environmental health. One result is the emergence of drug-resistant bacteria, or “superbugs” [5].

Antimicrobial resistance happens when microorganisms (bacteria, fungi, viruses, parasites) become “smarter” and “stronger” and develop resistance to medicine. As a result the medicine doesn’t work and infections aren’t treated, increasing the risk of spreading it.

In food animals, antibiotics are commonly used in cattle, chicken, and pigs and it is projected that in 2030 such use will increase up to 67% in the most populated countries of the world.” [5]

A global study showed that antibiotic use has increased 65%, from 2010-2015, in 76 countries [6]. Excessive use of antibiotics has been seen in animals, humans, over the counter and due to increased travel, poor sanitation, and through manure and feces residue from animals on antibiotics.

Prevent antibiotic overuse

  • If you experience antibiotic-related symptoms, ask your doctor
  • Take the full treatment of antibiotics
  • Don’t take antibiotics longer than instructed
  • Don’t use leftover antibiotics from previous prescriptions


IBD: could antibiotics be to blame?

A 2011 study published in BMJ Journal suggested a link between antibiotic use and IBD. This was a nationwide Danish cohort study exploring the link between the use of antibiotics and IBD in children [7].

The researchers gathered antibiotic prescription data between 1995 and 2004, including the type of antibiotic given, and all recorded diagnosis of IBD:

  • Data was collected on 577,627 children with an average follow-up time of about 5.5 years.
    • Most of the children (84.8%) had received at least one course of antibiotics.
  • 117 children had developed IBD (50 Crohn’s disease and 67 ulcerative colitis).
  • Researchers found that children who had taken an antibiotic prescription were 84% more likely to develop IBD during the follow-up than those who did not.

Keep in mind that this study doesn’t prove that antibiotic exposure causes IBD. Something to consider is that the children may have been more likely to have been prescribed antibiotics because of IBD symptoms, without knowing they had IBD at the time [7].

How to boost your healthy bacteria

The repeated use of antibiotics have been linked to decreased healthy gut bacteria. Without restoring and rebalancing your gut bacteria, you could have compromised gut health including impaired immunity, digestive issues, increased food allergies and sensitivities, increased inflammation, mood concerns, and even hormone and weight struggles.

Research shows that antibiotics can destroy helpful healthy bacteria and cause damage to the gut microbiome. Various sources of evidence suggest the important role of gut microbiota in IBS and IBD [8]. If you’ve taken antibiotics, it’s important to rebuild your healthy bacteria.

Note that these are general recommendations. If you suffer from IBD, you may need to practice more caution when it comes to food sensitivities or reactions, especially if you’re considering a flare-up. Consult your physician before changing your diet.


Focus on fermented foods

Fermented foods are foods that have been partially broken down by microbes. For instance, in yogurt, the bacteria ferment the lactose (milk sugar) to give yogurt its thicker texture and tart flavor. Other examples of fermented foods include cheese, sauerkraut, kombucha, kimchi, kefir, and miso.


Feed bacteria fiber

Fiber feeds healthy gut bacteria which helps them grow and populate. Higher fiber foods include nuts, seeds, beans, whole grains. In particular, prebiotic foods feed healthy bacteria. These include leeks, bananas, apples, flaxseed, onion, and asparagus.


Consider a high-quality probiotic

According to Dr. Liz Lipski in her book Digestive Wellness, aim for ones with Lactobacilli and Bifidobacteria. If you have chronic diarrhea, aim for Saccharomyces Boulardii. What’s most important is if the bacteria are still alive. Aim to buy a reputable brand who limits processing and conducts third-party testing.


Eat less sugar

Eating lots of processed foods and added sugar can decrease the amount of good bacteria in your gut. High amount of sugar have also been linked to increased inflammation, making IBD symptoms worse [9].


Reduce stress

Managing stress is important for all aspects of health, including gut health. Some studies have shown that psychological stressors can disrupt the balance of microbes. Also when certain bacteria strains (Lactobacillus and Bifidobacteria) were given to people suffering from chronic fatigue syndrome, they experience a decrease in anxiety symptoms [10].


Turn learning into action

Now you know what to do to boost the health of your microbiome, but applying these tummy tips can be tough. Nori Health is here to help you find actionable and easy steps towards a healthy lifestyle. Start a conversation with Nori Health today.


This article has been written by Lisa Booth, registered dietitian and nutritionist, and co-founder of Nori Health. Content is based on her professional knowledge, and our collection of 100+ scientific research study papers.