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Ulcerative Colitis and Antibiotics to Avoid

Antibiotics are prescribed to fight bacterial infection but have a substantial impact on gut bacteria. This makes their use in gastroenterological conditions somewhat complicated. It’s not that antibiotics should be completely avoided in cases of IBD, rather they should be used sparingly and with care. 

Here’s what you need to know when considering a course of antibiotics while managing IBD. 

Side Effects of Ulcerative Colitis Medication

Antibiotics & Gut Health in IBD 

Antibiotics target unwanted and damaging bacteria, but healthy gut bacteria get caught in the line of fire, leading to an imbalance of our gut microbiome known as ‘dysbiosis’. 

Our gut microbiome is home to trillions of bacteria, archaea, microeukaryotes, and viruses, making up a fragile ecosystem that plays a critical role in our adaptive immune system, energy homeostasis, and the nutrient breakdown and metabolite production. It regulates nearly every aspect of our health but when thrown out of balance, the reduced bacterial diversity can lead to the development of many diseases, including IBD, obesity, type 1 diabetes, and colorectal cancer. 

This may explain why antibiotics have been reported to cause flare-ups in IBD cases. Broad spectrum antibiotics reduce microbiota diversity, and this not only increases the risk of IBD but can exasperate symptoms of an existing condition.  

Can antibiotics trigger ulcerative colitis? 

Prior use of board-spectrum antibiotics has been associated with an increased risk of IBD

According to the research, just one prescription of antibiotics could raise the risk of IBD by 27%. Those administered 2 prescriptions were 55% more likely to develop IBD, and the numbers keep climbing with 5 or more prescriptions raising the risk to 236%. 

Can antibiotics cause a flare-up of ulcerative colitis? 

Antibiotics can cause UC flare-ups in some cases. 

Your doctor may prescribe a course to treat or prevent an inflection related to UC, but if the prescription is for an unrelated infection, make sure to alert your gastroenterologist so they know which antibiotics you’re taking and can help manage any symptoms that come up. 

Antibiotics to avoid when you have Crohn’s disease 

If you have Crohn’s disease, your doctor may prescribe antibiotics for abscesses and fistulas. The most common prescriptions for these complications are metronidazole and ciprofloxacin, which both have side effects to watch out for.  

  • Ciprofloxacin can lead to light sensitivity, tendonitis, tendon tears, oral thrush, QT prolongation (a heart rhythm disorder)
  • Metronidazole can cause GI issues, nausea, appetite loss, nerve damage 
  • Rifaximin side effects are rare but may involve joint pain and muscle tension 
  • Vancomycin can cause itching and redness in the upper body, neck, and face.

Pseudomembranous colitis 

In some cases, the eradication of healthy gut bacteria from antibiotics can lead to a condition called Pseudomembranous colitis (PC). This refers to an overgrowth of a bacteria called Clostridioides difficile in the lining of the large intestine. The overgrowth releases toxins that attack the intestinal lining and cause inflammation, swelling, and sometimes bleeding in the lining of the colon. It is a common cause of diarrhea after antibiotic use. 

Causes of Pseudomembranous colitis 

An overgrowth of C. difficile is directly caused by the loss of healthy bacteria from antibiotic use. The antibiotics with the highest risk factor are: 

  • Ampicillin
  • Clindamycin
  • Fluoroquinolones
  • Cephalosporins
  • Penicillin

Risk Factors of Pseudomembranous colitis 

Pseudomembranous colitis is uncommon in children, and rare in infants. The condition develops mostly in hospitalized patients, as healthcare providers can easily pass the bacteria from patient to patient. That said, a growing number of people outside of hospitals are developing Pseudomembranous colitis after taking antibiotics. 

Risk Factors: 

  • Older age (residents in nursing homes)
  • Long stays in a hospital 
  • Antibiotic use 
  • Recent surgery
  • History of pseudomembranous colitis
  • History of Crohn’s disease or ulcerative colitis 
  • Use of medicine that weakens the immune system 

Symptoms of Pseudomembranous colitis

  • Watery diarrhea (sometimes bloody) 
  • Abdominal cramps, pain, tenderness 
  • Fever
  • Pus or mucus in stool 
  • Nausea 
  • Dehydration
  • Loss of appetite 

When to go to the emergency room: 

  • Rapid heartbeat 
  • Abdominal tenderness 
  • Severe bloating, distention, and pain

How do I repair my gut after antibiotics? 

Research shows that it is possible to reset the microbiome after antibiotic treatment, although it may take around 3-6 months for healthy gut bacteria to return to completely normal levels.

1. Fermented Food 

Work with your dietician to find prebiotics and fermented food that will provide beneficial bacterial species. Studies show that those who eat yogurt and fermented milk have higher amounts of beneficial bacteria and lower levels of pathogenic bacteria like Enterobacteria and Bilophila wadsworthia. Kimchi and fermented soybean milk can also promote healthy bacteria in the gut. 

2. Stress Relief 

Research has illuminated the intricate connection between our brain, mood, and gut health via the gut-brain axis, a bidirectional line of communication that impacts our entire system, including the nervous system and immune function. Not only does poor gut health cause stress and mood imbalances, but stress and poor sleep can also have a damaging effect on the gut microbiome. 

There’s no better time to integrate stress relief tools into your daily routine. In fact, some tools will have a direct positive impact on your bacterial diversity, especially spending time in nature, gardening (there’s a plethora of beneficial bacteria in the soil), and cuddling pets. Yoga, meditation, mindfulness, and breathing techniques have also been found to improve stress levels. And, according to the latest research, simply listening to music you love has a calming effect on the mind and body. 

Many also use herbal remedies with adaptogens to help manage stress and the damage from chronic stress. 

3. Rest to Digest 

To support your gut after a course of antibiotics, make an effort to get good quality sleep

The gut microbiome is closely linked to our circadian rhythm, so it helps to give your gut an 8-10 hour window to process food while you rest. After dinner, wait until breakfast to eat again. This fast will help reduce inflammation, which in turn will protect you from further gut bacteria imbalances. 

4. Eat Clean 

To help your microbiome bounce back, it will help to reduce or avoid pro-inflammatory foods. 

Foods to Limit: 

  • Ultra-processed foods 
  • Red or processed meat 
  • Refines carbohydrates  
  • Sodas and ‘energy’ drinks 
  • Sugar and high-fructose corn syrup 
  • Artificial trans fats 
  • Alcohol

Try to cook as much as possible at home, and always go for the least processed and preserved options. Our guts love a variety of fresh food, so work with your dietician to increase a wider range of gut-healthy foods that will work for your condition. 

Medications and other UC Triggers

Apart from antibiotics, there are some other medications that should be used with care, or altogether avoided, when managing UC. 

Nonsteroidal anti-inflammatory drugs (NSAIDs) can cause flare-ups, so it’s best to avoid ibuprofen and naproxen, which can make bleeding worse.  

As for medications commonly used to treat UC itself, many have side effects so it’s worth knowing as much information as possible and discussing with your healthcare team.  






This blog is not intended to provide diagnosis, treatment, or medical advice. The content provided is for informational purposes only. Please consult with a physician or healthcare professional regarding any medical or health-related diagnosis or treatment options. The claims made regarding specific products in this blog are not approved to diagnose, treat, cure or prevent disease.


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