Reviving Gut Health: How to Recover After Prolonged Antibiotic Treatments

The scientific and healthcare community is becoming increasingly aware of the importance of gut health. In many ways, the gut is a crossroad to our overall health. There is scientific proof of connections between gut health and the brain, lungs, and thyroid. These are usually called axes, such as the gut-brain axis.

The balance and abundance of different gut-resident microbes partly determine gut health. Antibiotics play an essential role in healthcare by providing a first line of defense against bacterial infections. However, no treatment is perfect.

Prolonged use of antibiotics can lead to drug-resistant bacterial strains and also leave the body vulnerable to specific pathogens. Antibiotics disrupt the balance of microbes, often depleting beneficial bacteria and pathogens. Candida is a genus of fungi that is an opportunistic pathogen, living in the body under normal conditions and causing disease when it has the opportunity, such as when we take a long course of antibiotics.

Prolonged courses of antibiotics are used to treat various diseases, some mild, some very severe. These conditions include:

Chronic infections

    • Chronic sinusitis causes long-term inflammation of the sinuses, leading to congestion, pain, and difficulty breathing. It is commonly treated with doxycycline.
    • Chronic urinary tract infections cause persistent or recurrent pain and discomfort in the urinary tract, often requiring prolonged treatment. Nitrofurantoin is commonly used to treat them.
    • Chronic bronchitis is characterized by long-term bronchial tube inflammation, leading to persistent cough and mucus production. It is commonly treated with clarithromycin.

Specific medical conditions

    • Cystic fibrosis is a genetic disorder that causes severe damage to the lungs, digestive system, and other organs due to thick, sticky mucus buildup. Patients commonly experience bacterial infections of the lungs, which are commonly treated with tobramycin.
    • Lyme disease is an infectious disease caused by the Borrelia bacteria. It is transmitted through tick bites and leads to symptoms like fever, rash, and joint pain. It is commonly treated with doxycycline.
    • Autoimmune diseases occur when the immune system mistakenly attacks the body’s own tissues, sometimes triggered or worsened by bacterial infections. These can be treated with amoxicillin.

Recurrent bacterial infections

    • Skin infections are often caused by bacteria such as Staphylococcus aureus, which can lead to persistent redness, swelling, and pain, requiring treatment with antibiotics like cephalexin.
    • Gastrointestinal infections are often caused by bacteria such as Salmonella, C. difficile, or E. coli and lead to ongoing symptoms like diarrhea, abdominal pain, and nausea. They typically require antibiotic treatments like Ciprofloxacin.

Dental issues

    • Chronic periodontitis is a persistent inflammatory disease affecting the gums and bones supporting the teeth. It often requires antibiotic treatments like amoxicillin to manage the bacterial infection.
    • Bacteria often cause dental infections, which lead to persistent pain, swelling, and tooth damage and typically necessitate antibiotic treatments like penicillin.

While disruption of gut microbiome balance after or during a course of antibiotics can have significant implications for our overall well-being, there are solutions for recovery.

These solutions include treatment or supplementation to reduce the abundance of harmful microbes in the digestive system and replenish the levels of good microbes.

This article will discuss how damaging antibiotics can be, the importance of recovery, and strategies for regaining gut balance and overall health.

The Impact of Antibiotics on Gut Health

Antibiotics are important for treating many infections. However, prolonged usage can lead to poor gut health. Antibiotics are such an important tool against infection because they target a wide range of microbes without targeting human cells. However, they also target healthy microbes in addition to pathogens.

Beneficial bacteria in our gut are important for many reasons. These include aiding digestion, regulating the immune system, and suppressing the levels of harmful microbes. By taking prolonged courses of antibiotics, individuals can deplete the levels of beneficial bacteria in the gut and decrease the overall diversity of the microbiome.

Prolonged courses of antibiotics can have significant long-term impacts on gut health. Antibiotics lower gut microbiome diversity, which can take many months or even years to recover. As a result, pathogenic bacteria and fungi have an opportunity to overpopulate the gut and cause disease.

Furthermore, prolonged use of antibiotics creates an opportunity for pathogens to gradually develop resistance. Given the role of the gut microbiome in regulating the immune system, gut disruption naturally leads to immune dysfunction. This means increased opportunities for infection and the development of autoimmune diseases.

Disruption of the gut microbiome is also associated with metabolic disorders like diabetes and obesity. The gut-brain, gut-lung, and gut-thyroid axes are all disrupted by microbiome imbalances. Chronic inflammatory diseases such as inflammatory bowel disease and conditions like SIBO (Small Intestinal Bacterial Overgrowth) and SIFO (Small Intestinal Fungal Overgrowth) can be brought on by gut microbiome dysfunction.

Thus, antibiotics can have wide-reaching and damaging effects on overall health by disrupting the gut microbiome.

Some recent research suggests that microbial imbalance in the gut may play a role in a variety of mental health disorders, including anxiety and schizophrenia. This means that antibiotics can also impact mental health.

It may sound counterintuitive, but some microbes, like Candida and the bacteria C. difficile, can gain an advantage when we take antibiotics.

This occurs through multiple mechanisms, such as reducing competition for nutrients by depleting other microbes and promoting drug-resistant strains.

To be clear, antibiotics are essential for treating various diseases, and it is vital to take them when required. However, understanding their impact on the body is also important.

Understanding the Need for Recovery

The consequences of not maintaining gut balance can be disastrous. Candida overgrowth, in particular, can lead to the development of invasive candidiasis, which can be fatal. Thus, it is essential to be aware of factors like prolonged courses of antibiotics that can disrupt the gut and adopt preventative measures. Here, we highlight stories of our clients who developed issues likely due to a prolonged course of antibiotics.

“After several rounds of antibiotics over the years, and then two rounds back to back four years ago, I would develop rash, itching and sometimes hives when eating certain foods containing sugar and yeast. It was very annoying and restricted what I could eat/drink.“

Steve B. –

“I got candida and mold toxin from previous Lyme disease treatment, which involves years of antibiotic use. I suffered from symptoms of intense brain fog, anxiety, and mental fatigue for 19 years. This had a huge effect on learning and relationships/friendships since these symptoms consumed a huge amount of energy.”

Chris E. –

“I had massive antibiotic use from chronic urinary tract infections (UTIs). I don’t even know how long I was suffering from symptoms. They just became an everyday part of my life. I experienced fatigue, lethargy, weight gain, UTIs, vaginal yeast infections, bloating, digestive issues, skin rashes, or random itching without rashes.”

Jeanne D. –

As these stories indicate, antibiotics can have various adverse effects on different parts of the body. Let’s examine the impact of gut microbiome disruption on four key areas.

    • Digestive function: The gut microbiome significantly impacts digestion by helping to break down complex carbohydrates, fibers, and proteins that the body cannot digest alone. It produces enzymes and short-chain fatty acids, aiding nutrient absorption and energy production. A balanced microbiome ensures efficient digestion and prevents issues like bloating, gas, and constipation, while imbalances can disrupt digestive processes. An imbalanced microbiome can also cause food cravings and nutritional deficiencies in some cases.
    • Brain health: The gut microbiome also influences the brain and mental health. It produces neurotransmitters like serotonin and dopamine, which affect mood and cognition. The connection between the microbiome and the brain, known as the gut-brain axis, impacts stress response and emotional regulation. Imbalances in the microbiome are linked to anxiety, depression, and other mental health disorders like schizophrenia.
    • Lung health: Lung health is linked to the gut microbiome through the gut-lung axis. Microbial by-products, like short-chain fatty acids, influence immune responses and reduce inflammation in the lungs. A balanced microbiome supports respiratory health by enhancing immune defenses against infections and allergens. Conversely, imbalances in the gut microbiome can worsen conditions like asthma and chronic respiratory infections.
    • Skin health: The gut microbiome plays a crucial role in skin health. The gut-skin axis influences skin barrier function, hydration, and inflammation. Beneficial microbes produce metabolites that support skin integrity and immune response. Imbalances in the microbiome can lead to skin conditions like acne, eczema, and psoriasis.

Steps to Revive Gut Health

Restoring gut health can be a long and arduous process, depending on the nature of the imbalance and the patient’s commitment to the recovery program.

It’s important to understand from the outset that recovery from gut imbalances does not progress linearly. There will be times when you feel fantastic, like you have already recovered, and other times when you feel sick and like you have made no progress. Sticking to a recovery plan and returning to it quickly if you slip up is essential.

Here are some critical steps to take toward recovering your gut health.

1. Discovering the extent of the damage caused by antibiotics

Getting to grips with the problem is the first step toward solving it. There are important factors to consider when determining the extent of the damage caused by antibiotics. These include:

    • Antibiotic type: If you have been prescribed a broad antibiotic, the good bacteria in your system are more likely to have been depleted.
    • Length of treatment: The longer the course of antibiotic treatment, the more dysregulated your gut microbiome is likely to be.
    • Age: People of different ages are more or less susceptible to gut disruption. Those younger than 5 and those over 65 are more susceptible.

Comprehensive stool analysis can provide a direct report of what species of microbes are living in your gut. These analyses can tell you about the diversity of your gut microbiome and identify problematic bugs, like Candida, that may be causing issues.

2. Dietary adjustments

The gut microbiome adapts to the food we ingest. Therefore, improving our diet to optimize the microbiome is an essential first step. Diets rich in probiotics and prebiotics like fiber are important for restoring balance after a course of antibiotics. Probiotics are beneficial bacteria that help to promote a balanced gut and restore overall health. They can be found abundantly in fermented foods like yogurt. Prebiotics are foods for probiotics that help them to thrive and expand in number.

Conversely, foods that promote the growth of unwanted microbes and are low in nutritional value should be avoided, especially during recovery. It’s important to start slowly when integrating fermented foods, as taking too much too soon can lead to digestive discomfort. Here is a list of foods to eat and avoid during recovery.

High in probiotics:

    • Yogurt (greek sour)
    • Kefir
    • Kimchi
    • Kombucha
    • Sauerkraut (unpasteurized)
    • Other fermented foods

High in prebiotics:

    • Apples
    • Jerusalem Artichoke
    • Almonds (raw, fresh)
    • Garlic
    • Bananas (slightly green)
    • Chicory root
    • Whole oats
    • Onions

Foods to Avoid:

    • High sugar foods
    • Alcohol
    • Excessive caffeine
    • Highly processed foods
    • Potato chips
    • Fizzy drinks (beer, soda)

Some of our clients have found that the meat, eggs, vegetables, and yogurt (MEVY) diet, which avoids sugars and starchy vegetables, has been beneficial in restoring their gut balance.

Here is a complete shopping list to help you deal with Candida specifically*.

3. Probiotic Supplements and Prebiotics

Probiotics are beneficial gut bacteria and can be taken directly into the gut through supplementation. Probiotics help to support immune and digestive function and are important for keeping levels of unhealthy microbes at bay.

Many supplements provide probiotics, but often just a single species. CanXida Restore (Formula RST) contains six probiotic species and seven digestive enzymes, which help to repopulate the gut with healthy bacteria and restore digestive function. Beneficial probiotic strains include:

    • acidophilus
    • casei
    • plantarum
    • rhamnosus
    • longum
    • bifidum

Good sources of prebiotics are described in the section above.

4. Hydration and Detoxification

While we have recommended many different types of food to help restore gut function and balance, a core part of recovery is consuming enough water. Water is essential for the digestive process and directly supports healthy bacteria and the maintenance of the gut lining. Water can also help reduce constipation and inflammation in the gut. Staying well hydrated supports your immune system and the healthy bacteria you need to restore gut balance.

5. Naturopathic Approaches

Supplementation with natural products can play a huge role in helping you recover from prolonged antibiotic use. Many individual plant extracts have been scientifically shown to reduce the abundance of unhealthy microbes in the digestive tract. Complementing these extracts with probiotics, multivitamins, and mineral supplements is a solid step toward improving gut balance.

CanXida provides four supplements that help to achieve each of these goals.

    • CanXida Remove (Formula RMV) – All-natural supplement including plant extracts with scientifically proven activity against harmful bacteria, fungi, and parasites. Key ingredients include garlic, clove, and neem extracts.
    • CanXida Restore (Formula RST) – Formulation of six probiotic strains and seven digestive enzymes. These strains have been shown to help combat harmful microbes like Candida while the enzyme helps restore digestive function.
    • CanXida Rebuild (Formula RBD) – This is a comprehensive multivitamin and mineral supplement that helps to cover nutritional deficiencies and supports metabolism and the immune system.
    • CanXida ReChange (Formula RCH) – This powder formulation contains a wide range of premium ingredients that help support gut, liver, digestive, and brain health. It also includes clean sources of energy like Macha tea powder and medium-chain triglycerides, making it ideal for people with an active lifestyle who are recovering from antibiotic use.

Other naturopathic practices believed to restore gut balance include acupuncture, aromatherapy, and massage therapy.

6. Lifestyle changes

Stress management is crucial for restoring gut balance. However, this can be incredibly challenging during recovery because gut imbalance can cause us severe pain over a long period of time. Nonetheless, stress can significantly contribute to gut issues, so those in recovery must prioritize stress management.

Methods for dealing with stress include meditation and mindfulness. Consider seeking help from a mental healthcare professional to discuss strategies for stress management.

Sleep is essential for recovery, especially in helping to support the immune system. Again, it can be challenging to get enough sleep when we experience painful symptoms for prolonged periods. However, it’s important to prioritize sleep as a pathway towards recovery. Being active during the day, exercising, and reducing alcohol and caffeine intake can improve sleep duration and quality.

Special Considerations

Due to chronic infections and diminished immune systems, several specific groups of people may have a particularly difficult time restoring gut balance after long courses of antibiotics. Let’s examine two of these groups in more detail and provide specific guidance for attaining and maintaining gut balance.

1. Individuals with chronic and recurrent conditions

Individuals in this group are more likely to be prescribed long courses of antibiotics to address their issues. This can significantly disrupt gut balance and lead to the emergence of chronic yeast infections and overgrowth. However, many antibiotics may be required for continued healthcare. In these instances, individuals can focus on optimizing their diet and lifestyle to maintain a balanced gut.

    • Diet: Our diet is also the diet of our gut microbiome. Certain foods promote gut microbiome diversity while preventing the overgrowth of harmful microbes like Candida. Diet optimization can help people who must take antibiotics for a long time to maintain balance. See section 2 for a list of the best foods to eat.
    • Probiotics: These are beneficial bacteria that we can take directly into our bodies via supplementation. Many foods are also good sources of probiotics. CanXida Restore (Formula RST) is CanXida’s probiotic supplement that contains six powerful probiotic species and seven digestive enzymes to help restore balance to the gut.
    • Lifestyle adjustments: Stress and lack of sleep can affect gut health and microbiome balance. Removing unnecessary stress from your life and prioritizing high-quality sleep can help bolster your immune system and give you an edge in regaining gut balance.

2. Older adult patients

People over 65 can be at a higher risk of losing gut microbiome balance for several reasons, including a diminished immune system and a lack of a diverse and healthy diet. Taking a prolonged course of antibiotics could lead to a faster or more drastic loss of gut microbiome balance. Here are some tips that can help older adults maintain or regain balance.

    • Supplements: Older adults can often have specific nutrient deficiencies. This can be particularly true in care home settings or hospitals that don’t provide patients with a balanced diet. Furthermore, some older adults have difficulties swallowing, making it difficult to get all of the nutrients they need through food, even with a good diet. Thus, supplementation with a comprehensive multivitamin like CanXida Rebuild (Formula RBD) can help cover nutritional gaps important for maintaining immune function and gut balance.
    • Staying active: Older adults may not be able to exercise as much as they used to. However, exercising is vital to a healthy lifestyle and can help with gut issues. Regular exercise is associated with higher gut microbiome diversity and can help with digestive flow, which can be disrupted in older adults. Regular exercise reduces stress and can be a great way to socialize, enhancing the anti-stress effect. Lastly, exercise can help with weight management and the prevention of diseases like diabetes, which puts individuals at higher risk of gut problems.

Now, let’s examine some stories from our clients who developed problems after taking antibiotics. We’ve also provided a key lesson learned from each testimonial.

Jeanne’s Story

Jeanne D used antibiotics due to chronic urinary tract infections (UTIs). She experienced fatigue, lethargy, weight gain, more UTIs, vaginal yeast infections, bloating, digestive issues, skin rashes, and random itching without rashes.

About twenty years ago, Jeanne D started seeing a Naturopath mainly for help with the UTIs. Approximately seven years ago, she discovered information about Candida and realized that all of her random symptoms were connected. Her Naturopath provided her with Candidase, but it did not bring real relief. She started a candida diet, which helped quite a bit, but the results went away when she stopped the diet. Jeanne D saw regular improvement with CanXida products for 5-6 months. In retrospect, she feels that she should have stayed on the diet longer.

The Lesson: People commonly experience yeast overgrowths after taking long courses of antibiotics to treat conditions like UTIs. CanXida supplementation and an appropriate diet can help relieve symptoms, but the individual needs to remain committed to recovery and stick to the diet.

Kati’s Story:

Kati experienced fatigue and extreme sugar cravings, making food unsatisfying and leaving her feeling perpetually hungry. She viewed this as a lifelong battle, having grown up with unhealthy food, which made it challenging to eat healthily as an adult. Additionally, she suffered from perioral dermatitis, which she believed was a form of fungal infection because she could control it by managing her Candida levels. Before discovering this, she faced a difficult time as doctors recommended long-term antibiotics, which only worsened her condition. Kati tried cleanses with green smoothies or a raw food diet, which worked well but was difficult to maintain long-term.

Kati used CanXida Remove (Formula RMV) and has been using it off and on for the past year whenever she feels it is necessary. Candida was such a problem for Kati that she felt it took an army of products to find relief, so she was happy to find CanXida. She liked that it was a convenient pill that could be taken with or without food. She believed she would probably never be free of the struggle, but she found her mood was elevated after using CanXida. She has more energy and ambition and doesn’t crave sugar, which she really appreciates.

The Lesson: Courses on antibiotics can worsen fungal infection issues. Everyone has different needs when it comes to dealing with an imbalanced gut. Some do fine with just a diet, while others benefit enormously from supplementations such as those provided by CanXida.

Shelby’s Story:

Shelby’s yeast infections began occurring monthly as a teenager after using birth control pills and antibiotics. This led to a larger parasite infection, resulting in food intolerance and chronic constipation. She suffered for thirty-six years, dealing with mineral deficiencies, weakness, fatigue, anxiety, and adrenal fatigue. Shelby followed a gluten and dairy-free diet, consumed anti-parasite foods like garlic and pumpkin seeds, and took anti-parasite essential oils like oregano and green black walnut hull. She also used coffee enemas daily for the past six years. Although she reduced her parasite load, she had not cured it.

Shelby found an ad online and then watched a YouTube video about CanXida. Everything in the video resonated with her. She began using CanXida Remove (RMV) and felt some benefit after the first week. After five weeks of using CanXida, Shelby started to feel some improvement. She experienced less sensitivity to dairy and wheat, reduced gas and bloating, and noticed less candida in her stool. Shelby recommends this product, noting that no other products can help someone like her. She believes that with lifestyle and diet changes, CanXida can be very beneficial.

The Lesson: Individuals can suffer for many years without finding a solution to their problems. Some treatments can help with symptoms but do not completely clear up the underlying issue. A combined approach of supplementation, diet, and lifestyle changes can help restore digestive function after experiencing problems caused by antibiotics.


Maintaining a healthy gut microbiome is essential for overall health, and understanding the impact of antibiotics is crucial.

The gut microbiome is important for many bodily functions and tissues, including digestion, immune response, lung health, and mental health. Antibiotics are important for treating infections but are known to disrupt gut microbiome balance.

Prolonged antibiotic use can significantly reduce beneficial bacteria, paving the way for harmful microbes like Candida to thrive. Imbalances have far-reaching consequences and exacerbate chronic conditions.

Recovering from the adverse effects of prolonged antibiotic use involves a multifaceted approach. Dietary adjustments are a cornerstone of this recovery process. Incorporating probiotics and prebiotics into our diet can help restore the diversity and abundance of beneficial gut bacteria.

Probiotics, found in fermented foods like yogurt, kefir, and sauerkraut, introduce beneficial bacteria directly into the gut. Prebiotics, found in fiber-rich foods like garlic, onions, and whole oats, serve as food for these beneficial bacteria, helping them to thrive.

Alongside dietary changes, staying hydrated, managing stress, and ensuring adequate sleep are crucial for gut health. Hydration aids digestion, while stress management and quality sleep support overall immune function.

Naturopathic approaches, such as supplementation with targeted probiotics and plant extracts, can provide additional support in rebuilding the gut microbiome. Supplements like CanXida Restore, which combines multiple probiotic strains with digestive enzymes, can be particularly effective in combating harmful microbes and promoting gut health.

Moreover, lifestyle changes such as regular physical activity and stress-reducing practices like mindfulness and meditation can further enhance recovery. By understanding the extent of antibiotic-induced damage and implementing comprehensive recovery strategies, individuals can significantly improve their gut health and, consequently, their overall well-being.

Consult our product page for more information on CanXida products that can help gut recovery after prolonged courses of antibiotics. For educational support on the impact of antibiotics, visit our YouTube channel or check out these specific videos on antibiotics.

*These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure or prevent any disease.