
Antibiotics save lives. However, their presence can disrupt the intricately balanced gut microbiome, the rich and diverse ecosystem of microbial populations that thrive in the gastrointestinal tract and are crucial to good health. This is one reason we must be more circumspect about antibiotic use and learn how to restore gut health after antibiotics.
The Gut Microbiome
The gut microbiome refers to the entire microbial ecosystem in the gastrointestinal (GI) tract, commonly known as the ‘gut’. This ecosystem is the combination of microbial populations (i.e., microbiota), their environment (i.e., the gut and all its components), the interactions among these microorganisms and their environment, and the processes that define and determine these interactions.
Trillions of microscopic organisms make up the gut microbiota. These include:
- Bacteria
- Fungi
- Viruses
- Parasites
These microorganisms exist in stasis or equilibrium. This balance in your microbial gut ecosystem benefits your health, particularly that of your digestive, immune, and nervous systems, by:
- Helping break down complex carbohydrates and dietary fibres
- Producing enzymes the body needs to make or synthesise certain vitamins, including vitamin K and some B complex vitamins (e.g., B1, B9, B12)
- Metabolising bile in your small intestines
- Producing short-chain fatty acids that:
- Help lower blood cholesterol: reducing heart disease risk
- Contribute to keeping the gut barrier intact: preventing harmful microscopic organisms and toxins from entering the bloodstream
- Regulate gut inflammation: preventing hyper-reactivity that can lead to the development of autoimmune disease
- Positively affect mood, sleep and other nervous system functions, especially since some bacteria activate the production of certain neurotransmitters, such as serotonin
- Training your immune system so it can become better at distinguishing helpful from unhelpful microorganisms
- Competing for resources with potentially harmful microorganisms, which helps keep the pathogenic microbes’ population under control
What Antibiotics Do to the Gut Microbiome
Antibiotics kill bacteria, stop them from multiplying, or prevent them from growing. They do this through various means, such as destroying their cell walls, preventing them from synthesising certain proteins, or interfering with their DNA replication and repair functions.
Unfortunately, broad-spectrum antibiotics do not discriminate between harmful and beneficial gut bacteria. They target all bacteria, including the helpful ones, and this adversely affects gut health. Specifically, they:
- eradicate or appreciably reduce the bacterial population in the GI tract; and
- change the composition of whatever bacteria remain, since some bacteria are more susceptible to antibiotics than others.
This can lead to dysbiosis or gut microbiota imbalance, which, in turn, impairs the gut microbiome’s ability to perform its health regulation functions. Thus, you may experience stomach issues after taking antibiotics.
What’s alarming is that the frequent (and early) use of antibiotics can lead to long-term microbiota imbalance. Your gut microbiome’s ability to support your digestive, immune and nervous system health and functions is significantly diminished in this case.
Thus, it’s crucial that you learn how to heal your gut after taking antibiotics, specifically how to replenish good bacteria after antibiotic use.
How to Replenish Good Bacteria After Taking Antibiotics
You must cure the imbalance of microorganisms in your gut, and you do this by restoring your gut’s population of good bacteria. The following can help you accomplish this:
1. Take probiotic supplements.
A blend of probiotic strains during and after your antibiotic course may help. The best probiotics after antibiotic use include:
- Probiotic bacteria: Lactobacillus and Bifidobacterium
- Probiotic yeast: Saccharomyces boulardii
- Soil-based probiotics: Bacillus clausii
Probiotics may help resolve digestive issues after antibiotic intake, particularly antibiotic-associated diarrhoea.
2. Eat more whole and plant-based foods.
Eat fibre-rich foods to heal the gut after antibiotics, as these help good bacteria thrive. Your options include whole grains, leafy greens, nuts, and fruits. Eat a variety of fibre-rich foods to improve diversity in gut microbiota.
Note: If you are prone to bloating or gas, consult your doctor so they can recommend gut-bacteria-friendly foods (e.g., low-fructose fruits) that will cause less gas.
3. Eat more fermented foods.
Add fermented foods to your diet. These have live microbes that can improve the diversity of your gut microbiota, and they may be the best probiotics to take after antibiotics.
Examples of fermented foods include:
- Pickles
- Sauerkraut
- Kimchi
- Kefir
- Yoghurt
- Miso
- Tempeh
- Natoh
- Kombucha
4. Exercise.
Understanding how to rebuild the gut after taking antibiotics requires looking beyond food and probiotics. In particular, exercise can enhance the diversity of microbial species in the gut.
5. Get enough sleep.
Adequate sleep (i.e., between seven and nine hours) also contributes to gut health, as partial sleep deprivation can disrupt the gut microbiome.
How to Heal the Gut After Taking Antibiotics
To ensure gut recovery after a course of antibiotics, support your gut’s health by taking GcMAF supplements.
What is GcMAF? GcMAF stands for Gc protein-derived macrophage-activating factor. Macrophage-activating factors are white blood cells that naturally occur in the body. GcMAF is simply manufactured MAF, and like the naturally occurring MAF, GcMAF benefits the body by activating or triggering the action of macrophages.
What are macrophages?
Macrophages are part of the body’s immune system. They engulf and digest microbes, cell debris, dead cells, and foreign contaminants, helping to prevent infections and inflammation and promoting tissue repair. They also display fragments of antigens on their surface to activate T-cells and trigger subsequent immune system responses.
Macrophages in the gut also have a very specific role: to maintain the integrity of the gut lining. They interact with epithelial cells to produce proteins and mucus that strengthen the gut barrier and prevent leakage. Additionally, they help repair and regenerate damaged gut tissue.
How does GcMAF support gut health?
GcMAF supplements ensure you have sufficient levels of macrophage-activating factors in your body. MAF activates macrophages and regulates their activity. Therefore, with adequate MAF levels, your macrophages can reinforce your gut lining, which is crucial to maintaining the gut barrier, and stimulate the immune system response that will trigger gut wound healing and tissue regeneration.
How Long Does It Take to Repopulate the Gut With Good Bacteria
The balanced composition of your gut microbiota can be restored in a few weeks to a few months. In some cases, the process can take much longer, from several months to years.
The more severe the disruption, the longer it may take for the gut to recover after antibiotic use. Prolonged antibiotic use or multiple courses of antibiotic treatment can lead to longer gut-recovery timeframes.
How to Rebuild the Gut Microbiome After Taking Antibiotics
A depleted population of beneficial bacteria is a reason some people experience stomach problems after antibiotic intake. Broad-spectrum antibiotics, in particular, do not discriminate between unhelpful and helpful bacteria, so they kill both harmful and beneficial bacteria in the gut.
How do you fix the gut after taking antibiotics and restore the healthy, balanced and diverse gut microbiota? Take probiotics, eat fermented foods, consume whole and plant-based foods, exercise, and get enough sleep. Maintaining your gut’s healthy function is equally important to restoring the gut microbiome, so support your efforts to replenish your good bacteria population with GcMAF supplements.
Buy GcMAF supplements. Choose from GcMAF capsules, GcMAF powder, and GcMAf lollies. We deliver worldwide.
Author

Dr Toshio Inui
Doctor, expert in internal medicine and worldwide authority on GcMAF treatments, Dr. Inui is the visiting professor at Kagoshima University. He has dedicated his career to developing innovative treatments using MAF, and has 22 research works and 266 citations into macrophage activating factors.