Antibiotic Misuse: How It Affects Your Gut and Brain

By: Caroline Weed ^(a), Quinn Galbraith, MS ^(a), Matthew Weed, MD. 

^(a) Brigham Young University, Provo, UT, USA.

Medically reviewed by: O. Olatunbosun, MBBS, M.Sc. Microbiology and Parasitology.

September 17, 2026

 

Highlights

• Antibiotics save lives, but it is important to know how and when to use them, as misuse can have health-threatening effects on your body.

• Constant misuse of antibiotics can cause antibiotic resistance (AMR), making the antibiotic less effective in the future.

• The gut microbiome: When used incorrectly, antibiotics wipe out the delicate community of helpful bacteria in your body. Digestion and immunity are negatively impacted when this community is destroyed.

• Gut-brain axis: The gut microbiome works together with the brain to regulate mood and stress levels. When antibiotic misuse disrupts the gut, signals to the brain are disrupted, causing changes in mood and increased stress.

• Protect the power of medicine: Only take antibiotics that have been prescribed to you by a qualified healthcare professional, and always take them for the full dose given.

 

Introduction

You begin to feel feverish and extremely tired one day while working. As you return home, you stop by the local drug shop and pick up an antibiotic to treat your symptoms. After taking the medication for a few days, you begin to feel better and stop taking it. You then notice your sister with similar symptoms, so you offer her your leftover pills, assuming they will work just as well for her.

This is an extremely common practice in some communities around the world. Many people take an antibiotic as soon as they feel a fever or another symptom of illness. Because there are not often many nearby healthcare clinics, it is common to purchase antibiotics oneself at a pharmacy or market, to stop usage as soon as symptoms decline, or to save or share leftover pills (1). 

However, antibiotics do not function in the same way as a painkiller. They are much more powerful and are designed specifically to fight and kill harmful bacteria. When antibiotics are used in ways besides those for which they were created, there are many consequences, both noticeable and under-the-surface, that occur in the body. The more common this practice becomes, the less effective these crucial medications are to the pathogens they are supposed to kill.

This article will discuss what qualifies as antibiotic misuse, how antibiotic resistance occurs and why it is so pressing of an issue, as well as the unintended effect of antibiotic misuse on important systems and processes in your body.

 

How Antibiotic Misuse Affects Your Gut

What Are Antibiotics?

Antibiotics are medicines designed to target and kill or stop the spread of bacteria. They are manufactured to be specifically prescribed by medical professionals and are taken for a specified amount of time. Antibiotics are useless on colds, the flu, or other viral infections. Malaria is caused by a parasite, not bacteria, so taking antibiotics that haven’t been prescribed to you will not cure you.

When antibiotics are taken for a non-bacterial illness, or are stopped before the prescribed amount of time, the harmful bacteria do not die. Rather, they adapt and mutate in order to overcome the effects of the antibiotic and survive. This adaptation of bacteria is called antimicrobial resistance (AMR), and it is extremely dangerous (2).

Why Antibiotic Misuse Matters in Africa

Antimicrobial resistance has become a pressing issue throughout the world and notably in Sub-Saharan Africa, where there are low numbers of physicians and clinics in a majority of areas, especially in rural communities.

In these areas, physicians often prescribe antibiotics prematurely out of caution and because healthcare workers are so thinly spread (3). Additionally, antibiotics are often available in informal settings, such as in pharmacies and drug shops.

In many cases, the name of the drug is not even known, and they can be sold based on description to anyone, even children sent by their parents (S. Mugaya, BSN, personal communication, 24 August 2026). Because these medications are so easily accessible, they are often self-prescribed, shared, or stopped prematurely because symptoms have decreased (1).

This can cause significant difficulties for African families–

• Treatments become less effective: standard and affordable antibiotics no longer work against infections
• Higher mortality: infections and injuries that were previously treatable no longer have an effective cure and become life-threatening
• Wasted defense: when stopped prematurely, antibiotics only kill a portion of the pathogenic bacteria; the strongest bacteria survive and mutate into more advanced pathogens that are resistant to medication, and they spread through communities.
• Higher costs: because standard antibiotics no longer have an effect, families must look into secondary, more expensive treatment options (1).

 

What Is the Gut Microbiome?

The large intestine is home to about 38 trillion helpful bacteria and fungi (4), called the gut microbiome. It is a crucial part of the digestive tract and for effective bodily functioning. When healthy, the gut microbiome carries out a variety of essential functions (5):

• Digestion: breaks down complex starches and fibers that the intestine cannot otherwise digest
• Vitamin synthesis: essential vitamins for metabolic function and energy are synthesized
• Immune protection: shields from pathogens and blocks possible invasion into the bloodstream
• Barrier support: strengthens the inner lining of the intestines which prevents invasion of toxins into the body.

 

What Do Probiotics, Prebiotics, and Postbiotics Do?  

Good gut health is largely determined and maintained by three factors that work together– prebiotics, probiotics, and postbiotics (5).

• Probiotics: the bacteria and fungi that make up the gut microbiome. These healthy and helpful bacteria are found in many foods like porridge (such as uji), yogurt, kule naoto and other sour milks, and fermented roots (such as chikwangue).
• Prebiotics: the ‘fuel’ for probiotics– non-digestible carbohydrates and fibers that are found in fruits, vegetables, and grains. You are eating prebiotics when you eat things like plantains, cassava, beans, lentils, and whole grains.
• Postbiotics: When probiotics ‘feed’ on prebiotics, the results produced are enzymes, vitamins, and short-chain fatty acids. These are what build and support the stomach and intestinal lining and create barriers against harmful pathogens.

Eating foods high in both probiotics and prebiotics are helpful to the health of your gut microbiome and allow it to thrive. However, it’s important to note that eating these foods doesn’t replace seeing a healthcare professional for an illness or cure infections.

 

How Antibiotics Affect the Gut

Antibiotics are powerful, but they do not only kill the bacteria causing harm– they cannot tell the difference between pathogenic bacteria and helpful probiotics in your gut. Thus, an antibiotic goes in like a wildfire, destroying any bacteria it encounters.

When there is a large depletion and imbalance of protective microbes in your gut, it is called dysbiosis. This can cause problems both immediately and in the long term, such as:

• sudden stomach pain or diarrhea
• Unprotected and weak intestinal lining, making it easy for pathogens and infections such as C. diff to come in and flourish without any resistance (6).
• Most importantly: allowing antibiotic-resistant bacteria to thrive and grow without any roadblocks. Because there are no good bacteria to take space or food, they can easily multiply and overtake the gut microbiome (7).

A generally healthy body is resilient, and taking one round of antibiotics as prescribed is usually not a problem, because the body can tolerate dysbiosis for a short period of time until balance is restored. However, if antibiotics are taken repetitively or inappropriately, recovery can become extremely difficult, especially in areas with poor sanitation and nutrition (8).

The Gut-Brain Axis

The gut, in addition to providing key protection and support to the intestines and immune system, also plays a key role in brain function and in mental health regulation (9). The communication and relationship between the GI tract and the brain is referred to as the ‘gut-brain axis’. The gut and brain communicate in different methods, but are most notably and directly connected through the Vagus nerve– a long nerve running from the brain stem through the intestines. Chemical signals, electric impulses, and hormones are transferred across the Vagus nerve in order for the brain and gut to communicate.

The connection and communication between the gut and brain are commonly recognized in the signaling of satiety, or feeling full (9). There are signals sent to the brain from the stomach when eating that signal that the body does not need any more food. Knowledge on the communication between the gut and brain has expanded, however, and it is now understood that the gut-brain axis performs many other crucial functions in addition to satiety signaling.

When short-chain fatty acids are produced in the gut, these essential and helpful postbiotics stimulate certain cells in the intestine to produce serotonin– a hormone crucial to mood stabilization, happiness, and feelings of satisfaction and safety. Incredibly, over 90% of the body’s serotonin is produced in the gut (10). Following serotonin production, the gut sends calming signals to the amygdala and hypothalamus (the emotional control centers of the brain) through the Vagus nerve, which causes a lowering of baseline stress and anxiety levels (9).

 

How Antibiotic Misuse Can Affect the Brain

Because the gut plays such a big role in serotonin and other mood-regulating chemicals, dysbiosis of the gut through antibiotic misuse can also cause a shift in the brain chemistry.

When unnecessary antibiotics wipe out important bacteria in the gut, the amount of serotonin produced drops significantly. Because of the sudden drop in this ‘happiness hormone’, a stress loop is triggered in the brain in response. The body becomes flooded with a different hormone: cortisol, often called the ‘stress hormone’.

An excess of cortisol can have significant effects on the body: it acts like an acid, weakening and destroying the intestinal lining, wipes out even more probiotic bacteria, and allows for more harmful bacteria to enter and overtake the gut. The harmful bacteria then send signals of distress up the Vagus nerve from the gut, causing heightened anxiety and sadness, and triggering the release of even more cortisol (9).

 

Clearing Misconceptions about Mental Health

Mental health is an issue that is still generally misunderstood in a large number of communities in Africa. Many people see mental health issues such as anxiety or depression as diseases, or as supernatural consequences for one’s actions. This, however, is not true.

Mental health problems are illnesses that develop in the brain due to situations, genetics, or internal bodily factors; they need care and treatment, just as with malaria, the flu, or a broken bone.

Mental health problems are generally recognized when someone starts to show psychotic or manic behavior, but mental illnesses are often present long before this happens, and there are treatments and help that can aid in recovery.

People with mental illness need care and assistance from suitable medical facilities, as well as the support of their families and communities in order to heal (S. Mugaya, BSN, personal communication, 24 August 2026).

It is important to note that taking antibiotics does not cause depression or anxiety on its own; however, extreme or unnecessary use of antibiotics disrupts the functioning of the gut-brain axis, wearing down the body and brain’s resilience, and can lead to higher levels of anxiety or depression (9, 10).

 

What Africans Can Do to Protect Themselves from Effects of Antibiotic Misuse

• Never take antibiotics that haven't been prescribed to you– Getting the correct antibiotic and taking the proper dosage are crucial to getting effective treatment. Do not buy antibiotics from markets, kiosks, or pharmacies unless you have been given a formal prescription from a qualified physician or healthcare worker.

• Finish your dose– If you have been prescribed antibiotics, check to know the duration of your dose, and make sure you follow exactly what it says. If you have a 7- day prescription, make sure you take your antibiotic for all 7 days in a row, even if you start to feel better earlier. The full dose is needed to kill all the harmful bacteria, and stopping early leaves the strongest bacteria to grow and mutate (2).

• Never share or reuse medication– If you have been prescribed medication, that is for you only, during the time that you are sick. When you have finished your prescription, do not keep any extra pills around or give them to a friend or neighbor. Even if their illness looks the same, it could be caused by a virus or malaria, making the antibiotic harmful instead of helpful.

• Ask questions to your provider– Ask your healthcare provider questions about your illness to make sure you know all you need to know; questions like ‘is my infection caused by a virus or bacteria?’ or ‘is this an antibiotic?’ can make a difference.

• Feed your gut microbiome– Eat locally available fiber-rich vegetables, beans, and grains, as well as fermented foods to help the bacteria in your gut recover, grow, and thrive (5).

• Do your part to stop the spread– Wash your hands with soap and water, and drink only water that you know is safe (boiled or treated). These simple actions can prevent infections from growing and spreading, keeping you and your loved ones healthy.

 

When to Seek Medical Help

Self-medicating with antibiotics when you feel sick is extremely dangerous. Seek help from a medical professional if you or a loved one have any of the following symptoms:

• A fever that does not go down with rest and/or hydration.
• Severe stomach pain or bloody diarrhea
• Signs of severe dehydration (sunken eyes, dry mouth, extreme thirst, or dark urine)
• Persistent or constant feelings of hopelessness, severe anxiety, or sadness that impact your ability to do daily work or responsibilities

Additionally, see a physician if you are experiencing worsening symptoms after taking an antibiotic.

 

Conclusion

Antibiotics are one of the most helpful and needed medications, and are sometimes the only available option against an otherwise powerful or deadly bacterial infection or illness. They have saved and continue to save millions of lives in Africa each year. But, misuse of such a powerful medication has disastrous results, and as this practice continues, the effectiveness of the drug will eventually become zero.

It is crucial to use antibiotics strictly in their intended way, not only to fight against deadly pathogens, but also to protect the delicate balance of our gut microbiome that strengthens our immunity and ability to fight disease, protects and enhances digestive barriers, and keeps our minds in a calm, happy, and balanced state.

Even though antibiotics are extremely powerful, they are not to be feared. When used correctly and by order of a qualified professional, they are life-saving medications. It is the knowledge of their purpose that will make a difference both now and in the future in our communities and throughout the world.

 

Frequently Asked Questions

Can antibiotics treat the common cold, malaria, or the flu?

No. Antibiotics are only for bacteria. Malaria is caused by a parasite, while cold and flus are caused by viruses. Using an antibiotic for these infections will not help you return to good health, they will only weaken your gut microbiome and create space for antibiotic-resistant bacteria, causing you to become more susceptible to bacterial infections.

Will antibiotics permanently damage my gut?

Use of an antibiotic for one course of sickness will cause temporary dysbiosis of your gut, but a healthy body can usually restore balance and replenish within a few weeks. It is in the case of persistently repeated misuse that permanent damage occurs.

Should I buy probiotic supplements after taking an antibiotic?

No, supplemental probiotics are usually not necessary. You can get sufficient probiotics for your gut when you eat fermented foods such as yogurt and fermented porridges, as well as foods high in fiber such as root vegetables or beans and grains.

Will misusing antibiotics cause depression?

No, antibiotic misuse will not instantly cause depression. However, because the gut plays such a large role in the production of serotonin and other hormones important to mood and temperament, repeated misuse can disrupt the balance of your gut microbiome and leave you more susceptible to increased feelings of anxiety or sadness.

What can I do now?

Stop buying antibiotics over-the-counter without a prescription from a qualified physician or nurse. Seek medical counsel before beginning use of one of these powerful medications.

Are people with mental illnesses a threat to society?

No, the vast majority of people with mental illnesses are not a threat to society. Stigmatizing mental health conditions as inherently dangerous prevents people from seeking the care and support they need. Instead, they should be assisted to seek treatment and support from the appropriate medical facilities. 

 

References:

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2. US Centers for Disease Control (CDC). Antibiotic use and Antimicrobial Resistance Facts. [Internet]. 22 April 2024. [Accessed 3 August 2026]. Available from here.

3. Melariri H, Campbell P, Du Randt R, Truter I, Zulu S, Wiehahn BR, Ntunja A, Hutton-Willemse M, Ntlokonkulu Z, Mzimela N, Oyedele O, Melariri P. Knowledge, attitudes and practices on antimicrobial resistance among healthcare workers in sub-Saharan Africa: a systematic review and meta-analysis. Ther Adv Infect Dis. 2026 May 6;13:20499361251410677. doi: 10.1177/20499361251410677. Available from here.

4. Sender R, Fuchs S, Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLOS Biology. 19 August 2016. doi: 10.1371/journal.pbio.1002533. Available from here.

5. Ji J, Jin W, Liu S, Jiao Z, Li X. Probiotics, prebiotics, and postbiotics in health and disease. MedComm (2020). 2023 Nov 4;4(6):e420. doi: 10.1002/mco2.420. Available from here.

6. Cusumano G, Angeles Flores G, Venanzoni R, Angelini P. The Impact of Antibiotic Therapy on Intestinal Microbiota: Dysbiosis, Antibiotic Resistance, and Restoration Strategies. Antibiotics (Basel). 2025 Apr 3;14(4):371. doi: 10.3390/antibiotics14040371. Available from here.

7. Anthony W, Burnham C, Dantas G, Kwon J. The Gut Microbiome as a Reservoir for Antimicrobial Resistance. J Infect Dis. 2021 Jun 16;223(12 Suppl 2):S209-S213. doi: 10.1093/infdis/jiaa497. Available from here.

8. Joshi G, Rani S, Bharti D, Panda N, Chavan P, Mathpal S. The role of the gut microbiome in antibiotic-driven antimicrobial resistance. Front. Microbiol. 2026 June 6;17:1856738. doi: 10.3389/fmicb.2026.1856738. Available from here.

9. Cryan J, O’Riordan K, Cowan C, Sandhu K, Bastiaanssen T, Boehme M, et al. The Microbiota-Gut-Brain Axis. Physiol Rev 99: 1877-2013, 2019. doi: 10.1152/physrev.00018.2018. Available from here.

10. Margolis K, Cryan J, Mayer E. The Microbiota-Gut-Brain Axis: From Motility to Mood. Gastroenterology. 2021 Apr;160(5):1486-1501. doi: 10.1053/j.gastro.2020.10.066. Available from here.

 

Authors' declaration: AI was used as a consulting and editing device for this article. The contents, however, are completely human written.
 

 

Related: Antimicrobial Resistance in Africa: Causes and Solutions

 

Published: September 17, 2026

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