Antibiotics save lives, but they also come with a raft of potential serious side effects in children and adults. Cate Montana rounds up the evidence and offers some effective alternatives
In 2024, the Centers for Disease Control (CDC) in the US implemented its “Be antibiotics aware” campaign. It aimed “to improve antibiotic prescribing and use among target consumer and healthcare professional audiences to protect patient safety and combat antimicrobial resistance.”1
Today, doctors and many patients are aware of the growing issue of antibiotic resistance among many strains of quickly evolving bacteria. What they’re not aware of is the staggering fact that 700,000 people worldwide die due to antimicrobial resistance every year, a number the World Health Organization (WHO) predicts could rise to 10 million per year by 2050.2
Antibiotic overprescription and overuse has risen to epidemic proportions since penicillin, discovered in 1928 by Scottish bacteriologist Alexander Fleming, was brought into mass production during World War II. Today, many adults in the US and other Western nations receive an antibiotic prescription as often as once a year.
In the UK, nearly 480 metric tons of antibiotics were prescribed in 2019.3 In the US in 2023, 252 million outpatient antibiotic prescriptions were filled.4 Approximately 70 percent of US children receive at least one treatment with antibiotics for illness before age two—and they often suffer the consequences of ongoing conditions ranging from allergies to obesity.5
In US long-term care facilities, over 40 percent of residents receive an antibiotic every year.6 However, an estimated 85–95 percent of antibiotics prescriptions are given in outpatient settings worldwide.7 Of those, about 30 percent in the US8 and 20–30 percent in England9 are unnecessary.
People also aren’t aware of the inherent risks of taking antibiotics. We tend to believe antibiotics are totally safe and totally harmless. And yet a study at Johns Hopkins University in 2017 found one in five hospitalized adults suffers side effects after taking antibiotics prescribed by their doctor, nearly 20 percent of which were unnecessary in the first place.10
“We’ve been marketed to and sold the idea that we need an antibiotic anytime we don’t feel well,” says Piper Dobner, ND, founder of Biome Basics in Nampa, Idaho (drpiperdobner.com). “Antibiotics as a whole have saved countless lives. They’re a blessing. But the long-term implications and outcomes of people taking them broadly are significant.
“I’ve seen people lose tolerance to food. I’ve seen people with increased neuroinflammatory symptoms. Some people get super anxious, some get insomnia, some get diarrhea. I’ve seen depression as a side effect of antibiotics; I’ve seen constipation, even tendon ruptures. Everybody reacts to antibiotic use and overuse in a different way.”
Why are the reactions to antibiotics so diverse? The answer is the gut. There are around 30 trillion cells in the human body and around 38 trillion smaller bacterial cells, most of which live in the gut.11
The bacteria constituting the gut microbiome affect virtually all aspects of human health. The gut microbiota has a regulatory role over growth and development, the immune system, digestion, mood regulation, cognition and sensory processing via the gut–brain axis.12
Over 1,000 strains of bacteria have been identified in the gut microbiota, and the overwhelming majority of genes in our bodies are microbial; more than 10 million microbial genes are running the show. Keeping these bacteria and microbes in a state of balance—aka homeostasis—is essential for health.13
Antibiotics, of course, work specifically against live, single-celled bacterial organisms that reproduce independently. Antibiotics can be natural, produced by fungi, molds or other bacteria. They may be semi-synthetic and modified from natural compounds. Or they can be synthetic and designed entirely in the lab.
In any case, the sole purpose of all of them is to either kill problematic bacteria outright (bactericidal) or to stop them from reproducing (bacteriostatic). And most, especially those that are broad-spectrum, are not particular about which bacteria they kill. The basic attitude is “kill the Bad Guys now, figure out the consequences for the Good Guys later.”
And those consequences are severe. “In my practice, I see a lot of complex chronic illness driven by a decimated gut microbiome that’s accompanied by things like mast cell activation syndrome (MCAS), where people’s immune systems are just exploding,” says Dobner.
“They’re having hyper-reactive expressions in the immune system—tissue swelling, hives, shortness of breath, intense and even life-threatening anaphylaxis—because they don’t have that richness of the biome to tell the immune system to calm down, to help assist and aid in metabolic health. It’s heartbreaking on a scale that I don’t know how to articulate.”
It’s taken decades for the adverse effects of antibiotics to be identified, partly because many common side effects are masked by the effects of the illness or infection the antibiotics are being used to treat. Some side effects show up after treatment is complete.
And finally, the sheer number of side effects, from nausea and vomiting to decreased libido, abnormal weight loss, hepatitis, jaundice and liver cell death, makes direct causation difficult to determine.14
One of the most common side effects of antibiotic use is an outbreak of Clostridioides difficile, aka C. diff. One of the major causes of diarrhea in the Western world, “C. diff is usually dormant in most of us,” says Anu Simh, board-certified functional health coach and founder of 9 Arms of Wellness (9armsofwellness.com).
“They’re like little spores that are just lying around in the gut along with beneficial bacteria, which normally convert primary bile acids from the liver into secondary bile acids. But when antibiotics come in and kill a lot of those good bacteria, the primary bile acids wake up the C. diff spores and they start causing havoc—diarrhea, colitis and a lot of issues that, ironically, are often treated with yet another round of antibiotics.”
Antibiotic-associated colitis is almost always caused by C. diff proliferation and most commonly develops after using fluoroquinolones, amoxicillin/clavulanate, clindamycin and third-generation cephalosporins.15 Hemorrhagic colitis is associated with the use of amoxicillin. And people who take antibiotics are nearly twice as likely to develop inflammatory bowel disease (IBD) as those who never take them.16
Antibiotic use has been linked to gut microbiome dysbiosis and metabolic disorders, and recurring use has been linked to an increased risk of type 2 diabetes both in children17 and in adults.18 Aminoglycoside antibiotics affect neurotransmitter levels in the brain and alter blood flow in the inner ear, causing dizziness, hearing damage and hearing loss that can be irreversible.19
Sihm recounts the story of an uncle who irreversibly lost his hearing after taking gentamicin back in 2005. “His whole life changed,” she says. “He went from being this very articulate gentleman to someone whose quality of life seriously decreased.”
A recent study shows that up to 57 percent of children treated with aminoglycosides experience hearing loss.20 Sulfonamides can cause painful scarring in the inner eyelid and whites of the eyes. Tetracyclines can irreversibly discolor the whites of the eyes. And fluoroquinolones are powerful antibiotics that increase the risk of retinal detachment.21
Side effects aren’t limited to physiological conditions, either. Microbes in the gut impact brain function by acting on the vagus nerve and by changing the production of short‐chain fatty acids affecting the production of the amino acid tryptophan, the building block of serotonin. They also affect the hypothalamic–pituitary–adrenal axis, reducing levels of the feel-good hormone oxytocin in the brain.22
Antibiotic treatment with fluoroquinolones is closely related to increased psychiatric disorders, including anxiety, depression and delirium.23 Long-term and recurrent use of antibiotics is associated with an increased risk of depression.24 Quinolones such as ciprofloxacin, ofloxacin, pefloxacin, iprofloxacin and levofloxacin can induce psychotic episodes.25 Animal studies also provide evidence that early antibiotic exposure may increase the risk of autism.13
Finally, lest we forget where we started, antibiotic and antimicrobial resistance is the most stunning side effect that has developed over decades of use and misuse of antibiotics—with major global ramifications.
Antibiotics save lives. It’s impossible to get around that fact.
But neither antibiotics nor patients are created equal. Here are some things to consider before, during and after treatment to make sure your body—especially your gut—suffers the smallest possible impact.
Before. Prepare your body by feeding your gut a broad variety of plants and make sure to get some fermented foods, like kefir and kimchi, into the mix. Prepare questions to ask your doctor, such as these:
Consider your unique patient profile. Do you have any cognitive or emotional issues that could be exacerbated by using fluoroquinolone antibiotics like gatifloxacin and temafloxacin, which are significantly associated with anxiety, depression and delirium?
Are you on proton pump inhibitors, steroids or SSRIs? All these substances significantly reduce gut health, and you can seriously impact your situation by taking an antibiotic on top of any of them.
During. Take probiotics, especially if there’s a risk of diarrhea. The Akkermansia group of bacteria is a great probiotic choice, as are Saccharomyces boulardii and Lactobacillus rhamnosus GG.
As well, take them several hours before or after taking the antibiotic so it doesn’t immediately kill them. Ease off high-fiber foods to simplify digestion for the duration. Avoid alcohol and be careful with caffeine consumption, which can cause side effects when combined with antibiotics.
After. For two to six weeks after finishing your course of antibiotics, Anu Simh advises recognizing food as “the biggest needle-mover when it comes to gut health.” Be sure to start eating and adding foods that microbes like, especially a wide variety of vegetables. If you’ve struggled with antibiotic-induced diarrhea, work up to adding beans and lentils and other high-fiber foods that require a lot of digestive power.
“Start with a basic foundational layer of diverse veggies that will increase the diversity of your microbes coming from plant sources,” Simh says. “Don’t eat a mono-diet or the same three or four veggies. Think beyond that.
“Look at farmer’s markets. Look at seasonal foods and explore international markets for more diversity. And then slowly add fermented foods like kimchi and sauerkraut and kefir—foods that, within a week or two, will facilitate an incredible blooming of new microbes.”
Don’t forget good fats like avocado, coconut and olive oils or herbs and spices like cloves, star anise, oregano and peppermint that are high in polyphenols. Dark berries help to build up polyphenol stores that support keystone bacterial species (see below) and increase insulin sensitivity. And be sure to consume functional beta-glucans from oat bran, shiitake mushrooms and barley to help grow and increase microbial diversity.
“Some bacteria and microbial species bounce back after a round of antibiotics, and others don’t, which leaves gaps for pathogens to move in post-antibiotic use,” says Simh. “Studies show the microbiome as ‘mostly normal’ around six weeks after a course of antibiotics.
“But keystone species are usually still missing, which is why some people feel ‘off’ long after a prescription ends. So, pay attention to getting those keystone species back into your gut. They play a very pivotal role in your health.”
Foods that help to increase some bacteria tend to decrease others. These balancing effects are a major reason it’s important to eat a varied diet.
A natural antibiotic is a substance produced by microorganisms, such as fungi and molds, that inhibits or kills other microorganisms. Semi-synthetic antibiotics are natural antibiotics that have been chemically altered to increase potency and decrease side effects.
Synthetic antibiotics, such as iboxamycin, are chemically designed in the lab. Different classes of antibiotics do their jobs in different ways. Some, like penicillin, attack the bacterial cell wall. Others reduce bacterial DNA replication or mimic bacterial “food” and poison them.
The following are the major classes of antibiotics, their uses and their side effects.
Aminoglycosides are broad-spectrum drugs including delafloxacin and gemifloxacin that inhibit protein synthesis inside bacteria. Effective against heavy hitters such as Staphylococcus and Mycobacterium tuberculosis bacteria, aminoglycosides are often combined with other antibiotics. Not well absorbed orally, they’re often delivered via IV.
Side effects include impaired kidney function and hearing loss, which is often permanent.
Cephalosporins are derived from the Acremonium mold and work similarly to penicillins, binding to and blocking enzymes that build cell walls in various bacteria. They are broad-spectrum antibiotics commonly used to treat bone, ear, skin and respiratory infections as well as bacterial meningitis and urinary tract infections (UTIs).
Side effects include nausea, vomiting, abdominal pain and allergic reactions such as rashes, hives and swelling. In rare cases, they can cause anaphylaxis and colitis.
Fluoroquinolones inhibit the production and action of enzymes essential for bacterial DNA replication. They are commonly used to treat Mycobacterium tuberculosis bacteria, UTIs, chlamydia and respiratory infections. Fluoroquinolones, such as ciprofloxacin (Cipro) and levofloxacin (Levaquin), are potent and are strongly associated with psychiatric and mood disorders, including anxiety, depression and delirium.
Side effects include severe hepatic (liver) toxicity, cardiac toxicity, renal (kidney) failure, hepatotoxicity, anemia and hypoglycemia, which have caused many fluoroquinolones to be withdrawn from the market.
Macrolides are mostly natural substances such as erythromycin and are primarily used as substitutes for penicillin. They’re commonly used to treat infections like pneumonia, sinusitis, pharyngitis, and tonsillitis, simple skin infections and ear infections in children.
Side effects include nausea, vomiting, abdominal pain and diarrhea, cardiac arrhythmias, hearing problems and irreversible hearing loss.
Penicillins come from the fungi Penicillium. They’re most commonly used to treat respiratory, ear, urinary tract, dental and skin infections.
Side effects include diarrhea, nausea, abdominal pain, skin rashes and hives. Severe side effects include rapid heart rate, anaphylaxis, lightheadedness and fainting.
Sulfonamides are made from a sulfur-containing chemical called sulfanilamide, and they work by inhibiting bacterial protein production. They’re used to treat eye and ear infections, UTIs, bronchitis, and bacterial meningitis.
Side effects include nausea, vomiting, dizziness, headache, lethargy, skin rashes, sun sensitivity and kidney damage. Sulfonamides can increase the blood-thinning effects of warfarin (Coumadin), a commonly prescribed anticoagulant medication.
Tetracyclines inhibit bacterial protein synthesis and are used to treat a wide variety of skin infections, including acne and rosacea. These antibiotics are also used to treat intestinal and respiratory tract infections, UTIs, chlamydia, syphilis and gonorrhea. Tetracyclines can interfere with the action of birth control pills and is easily passed into breast milk, possibly affecting bone and tooth development in nursing babies.
Side effects include sores, swelling and itching in genital and rectal areas as well as nausea, vomiting, diarrhea, mouth sores, swollen tongue and difficulty swallowing.
Green tea
Green tea (Camellia sinensis) has been used for hundreds of years against microbial infections, and modern studies show its effectiveness against drug-resistant microorganisms such as MRSA, Pseudomonas aeruginosa and Candida albicans.1
Cinnamon
As well as being neuroprotective and effective for treating diabetes, numerous studies show that cinnamon has antibiotic properties against Salmonella typhi, Salmonella paratyphi A, Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae and others.2
Coconut oil
Virgin coconut oil is antimicrobial and has been found effective against S. aureus.3 Frequently used as a topical antibiotic, coconut oil is effective against atopic dermatitis (eczema).
Colloidal silver
Silver was used to treat bacterial infections in ancient days. Colloidal silver has been proven to work against multidrug-resistant bacteria such as Acinetobacter baumannii, P. aeruginosa, E. coli, K. pneumoniae and S. aureus.4
Turmeric
The deep-yellow rhizome turmeric (Curcuma longa) contains curcumin, a compound well known for its antimicrobial and antioxidant properties that can help eliminate antibiotic-resistant microbes.5 Curcumin may be most effective within turmeric rather than isolated from it,6 and it becomes even more bioavailable with piperine, found in black pepper.
Echinacea
Echinacea extracts have been used traditionally to treat the immune system and respiratory symptoms caused by bacterial infections as well as to promote wound healing. Lab testing shows they have proven antioxidant and antimicrobial effects.7
Garlic
The organosulfur compounds of garlic have antibacterial properties and are proven effective against a wide range of bacteria, including multi-drug-resistant strains. They have “enormous potential to be developed into novel antibacterial agents.”8
Manuka honey
Manuka honey is made by bees harvesting nectar from the Manuka plant. It’s dark and rich in phenols that make it effective against a wide range of pathogens. Honey has a natural ability to inhibit cell growth by altering bacteria shape and size, and Manuka honey’s other unique components enhance its effectiveness.9
Mustard
Mustard seed extract has high-level antimicrobial and anti-inflammatory effects for treating a variety of oral microorganisms.10
Myrrh
An ancient treatment, myrrh is resin extracted from the Commiphora molmol gum tree. It is effective against the multidrug-resistant S. aureus and P. aeruginosa.11
Rose oil extract
With antibacterial and antifungal properties, rose petal extracts can be applied topically to treat skin infections and gargled to treat throat infections.12
Thyme
The common kitchen herb thyme (Thymus vulgaris) is known since ancient times to have anti-inflammatory and antimicrobial properties. Effective against bacteria caused by dental cavities, it reduces growth of E. coli, MRSA and many other bacteria.13
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