Antibiotics: Risks and Alternatives

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Antibiotics are one of the cornerstones of modern medicine. But this once lifesaving medication has been overused, with catastrophic results—including antibiotic-resistant bacteria, disrupted gut microbiomes, and associated chronic health problems. Read on to learn about the perils of abusing antibiotics and what alternatives medical professionals can consider.

Antibiotics were discovered accidentally in 1928, when Alexander Fleming noticed that a mold killed Staphylococcus bacteria. Between 1940 and 1962, 20 classes of antibiotics were developed, but only two new classes hit the market from 1962 until 2011. (1) Within the past couple of decades, antibiotics have been losing their effectiveness and wreaking havoc on the human gut.

Antibiotics Are Overused and Abused

Overuse and abuse are mostly to blame for weakening antibiotics’ arsenal. Consider the following:

  • One out of every five pediatric acute-care visits results in an antibiotic prescription (2)
  • Forty percent of women receive antibiotics during labor (3)
  • The average child receives 10 to 20 courses of antibiotics by age 18 (4)

Of course, antibiotics can be lifesaving, but most of the illnesses for which antibiotics are prescribed are self-limiting. Even the CDC admits that one out of three antibiotic prescriptions is unnecessary, (5) although I would wager the actual figure is much larger.

Treating infections in the age of antibiotic resistance

The Gut’s Connection to the Rest of the Body

While fighting a bacterial infection, antibiotics also kill off many of the beneficial microbes living in harmony in our guts. The vast majority of gut microbes live in the colon and feed on the undigested and poorly absorbed complex carbohydrates and fiber from our diets.

The gut microbiome is considered a distinct organ by many microbiologists today due to its involvement in a variety of body processes. For starters, 70 percent of the immune system resides in the gut. (6) Developing the adaptive immune response is especially important early in life and has a huge impact on long-term health. (7) We are still discovering all the ways in which the gut microbiome is linked to health, but some of its functions include: (8, 9)

  • Influencing hormone signaling, such as pylori’s effects on ghrelin and leptin
  • Extracting energy from food, such as Bacteroides in the colon that synthesize vitamin K
  • Regulating gene expression
  • Providing accessory growth factors
  • Promoting differentiation of mucosal structure and function

Because of its connection to so many body processes, anything that disrupts the gut—such as multiple antibiotic courses—will undoubtedly affect overall health.

Antibiotics Have Changed Human Gut Profiles

The human gut microbiome took millions of years to systematically evolve alongside humans, but modern-day hygiene, Western diets, and antibiotics have drastically altered our microbiome over a comparatively very short period of time. Stool samples indicate that modern hunter–gatherers have closer microbiota profiles to ancient samples than people from Westernized nations. (10, 11) Similarly, microbiomes from rural populations in South America and Africa have a greater richness and variety than Westernized nations. (12, 13, 14)

The bottom line is that we don’t fully understand the long-term health consequences of meddling with human gut microbiota in the way that antibiotic overuse does.

Risks of Antibiotic Usage

Drug-Resistant Bacteria

Antibiotic-resistant bacteria are a serious consequence of excessive antibiotic usage. The CDC reports that two million people each year contract a bacterial infection that is resistant to one or more antibiotic medications, resulting in 23,000 deaths. (15) Certain strains of N. gonorrhoeae, M. tuberculosis, and C. difficile are especially threatening.

Most antibiotic classes were developed before 1962, like tetracycline, erythromycin, and vancomycin, are quickly losing their effectiveness. In response, doctors are resorting to once-abandoned antibiotics such as colistin, which is still effective for stronger strains of salmonella and E. coli, but is toxic to the kidneys.

Gut Microbiome Is Changed and Doesn’t Recover Easily, If Ever

In young children especially, whose body systems are still developing, the gut microbiome takes a heavy blow from antibiotics. A study from 2016 showed that one course of macrolide caused significant changes to children’s guts that were not resolved until two years later. (16) With a dozen or more antibiotics usually given by age 18, most children won’t have two years between antibiotic prescriptions, which means that their guts may never fully recover. (17) Antibiotic overuse in children disrupts the proper development of a normal adult microbiota. (18)

Adverse Reactions and Drug Interactions

Each year, adverse reactions from antibiotics result in 140,000 ER visits in the United States, with nearly 80 percent due to allergic reactions. (19) Antibiotics can cause a variety of other unpleasant side effects, including nausea, diarrhea, and stomach pain. Furthermore, antibiotics can interact with other medications. Hormonal contraceptives, for example, can lose their effectiveness if antibiotics are taken concurrently.

Diseases and Health Problems

Antibiotic usage is linked to many diseases and health problems, including:

  • Inflammatory bowel disease (20, 21)
  • Crohn’s disease (22)
  • Obesity (23, 24)
  • C. difficile (25)
  • Candida infection (26)
  • Mental health issues (27, 28)
  • Autoimmune diseases (29)
  • Celiac disease (30)
  • Metabolic disease (31)

Healing the Gut to Avoid Antibiotics

An ounce of prevention is worth a pound of cure. Since 70 percent of the immune system resides in the gut, healing the gut to prevent serious infections in the first place is the best way to avoid needing antibiotics.


Probiotics help repopulate the gut with helpful microbes. The most common probiotic supplements are Lactobacillus and Bifidobacteria.

Although probiotic supplements can be effective, a manufactured product cannot achieve the diversity of a healthy gut flora on its own. Homemade, naturally fermented foods like kefir, beet kvass, sauerkraut, kombucha, and kimchi can help increase microbe diversity.


Prebiotics (soluble fiber and resistant starch) are better than probiotics at promoting the growth of beneficial bacteria. (32) Good food sources of soluble fiber include carrots, winter squash, turnips, rutabagas, parsnips, beets, plantains, starchy tubers, taro, and yuca.

Green bananas and unripe plantains are dietary sources of resistant starch and are more palatable as part of a smoothie. For a controlled dose of resistant starch, I often recommend Bob’s Red Mill unmodified potato starch, green banana flour, or green plantain flour. Patients can start very small, at one teaspoon per day or less, and slowly work up to two to four teaspoons per day. If resistant starch is not well tolerated, Prebiogen is an inulin-free prebiotic option

Alternatives to Antibiotics

Many botanical alternatives to antibiotics can shorten infection duration, improve immunity, and provide symptom relief. The effects that botanicals have on the gut flora are generally less pronounced than pharmaceutical antibiotics. I was trained as an herbalist to properly prescribe the correct combinations, dosages, and preparations of botanicals. A great resource is Stephen Buhner’s book Herbal Antibiotics.

Antiviral Botanicals

Bacterial infections often present very similarly to viral infections. One of the mottos of my practice is, “Test, don’t guess.” If the infection is viral, some options are Chinese skullcap, isatis, licorice, houttuynia, lomatium, yerba santa, elephant tree, osha, and pleurisy root.


Lauricidin is an antimicrobial that also breaks up the tough, protective bacterial biofilm. It is quite effective against gram-negative bacteria, which are becoming increasingly antibiotic-resistant. Other antimicrobial options include undecylenic acid, uva ursi, cat’s claw, wormwood, goldenseal, pau d’arco, olive leaf extract, garlic, barberry, Oregon grape, and oregano oil extract.

Biofilm Disruptors

In addition to Lauricidin, other biofilm disruptors include lactoferrin and apolactoferrin, which are also used as iron chelation agents. Enzymatic options are lumbrokinase and nattokinase. Klaire Labs carries N-acetylcysteine, another biofilm disruptor.

Immune Support

Equal parts astragalus, cordyceps, and rhodiola make an effective immune-support botanical tincture. For illness prevention, ¼ teaspoon three times a day is a sufficient dose. To treat an illness, ½ teaspoon up to six times a day can be used.

Ginger tea, which is extremely potent when following my recipe, is also great for the immune system.

The following micronutrients can help the immune system fight off an infection:

  • vitamin C, 1000 to 4000 mg/day, in liposomal form
  • iodine, from sea vegetables and fish heads, or one mg/day as a kelp capsule
  • selenium, 200 micrograms/day, three to four times a week (short-term use only)
  • zinc, from oysters or 30 mg/day of zinc picolinate or zinc gluconate
  • elderberry syrup, one teaspoon twice per day
  • vitamins A and D together, from cod liver oil

Fecal Transplants

Fecal transplants were first mentioned more than 1,500 years ago (33) and have been used in the past to treat diarrhea, colitis, and dysentery. Once practitioners and patients get over the “yuck” factor, many compare it to an organ transplant.

In recent years, fecal transplants have been very successful in treating C. diff. (34) Scientists have also been exploring fecal transplants for IBD and metabolic syndrome, and I hope to see it expand to other diseases.

Rest and Wait

Many illnesses are self-limiting and cleared by a properly developed immune system. For mild infections, a watch-and-wait approach, along with some immune-boosting micronutrients, fights off many illnesses without the need of harsh interventions.

A key to this approach, however, is to truly REST—something that is extremely underrated in our society.


  1. I am always shocked about being prescribed antibiotics as a preventative measure in the US.
    This is not something I have experienced in Europe.
    Having also suffered gut damage due to a hard to detect parasitic infection, promoted by a long course of (the wrong) antibiotics, I’m very weary of taking antibiotics.
    I have always refused taking them to prevent infections, which most US doctors seem to automatically prescribe for small procedures, and have always been fine and infection free.
    When researching the risks of infections associated with these procedures I always found it was very low, yet the antibiotics course seems automatically prescribed to everyone undergoing the procedures.
    I trust my body would let me know in the off chance I contracted an infection, in which case I would be able to seek treatment then, only if truly needed.

  2. A while back I figured that antibiotics were not an answer to our problem, but a window of opportunity to get our house in order, and that window is closing pretty fast. Our immune system is the last line of defense against microbes, but we treat it like the first and only line of defense.

    We removed lions from our midst for good reason, the same rule needs to apply to microbes. We have the technology and the means to create environments from which microbes are totally excluded but we choose to use these resources elsewhere. The repeated assault on our immune system causes “crashes” which result in the formation of auto-antibodies, and vaccines have a compounding effect (multiple assaults simultaneously – it is like a production line being asked to produce multiple products at the same time- the result is chaos).

    Antibiotics are a help, but a temporary one and soon they will all be useless and we will be in the same environment, only worse since the microbes that prevail will be those that have not adapted to their host, they will be serial killers.

    Probiotics and prebiotics and biologicals are an extension of the “window of opportunity theme” and do not provide a definitive answer. Until we remove ourselves from the environment occupied by microbes, we will be destroyed long before the sun would do the same to us.

    This may sound like science fiction, but it is the only rational and logical answer to our health crisis. It requires a totally different approach, and away from the pharmaceutical directed palliative approach. Our governments collect our wealth and it is misused, this therefore also calls for a move away from our current political structures to one where our interest and well-being is given priority. Universal healthcare under the current palliative approach model is not the answer.

  3. Hi Chris!

    Great article!

    We should be careful with our use of botanical antimicrobials, because they could lead to bacterial resistance. I recently published a paper on the Journal of Evolution and Health on the very topic:

    Just like you have been saying for the past 8 years, always use the help of a practitioner when treating infections. “Test don’t Guess” is exactly the only way we can avoid the development of super bugs.

    Thank you for all your awesome work!

  4. Hi Chris,
    I am trying to get rid of blasto homminis with a patient and tried a lot of different herbal protocols. What do you see as the most effective treatment? Would you recommend the triply therapy from Australia?