Antibiotics: Risks and Alternatives*

AntibioticsOveruse & Abuse

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.

Damaging the Gut Microbiome

While fighting a bacterial infection, antibiotics also kill off many of the beneficial microbes living in harmony in our guts.

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.

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.

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.

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Antibiotic Resistance

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.

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

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

Herbal Antibiotics

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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.

When using botanicals as an alternative to antibiotics, it’s important to know the specifics of what you are treating (test-don’t guess), and understand which botanicals target the specific infectious colonies. A clinical herbalist should have an in depth understanding of the various antibiotics, antivirals, and antimicrobials.

Immune Support

Design an immune support plan with your primary care physician. 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.

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


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.


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.

Unwind & Wait it Out

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 and DESTRESS—something that is extremely underrated in our society.


*Article Adapted from the Kresser Institute. Thank you Chris Kresser! Readers, check out his fantastic web page!

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