How To Effectively Counter The Harmful Effects Of Antibiotics

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There is no doubt that antibiotics save lives, but what’s the best way to counter the damage to our microbiome when we have to use them.

My mother was an officer in the Army Nurse Corp in World War II. She witnessed the horrifying consequences of battle first hand. She told me that the wounded were crowded into cargo ships and ferried across the Atlantic to hospitals in the US. Most didn’t make it. The only pain drug was morphine. There was little to do for infections but keep wounds clean, or amputate an infected limb. Antibiotics were new, and there was just one kind: penicillin. She said they often ran out before reaching port.

In previous wars, more people died from infected wounds and disease than were killed in combat. In World War II, penicillin changed everything. Antibiotics transformed medicine.

But, like many great medical advances, the discovery of antibiotics was an accident. On the morning of September 3rd, 1928, while British researcher Alexander Fleming cleaned up his disorderly lab, he eyed one plate that had mold in the shape of a ring while the area around it remained free of Staphylococcus bacteria. That mold was Penicillium notatum.


But most antibiotics don’t come from kitchen mold; they come from dirt. By 1939, scientists were studying microorganisms in soil from Spain in an attempt to find how these organisms helped to keep soil disease free. In the same year, the American microbiologist Selman Waksman invented the term “antibiotic” to describe a compound that killed bacteria without being toxic to human cells. The label stuck.

By 1940, Oxford University scientists found ways to purify penicillin and started testing with mice, then on humans. With the outbreak of World War II (1939-1945), the wounded crowded into inadequately stocked hospitals. Infections were rampant. A team of scientists rushed to develop penicillin in sufficient quantities to fight bacterial infections of the injured troops.

By 1942, penicillin was mass-produced by British pharmaceutical companies. Through the use of penicillin, many soldiers were saved from the infections that developed after battle wounds. From wartime to peacetime, penicillin found its way into the daily practice of medicine.

Penicillin reduced the rate of death from bacterial pneumonia. At the time, pneumonia killed 60 to 80 percent of people infected, but penicillin lowered the rate to 1 to 5 percent. Before penicillin, special wards of hospitals were reserved for syphilis cases. Approximately 10 percent of Americans had syphilis. By 1945, cases plummeted by more than 75 percent with penicillin use. In 1975, there were few cases in the US, and the death rate from syphilis approached zero.

Contemporary researchers acknowledge the effectiveness of penicillin to wipe out syphilis in the US and other advanced nations. They also consider the relationship of syphilis to penicillin as historically unique. Wider use of antibiotics based on the enthusiasm from witnessing the miraculous benefits in infected wounds and syphilis, lead to the rapid advance of antibiotic resistant bacteria. And, mass antibiotic overuse resulted in unforeseen consequences.

The Reputation Of Modern Medicine’s Miracle Drug Is Tainted

Using antibiotics makes our immune system more vulnerable to pathogens and destabilizes our microbiome. Bacteria are not passive; they fight back. Antibiotic resistance occurs when an antibiotic loses its ability to kill bacteria. Resistant bacteria become stronger than their predecessors and more dangerous.

Resistance is a natural biological phenomenon. Bacteria and viruses are always adapting, and they evolve fast. Bacterial resistance to antibiotics is the consequence of antibiotic use, but the results of healthy adaptation. A bigger problem happens as resistant strains spread from person to person by coughing or contact with commonly touched surfaces like doorknobs.

The good news is that antibiotic use has dramatically declined in higher-income countries, like the United States. However, antibiotic use has increased significantly in Africa, the Middle East, and South America. The bad news, according to health economist Ramanan Laxminarayan, is that bacteria are evolving fast and have achieved natural antibiotic resistance. That may mean that if a resistance tipping point is reached, antibiotics won’t work at all.

Overuse of antibiotics can decimate your gut’s ecosystem. But, in only a few days it’s bouncing back. However, it takes several months to return to healthy populations of friendly bacteria after a single course of antibiotics. Some strains of probiotic organisms may never go back to normal levels. In this imbalanced environment, unfriendly bacteria or potentially pathogenic bacteria thrive.

While scientists and medical doctors research ways to counter antibiotic resistance, patients are left on their own to find how to counter the adverse effects of antibiotics in their bodies.

Why Are Probiotic Supplements Minimally Effective?

I’m an advocate for probiotic supplementation. Much of the science about probiotics is excellent. Some probiotics, like Saccharomyces boulardii for diarrhea caused by antibiotics, work fast. But most commercial probiotics don’t work well enough. The problem is simple. We’re up against overwhelming odds from the bacterial world.

It’s difficult to determine our gut microbiome because it is composed of some 100 trillion microbes made up of thousands of different species. However, laboratory science is getting better. The lab test I use for my patients (GI Effects Comprehensive Stool Analysis from Genova Diagnostics) assays for 25 different commensal bacteria. That’s not enough to get much clinical insight, but it’s sufficient to get an idea of dysbiosis – a biologically imbalanced gut microbiome.

Because naturally occurring commensal bacteria and live bacteria found in pharmaceutical grade probiotics are living organisms, they need the right matrix to thrice. Just like plants require healthy, nutrient-rich soil to grow, probiotic bacteria need a rich prebiotic “soil.”

When the gut microbiome is already sick, simply adding probiotic supplements is not enough to make a significant difference. A therapeutic strategy for multiple actions is required. I often have to dampen the activity of potentially pathogenic bacteria with antimicrobial botanical extracts, or add building blocks like butyrate, and support implantation success with prebiotics.

But, even with a comprehensive strategy for rebuilding gut health, the probiotic species available to doctors and patients are limited. There are not enough of the right bacteria to do the job effectively.

How To Counter The Negative Effects Of Antibiotic Therapy

All things, living and nonliving are interrelated. We need to breathe oxygen to live. We must eat to produce energy. Air, food, and water come from the biosphere, a biological soup of trillions times trillions of countless living microorganisms.

There’s no way around it. We must all live together, bugs and us. People are a composition of microbes and human parts. Our body harbors far more bacteria than human cells.

If you have to take antibiotics, disruption will occur. Most of the time, it’s relatively minor, and the body rebalances itself. But, repeated use takes a toll. What is the best way to protect your body’s microbiome?

Justin Sonnenburg of Stanford University School of Medicine advises a “two-step” approach. Diet and probiotic supplementation play equally important roles, but so do exercise and gardening – both activities that favor a healthy gut microbiome. Two steps become four cornerstones, and eventually the entire foundation of human health.

Diet plays a significant role in supporting a thriving inner microbiome. Getting enough fiber is critical for microbial health. The primary energy sources of probiotics are microbiota-accessible carbohydrates (MACs). If you don’t have enough MACs in your diet, due to overeating refined carbohydrates, bacteria turn to eating your gut’s mucosal lining. The result produces increased inflammation and leaky gut syndrome.

Cultivating a healthy gut microbiome may be the most important goal we achieve to prevent and treat chronic disease. Here’s what I recommend for my patients:

Take Probiotics: Take Saccharomyces boulardii for diarrhea caused by antibiotics. Use Lactobacillus sporogenes. It is resistant to the acid bath in the stomach so is a powerful probiotic to help recolonize the gut. Research shows that probiotic supplements reduce IBS symptoms. No one type of probiotic is better than others. I recommend a high dose (at least 25 billion units) of a probiotic combination that includes Lactobacillus acidophilus, Lactobacillus plantarum, Lactobacillus rhamnosus, Bifidobacterium breve, Bifidobacterium lactis, Bifidobacterium longum, and Streptococcus thermophilus.

Increase Soluble Fiber and MACs: According to the research, wheat bran has the most beneficial effect. If you are wheat sensitive, this choice is not for you. Instead, expand your dietary choices to include quinoa, wild rice, millet, and legumes like lentils and black beans.

Take Prebiotics: Commercial prebiotics come in capsules or as powders you mix in water. For my patients with chronic fatigue syndrome and IBS, I always recommend including prebiotics along with probiotics. Prebiotics include inulin from Jerusalem Artichokes, Larch Arabinogalactans from Larch tree bark, and Beta Glucan from nutritional yeast.

Include Fermented Foods: Small amounts of naturally fermented plant-based foods consumed daily benefits your gut. Fermented foods include miso, tempeh, kimchi, sauerkraut, and Kombucha.

Increase Dietary Sources Of Short Chain Fatty Acids (cooked green bananas, sweet potatoes, ghee, apples): Ghee is rich in natural antioxidants and is composed primarily of short chain fatty acids. These short chain fatty acids are metabolized and used for energy by the liver, and help control metabolism, and inflammation. Short chain fatty acids are necessary tools for rebuilding the gut microbiome. The most useful food for restoring short chain fatty acids is green bananas (plantains).

Supplement With Butyrate: Sodium or calcium-magnesium butyrate is a short chain fatty acid necessary for gut health. In patients with dybiosis, one of the most frequent findings on a comprehensive stool test is a deficiency of butyrate. Getting your butyrate levels back to normal is important. High levels of butyrate slow cancer growth and support a robust gut microbiome. Take 300-600 mg daily.

Some day, we’ll be wiser. Doctors will prescribe fewer antibiotics, reserving the most powerful ones for life-threatening infections. If antibiotics are necessary, patients will take specific gut-protective drugs along with antibiotics, followed by recommendations for a gut-friendly dietary and a prescription for symbiotics – combinations of prebiotics and probiotics. We may even learn to bioengineer our gut ecosystem back to balance with designer microbial cocktails.

Wiser may mean living like a native, finding balance with nature without and within, eating a plant-based diet, including superfoods included fermented products, organic gardening, and alternative technologies and therapies to keep us healthy. We’ll respect the laws of coevolution between humans and microbes.

We need a complete rethink in our understanding of nature and how we use technology, not just overuse of antibiotics. It’s a citizen revolution, and we’re doing it now. I encourage you to take part in restoring planetary balance by rebuilding your gut microbiome.

Dr. J. E. Williams


Dr. Williams is a pioneer in integrative and functional medicine, the author of six books, and a practicing clinician with over 100,000 patient visits. His areas of interest include longevity and viral immunity. Formerly from San Diego, he now resides in Sarasota, Florida and practices at the Florida Integrative Medical Center. He teaches at NOVA Southeastern University and Emperor’s College of Oriental Medicine.

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