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Recovering From Antibiotics: The Best Strategies For A Healthier Gut

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"Penicillin is not a magic bullet. It is not for nothing that the public has become aware of the dangers of the thoughtless use of antibiotics. If we continue to use them unwisely we will soon be faced with a race between the antibiotic and the microbe."

—Alexander Fleming, the discoverer of penicillin


Last year around Halloween, I was hit pretty hard by some sort of respiratory illness that had lingering effects for a good 21+ days afterward.  I was hoping it was viral but it lingered and ultimately proved to be bacterial.  I dragged my feet on getting (then taking) the antibiotic and the inhaler but realized the pros outweighed the cons and I swallowed the pills I tried hard to avoid. 

They probably helped me recover more quickly and I was glad the illness was behind me but now I had a new dragon to slay: the effects of the antibiotics. Antibiotics are powerful little things that can have a significant impact on your health whether you know it or not. Here I lay out the issues with antibiotics and my protocol for recovering from antibiotics to restore your health.

The Concerns With Antibiotics

In the realm of modern medicine, antibiotics can be literal lifesavers, combating an array of bacterial infections that once posed significant threats to human health. The indiscriminate use of these powerful drugs, however, has inadvertently created a formidable foe—antibiotic resistance and a devastated microbiome.

Antibiotic Resistance

The early 20th-century discovery of antibiotics, particularly Penicillin, revolutionized medicine, offering a potent weapon against once-devastating bacterial infections. This breakthrough significantly reduced mortality rates from infections like pneumonia and meningitis. However, the extensive and often inappropriate use of antibiotics has fueled the emergence of antibiotic-resistant strains. Resistance develops as bacteria evolve mechanisms, including acquiring resistance-conferring genes, altering cell walls to resist penetration, or developing efflux pumps that expel antibiotics from cells.

According to Bill Bryson, author of The Body, the rise of antibiotic resistance has given rise to highly resistant bacteria, such as MRSA and CRE, which are projected to cause 10 million deaths annually. The growing threat of these superbugs has even prompted some surgeons to reconsider performing common surgeries like hip replacements due to the elevated risk of infection.

One of the primary drivers of antibiotic resistance is the overuse of these medications for conditions that they are not effective against. Out of the 40 million antibiotic prescriptions written each year, a staggering 75% are for illnesses, such as acute bronchitis, that cannot be treated with antibiotics. This inappropriate use of antibiotics, coupled with the consumption of antibiotics through food sources, has fueled the development of resistant bacteria. In fact, an alarming 70% of all antibiotics used worldwide are administered to animals for agricultural purposes.

The Microbiome

The gut microbiome is a thriving community of trillions of microorganisms, each playing a vital role in maintaining our overall health. It's only been in recent years that we've recognized the importance of the gut microbiome, a vast community of microorganisms in our digestive system.  While research is still in its infancy, we now know that a high microbial diversity in the gut is linked to a variety of health benefits such as mental health, immune system, and even the development of neurodegenerative diseases.

When antibiotics disrupt this delicate balance by indiscriminately eliminating both harmful and beneficial bacteria and creating a low microbiome diversity. This is linked to inflammatory disorders like IBS, obesity, diabetes, anxiety, and depression. The gut-brain axis, a bidirectional communication system, is pivotal, with 90% of serotonin (the feel-good neurotransmitter) produced in the gut.  This low diversity leaves our guts vulnerable and susceptible to further infections and a range of health issues.

Recovering From Antibiotics

My personal experience with antibiotics highlighted the need for a holistic approach to gut health, including dietary modifications and lifestyle changes. As soon as I was on the mend from my sickness, I was on a microbiome-improving quest to heal my gut microbiome and get it better than where it was before. 

My Antibiotic Recovery Protocol

Here are some of the strategies I'm using to restore the good bacteria in my gut:

  • Eat more fermented foods.  Fermented foods, considered to be nature’s gift to gut health, have been shown to be one of the best avenues to gut restoration post-antibiotics. Fermented foods are teeming with beneficial bacteria, known as probiotics, which act like reinforcements for our depleted gut microbiome. Probiotics help to restore diversity, promote overall health, and enhance the gut's ability to fend off harmful bacteria.

    • Kefir and yogurt are staples in our fridge but when my family or I take antibiotics, we double up. I add even more to my protein shakes and have more post-dinner dessert yogurt bowls. 

      1. I go in waves of adding kimchi to my lunches.  I've hopped back on the train and now I'm trying to get some kimchi at least once a day.

      2. Usually, my food shopping "treat" for my wife is a bottle of kombucha so I've been doubling up and getting one for myself as well.

      3. Sauerkraut tends to be one of the best sources of fermented foods but I just cannot find a way to eat it without gagging despite many attempts. 

  • Eat more prebiotic foods.  Prebiotics, non-digestible fibers found in foods like green bananas, garlic, onions, and apples, serve as the fuel that nourishes the beneficial bacteria in our gut. They provide a substrate for these microorganisms to thrive, enabling them to proliferate and restore balance within the gut microbiome.

    • Examples include green bananas, garlic, onions, and apples.  They're also in the probiotic capsule I take--see the next point.

  • Take a probiotic.  The antibiotic kills life, the probiotic promotes it.  I tried probiotics way back in the day and didn't notice an effect so I stopped taking them but since this antibiotic regimen, I ordered a new type of probiotic from Primal Kitchen called Primal Probiotics (MINDBODYDAD for 10% off).  It contains 200mg of prebiotics as well as 10 billion CFU of 4 types of probiotics (Lactobacillus acidophilus, Lactobacillus rhamnosus, Lactobacillus reuteri, and Bacillus coagulans).

  • Add more fiber to your diet.  Research has shown a strong interplay between the microbiome-promoting aspects of fiber. but this study says it all when it comes down to the best: Soluble Dietary Fiber, One of the Most Important Nutrients for the Gut Microbiota.

    • The best sources of soluble fiber include black beans, brussels sprouts, avocados, and sweet potatoes.

  • Get more sleep.  Research has shown that a disruption in your sleep is linked to your gut microbiome as well. 

    • While I'm always factoring in ways to improve my sleep I've been more diligent recently, wearing my blue light blockers more often and trying to adhere to a nightly reminder to get to bed by 9.

Seeking Professional Guidance

While self-care is essential for maintaining gut health, consulting with a healthcare professional is important to address specific needs and concerns. They can provide personalized advice on dietary changes, probiotic supplements, lifestyle modifications, and appropriate antibiotic use.




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