The long-term effects of antibiotics

The long-term effects of antibiotics

Have you had a round of antibiotics recently? With over 40% of adults and 70% of children taking one or more antibiotics every year there’s a good chance you have.  When it comes to fighting off a serious bacterial infection, an antibiotic can be life-saving (It was an intervenous antibitoic that saved my life in Thailand when I had life-threatening food poisoning), but the negative effects of their overuse and misuse are highlighting a need for us to get smarter about how and when these are handed out.

Over 10% of those taking antibiotics suffer from a growing list of negative side-effects

On the lining of our gut lives a very delicate balance of over 100 trillion bacteria, which works out to be around 3 pounds worth! These bacteria are known as our healthy gut flora and play a vital role in immunity, in the absorption of essential nutrients, controlling the breakdown of glucose for energy, in the development of obesity, and can even determine our behaviour.

All these functions can be slowed down or altered as an antibiotic unintentionally targets our gut flora, leading to depleted bacterial colonies that are no longer finely balanced. New information is beginning to show that this direct effect is only part of the story, and the rest of the developing picture is a whole lot more complicated than we thought.  In obesity, as I wrote about here, researchers have been linking a disruption in the balance of flora to an increase in weight. Dr. Katherine Pollard, a genetics scientist, says that this explanation is just too simple. She sees that the size of the genetic material (the genome) from the bacteria in our gut could be a more important indicator for obesity.


Spread out, the lining of our intestine would cover an area equivalent to a basketball court

Further, research out of Oregon State University has suggested that the use of antibiotics may also destroy the cells lining our intestine. This is a consequence far worse than we could have imagined.

The cells that line our intestinal walls are known as the intestinal epithelium, and just as the bacterial colonies living on them, they are vital in digestion, immunity, and are a wall of defence against invading pathogens. In these cells lives the powerhouse of all living cells, the mitochondria. This is the cells’ battery pack that converts food to energy, and its health is vital for our overall health. The study found that adding antibiotics to mouse models disrupted the function of mitochondria in the epithelium, and in turn killed the cells.

Why would antibiotics target mitochondria? Mitochondria are actually believed to have evolved from bacteria as they share some characteristics, and so it’s understandable that an antibiotic would mistake this for an unwanted pathogen.

The Dangers Of Overusing Antibiotics

One of the greatest issues we face in our modern world is the antibiotic resistant pathogens that are threatening the safety of our hospitals. As Dr. Edward Belongia and Benjamin Schwartz state in a 1998 article in the British Medical Journal, “Recent antibiotic use is a well documented risk factor for infection or colonization with resistant pathogens. Despite this recognition, unnecessary antibiotic prescribing remains common. In the United States more than a fifth of all antibiotic prescriptions for children and adults are written for upper respiratory tract infections or bronchitis, conditions are are almost always viral. This finding are consistent with results from focus groups among doctors, in which participants have estimated that 10% to 50% of outpatient antibiotic prescriptions are unnecessary.”

More recent papers published in the Oxford Journals of Medicine & Health Promotions (2007) and theCanadian Medical Association Journal (2012), demonstrations that the issue of the overuse of antibiotics continues. The threat we face from antibiotic resistant pathogens is becoming more and more of a concern to the point where in 2015 the CDC (The Centers for Disease Control and Prevention) launched the Get Smart About Antibiotics Week to raise awareness in doctors and patients about the threat of antibiotic resistance and the importance of appropriate antibiotic prescribing and use.

The researchers suggest that a better way of dealing with a bacterial infection may be to boost our healthy gut flora so they can outcompete any unwanted ones.  So what can you do to maintain and boost a healthy gut flora?

How To Maintain A Healthy Gut Flora

Reduce or Eliminate When You Can:

Why? These destroy the beneficial bacteria in your gut and feed the harmful bacteria and yeast.

  • Unnecessary antibiotics and meat grown with antibiotic feed
  • Corticoid-steroids
  • Birth control pills and hormonal contraceptives
  • Sugar: Read more here
  • Processed and refined foods
  • Chlorinated water
  • Antibacterial soap and chemical cleaning agents
  • Pesticides

Introduce / Increase:

Why? These are non-pasteurized, probiotic-packed fermented foods.

  • Sauerkraut – fermented cabbage
  • Fermented vegetables*
  • Kimchi – spicy Korean dish of fermented cabbage
  • Miso – fermented soybeans **
  •  Tempeh – fermented soybeans **
  •  Kefir – fermented milk **
  • Natto – fermented soy **
  • Tamari – fermented soy**

*Fermented vegetables – carrots, beets, cucumber and ginger are all examples of vegetable that can be fermented. Commercial varieties are available in the refrigerator section of your local health food store. They can also be made at home.These fermented foods have been used traditionally by different cultures but do contain allergens or intolerances that can be problematic for some people. Fortunately the fermentation process can assist in the digestion of these foods and may eliminate the negative symptoms of ingestion.

** Provided you do not have an intolerance or allergy


1. R. A. Weinstein: “Controlling antimicrobial resistance in hospitals: infection control and use of antibiotics.” Emerg Infect Dis. 2001 Mar-Apr; 7(2): 188–192. PMCID: PMC2631704
2. Morgun, Andrey, Amiran Dzutsev, Xiaoxi Dong, Renee L. Greer, D. Joseph Sexton, Jacques Ravel, Martin Schuster, William Hsiao, Polly Matzinger, and Natalia Shulzhenko. “Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks.” Gut (2015): gutjnl-2014.
3. Gladstone Institutes. “Mapping the gut microbiome to better understand its role in obesity.” ScienceDaily. February 19, 2015
4. Peterson, Lance W., and David Artis. “Intestinal epithelial cells: regulators of barrier function and immune homeostasis.” Nature Reviews Immunology 14, no. 3 (2014): 141-153.
5. G.G.Khachatourians: “Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria” CMAJ November 3, 1998 vol. 159 no. 9
6. Edward A Belongia, Benjamin Schwartz: “Strategies for promoting judicious use of antibiotics by doctors and patients.” British Medical Journal, International edition317.7159 (Sep 5, 1998): 668-71.
7. Sonia E. Wutzke, Margaret A. Artist, Linda A. Kehoe, Miriam Fletcher, Judith M. Mackson and Lynn M. Weekes: “Evaluation of a national programme to reduce inappropriate use of antibiotics for upper respiratory tract infections: effects on consumer awareness, beliefs, attitudes and behaviour in Australia” Oxford Journals Medicine & Health Health Promotion International Volume 22, Issue 1Pp. 53-64.2007
8. France Légaré, MD PhD⇓, Michel Labrecque, MD PhD, Michel Cauchon, MD, Josette Castel, MD MSc, Stéphane Turcotte, MSc, Jeremy Grimshaw, MB ChB PhD: “Training family physicians in shared decision-making to reduce the overuse of antibiotics in acute respiratory infections: a cluster randomized trial.” CMAJ September 18, 2012 vol. 184 no. 13 First published July 30, 2012, doi: 10.1503/cmaj.120568
9. The Centers for Disease Control and Prevention: Get Smart About Antibiotics Week is an annual one-week observance to raise awareness of the threat of antibiotic resistance and the importance of appropriate antibiotic prescribing and use.
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