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What are antibiotics?

Antibiotics are drugs that either kill bacteria or interfere with their reproduction and growth. They are used to treat and prevent bacterial infections and have been a powerful tool in managing bacterial diseases.1 Examples of diseases that can be successfully treated with antibiotics are urinary tract infections, pneumonia, and meningitis.

Although antibiotics can be used to treat bacterial infections, they do not work against viruses. The severity or length of common viral infections such as the cold or influenza will not be affected by antibiotics, though antibiotics can be helpful in preventing or treating secondary, bacterial infections.

Antibiotics can save lives. Life spans worldwide and in the U.S. have increased in the last 80 years, partly due to antibiotic use.

However, antibiotics have also been overused. Antibiotic drug use increased worldwide by 35% between 2000 and 2010, mainly in developing countries. That said, the U.S. was the third largest consumer of antibiotics in 2010, after India and China.2 Increasing consumption of antibiotics – along with inappropriate prescriptions, extensive use in agriculture, and lack of new drug development – have contributed to antibiotic resistance, which endangers their efficacy.3

What are antibiotics mechanism of action?

Antibiotics are mainly used to treat infectious diseases caused by bacteria. Antibiotics can prevent growth or even kill microbes by interfering with essential processes in microbial cells, such as4:

  • Synthesis of cell walls
  • Protein synthesis
  • Nucleic acid synthesis
  • Metabolic pathways

While most antibiotics are safe to use in most humans, some can cause side effects, depending on how much and how often they are used. The most common side effects of antibiotics are (in order of frequency)5:

  • Hypersensitivity: drug fever, drug rash, anaphylactic reactions, photosensitivity
  • Gastrointestinal: nausea and vomiting, diarrhea, acute pancreatitis
  • Hematologic: reduction in number of blood cells
  • Hepatic: liver inflammation and malfunction

Other than drug fever and drug rash, which can occur with many types of antibiotics, most of these side effects are specific to a certain antibiotic. Most side effects are rapidly reversible by stopping the medication.5

 Antibiotic resistance

Antibiotic resistance occurs when microbes are no longer sensitive to antibiotics, making it more difficult to treat infections. There are a few ways in which bacteria can become resistant to an antibiotic. One mechanism is genetic mutation, which occurs spontaneously and quite frequently in bacteria, especially in rapidly growing bacterial species. Another way of becoming resistant to an antibiotic is if a bacterium receives resistant genes from a neighboring bacterium in a process called horizontal gene transfer.6

Overconsumption and inappropriate prescription of antibiotics have contributed to the development of antibiotic resistant bacteria worldwide.7 These bacteria can spread between humans or animals, resulting in infections with few treatment options. The increasing types of resistant bacteria makes treating infections more difficult and expensive, since the medicines available are limited.8

In general, countries with high antibiotic consumption have higher rates of antibiotic resistance.7 In 2015, antibiotic resistant pathogens were estimated to cause over 50,000 deaths a year in Europe and the U.S.9 The economic burden on the U.S. economy by antibiotic resistant infections is approximately $20 billion in health care costs and $35 billion a year in lost productivity, not counting its effect on families and communities.3

How does this topic relate to my microbiome?

Antibiotics are often used to treat a bacterial infection, such as strep throat, pneumonia, or meningitis. Unfortunately, these drugs cannot distinguish between the bacteria that cause the infection and some of those that naturally live in and on our bodies. As a result, taking antibiotics to treat an infection will often result in “collateral damage”. In particular, antibiotic consumption can alter the gut microbiome, sometimes resulting in dysbiosis (a disturbance in the composition and function of gut microbiota). After ending antibiotic treatment, the gut microbiota is capable of restoring itself, but it often fails to completely recover.10

A gut microbiome altered by antibiotics can lead to9,10:

  • Accumulation of antibiotic resistances
  • Antibiotic-associated diarrhea
  • Clostridium difficile infections
  • Compromised immune balance and tolerance, which – together with genetic and other factors – could contribute to atopic, inflammatory, and autoimmune diseases (allergies, asthma, necrotizing enterocolitis, inflammatory bowel disease, irritable bowel syndrome, etc.)
  • Deregulated metabolism (obesity, metabolic syndrome, diabetes)
  • Increased susceptibility to infections

How can people take action?

Antibiotic resistance is a global economic and health crisis. The Centers of Disease Control and Prevention (CDC) and other organizations have made recommendations to various health care providers and facilities, such as11:

  • Adopting an antibiotic stewardship program
  • Improving diagnosis, tracking, and prescribing practices
  • Optimizing therapeutic regimens
  • Preventing infection transmission

Actions that consumers can take to limit antibiotic resistance are6,12:

  • Washing hands often and thoroughly with regular soap and water
  • Not asking for antibiotics in the case of a viral infection
  • Taking antibiotics exactly as prescribed and completing the full course of treatment
  • Not taking antibiotics that were left over from another treatment or patient
  • Buying meat and produce that were produced without antibiotics


1. Sengupta, S., Chattopadhyay, M. K., & Grossart, H. P. (2013). The multifaceted roles of antibiotics and antibiotic resistance in nature. Frontiers in Microbiology, 4(MAR), 1–13.

2. Van Boeckel, T. P., Gandra, S., Ashok, A., Caudron, Q., Grenfell, B. T., Levin, S. A., & Laxminarayan, R. (2014). Global antibiotic consumption 2000 to 2010: An analysis of national pharmaceutical sales data. The Lancet Infectious Diseases, 14(8), 742–750.

3. Ventola, C. L. (2015a). The antibiotic resistance crisis: part 1: causes and threats. P & T : A Peer-Reviewed Journal for Formulary Management, 40(4), 277–283.

4. Ren, B., Huang, P., Zhang, J., He, W., Han, J., Liu, X., & Zhang, L. (2015). Main Applicatons of Antibiotics. In S. Sanchez & A. L. Demain (Eds.), Antibiotics (pp. 19–47). Caister Academic Press.

5. Cunha, B. A. (2001). Antibiotic Side Effects. Medical Clinics of North America, 85(1), 149–185.

6. Levy, S. B. (1998). The challenge of antibiotic resistance. Scientific American, 278(3), 46–53.

7. Goossens, H. (2009). Antibiotic consumption and link to resistance. Clinical Microbiology and Infection, 15(SUPPL. 3), 12–15.

8. Rather, I. A., Kim, B. C., Bajpai, V. K., & Park, Y. H. (2017). Self-medication and antibiotic resistance: Crisis, current challenges, and prevention. Saudi Journal of Biological Sciences, 24(4), 808–812.

9. Langdon, A., Crook, N., & Dantas, G. (2016). The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Medicine, 8(1), 39.

10. Francino, M. P. (2016). Antibiotics and the human gut microbiome: Dysbioses and accumulation of resistances. Frontiers in Microbiology, 6(JAN), 1–11.

11. Ventola, C. L. (2015b). The antibiotic resistance crisis: part 2: management strategies and new agents. P & T : A Peer-Reviewed Journal for Formulary Management, 40(5), 344–352.

12. Francois Watkins LK, Sanchez GV, Albert AP, Roberts RM, Hicks LA. (2015). Knowledge and Attitudes Regarding Antibiotic Use Among Adult Consumers, Adult Hispanic Consumers, and Health Care Providers — United States, 2012–2013. Morbidity and Mortality Weekly Report 64(28);767-770.