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Microbes: What They Do & How Antibiotics Change Them

Maura Meade-Callahan


Antibiotics and antibacterials can do more damage than good when they:

  • kill good bacteria inside the human body
  • destroy microbes that clean up pollution
  • lead to antibiotic resistance in microorganisms
  • make treatment of some diseases difficult when overused

January 2001


Antibiotics allow naturally resistant variants of microbes within a population to survive and reproduce. Source: Microsoft Images.

Antibiotics and antibacterials have made microbes tougher.

Microorganisms — bacteria, archaea, fungi, algae, viruses and protists — are often easy to overlook. For the most part (except fungal fruiting bodies seen as mushrooms) we can’t see microbes. The effects of microbes we feel are usually associated with an illness. Most people know that bacteria and viruses can act as “germs” and cause disease. Because of this it seems perfectly acceptable to try to wipe all of the germs out of our environment by using antibacterial agents (found in everything from hand soap to sweat socks) and antibiotics. However, our use of antibiotics and antibacterial agents is changing the microbes in our environment, making the germs tougher to beat and eliminating some beneficial microbes.

Beneficial functions of microorganisms

Microorganisms are essential to our very existence. They are ubiquitous, found in common environments such as soil, water, and air as well as exotic locales as diverse as deep sea hydrothermal vents and soda lime lakes. In these natural environments microorganisms have very specific jobs. They are responsible for recycling nutrients in our soil and purifying our water. We also use microorganisms in constructed environments to serve our own functions.

Microbes recycle nutrients in our environment.
  • Nutrient Recycling. When plants and animals take up nutrients, they are not available to other living organisms. When the plants and animals die, the nutrients remain in the carcass. If the dead material, or detritus, is not broken down by microbes, those nutrients will never become available to help sustain the life of other organisms. There are a finite amount of nutrients available in the environment and we cannot simply make more. The nutrients that are trapped in detritus must be released in order for life to continue. It is the microbial population of the environment that is responsible for this nutrient recycling.
Good bacteria inside us destroy invasive, harmful bacteria.
  • Health. We depend on having a microbial population, called our microbiota, for our health. There are normally 10 times more microbial cells on/in a human body than human cells. The good bacteria that live on and in us protect us from the bad invaders that might come our way. Without the good bacteria, the bad ones can slip in and easily cause us problems. Our own digestion has also evolved to use bacteria for assistance, allowing us to gain nutrition from plant polysaccharides that our own enzymes will not degrade. This is one of the reasons why taking antibiotics can lead to episodes of diarrhea - we have disrupted our natural gut biota.
Microbes provide food for us through fermentation.
  • Food. Microbes have been used for centuries to provide us with food. Bread is the result of a microbial fermentation of sugars to produce carbon dioxide — the bubbles that make bread rise. We owe our beer and wine to similar little yeast that convert sugars into alcohol for our consumption. Yogurt and cheese are produced by bacterial fermentation of lactose, the sugar in milk. Microbes such as phytoplankton also serve as the nutrient source that indirectly feeds all marine animals. And microbial symbioses with plants allow them to grow strong and increase productivity — sometimes they are even essential for plant survival.
Microbes can eat waste and pollution.
  • Biodegradation. Microorganisms are responsible for getting rid the waste generated by industry and households. They detoxify acid mine drainage and other toxins that we dump into the soil and water. The nutrients gained from the breakdown of these products then go to feed plants or algae, which in turn feed all animals.
Microbes purify waste water.
  • Waste Water Treatment. When we flush things down the drain or the toilet, they go to a septic system or waste water treatment plant at the end of the line. After primary mechanical treatment and aeration microbes remove organic materials from the filthy waters that flow into these systems and, eventually, water can safely be returned to the rivers and streams. The methane produced during treatment can even be used to generate heat or electricity for the operation!
Microbes are builders, making products such as vitamin C.
  • Biosynthesis. We have discovered that microorganisms are useful for making things as well. Products such as xanthan gum (a food thickener) are harvested from their bacterial producers. Most of our vitamin B12, riboflavin, and vitamin C are produced by bacterial fermentation. Approximately 70% of antibiotics currently in use are also the product of microbial fermentation.

Sources of antibiotics in the environment

In spite of all of the benefits of having a healthy microbial population, antibiotics and antibacterial agents are added to the environment at a rate of over a million pounds per week. There are several routes of entry of antimicrobial agents into the environment. Studies have shown that introduction by these routes has changed the antibiotic susceptibility of the microbes in those environments and/or changed the predominant microbes.

  • Sewage. The antibiotics that we take in are not all processed by our bodies. Some of them are expelled as waste and wind up in our waste water treatment plants. Of bacteria isolated from sludge remaining after wastewater treatment at one plant, 46.4% were resistant to multiple antibiotics. Sewage from hospitals and pharmaceutical plants has been shown to contribute to antibiotic resistance in treatment plants. Rivers contaminated with urban effluent and agricultural runoff have also been shown to have greater antibiotic resistant bacterial populations than areas upstream of the contamination source. Antibiotic resistance in streams is also indirectly selected for by an increase in industrial wastes containing heavy metals.

  • Medical waste. The dispensing of antibiotics in a medical facility inevitably leads to waste. Discharge from hospitals has been shown to cause an increase in bacterial populations resistant to certain antibiotics such as oxytetracycline.

Microbes are becoming resistant to antibiotics due to environmental pollution, overuse of antibiotics, and antibacterial agents.
  • Production. Antibiotic sales total more than $8 billion worldwide each year. That is 50 million pounds produced each year, 25 million pounds of which are prescribed for human use. Discharge of wastewater from pharmaceutical plant has been associated with an increase in the prevalence of single- and multiple-antibiotic resistance in indicator organisms.

  • Household products. Over 700 “antibacterial” household products have been introduced in the past five years. These include such items as sweat socks, toothpastes, kitchen plastics, cement and paints. The more common antibacterial ingredients in these formulations are triclosan, quartenary ammonium compounds, alcohol, and bleach. Microbes resistant to each of these compounds have been documented in nature and in some human pathogens. These products wind up in the sewage or landfill after being used in our households.

  • Sprayed on crops. About 300,000 pounds of antibiotics are used in plant production each year. They are sprayed on high-value crops such as fruit trees to prevent bacterial infections. This can select for resistant bacteria on our crops. Not all of the spray remains on the fruit. Most of the antibiotics are washed into the soil and eventually end up in the ground water.

  • Animal production. Antibiotics are commonly added at subtherapeutic levels to animal feeds as growth promoters. They are also added to fishery waters. About 24 million pounds of antibiotics are fed to animals every year. Due to this practice antibiotic resistance in foods has become a health concern. Bacteria such as drug resistant Salmonella typhimurium, Escherichia coli and Enterococcus have increased clinically as animal antibiotic use has risen. It is also possible that our normal gut microbiota have gained antibiotic resistance from antibiotic-exposed food animals. A popular theory is that vancomycin resistant strains of the bacterium Enterococcus (VRE), a major cause of postsurgical infections, have arisen in Europe due to the use of the antibiotic avoparcin as an animal growth promoter. At least one study, however, shows that in minced beef and pork, VRE occurs very rarely. The use of oxytetracycline in aquaculture has been shown to cause a seasonal shift in bacterial species towards Enterobacteriaceae and is associated with increased antibiotic resistance.

Mechanisms of spread of antibiotic resistance

Antibiotic resistance is encoded in the microbe’s DNA.

Antibiotics do not, in themselves, cause resistance. Instead, they allow naturally resistant variants within a population to survive and reproduce while those individuals without the resistance factor die. Once in a bacterial population, antibiotic resistance can spread rapidly. Even unrelated bacteria can gain resistance from their neighbors in a phenomenon called horizontal gene transfer. Resistance to antibiotics is encoded in DNA, the genetic blueprint for life. Bacteria are able to exchange DNA, especially in the form of plasmids (small, self-replicating circles of DNA) and pass resistance very rapidly.

  • Conjugation. Bacteria can fuse and exchange plasmids and sometimes chromosome fragments. Increase in mobilizing plasmids has been associated with use of antibiotics in swine husbandry. These plasmids have a broad host range and are able to cross genus lines during transfer.

  • Transfection. Viruses can infect bacteria and fungi, passing along genes from one infected organism to the next. These genes sometimes encode resistance factors. The use of antibiotic growth promoters in animal husbandry may increase the amount of free phage in intestines and may contribute to the spread of antibiotic resistance.

  • Transformation. When a bacterium lyses in its environment, any other actively-growing bacteria in that vicinity can pick up its DNA. This is another mechanism of resistance spread, since plasmids (including resistance or R plasmids) are more easily used by the recipient bacterium than chromosomal material.

Some diseases are no longer treatable with antibiotics.

Microbial populations have been shown to change due to exposure to antibiotics and antibacterial agents. We are seeing a rise in antibiotic resistance all around the world. Some diseases that were previously susceptible to a variety of antibiotics now are untreatable. According to the Center for Disease Control (CDC), approximately 70 percent of infections that people get while hospitalized are now resistant to at least one antibiotic. Resistance to antibiotics is rapidly outpacing our ability to synthesize new drugs. While only a very small proportion of bacteria in our lives can potentially harm us, we are losing our arsenal to treat these rare infections.

Curbing spread of antibiotic resistance

Antibiotic resistance is inevitable. However, there are a few things that we, as consumers, can do to control the spread of antibiotic resistance.

Antibiotics have no effect on viral ailments but people continue to use them.
  • Do not seek antibiotics for the treatment of viral infections such as the common cold, sore throat, bronchitis, or flu. Antibiotics have no effect on viral diseases. Taking antibiotics improperly simply leads to more antibiotics in the sewage and a buildup of antibiotic resistant bacteria in your microbiota.

  • Take the full course of antibiotics when they are prescribed. Stopping when you feel better means that some bacteria in your body were exposed to only small doses of the antibiotic and have survived. They are now resistant to small amounts of the antibiotic. The next time you get an infection they will not be so easily killed.

Antibacterial soap and other household products destroy good bacteria.
  • Avoid unnecessary antibacterial household products. We need the bacteria that surround us, and it is possible that trying to kill them is causing harm. By introducing antibacterial products into the landfills and sewage we are ensuring that only the microbes that are resistant to these products survive. Research is underway to determine if we are selecting for resistant bacterial populations causing antibacterial agents, like antibiotics, to lose their effectiveness or disrupt the effectiveness of the wastewater treatment plants or nutrient cycling in the soil. Use antibacterial hand soaps only when dealing with ill and immunocompromised individuals.

  • Wash your hands. The best way to stop the spread of any bacterial infection is through simple hygiene measures. Washing hands in warm soapy water for at least 20 seconds is enough to eliminate most of the potential pathogens. Also be sure to wash all fruits and vegetables well before eating them.


Microbes are an essential part of all life on earth. The addition of antibiotics and antibacterial compounds is changing the microbial populations of the soil, water, and our own microbiota. Recognizing the numerous invaluable functions of microbes should decrease the germophobia prevalent in Western societies.

Maura Meade-Callahan, Ph.D., is a professor of biology at Allegheny College in Meadville, PA. There she teaches biology, microbiology, and antimicrobial agent resistance in bacteria. She earned her Ph.D. in plant pathology at North Carolina State University. She is actively involved in a graduate research ethics project of the Association for Practical and Professional Ethics and in various aspects of undergraduate microbiology education through the American Society for Microbiology. She serves as a reviewer for several journals, textbooks, and web sites.

4/09 update: Unable to locate Dr. Callahan’s current information online.

Microbes: What They Do & How Antibiotics Change Them

Antibiotic resistance links

Environment Literacy Council provides basic information about antibiotic resistance with several notable links to learn more about the problem.

Food and Environment Electronic Digest

FEED is a free email newsletter that will keep you informed about food production and safety issues.

Microbiology portal is a good starting point for finding information concerning microbiology.

Infectious diseases guidance, U.K.

The Health Protection Agency (HPA) is a national organization for England and Wales “dedicated to protecting people’s health and reducing the impact of infectious diseases, chemical hazards, poisons, and radiation hazards.”

Food Animal Agriculture

The 2004 USDA report, “Strategies to Reduce Antimicrobial Resistance in Food Animal Agriculture.”

“The rise of antibiotic-resistant infections”

An article by Ricki Lewis, Ph.D. in the U.S. Food and Drug Administration (USFDA) Consumer Magazine (1995) reviewing the problem of antibiotic resistance and the mechanisms by which bacteria become resistant to antibiotics and other environmental chemicals.

Read a book

Natural Alternatives to Antibiotics by John McKenna offers information on the herbal remedies, nutritional supplements, and dietary changes that can combat bacterial infections without the use of antibiotics (Avery Publishing Group, 1996).


Understanding Evolution

Your one-stop source for information on evolution. Learn the facts in Evolution 101, browse the resource library, read about evolution in the news, or discover a wealth of materials to help educate others about evolution and related concepts—it’s all right here!

Alliance for the Prudent Use of Antibiotics

“…dedicated to promoting proper antibiotic use and curbing antibiotic resistance worldwide. We promote global public health by raising public awareness through education and research projects on proper antibiotic use and antibiotic resistance.” Get involved options on home page.

Center for Science in the Public Interest Antibiotic Resistance Project

“CSPI is a nonprofit education and advocacy organization that focuses on improving the safety and nutritional quality of our food supply…It represents citizens’ interests before legislative, regulatory, and judicial bodies; and it works to ensure advances in science are used for the public good.” original lesson

This lesson has been written by a science educator to specifically accompany the above article. It includes article content and extension questions, as well as activity handouts for different grade levels.

Lesson Title: Microbes: Too Smart for Antibiotics?
Levels: middle school - undergraduate
Summary: This lesson focuses on examining why microbes become resistant to antibiotics, as well as their roles in human health and the environment. Students can produce public-awareness campaigns on antibiotic use, create yogurt recipe cards, develop a commercial bioremediation product, experiment with simulated germs… and more!

Download/view lesson.
(To open the lesson’s PDF file, you need Adobe Acrobat Reader free software.)

Useful links for educators: extension activities

The following links will take you to middle - high school level activities that will complement some of the activities suggested in the above original lesson:

Useful links for student research

In addition to the links in the “learn more” section above:


Two glossaries of terms. The second link also includes phytoremediation terms.


  • » Alekshun, M.N. and S.B. Levy. 1999. “The mar regulon: multiple resistance to antibiotics and other toxic insults.” Trends Microbiol 7: 410-13.
  • » Levy, Stuart. 1998. “The challenge of antibiotic resistance.” Scientific American, May issue.
  • » McMurray L.M., Oethinger M., Levy S.B. 1998. “Triclosan targets lipid synthesis.” Nature 394: 531-2.
  • » Meade, M.J. and T.M. Callahan. 2000. “Unique mechanism of triclosan resistance identified in environmental isolates.” Abstracts of the 100th annual meeting of the American Society for Microbiology, Los Angeles, CA.
  • » Meade, M.J. 2000. “The horror in your hand soap: triclosan resistance in environmental microbes.” Presentation at Slippery Rock University.
  • » Rook, G.A.W. and J.L. Stanford. 1998. “Give us this day our daily germs.” Immunol Today 19: 113-6.
  • » Russell, A.D. et al. 1998. “Possible link between bacterial resistance and use of antibiotics and biocides.” Antimicrob Agents Chemother, 42: 2151.


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