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Bacteria: More Than Pathogens

Trudy M. Wassenaar


There are more bacteria on Earth than there are humans. Bacteria:

  • inhabit every environment on the planet, playing a key ecological role
  • can be good for our health — for example, by helping us digest food
  • can cause disease, but the human body is not the natural host for many bacteria

July 2002


Bacteria are associated with the three D’s: dirt, disease and death but not all of them are harmful. Source: Microsoft Images.

Misunderstood bacteria

Bacteria are usually associated with dirt, disease, and death.

Bacteria suffer from negative public relations. You probably associate bacteria with the three D’s: dirt, disease and death. And indeed, for centuries bacterial infections were the major cause of infant and child mortality worldwide. Child mortality began to decline after people were educated about better hygiene. The decline continued with the introduction of antibiotics for better treatment and vaccination for prevention of common deadly diseases.

Bacteria are certainly involved in dirt, disease and death, to which we should add decay. Spoilage of leftover food, decomposition of garden cuttings, decay of dead bodies, or smelly water in a forgotten vase, are all the result of bacterial activity. As is body odor, caries, strep throat, or bubonic plague, to name a few diseases from both ends of the spectrum. No wonder that bacteria receive a bad press.

Bacteria that caused large-scale disease in our history may be close to extinction.

Commercials want us to believe that the only good bacterium is a dead bacterium. Antimicrobial agents are added to tooth paste, soaps, detergents, and plastics. There is no Society for the Protection of Bacteria, although there is a satirical initiative for the Ethical Treatment of Bacteria.1 Some bacteria may even hover on the edge of extinction, and it is no coincidence that these are pathogenic (disease-causing) bacteria such as Salmonella typhi (the cause of typhoid fever) or Yersinia pestis (the cause of plague). Fortunately for the little critters, populations survive in remote areas where they are not efficiently hunted with vaccines and antimicrobials, and people are still at risk for the diseases they cause in these places.

The bacterial kingdom

It is about time we take a closer look at the Bacterial Kingdom, with capitals. For a Kingdom it is, biologically speaking, and the ancient lineage, diversity, and evolutionary power of its inhabitants deserve royal treatment rather than disgust.

Before kindling fascination for the world of bacteria, a common misconception must be cleared: bacteria are not viruses.

A bacterium differs from a virus in its structure and in the way it inhabits a host.
  • Whereas most bacteria live as independent cells with a membrane to separate them from the outside world, viruses can only multiply inside, and to the detriment of, the cells they infect. Interestingly, some viruses, called bacteriophages, have specialized to infect bacteria.2,3

  • Viruses consist only of genetic material (DNA or RNA) surrounded by a protein shell. They cannot metabolize and once inside a host cell, their genetic material hijacks the cell’s machinery to produce replicas of the virus.

  • Bacteria are much more similar to you and me. They exhibit the basic characteristics of all living things — they breathe, metabolize, produce waste, and maintain a membrane potential. However, they do not have a nucleus in which their DNA is separated from the rest of the cell, as plants and animals do, and that is the major distinction between prokaryotes (a type of cell that most microorganisms are made of, including all bacteria) and eukaryotes (a different type of cell making up nucleated microorganisms, such as yeasts, or cells in an organism, e.g., human).

  • Both viruses and bacteria can cause disease. However, not all types of viruses cause disease in humans, and not all bacteria cause disease.

The majority of bacteria are harmless and some are beneficial.

Another common misconception is that all bacteria are bad for you. Some bacteria you’d better not meet, but the majority of them are completely harmless, and some are highly beneficial to us. Confusingly, certain bacteria can be beneficial to some animals, and pathogenic to others. More commonly, pathogenic bacteria are harmful only to a limited number of hosts, or even only to one, whereas they live happily within other hosts without causing trouble. If the suffering host happens to be human, the culprit bacteria are called human pathogens; however, from the bacterial point of view, humans are just the wrong host to be in. So who is to blame for the disease?

Most bacteria are completely harmless

Harmless bacteria can become deadly in certain circumstances.

Although a tree can kill a person when it falls, we usually don’t regard trees as harmful. The same is true for most bacteria — although they may cause problems under specific conditions, they usually live their lives without interfering with ours. An example is Pseudomonas aeruginosa, which commonly lives in soil without doing harm. However, if it is inhaled by a person with Cystic Fibrosis, it can colonize their lungs and cause lethal infections.4

For many bacteria, the human body is not the right place to live in at all.

  • They couldn’t cope with the lack of oxygen (inside our cells the oxygen concentration is lower than that of air) or with the presence of oxygen (for bacteria that live in oxygen-deprived environments, oxygen is toxic).
The human body is not the natural environment for many bacteria.
  • They couldn’t withstand our defense mechanisms such as the salt present on our skin and in our tears, the lack of iron (a smart device keeps iron, a vital element to all living organisms, inaccessible to most microorganisms in our body), or with the toxic radicals that cells release when under attack of bacteria.

  • It could be too warm for them, or too cold, as certain bacteria have specific temperature requirements to grow.

  • Or they could be deprived of food, as the members of the Bacterial Kingdom have specialized to live on almost anything, but each species has specific nutrient needs.

  • In conclusion, we have little to fear from most bacteria that we encounter.

Our bodies can resist most bacterial attacks.

It is no big surprise that we are relatively inert to bacteria. After all, mammals have evolved in the presence of bacteria, and have developed specialized strategies to keep bacteria under control. In contrast to what your mother taught you, soap is not essential to survive. Our body can resist the bombardment of bacteria it receives every day quite efficiently. Just as well that we can’t see them (for the idea is unpleasant) but with every breath of air, every bite we take, little bugs are unknowingly entering our body. And this shouldn’t worry you in the least. As long as you keep the troublemakers — the real pathogens — out.

We couldn’t live without bacteria

The human body is home to millions of beneficial bacteria.

We house millions of bacteria on our skin and in our nose, mouth, and gut:

  • up to 500 species can be found as normal oral flora5
  • there can easily be 25 species living in a single mouth
  • a milliliter of saliva can contain as many as 40 million (4 x 107) bacterial cells6
  • 108 bacterial cells present in the cecum (the initial part of the colon) per milliliter of content is normal and many of these species are different from those found in the mouth7
Antibiotics can wipe out our body’s beneficial bacteria, causing unwanted health consequences.

Strictly speaking, the inside of our mouth, stomach and intestines are part of our outer surfaces. Although they are inside our body, their surfaces are in direct contact with the outside world, and as food particles pass the mucosal inner lining of our intestines, hitchhiking bacteria can stay there and multiply. We are born sterile (free of bacteria) but within hours we are colonized by our little friends, not to be left alone again.

Without bacteria we would not survive. They help us digest our food, produce vitamins, and occupy niches that would otherwise be available for competing pathogens. This competitive effect becomes apparent when we wipe out a large proportion of our intestinal flora, for instance by an antibiotic that is prescribed to treat a bacterial infection. Diarrhea is frequently the unwanted result, as ‘foreign’ bacteria take their chance to occupy the ‘empty’ niches. Healthy bacteria take over in time, so that in most cases the side effects of antibiotics are soon gone. Bacterial populations grow into a state of equilibrium until some external factor disturbs it again.

Certain bacteria are good for you

For centuries, people have eaten certain food deliberately for the bacteria it contains and have used bacteria in food preparation.

Certain foods and the way we process food depend on bacteria.
We can buy supplements or foods with beneficial bacteria.
  • The best-known example is the consumption of yogurt and other fermented milk products, which have the combined effect of reducing spoilage, and enhancing tolerance for partially lactose-intolerant individuals.

  • A major industry has developed to produce bacterial preparations, in the form of powders, drinks, and dairy products; all sold as healthy and beneficial (and sometimes tasty) supplements. Although some of their promises are unrealistic (some products don’t even contain viable bacteria), it is generally accepted that certain bacteria are beneficial, especially when intestinal flora is unbalanced (as with antibiotic-associated diarrhea). The most commonly used bacterial species as so-called probiotics are lactobacilli and bifidobacterium.8

  • A number of bacterial species are required for the preparation of food, and may or may not arrive on our plate alive.9 Notably, many cheese varieties are dependent on their characteristic bacterial starter culture. Fermenting bacteria are required to produce sausages and sauerkraut; they even help cacao and coffee beans to attain their desired flavor.10

Earth: the planet of bacteria

In a gram of soil, approximately 108 bacteria are present11 and these are estimated to represent over 10,000 species. Interestingly, there are more than 1030 bacteria on earth, compared with fewer than 1010 humans.12

Conclusion: Bacteria are essential to human health and the world’s ecosystems.
  • Bacteria were the first living organisms found on Earth.
  • They inhabit deserts, ice caps, oceans and hot springs.
  • The number of bacterial species worldwide is estimated to be more than a thousand million.11 Their individual sizes may be insignificant, but their number and diversity is unimaginably large.
  • Bacteria contribute substantially to the total biomass in marine environments.13 And, since oceans cover 70% of our planet’s surface, bacteria make up a significant part of the total biomass on Earth.

These facts are truly impressive for organisms so small that they are invisible to the eye. It is to our advantage to look at bacteria as more than just pathogens.

Trudy Wassenaar, Ph.D., is a molecular biologist specializing in microbiology. She has done research at the University of Amsterdam and the University of Utrecht (The Netherlands), as well as at the University of Mainz (Germany), for over 15 years. In 2000, she founded a consulting company to assist research groups in academia and governmental agencies with the development of research strategies and dissemination of results. She is Curator of the Virtual Museum of Bacteria (supported by the Foundation for Bacteriology).

Bacteria: More Than Pathogens

Virtual Museum of Bacteria

This site brings together information and links on bacteria, bacteriology, and related topics available on the web, as well as images of bacteria.

CELLS Alive!

Unique images of microorganisms that cause illness, and the blood cells that do battle to keep you well. Includes links to sites offering further information on microbiology, infectious diseases and cell biology.

The Microbe Zoo

A visually stimulating visit to Dirtland, Water World, and other pavilions in this virtual zoo to discover the microbes that inhabit different environments. Good introduction to microbes for young people and adults who know little about the critters.

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


MyMicrobiologyPlace is a central place for students to access the online materials that will help them succeed in their microbiology course. This 24/7 personal study site lets students make the most of their valuable study time with book-specific materials for learning, practicing, and self-quizzing.

MicrobeWorld Radio Archives

MicrobeWorld Radio was an educational outreach initiative that revolved around a daily, 90-second radio and podcast series designed to increase public understanding and appreciation of the vital role microbes play on our planet and to promote the science of microbiology. MicrobeWorld Radio debuted in January 2003 and was discontinued in November 2008. Below is a searchable database of the show’s archives containing over 1,000 episodes on a wide variety of subjects.

Clean Hands campaign

The American Society for Microbiology asks you to spread the “importance of handwashing.” The site offers educational materials designed for healthcare professionals and consumers including posters, a brochure, and stickers, which can be downloaded from the site.

Virology meetings worldwide

A compendium of current events in virology, with information on meetings and registration. Of interest to professionals and students. 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: Bacteria: Friend or Foe?
Levels: middle school - undergraduate
Summary: This lesson explores “good” and “bad” bacteria. Students can draw “Wanted!” bacteria mug shots, create composting trials and designs, produce a skit involving a boastful virus and bacterium, experiment with soil and ordinary objects in the lab, write a news story about an outbreak, complete a multiple-choice bacteria quiz … and more!

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

Useful links for student research

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


  1. “Resolution of the National Organization for the Ethical Treatment of Bacteria,” a satirical campaign, accessed online 7-02 but no longer available (was
  2. “Bacteria can be ill.” Cells Alive!
  3. “Oh goodness, my E. coli has a virus!” Cells Alive!
  4. Brennan AL, Geddes DM. 2002. “Cystic fibrosis.” Curr Opin Infect Dis; 15:175-182.
  5. Paster BJ, Boches SK, Galvin JL, Ericson RE, Lau CN, Levanos VA, Sahasrabudhe A Dewhirst FE. 2001 “Bacterial diversity in human subgingival plaque.” J Bacteriol; 183:3770-3783.
  6. Aps JK, Van den Maagdenberg K, Delanghe JR, Martens LC. 2002. “Flow cytometry as a new method to quantify the cellular content of human saliva and its relation to gingivitis.” Clin Chim Acta; 321:35-41
  7. Marteau P, Pochart P, Dore J, Bera-Maillet C, Bernalier A, Corthier G. 2001. “Comparative study of bacterial groups within the human cecal and fecal microbiota.” Appl Environ Microbiol; 67:4939-4942.
  8. Saarela M, Mogensen G, Fonden R, Matto J, Mattila-Sandholm T. 2000. “Probiotic bacteria: safety, functional and technological properties.” J Biotechnol; 84:197-215.
  9. “Good bacteria in food.” The Virtual Museum of Bacteria. 4/9/09: Link no longer available.
  10. “What role, if any do yeasts play in the cocoa production process?” International Cocoa Organization.
  11. Bach HJ, Tomanova J, Schloter M, Munch JC. 2002. “Enumeration of total bacteria and bacteria with genes for proteolytic activity in pure cultures and in environmental samples by quantitative PCR mediated amplification.” J Microbiol Methods; 49:235-245.
  12. William B. Whitman, David C. Coleman, and William J. Wiebe. 1998. “Prokaryotes: the unseen majority.” PNAS 95: 6578-6583. Editor’s Note (11/02): The biomass of the world’s humans plus their domestic livestock is only exceeded by the estimated combined biomass of the world’s bacteria, according to the World Atlas of Biodiversity: Earth’s Living Resources for the 21st Century, United Nations Environment Programme World Conservation Monitoring Centre (University of California Press, 2002).
  13. Fukuda R, Ogawa H, Nagata T, Koike I I. 1998. “Direct determination of carbon and nitrogen contents of natural bacterial assemblages in marine environments.” Appl Environ Microbiol; 64:3352-3358.


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