The University of Arizona Learn About Germs


UA College of Public Health






The Good Microbes

Did you know?   It’s a shame that the microbes’ good work goes unnoticed until something goes wrong” Dr Paul Humphrys, senior lecturer in microbiology at Huddersfield University’s School of Applied Sciences in an article by Andrew Flynn, Huddersfield Daily Examiner Feb 19 2008.

Although the focus of this website is on the “bad bugs”, it is imperative that we give credit to the many good microbes on the planet. In fact, you will be relieved to know the number of good guys far outnumber the bad. A microbiologist, in a 1941 Census of Bacteria in the United States, claimed that there were 10,031 quintillion good microbes against less than 3008 quintillion bad ones. This translates into 1 harmful germ for every 30,000 good bacteria! This certainly puts a different perspective on the role that microbes play in our lives.
There are three main areas where microbes are beneficial to us: In food production, in and on the human body, and in our environment. Microbes are also frequently used in research and industry.


Did you know?   Mother Noella is a Benedictine nun at the Abbey Regina Laudis in Conneticuit where she teaches Gregorian chant. She is passionate about cheese making and the microbes involved in the process.She obtained a Ph. D. in microbiology studying the microorganisms that make Bethlem cheese. She stared in a PBS documentary titled “The Cheese Nun: Sister Noella’s Voyage of Discovery”. She first produced a St. Nectaire –type Bethlehem Cheese in 1978 and continues to make cheese to this day. In an interview by Seattle Times staff reporter Karen Gaudette, published in the May 16 2007 issue of the Gazette, she was asked: “ Is there any type of cheese that intimidates you?” Mother Noella’s response: “ I wouldn't be afraid to try anything. It's alive. You are actually eating, in a sense, decay, because microorganisms are breaking down this cheese, and we're eating byproducts of that.”

We can thank the group of food fermentating bacteria for the production of sour-dough bread, alcoholic beverages, fermented milks, and pickled vegetables. There are three types of fermentating bacteria. The lactic acid bacteria are described as microaerophilic, as they carry out their reactions with very little oxygen. These gram positive, non-spore forming bacteria produce lactic acid as the major end product of the fermentation of carbohydrates. Lactobacillus, Leuconostoc, Pediococcus and Streptococcus comprise some of the major players. A second group of bacteria of importance in food fermentations are the acetic acid producers from the Acetobacter species. A third group of bacteria are those which bring about alkaline fermentations - the Bacillus species. Of note are Bacillus subtilis, B. licheniformis and B. pumiliu. Although this third group is less known, they are important in that they provide inexpensive, high protein foods from leaves, seeds and beans to millions of people in Africa and Asia.

  • Yogurt. Yogurt is produced by bacterial fermentation of lactose, the sugar in milk. The increased acidity causes milk proteins to curd and also prevents the growth of potentially pathogenic bacteria. Some of the bacteria found in yogurt are Streptococcus salivarius subsp. thermophilus and Lactobacillus delbrueckii subsp. bulgaricus. L. acidophilus, L. casei and Bifidobacterium species may also be present.
  • Cheese. The type of bacteria used to produce cheese determines the taste, so every cheese has its own unique flavor due to the specific bacteria used in the cheese making process. Swiss cheese is made using Propionibacterium shermanii. The holes are made by large bubbles of gas produced by the bacterium in the cheese-ripening process. Streptococcus thermophilus , Streptococcus durans and Streptococcus faecalis can be used to make cheddar cheese. Blue Cheese is made by a species of Penicillium. Brevibacterium linensis is responsible for the unique taste of Limburger.
  • Other dairy. Foods such as sour cream, cottage cheese, cultured buttermilk and starter cultures rely on Leuconostoc dextranicum , Streptococcus lactis and Streptococcus cremoris bacteria.
  • Vegetables. Leuconostoc mesenteroides is a bacterium associated with the fermentation process required for making sauerkraut and pickles.
  • Mushrooms. Mushrooms are the spore-forming fruiting bodies of a filamentous fungus. Although many mushrooms are poisionous, Agaricus bisporus (the button mushroom) is one of the most widely cultivated edible mushrooms in the world.
  • Vinegar. Production of vinegar is a two stage process. First, yeasts convert sugars into alcohol then Acetobacter oxidise alcohol to acetic acid.
  • Alcoholic drinks. Brewers yeast is used in beer and wine making, converting sugars into alcohol.
  • Bread. Bakers yeast used in bread making results the microbial fermentation of sugars to produce carbon dioxide, in turn producing the bubbles that make the bread rise.
  • Vitamins. A variety of bacteria, yeasts and fungi are used for the commercial production of vitamins and supplements for consumption by humans and other animals.
  • Food flavorings. Flavorings such as monosodium glutamate (MSG) and the artificial sweetener aspartame rely heavily on the fermentation processes of microbes such as brevibacteria. Soy Sauce is made by adding mold spores of Aspergillus oryzaeto or Aspergillus soyae to soybeans and wheat. The mold, with the help of yeast and lactobacillus bacteria, produces amino acids and peptides that contribute flavor. As with cheese, different microbes can produce different tasting soy sauces.
  • Fish and other marine life. Photosynthetic algae and cyanobacteria are a major a component of marine plankton which provide a nutrient source to feed most other marine life.
  • Sausage and vacuum-packaged meats. These foods contain Lactobacillus sakei. The acidity and saltiness produced by the bacteria preserves the microbial quality of the meat by inhibiting other bacteria that would spoil the meat.
  • Legumes. Bacteria called Rhizobium attach themselves to the roots of legumes such as peas and beans creating a symbiotic relationship between the microbe and plant. The plant provides the microbe with a necessary environment, while the microbe performs a process known as “nitrogen fixation”, taking nitrogen from the air and making it into a form of “fertilizer” for the plant.
  • Chocolate! Microbes are responsible for transforming the seed of the cocao tree into chocolate. When the seeds of the tree are deposited on the ground, the yeasts initially dominate, breaking down the seed coat allowing the bitter chemicals to be removed. The yeast produce a large quantity of alcohol in this process, and eventually cause their own demise. From here the lactobacilli create a clear type of cacao vinegar. This is drained off and the acetic acid bacteria, in the presence of oxygen, finish the fermentation process on the beans. Subsequently, the beans are dried and taken to chocolate factories to be roasted, ground and mixed with sugar to make the final product.

In Our Bodies

Did you know?   Ninety five percent of all the cells in the body are bacteria, and most of these are found in the digestive tract.

Microbes colonize the human body shortly after birth, and remain with us throughout our life. These so-called “normal flora” or "indigenous microbiota" as scientists prefer to call them, are on our skin, in our nose, mouth, and urinary tract, and digestive system. Strangely, scientists still don’t know much about the human flora because they can be difficult to grow outside of the body. However, The National Institutes of Health Human Microbiome Project (HMP) is underway with the goal of identifying and characterizing the microorganisms which are found in humans.
In the acid environment of the stomach only a small number of microbes are able to survive. The small intestine usually contains small numbers microbes including Streptococci, Lactobacilli, and yeasts, such as Candida Albicans. By far, the majority of microbes are in the large intestine where an estimated one hundred trillion microbes reside. It is thought that some 500 different species reside in the gut, but probably 40 or so species predominate the mix. Some of the genera include Bacteroides, Clostridium, Fusobacterium, Eubacterium, Ruminococcus, Peptostreptococcus, and Bifidobacterium. Other genera such as Escherichia and Lactobacillus are present to a lesser extent. Fungi such as Candida and Aspergillus as well as protozoa can also be found in the digestive flora. The multitude of digestive flora are beneficial to us in many ways:

  • Digestion. They not only help us digest our food but also break up the more complex material such as the cell walls of plants, subsequently using this material to grow and multiply, and finally transforming the remains into a digestible product.
  • Vitamin production. Enzymes produced by intestinal bacteria are important in the metabolism of several vitamins including vitamin K and some of the B vitamins.
  • Immunity. Since we have digestive microbes in our gut as infants, the immune system is well trained to fight off invaders, while at the same time not attacking the good microbes. This helps protect us from infection and disease.
  • Competitive Exclusion. Good microbes in the body create competition for the germs and thus check the growth of harmful microbes. This very beneficial effect has been shown to take place in the throat, intestine, on the skin, and in the vaginal areas.
  • Antibiotic Effect. Scientists are finding that our normal flora can excrete their own antibiotics to ward off other microbes that may invade the gut and make us sick.
  • Antagonistic Effect. In addition to producing the antibiotic effect, microbes in our body can produce substances such as fatty acids, which inhibit or kill non-indigenous species.
  • Source for Prescription Antibiotics. When the bad bugs invade our bodies, the good bugs help by providing us with a way to manufacture prescription antibiotics to help fight infection. Actinomycetes are one of the primary sources for the production of the antibiotics. Actinomycetes, mainly Streptomyces species, produce tetracyclines, streptomycin, erythromycin, chloramphenicol, and many other antibiotics. Bacillus species, such as B. polymyxa and B. subtilis produce polymyxin and bacitracin. The molds Penicillium and Cephalosporium produce antibiotics such as penicillin and cephalosporin.
  • Source for Vaccines. Administration of vaccines derived from microorganisms helps immunize us against disease. Usually it is the microbe that is the causes the disease that is the source for the vaccine. Some diseases, such as smallpox, have been eradicated thanks to the widespread use of vaccination.

In the Environment

Decomposition of Biological Waste

Did you know?   There is perhaps no greater favors microbes do for us than eating our poop when we live and eating us when we die” A quote from Jeanette Farrell in her book “Invisible Allies”.

Most microbes in soil and water are heterotrophic, that is, they use a carbon source derived from organic matter as food. They may carry out respiration or fermentation, and may be aerobic or anaerobic. These microbes, including a consortium of bacteria, fungi, actinomycetes, and algae, are responsible for the decomposition of biological waste material. This includes human and other animal waste, dead plants, dead animals and food waste. Without such decomposition, the planet would be overrun with waste. Thanks to microbes, our biological waste is eaten and the primary elements that make up all life, including carbon, oxygen and nitrogen, are released and recycled in the process so that new life can be made and fed.
The processes of biological decomposition are taken advantage every day and in a multitude of ways.

  • Municipal wastewater treatment plants. Sewage treatment plants throughout the world rely on microbes to decompose human waste from sewer systems. This results in the destruction of many of the germs found in the sewage. The resulting product can be used as fertilizer.
  • Septic tank systems. Home septic systems are an alternative way to decompose human waste when municipal waste treatment facilities not available. Anaerobic bacteria naturally present in the tank decompose
  • Composting. Recycling of wastes such as food scraps and paper products in home or industrial composting is made possible by the actions of microbes. Microbes decompose the organic matter and the recycled the waste material is used as compost or mulch for agriculture or home gardening use.
  • Decomposition of some of the material in landfills. The three stages of decomposition in landfills require aerobic bacteria (using oxygen to break down the biodegradable waste into carbon dioxide and water), anaerobic bacteria that do not need oxygen (further break down wastes into hydorgen, ammonia, carbon dioxide) and finally microbes produce methane gas .
  • Decomposition of environmental materials. Microbial decomposition of leaf litter, and other organic wastes provides for nutrient recycling in the soil for plant growth. This is major source of nutrients in forest ecosystems.
  • Production of energy. Waste gases such as methane that are the result of the anaerobic decomposition process can be captured and used to generate electricity or make ethanol to fuel automobiles.

Degradation of Organic Compounds (Biodegradation)

Did you know?   In March 1989, 33,000 tons of crude oil accidently spilled from the Exxon Valdez into the Prince William Sound in Alaska. On July 26 the EPA informed Exxon that it would support a proposal by the company to use bioremediation in an effort to help with the clean-up. Fertilizers that had the ability to adhere to the oil were added to the contaminated ocean water. Consequently, the number of microbes that could degrade the oil increased. Scientific studies concluded that there was a 3 to 8 fold increase in the rate of biodegradation due to the addition of these nutrients. Bioremediation is currently approved by the United States Environmental Protection Agency.

There are a variety of hazardous organic compounds manufactured by humans that ultimately make their way into the environment. Some organisms (generally bacteria and fungi) have the unique ability to grow and reproduce by utilizing these organic chemicals as a food source. During this process wastes are degraded (used up) or converted into a less harmful form. Scientists are now researching this phenomenon of biodegradation and applying the principle to the clean-up of environmental pollution existing in soil as well as surface and ground waters. While some of these microbes exist naturally in the environment, the process of biodegradation can be enhanced by adding nutrients to a contaminated site to encourage the growth of the indigenous microbe population. Alternatively, a large number of beneficial microbes can be introduced into a toxic site. Bioremediation, as defined by the American Academy of Microbiology is "the use of living organisms to reduce or eliminate environmental hazards resulting from accumulations of toxic chemicals and other hazardous wastes".
Some of the toxic substances and the microbes responsible for biodegradation are listed below. In many instances, more than one microbe is involved along the pathway of degradation.

  • Petroleum or hydrocarbon products such as gasoline, diesel, fuel oil: Pseudomonas, Proteus, Bacillus, and Penicillum.
  • Herbicides (weed killers) and pesticides (insect killers): Alcaligenes eutrophus
    and Burkholderia cepacia degrade the pesticide 2,4-D.
  • Hazardous crude oil compounds such as benzene, toluene, xylene, naphthalene: Aspergillus niger, Micrococcus and Pseudomonas.
  • Polychlorinated biphenyls (PCB’s) coolants found at industrial sites: Comamonas, Pseudomonas, Rhodococcus spp.
  • Chlorinated solvents such as trichloroetheylene from manufacturing: Mycobacterium, Pseudomonas,Bbulkholderia

Remediation of Toxic Inorganic Compounds

Did you know?    One of the most common methods for the treatment of metal contaminated water is the use of microbial biofilms. A biofilm is a combination of organic matter and microorganisms that proliferate by attachment to the surface of an object. Many metals are attracted to and attach to these biofilms, thus removing them from the water. This ability of microorganisms has been so successful there are now commercial biomass products on the market for use in metal recovery from contaminated waters.

Toxic inorganic compounds are on the rise in our environment, and are cause for concern. The source of these compounds includes both industrial and home sources. Inorganic compounds contain no carbon source, yet some microbes can transform these compounds into other less toxic forms or concentrate them to make them easier to remove from the environment. Scientists are currently studying this microbial property in hopes to harness this ability and facilitate the removal of toxic compounds from the environment. Some of these compounds and the microbes that help with the remediation include:

  • Heavy metals such as selenium, arsenic, mercury (such as in batteries) and uranium.
  • Chromium: Alcaligenes, Pseudomonas.
  • Cadmium: Staphlococcus, Bacillus, Pseudomonas, Citrobacter.
  • Copper: Escherichia, Pseudomonas.
  • Chemical Fertilizers, including nitrate and phosphate.

Industry and Research

Microbes contribute to industry in a variety of ways.

  • Medical. In the health field they provide a way to synthesize antibiotics, create vaccines, and produce vitamins.
  • Food. As previously discussed, microbes are important in the production of various foods including cheese, alcoholic beverages and breads.
  • Agriculture. Microbes produce organic fertilizers from the decomposition of waste material. Some microbes live in association with plant roots and provide plants with essential nitrogen fertilizer.
  • Remediation. Industries involved with clean-up of contaminated sites sometimes use the actions of microbes for the remediation or stabilization of these sites.
  • Research. Microbes are a source of DNA for ongoing research and development, including recombinant DNA techniques. Applications can be found in the medical field, such as in the production of recombinant insulin. In agriculture scientists have genetically engineered plants for insect and virus resistance.