Microbiology and You: An Introduction
Chapter 1
Microbiology as a discipline has been growing and evolving since the 1600's. The topics studied in microbiology are as varied and wide ranging as the organisms or entities involved. Microbiologists can study bacteria (bacteriology), or viruses (virology), or fungi (mycology) or protozoans, or algae, or human response to infection (immunology), or multi-cellular animals (parasitology - study of parasitic protozoans and worms) or recombinant DNA technologies. The only 'requirement' is that the object of study has a microscopic stage of development. So the word microbe or microorganism is a very generic term and can apply to vastly different types of organisms.
Your first thoughts about microbiology and microorganisms are probably very negative and may include memories of your last bout with strep throat or some random skin infection. Although, some microorganisms are pathogenic, i.e., they cause disease, most are not harmful and in fact many of them are essential for the existence life on earth as we know it today. Pathogens are certainly important and it is essential that we understand these microbes, their capabilities, their pathogenic mechanisms and their susceptibilities to treatment.
Microorganisms are found nearly everywhere and are essential for life on earth. Bacterial have been isolated from boiling water in hot springs (see image to the right) and from ice cores from glaciers. They are in the air, water, soil and on your skin. And again, most of these organisms are not pathogenic but necessary as part of the normal flora. Environmentally, microbes are important in recycling organic debris, fixing nitrogen gas from the atmosphere into an organic form usable by all forms of life, absorbing carbon dioxide and releasing molecular oxygen through photosynthesis, and biogeochemical cycling of nutrients, just to name a few of their roles. In us microbes play an essential role in maintaining our health. Our normal flora helps protect us from pathogens. E. coli, a well known intestinal bacterium, is present in the colon of every human. This organism produces vitamin K and secretes it into the lumen of the colon. Our bodies own cells do not produce enough vitamin K to meet our needs. Vitamin K is essential for the blood clotting cascade; without vitamin K minor cuts would bleed uncontrollably. So you should thank E. coli every time you get a paper cut.
Microbes, microbial enzymes and microbial products are also the mainstay of biotechnology and commercial industries today. Today, pharmaceuticals including vitamins, antibiotics, alcohols and other drugs are made using microbes and microbial pathways. At one time diabetics were dependent on insulin derived from pig and cow pancreases to control their diabetes. The availability of insulin was directly dependent on the availability of these meat products. In the 1970's when Americans began to eat more healthily, the supermarket demand for pork and beef decreased and the supply of insulin decreased also. By the 1980, biotechnologists had isolated and introduced the gene for insulin in humans E. coli. The product, Humulin was not subject to the whims of the meat market and had the added advantage that it was human insulin and therefore would not cause any type of immune reaction.
The food, clothing and household products industries also utilize microbes and their enzymatic pathways. Foods such as sauerkraut, yogurt, vinegar, miso, soy sauce, beer, wine, pickles, bread, soup and ice cream all either directly or indirectly use microbial enzymes or products. The clothing industry uses microbial enzymes to soften denim, bleach or color fabric, and to make biodegradable plastics. Microbial enzymes are also used around the house to clear slow moving drains, remove stains from clothing, remove pet odors and tenderize meats.
Hopefully, you realize now that microbiology is everywhere. It impacts every aspect of your life.
Classification and the naming of things in our world appears to be an inherently human trait. Very young children spend much of their time trying to identify and characterize things in their world. Throughout history scientists have done the same thing. For centuries, all living things were classified as either plants or animals. Early schemes of classification were based on physical appearance. Within the Animal Kingdom organisms were further classified by these observable differences. Did the organism walk? Did it walk on 2 legs or 4? Did it have hair? The Kingdom scheme of classification was then expanded to include 5 Kingdoms, i.e.., Animalia, Plantae, Fungi, Protista, and Monera (bacteria). In the 1970's yet another classification scheme was proposed by Carl Woese that was based on the cellular organization of organisms and evolutionary linkages. He proposed a 3 Domain system,i.e.., Eukarya, Archaea, and Bacteria or Eubacteria. Domain Eukarya includes all of the eukaryotes or organism's whose cells contain a nucleus. This Domain would include the protistan, fungus, plant and animal groups from previous schemes of classification. The Archaea Domain includes very unique, possibly primitive forms of prokaryotic organisms. Members of this Domain live in extreme environments like hot springs or deep in the ocean. Many of these prokaryotes lack a cell wall and those with a cell wall lack the macromolecular, scaffolding molecule peptidoglycan which is found in the Bacteria or Eubacteria. The members of the Domain Bacteria are the prokaryotes that are familiar to most of us. They lack internal double membrane-bound organelles and have cell walls containing peptidoglycan.
Classification schemes continue to evolve. Although Woese's three Domain system is the most commonly subscribed to system of classification others do exist and play an important role in microbiology. Numerical taxonomy is a classification methodology that is commonly applied to bacteria, archaea and viruses. This taxonomic method uses mathematical modeling to classify organisms based on similarities and differences at the molecular level. Whereas, Woese's three Domain system is based on cellular organization, numerical taxonomy relies on molecular similarities and differences.
Consistency in naming things is essential. When I say the sky is blue, everyone understands what I am saying. If we didn't have a standard meaning for words then confusion would be common. However, if I were to say I saw a bear in the backyard your interpretation of that word bear would depend on where you lived. Here in Georgia you might think I was referring to the American black bear, if you lived in Idaho you might think I saw a grizzly bear and if you lived in Alaska or Canada you might think I was referring to a polar bear. Scientists can't have that kind of ambiguity! If I am referring to a specific pathogen it is essential that everyone around the world understand to which specific organism I am referring. The most commonly used naming system used today was developed by Carolus Linnaeus in the 1700's. It is called the Linnaean system of binomial nomenclature. Binomial literally means two names and a nomenclature is a naming system. So the Linnaean system of nomenclature is a two name naming system. Each organism is given two names, the first name is the genus and the second name is the species. For example, humans are scientifically known as Homo sapiens. Our genus is Homo (homo means 'man') and our species designation is sapiens (sapiens means 'wise'). By convention, the first letter of the genus name is always capitalized and the first letter of the species name is written in small case. Additionally, the genus and species names should be either italicized or individually underlined. The following are correct ways to write the scientific name for the American black bear: Ursa americana, U. americana, Ursa americana, U. americana. These are the only correct ways to write this organism's name in scientific parlance.
Microbes are also named using this nomenclature. Microbes historically have been named by their discoverer. The name given to the organism typically reflects the organism's morphology, arrangement, colonial appearance, discoverer, or disease characteristics. Streptococcus pyogenes for example was named because the organism is spherical (coccus), forms long chains (strepto) and is associated with pus generation (pyogenic). E. coli or Escherichia coli was named for its discoverer and for the sample from which it was isolated. Theodor Escherich was studying the flora of infant feces. He noted that one organism seemed to be universally found in baby diapers. So E. coli is named for its discoverer, Theodor Escherich and for the colons from which the bacteria originated.
Bacteria (sing. bacterium) are small, single-celled prokaryotic organisms. Prokaryotes lack internal double layered membranes, like the nuclear membrane. 
They do have DNA in the form of a single, double-stranded circular chromosome, it is just not contained within a nuclear envelop. Cells can have multiple copies of their one chromosome. Bacteria structurally and metabolically are relatively simple. The eubacteria or true bacteria are the bacteria we typically study and think about. The archaea (ancient) are prokaryotic but live in extreme environments like hot springs and are structurally different than eubacteria.
Bacteria are single-celled organisms. The cells are typically either spherical (coccus), oblong or hotdog shaped (bacillus) or spiral (vibrio, spirillum, spirochete). Cells can occur individually or in packets of cells. Some bacteria form long chains, others packets of 2 or 4 cells and still others form random clusters of cells. The arrangement of cells is derived from the divisional plane for the organism. Bacteria divide through a process called binary fission. The cell enlarges, duplicates the cell machinery and then pinches in half. If the cell always pinches in half in the same orientation and chain is formed. If the cell divides along random planes then grape-like clusters of cells result.
Most bacteria have a cell wall. The cell walls of the eubacteria are composed mostly of either peptidoglycan or a lipopolysaccharide layer. Members of the archaea may not have cells walls, but if they do they lack peptidoglycan.
The protozoans are unicellular eukaryotes. They are single-celled organisms that have a nucleus. Protozoans can be classified by their means of locomotion. 
Bacteria if motile, move by mean of flagella or gliding. Protozoans move by cilia, flagella, or pseudopods. One group of protozoans have no motile stage. All of these non-motile organisms are pathogens.
Protozoans are diverse. Some are free-living and some are pathogenic. Some have photosynthetic capabilities, but most are heterotrophic. Protozoans can divide asexually by mitosis or participate in meiosis and sexual reproduction.
The fungi are either single-celled (yeasts) or multi-cellular (molds) eukaryotic organisms. Yeast colonies typically appear slimy and mold colonies appear fuzzy.
Common fungal organisms include mushrooms, puffballs, molds, and yeasts. Fungi reproduce both asexually and sexually. They are classified by the type of sexual spore they produce. The cell walls of fungi contain a compound called chitin, the same compound found in insect exoskeletons. Fungi are heterotrophic, ie. they get their nourishment from eating other organisms or other combined sources of carbon.
Algae can be either unicellular or multi-cellular. They are photosynthetic (autotrophic) eukaryotes. They utilize sunlight in photosynthesis to fix carbon dioxide into organic molecules and produce oxygen as a waste product. As photosynthetic autotrophs, they are considered producers in the environment and can be the basis for food chains/webs. Their cells walls contain cellulose. Some of them (diatoms) also produce an outer "shell" composed of silica.
A number of animal groups are studied by microbiologists either as the primary cause of infection (roundworms, flukes and tapeworms) or as the vectors or carriers of disease (ticks, mosquitoes). Animals are multi-cellular eukaryotes.
Viruses are not truly living because they do not meet the classical definition for life. They are considered infective particles or infective nucleoproteins. Viruses are very tiny and cannot replicate outside of a living cell. They do not grow and cannot perform energy generating metabolism. Viruses are composed of a nucleic acid, either RNA or DNA, but never both, surrounded by a protein coat. This protein coat may be surrounded by a membrane (envelope). Viruses are classified by the type of nucleic acid they contain, its strandedness (single, double-stranded DNA), and by whether or not it has an envelope.
Microbiology is a relatively young science with its first advances occurring in the 1600's. Sciences, all sciences, progress hand in hand with technology. Appropriate technological tools have to be in place for science to further discoveries in the field.
Although we take the existence of cells for granted today, it was not until microscopes were invented that cells could actually be seen. The invention of the microscope was the first major advance in cell biology. It was not until the 1600 that lenses could be made that would allow magnification of very small objects. The first microscope, a simple microscope was a single well ground glass bead on which a specimen could be viewed. By the mid 1600 early microscopists were fine tuning the design of the microscope. Robert Hooke modified his microscope to include two aligned lenses. A microscope is called a compound microscope when two or more lenses or mirrors are used to create an image. In 1665, Robert Hooke using his modified compound microscope was the first person to view and describe cells. He was viewing a thin section (image to the right) from the bark of a tree. Bark is a dead plant tissue. Cells in bark lack cytoplasm and organelles. What he saw when he looked at the thin section of bark were very regular, empty box-like rectangles. He said these boxes reminded him of the cells, the unadorned empty rooms in monasteries, in which monks slept. The discovery of bacteria and protozoa occurred a short time later. Anton van Leeuwenhoek examined water, vinegar, and his own bodily tissues and wastes looking for "animicules". He drew and published representations of his animicules that are still identifiable today (see below). Van Leeuwenhoek was apparently quite a character. He was a gentleman scientist. In one of his writings he described a party at which his microscopes provided the entertainment. He wrote about how the ladies swooned when they viewed vinegar eels on the microscope.
For thousands of years, if not longer, life was thought to arise from lifelessness.... life came from the air, water or soil. While this seems silly to us now, we need to remember that hundreds of years ago people did not even know about the cellular basis for life. Just as an example, if you were to throw out an old piece of food you might return in a couple of days to find that food teeming with fly maggots. You might assume the flies arose from the dead meat. These types of ideas were very common. People thought malaria (literally means bad air) came from bad air. Some other historical misconceptions are that insects come from damp bamboo, bees arise from dead cows, and frogs and snakes come from the mud of the Nile River. The idea that life arises from lifelessness is known as Spontaneous Generation.
As hard as it may be to believe today, spontaneous generation and arguments supporting or detracting from this idea were very contentious. Several scientists are credited with putting the nails in the coffin of spontaneous generation. We will review their contributions and some of the pro-spontaneous generation experiments also. Francesco Redi, an Italian physician and scientist was the first person to critically examine spontaneous generation. He took two jars and placed a piece of decaying meat in each. He sealed one jar with a cork and left the other jar open to the environment. Within days the meat in the open jar was covered in fly maggots. The meat in the sealed jar was maggot-free. Critics of the experiment claimed that by sealing the jar Redi excluded the essential life force needed to create maggots, so of course there were no maggots. In response, Redi repeated the experiment but instead of sealing the second jar he covered it with cheesecloth. Cheesecloth allowed air to pass into and out of the jar but would not allow flies into the jar. No maggots developed on the meat in the jar covered with cheesecloth, although fly eggs and later maggots were found on the cheesecloth itself. The repetition of the experiment with the cheesecloth covered jar is the first documented case of using a control in a scientific experiment.This experiment would seem to answer the question that life generates life, but not so. In 1745 John Needham heated vegetable broth and chicken stock and then poured the solutions into covered flasks. In a short period of time the flasks developed lush microscopic life. Needham suggested that organisms were created spontaneously from the nutrient broths. Lazzaro Spallanzani did a similar experiment, except he boiled the nutrient broths after sealing the containers. Nothing grew in Spallanzani's experimental flasks. Needham suggested that by boiling the flasks Spallanzani had destroyed the vital force and then excluded it by sealing the flasks. Air had been shown to be essential to animal life so the exclusion of the air was key to discounting Spallanzani's work. So arguments went back and forth for the next 100 years.
In the mid 1800's, Rudolf Virchow a German scientist proposed the Theory of Biogenesis. The Theory of Biogenesis states that life comes from pre-existing life, so all cells arise from other cells. Again, this isn't earth shattering news to us in our day and age but in the 1800's this was a revolutionary sentiment. Unfortunately, Virchow was never able to prove this point. It wasn't until Louis Pasteur approached the problem that spontaneous generation was laid to rest and the Theory of Biogenesis was proven. Louis Pasteur was an amazing scientist and he made numerous significant contributions to science. Probably, his greatest contribution was disproving spontaneous generation. Pasteur designed what he called swan-necked flasks. The flasks had an enlarged reservoir which tapered to a narrow inlet tube. The tube was bent into an S-shape. The flask was open, not sealed. Pasteur filled the flasks with broth and then boiled them. The flasks remained microbe free. Critics claimed the broth must have been poisoned. So Pasteur broke open the neck of a flask. Within days microbes were present in the broth, disproving the poisoned broth criticism. Pasteur suggested that microbes were present in the air and on dust particles in the air. These microbes and dust particles settled out onto the first bend in the S-shaped neck of the flask and were not carried into the broth. In one elegant, but simple experiment Pasteur disproved spontaneous generation. Today, some of the original swan-necked flasks have been preserved and can be seen in the Pasteur Institute.
The culmination of the work of Hooke, van Leeuwenhoek, Virchow, Schleiden, Schwann and Pasteur was the establishment of the three tenets of cell theory. Cell theory states that the cell is the fundamental unit of all life, that all living things are composed of cells and that cells come from pre-existing cells.
The refinement of the microscope, an understanding of cell theory and the development of aseptic technique and culturing methods led to an explosion of new discoveries between 1857 and 1914. This period is often referred to as the Golden Age of Microbiology. During this period microbiology was established as a science and an exceptional number of discoveries were made.
The average life expectancy in the 1700's was 25 years of age. Up until the mid-1900's the top four killers in the world were infectious diseases. Today, in the USA the average life expectancy is 78 years and the top killers of people in middle and high income countries include heart disease, cardiovascular disease (stroke), cancer, pulmonary disease and Alzheimer's disease. There are many factors that have led to these dramatic changes, not the least of which is a better understanding of germ theory. Cell theory established that cell were the fundamental unit of life; germ theory established that microbes were the causative agents of disease.
Before the acceptance of the germ theory of disease, most cultures thought disease was caused by transgressions, sins, committed by the affected person. Ill people were, it was thought, being punished by a deity. The other common perception was that disease could be caused by bad air or miasma. Pasteur and his work on fermentation and silk worm disease offered the first alternative causation of disease. Pasteur was asked by French vintners to determine why their wine was spoiling. He found that wine casks were contaminated with bacteria not yeast. Under preferred conditions, yeast ferment grape sugars to produce alcohol or wine. However, the bacteria contaminating the casks converted sugars, through fermentation to acetic acid or vinegar. He solved this problem by heating the grape juice which killed the spoilage bacteria. This process which is still widely used bears his name, pasteurization. He was also asked to investigate silkworm disease. Marco Polo had returned from China with silkworms which led to the beginning of a vibrant silk industry in Europe. However, silkworms were dying, the industry was suffering and no cause could be found. Pasteur identified a microbe (an 'invisible' protozoan) infecting silkworm eggs. He recommended procedures for minimizing infection and death of eggs. Pasteur's work with wine spoilage and silkworm disease laid the groundwork and supported the germ theory of disease. He showed that microbes can alter their environment in an unfavorable way (for humans) and that microbes can directly affect the health and survivability of animals.
Ignaz Semmelweis was another pioneer in medicine and antisepsis. Semmelweis was a physician who was aware of the 'invisible' world of microbes. During his time little care was taken by healthcare professionals to maintain routine cleanliness. Doctor's operated in street clothes. Doctors would go from the autopsy theater to the wards without washing their hands or changing clothes. Hand washing was not routinely performed by anyone. Childbirth fever or puerperal fever was very common and often fatal during his time. Doctor's would move from patient to patient, transmitting disease along the way. Women delivering their children in a hospital were more likely to die than those delivering at home. Mortality, from post-delivery infection was as high as 35%. Semmelweis insisted that wash basins containing chlorinated lime solutions be installed in the wards where his patients were housed. He routinely washed his hands before touching his patients. Patient mortality dropped to less than 1% in wards where hand washing was routinely done. Unfortunately, his work was not well regarded during his lifetime and it was not until years later with the work of Pasteur that antiseptic practices were commonly implemented in the medical community.
Joseph Lister, a surgeon built upon Semmelweis' work to extend antiseptic techniques to surgery and patient care. Lister used carbolic acid (phenol) a potent disinfectant to treat wounds, surgical instruments, and even the air in the operating theater. He had a vaporizer in the operating room that would create a thick fog of phenol. Because phenol is so abrasive, he started the practice of using gloves to protect his hands. He also recommended that surgical instruments be made of non-porous materials to decrease potential sources of infection.
Watch the following video and then answer the questions in the Quiz Group.
The causal relationship between microbes and disease was first clearly and definitively demonstrated by Robert Koch in 1876. He studied anthrax a common and deadly disease affecting sheep and cattle. He isolated a rod-shaped bacterium, later named Bacillus anthracis from the blood of infected cattle. He then grew the bacterium on medium. He made an inoculum of the bacteria from the medium and injected it into a healthy cow. The cow developed anthrax. He then re-isolated the bacterium from the sick cow. Koch's postulates describe the steps he followed and establish the clear linkage between an organism and the disease it causes. These postulates have guided scientists for over hundred years. However, it is important to understand that Koch's postulates are modified in the area of human health. For example, HIV is the causative agent for the syndrome known as AIDS. It would not have been ethical for early experimenters to inject putative causative agents of AIDS into human subjects. Another complication is that some causative agents like HIV can not be grown on a Petri dish, but require a different type of cell culture.
Koch's Postulates
Small pox is an old world disease that ravaged not only Europe but is thought to have devastated Native American populations during early European colonization of the Americas. Small pox killed millions worldwide. Survivors suffered from its effects, deafness, blindness and horrendous scarring for the remainder of their lives. Worldwide vaccination efforts sponsored by the World Health Organization led to the eradication of small pox from the world in 1977.
Edward Jenner, a British physician is credited with developing the vaccination for small pox in 1796. A milkmaid told Jenner that she couldn't get small pox because she had contracted cow pox previously. Jenner obtained and ground up cow pox scabs. He used a sharp needle contaminated by this ground up powder to scratch a healthy young boy in whose family there was a small pox outbreak. The boy's arm blistered and he was ill for a few days, but he never contracted cow pox again or small pox. Jenner concluded that exposure to the cow pox scabs conveyed resistance to the infection. Jenner never knew what caused the disease or how his treatment worked. Germ theory was still unknown. His work did meet with some resistance as the image to right indicates.
This process of exposing healthy subjects to related or weakened disease agents to protect them from the pathogenic agent is now known as vaccination. The word vaccination was coined by Louis Pasteur to honor Jenner's work. Vacca is Latin for cow.... Interestingly, evidence of vaccination in China can be found centuries before Jenner's work in Europe. Chinese medical practitioners would take dry small pox scabs, grind them to a fine powder and then blow them up people's noses. This would expose the mucosa to a weakened form of the virus and lead to an immune response that would eventually convey immunity to the disease.
In our time, with the easy availability of over the counter antiseptics and antibiotics it is difficult to imagine dying of a minor skin infection. Yet for most of mankind's history death from infection was commonplace. Infection led to sepsis and sepsis to death. As recently as World War II more soldiers died of infection and blood loss than from the extent and immediacy of their original wounds. Death by infection decreased significantly with the development of chemotherapeutic agents. Chemotherapy is the use of chemicals in the medical treatment of disease. Using a liberal interpretation of chemotherapy you could include everything from hot tea with honey to the most recent cancer fighting drugs as chemotherapeutic agents. Historically, chemotherapeutic agents have been divided into two groups, antibiotics and synthetic drugs. Until the 'discovery' of antibiotics in the late 1920's, most chemotherapeutic agents were synthetic drugs or chemicals made in the chemistry lab or plant-derived products (quinine for malaria). Sulfur, in mineral form was used as a treatment for open wounds. Medics during the Civil War would carry rocks of sulfur and grind it into powder to be poured into the wounds of soldiers. In the late 1800s and early 1900s derivatives of arsenic and mercury were used for the treatment of Frenchman's Disease or syphilis. Paul Ehrlich, a German physician, coined the term "magic bullet" in reference to the development of a chemotherapeutic agent that would selectively kill pathogens and not harm the host. He discovered Salvarsan the arsenic derivative just mentioned. Mercury and Salvarsan were used to treat syphilis. Although both treatments killed the bacterium, Treponema pallidum, the causative agent of syphilis they also caused rashes, liver damage, loss of limbs and life. These side effects have been attributed to improper handling of the drug. Regardless, a Salvarsan derivative (neosalvarsan) was the only treatment for syphilis until the use of antibiotics in the 1940. Dyes, like crystal violet were also used in the treatment of infection. Old nursing texts include mentions of using crystal violet IV drips on patients with septic bacterial infections.
Antibiotics are compounds produced by bacteria and fungi that inhibit or kill other microbes. The current prevalence of antibiotic use can be attributed to a discovery made by Alexander Fleming. Fleming noticed that a mold growing on some old agar plates inhibited the growth of bacteria inoculated on the plate. Rather than just throw the plate out he recognized the potential importance of this fungus and its by-products to chemotherapy. The mold Penicillium notatum is probably the world's most famous fungus. It produced penicillin which was truly a magic bullet. Commercial mass production of a stable, safe form of penicillin still did not occur for more than a decade after its discovery. For decades following this initial discovery drug companies actively searched native environments for antibiotic producing fungi and bacteria. The search continues although today more emphasis is placed on the in vitro development of drugs based on the molecular mode of action. Another problem we face today is antibiotic resistance. The overuse and misuse of antibiotics has led to an increasing number of antibiotic resistance strains of bacteria. This issue will be discussed in more detail later in the course.
Microbiology is a relatively young science. Advances in technology push the science ahead. The timeline below shows only some of the major advances that have ocurred during the last 500 years. What do you notice as you scroll through the timeline? What would you like to know more about?
Microbes are everywhere in nature. They play an essential role in many aspects of the environment and in human health. The study of microbes and their interactions is called microbial ecology.
Sergei Winogradsky and Martinus Beijerinck were the first microbial ecologists. They studied the role microbes played in the cycling of nutrients in the biosphere. Although we don't think about it very much, the Earth is like a giant terrarium. We get a constant input of energy from the sun, but for the most part all of the elements on Earth today were here at the very beginnings of the Earth's formation. The water molecules in the coffee you drank today, could have been in the urine of a dinosaur 400 million years ago.... For an even more disgusting example, consider all of the road kill you have seen in your lifetime. Now consider what would happen if microbes did not degrade that organic material through decay processes. We would be up to our eyeballs in dead animals. Microbes recycle these organic compounds. They breakdown organic molecules to their fundamental parts. These parts are then available to be reassembled into new molecules. The elements are the same, they just are cycled from one compound to another. Microbes play a critical role in this cycling. They take the wood in that tree that fell in the storm and break it down to carbon dioxide which is released into the air and other elements that are deposited in the soil. Once in the air the CO2 can be taken in by a plant to form sugars, which in turn can be eaten by someone else. Microbes play an essential role in cycling not only carbon, but nitrogen, sulfur and phosphorus.
The natural ability of microbes to degrade compounds has been exploited effectively in a number of ways to benefit people. Sewage treatment is one example. Effective water and sewage treatment is necessary for the health and well being of society. Sewage treatment is a multi-step process that involves physical removal of large or recalcitrant solids and the biological digestion of organic materials. The biological digestion of organics occurs under aerobic and anaerobic conditions and ultimately produces an effluent that is low in organic content and microbial load. By-products of the process include methane gas which is used in some communities to power the treatment plant and fertilizer (Milorganite) can be made from the composted solids left over from the entire process.
Bioremediation involves using microbes or their enzymes to remediate (correct fault or deficiency) soil, water, air, or clothing. Bioremediation is used to clean up oil spills, chemical spills, toxic waste sites and stained clothing. Bacteria and their enzymes can be thought of as nature's cleansers. Bacteria can also be used as natural pesticides. Bacillus thuringiensis in powdered form can be used to coat seeds or sprinkled on the leaves of plants. The bacteria begin replicating once they are ingested by plant pests (caterpillars and boring insects) eating the plant leaves. They then produce a toxic protein that kills the plant pest. The bacteria are not harmful to people and are not residual in the environment like chemical pesticides.
One of the first things babies do after being born is cry and lick their lips. That is their first taste of their new world and their first exposure to bacteria. The uterus is a sterile environment with respect to bacteria and microbes. Studies have shown that the bacteria in a woman's vagina experience explosive growth in the 48 hours before delivery. The organisms in the vaginal flora once swallowed are the first to colonize the baby's gut. Throughout our lifetimes we acquire microbes that live in us and on our body surfaces. These organisms make up our natural flora or normal microbiota. We need them to maintain our health. They take up space which prevents pathogens from colonizing the same space, they produce compounds that inhibit other organisms and in some cases they produce essential nutrients, like vitamin K, that they "share" with us. Vitamin K is produced by E. coli a natural inhabitant of our colon. When we remove our normal flora, we diminish our resistance to infection and open ourselves up to illness.
Bacteria in the real world are found growing as biofilms. A biofilm is a mixture of many different types of bacteria or microbes that share a surface. Dental plaque is one example. Dental plaque is composed of a bacterial community and the ions they precipitate around themselves. Biofilms benefit the community members by providing a substrate on which the organisms grow, they can protect the community from antibiotics or antiseptics and can allow community members to the share nutrient resources. Biofilms can be beneficial or deleterious to health. Biofilms of normal microbiota protect human tissue. However, pathogens can also produce biofilms and thrive on medical implements and prostheses.
Infectious diseases are diseases caused by the introduction, replication of agents in the body that lead to diminished health or disease states. They are contracted by contact with the agent through wounds, through various body surfaces (skin, mucosa) or via vector or fomite. The introduction of government mandated sanitary practices and vector/insect control have gone a long way in controlling the spread and prevalence of infectious disease.
While many of the formerly endemic diseases (small pox, polio) found in human society appear to be disappearing, others are re-emerging and still more, 'brand new' agents appear to be on the increase. These new diseases are called emerging infectious diseases (EID). Recent infectious diseases that are considered emerging include H1N1 influenza, Ebola and Marburg viruses, BSE (mad cow disease), AIDS, SARS and MRSA (methicillin resistant Staphylococcus aureus). 
Several factors contribute to the "emerging" nature of these infective agents. Viruses like HIV and Ebola have probably been around for quite awhile. They have existed in non-human animal populations (reservoirs). Their crossover into previously unknown hosts, humans has led to their classification as EID. New diseases coupled with the global nature of society have created concern within the healthcare community. When SARS emerged in China, it took less than 48 hours for the disease to appear in the Americas. One contagious person, one airplane and a global outbreak is possible.