Chapter 1 Microbiology

Bacteria

(Singular: bacterium). Are relatively simple, single celled (unicellular) organisms. Because their genetic material is not enclosed in a special nuclear membrane, bacteria are called prokaryotes, from the Greek words meaning prenucleus. Prokaryotes include both archaea and bacteria. Bacterial cells have several shapes: bacillus (rodlike), coccus (spherical or ovoid), and spiral (corkscrew or curved) are the most common shapes. They can also be star shaped or square. Individual bacteria may form pairs, chains, clusters, or other groupings. Such formations are usually indicative of a particular genus or species.

First Golden Age of Microbiology

1857 - 1914. Rapid advances, spearheaded mainly by Pasteur and Robert Koch, led to the establishment of microbiology. Discoveries included both the agents of many diseases and the role of immunity in preventing and curing disease. During this productive time, microbiologists studied the chemical activities of microorganisms, improved the techniques for performing microscopy and culturing microorganisms, and developed vaccines and surgical techniques.

Parasitiology

A branch of microbiology. The study of Protozoa and parasitic worms. Because many parasitic worms can be seen with the unaided eye, they have been known for thousands of years. Clearing of rain forests has exposed laborers to previously undiscovered parasites. Parasitic diseases unknown until recently are also being found in patients whose immune systems have been suppressed by organ transplants, cancer chemotherapy, and AIDS

Bacteriology

A branch of microbiology. The study of bacteria.

Mycology

A branch of microbiology. The study of fungi. Includes medical, agricultural, and ecological branches. Fungal infection rates have been rising during the past decade, accounting for 10% of hospital acquired infections. Climactic and environmental changes (severe drought) are thought to account for a tenfold increase in Coccidioides immitis infections in California.

Koch's Postulates

A sequence of experimental steps for directly relating a specific microbes to a specific disease. The first proof that bacteria actually cause disease came from Robert Koch in 1876. He was a German physician and Pasteur's rival in the race to discover the cause of anthrax, a disease that was destroying cattle and sheep in Europe. Koch discovered a rod-shaped bacteria now known as Bacillus anthracis in the blood of cattle that died of anthrax.

Microbiome

Aka microbiota. Microbes that live stably in and on the human body. Humans and many other animals depend on these microbes to maintain good health. Bacteria in our intestines, including E. coli, aid digestion and even synthesize some vitamins that our bodies require, including B vitamins for metabolism and vitamin K for blood clotting. They also prevent growth of pathogenic (disease causing) species that might otherwise take up residence, & they seem to have a role in training our immune system to know which foreign invaders to attack and which to leave alone. Even before birth our bodies begin to be populated with bacteria. As newborns we acquire viruses, fungi, and bacteria. For example, E.coli and other bacteria acquired from foods take residence in the large intestine. Microbes can only colonize those body sites that can supply appropriate nutrients (temperature, pH, and the presence or absence of chemical compounds are some factors).

Microbes

Aka microorganisms, are minute living things that individually are too small to be seen without a microscope. The group includes bacteria, fungi (yeasts and molds), Protozoa, and microscopic algae. It also includes viruses, the non cellular entities straddling the border between life and non life.

Nomenclature

Aka naming. The system of nomenclature for organisms in use today was established in 1735 by Carolus Linnaeus. Scientific nomenclature assigns each organism two names - the genus (plural:genera) is the first name and is always capitalized; the specific epithet (species name) follows and is not capitalized. The organism is referred to by both the genus and the specific epithet, and both names are underlined or italicized. After a scientific name has been named once, it can be abbreviated with the initial of the genus followed by the specific epithet. Scientific names can, among other things, describe and organism, honor a researcher, or identify a habitat or species.

Algae

Algae (singular: alga) are photosynthetic eukaryotes with a wide variety of shapes and both sexual and asexual reproductive forms. The algae of interest to microbiologists are usually unicellular. The cell walls of many algae are made of a carbohydrate called cellulose. Algae are abundant in freshwater and saltwater, in soil, and and in association with plants. As photosynthesizers, algae need light, water, and carbon dioxide for food production and growth, but they do not generally require organic compounds from the environment. As a result of photosynthesis, algae produce oxygen and carbohydrates that are then utilized by other organisms, including animals. Thus, they play an important role in the balance of nature.

Vaccination

Almost 70 years before Koch established that a specific microorganism causes anthrax, Edward Jenner, a young British physician, embarked on an experiment to find a way to protect people from smallpox. This disease periodically swept through Europe, killing thousands, & it wiped out 90% of the Native Americans on the East Coast when European settlers first brought the infection to the New World. A young milkmaid informed Jenner that she couldn't get sick from smallpox because she had already been sick from cowpox - a much milder disease. Jenner collected scrapings from cowpox blisters with which he inoculated a healthy 8 year old volunteer by scraping the child's arm with a pox contaminated needle. The scratch turned into a raised bump. In a few days the volunteer became mildly sick but recovered and never again contracted either cowpox or smallpox.

Multicellular Animal Parasites

Although multicellular animal parasites are not strictly microorganisms, they are medical importance. Animal parasites are eukaryotes. The two major groups of parasitic worms are the flatworms and the roundworms, collectively called helminths. During some stages of the life cycle, helminths are microscopic in size. Lab identification of these organisms includes many of the same techniques used for identifying microbes.

Fungi

Are eukaryotes, organisms whose cells have a distinct nucleus containing the cells genetic material (DNA), surrounded by a special nuclear envelope called the nuclear membrane. Organisms in the Kingdom Fungi may be unicellular or multicellular. Large multicellular fungi, such as mushrooms, may look somewhat like plants, but unlike most plants, fungi cannot carry out photosynthesis. True fungi have cell walls composed primarily of chitin. The unicellular forms of fungi, yeasts, are oval microorganisms that are larger than bacteria. The most typical fungi are molds. Molds forms visible masses called mycelia, which are composed of long filaments called hyphae that branch and intertwine. The cottony growths sometimes found on bread and fruit are mold mycelia. Fungi can reproduce sexually or asexually. The obtain nourishment by absorbing organic material from their environment - whether soil, seawater, freshwater, or an animal or plant host. Organisms called slime molds are actually ameba-like Protozoa.

Viruses

Are so small they can only be seen with an electron microscope. They are acellular (that is they are not cells. They are structurally very simple. A virus particle contains a core made of only one type of nucleic acid, either DNA or RNA. This core is surrounded by a protein coat, which is sometimes encased in a lipid membrane called an envelope. All living cells have DNA and RNA, can carry out chemical reactions, and can reproduce as self sufficient units. Viruses can reproduce only by using the cellular machinery of other organisms. Thus on one hand, viruses are considered to be living only when they multiply within host cells they infect. In this sense viruses are parasites of other forms of life. On the other hand, viruses are not considered to be living because they are inert outside of living hosts.

Classification of Microorganisms

Before the existence of microbes was known, all organisms were grouped into either the animal kingdom or the plant kingdom. When microscopic organisms with characteristics of animals and plants were discovered late in the 17th century, a new system of classification was needed. In 1978, Carl Woese devised a system of classification based on the cellular organization of organisms. It groups all organisms into 3 domains as follows: 1. Bacteria (cell walls contain a protein-carbohydrate complex called peptidoglycan). 2. Archaea (cell walls, if present, lack peptidoglycan). 3. Eukarya: include the following Protists (slime molds, protozoa, and algae) Fungi (unicellular yeasts, multicellular molds, and mushrooms) Plants (mosses, ferns, conifers, and flowering plants) Animals (sponges, worms, insects, and vertebrates)

Antibiotics

Chemicals produced naturally by bacteria and fungi that act against other microorganisms.

Synthetic drugs

Chemotherapeutic agents prepared from chemicals in the lab.

Cell Theory

In 1665, after observing a slice of cork under a crude microscope, Englishman Robert Hooke reported that life's smallest structural units were "litter boxes" or "cells". Using his improved microscope, Hooke later saw individual cells. His discovery marked the beginning of cell theory - the theory that all living things are composed of cells. Though Hooke's microscope was capable of showing large cells, it lacked the resolution that would have allowed him to see microbes clearly. Dutch merchant and amateur scientist Anton van Leeuwenhoek was probably the first to observe live microorganisms through the magnifying lenses of more than 400 microscopes he constructed. Between 1673 and 1723, he wrote about the "animalcules" he saw through his simple, single lens microscopes. He made detailed drawings of organisms he found in rainwater, feces, and material scraped from teeth. The drawings have since been identified as representations of bacteria and Protozoa.

Theory of Biogenesis

In 1858 Rudolf Virchow challenges the case for spontaneous generation with the concept of biogenesis, hypothesizing that living cells arise only from preexisting living cells. Because he could offer no scientific proof, arguments about spontaneous generation continued until 1861, when the issue was finally resolved by the French scientist Louis Pasteur. Pasteur demonstrated that microorganisms are present in the air & can contaminate sterile solutions, but the air itself does not create microbes. He filled several short-necked flasks with beef broth and then boiled their contents. Some were then left open and allowed to cool. In a few days, these flasks were found to be contaminated with microbes. The other flasks, sealed after boiling, were free of microorganisms. From these results, Pasteur reasoned that microbes in the air were the agents responsible for contaminating non living matter. Pasteur next placer broth in open ended, long-necked flasks and bent the necks into S-shapes curves. The contents were then boiled and cooled. The broth in the flasks did not decay and showed no signs of life, even after months. Pasteurs unique design allowed air to pass into the flask but the curved neck trapped any airborne microbes that might contaminate the broth. Pasteur showed that microorganisms can be present in non living matter - on solids, in liquids, and in the air. He also demonstrated conclusively that microbial life can be destroyed by heat and that methods can be devised to block the access of airborne microorganisms to nutrient environments. These discoveries form the basis of aseptic techniques, procedures that prevent contamination by unwanted microorganisms, which are now the standard practice in labs and many medical procedures.

Joseph Lister

In 1860s, an English surgeon named Joseph Lister, applied germ theory to medical procedures. Luster was aware that in the 1840s, the Hungarian physician signal Semmelweis had demonstrated that physicians, who at the time did not disinfect their hands, routinely transmitted infections (puerperal, or childbirth, fever) from one obstetrical patient to another. Disinfectants were not used at the time but Lister knew that phenol (carbolic acid) kills bacteria, so he began treating surgical wounds with a phenol solution. The practice so reduced the incidence of infections and deaths that other surgeons quickly adopted it. His findings proved that microorganisms caused surgical wound infections.

Bacterial Cell Wall

Largely composed of a carbohydrate and protein complex called peptidoglycan. (By contrast, cellulose is the main substance of plant and algal cell walls). Bacteria generally reproduce by dividing into two equal cells, this is called binary fission.

Archaea

Like bacteria, archaea consist of prokaryotic cells, but if they have cell walls, they lack peptidoglycan. Archaea are often found in extreme environments, and are divided into 3 main groups. The methanogens produce methane as a waste product from respiration. The extreme halophiles (halo=salt, philic=loving) live in extremely salty environments such as The Great Salt Lake and the Dead Sea. The extreme thermophiles (therm=heat) live in hot sulfurous water, such as hot springs at Yellowstone National Park. Archaea are not known to cause disease in humans.

Molecular Biology

Looks at how genetic information is carried in molecules of DNA.

Bacterial Nutrition

Most bacteria use organic chemicals, which in nature can be derived from either dead or living organisms. Some bacteria can manufacture their own food by photosynthesis, and some can derive nutrition from inorganic substances. Many bacteria can "swim" by using moving appendages called flagella.

Fermentation & Pasteurization

One of the key steps that established the relationship between microorganisms and disease occurred when a group of French merchants asked Pasteur to find out why wine and beer soured. They hoped to develop a method that would prevent spoilage when those beverages were shipped long distances. At the time, many scientists believed that air converted the sugars in these fluids to alcohol. Pasteur found instead that microorganisms called yeasts convert the sugars to alcohol in the absence of air. This process is fermentation and is used to make wine and beer. Souring and spoilage are caused by different microorganisms, called bacteria. In the presence of air, bacteria change the alcohol into vinegar (acetic acid). Pasteurs solution to spoilage was to heat the beer and wine just enough to kill most of the bacteria that caused the spoilage. The process called pasteurization, is now commonly used to reduce spoilage and kill potentially harmful bacteria in milk and other beverages, as well as in some alcoholic beverages.

The First Synthetic Drugs

Paul Ehrlich, in 1910, after testing hundreds of substances, found a chemotherapeutic agent called Salvarsan, an arsenic derivative effective against syphilis. Before this, the only , the only known chemical in Europe's medical arsenal was quinine, an extract from the bark of a South American tree, which had been used by conquistadores to treat malaria. By the late 1930s researchers had developed several other synthetic drugs that could destroy microorganisms. Most of these drugs were derivatives of dyes. This came about because the dyes synthesized and manufactured for fabrics were routinely tested for antimicrobial qualities by microbiologists looking for a magic bullet. In addition sulfonamides (sulfa drugs) were synthesized at about the same time.

Protozoa

Singular: protozoan. Unicellular eukaryotic microbes. Protozoa move by pseudopods, flagella, or cilia. Amebae move by using extensions of their cytoplasm called pseudopods (false feet). Other Protozoa have long flagella or numerous shorter appendages for locomotion called cilia. Protozoa have a variety of shapes and live either as free living entities or as parasites (organisms that derive nutrients from living hosts) that absorb or ingest organic compounds from their environments. Some Protozoa like Euglena are photosynthetic. They use light as a source of energy and carbon dioxide as their chief source of carbon to produce sugars. Protozoa can reproduce sexually or asexually.

Microbial genetics

Studies the mechanisms by which microorganisms inherit traits.

Antibiotics

The first antibiotic was discovered by accident. Alexander Fleming, a Scottish physician and bacteriologist, almost tossed out some culture plates that had been contaminated by mold. Fortunately he noticed the curious clear area where the bacterial growth had been inhibited by the mold. Fleming was looking at mold that inhibited the growth of a bacterium. The mold became known as Penicillium chrysogenum, and and the molds active inhibitor was called penicillin. Thus penicillin is an antibiotic produced by a fungus. Thus the Second Golden Age of Microbiology began in the 1940s, when the enormous use of penicillin became apparent and the drug came into common use.

Germ Theory of Disease

The idea that microorganisms might cause disease. At the time, the causes of diseases were unknown. Effective treatments for many diseases were discovered by trial and error. The realization that yeasts played a crucial role in fermentation was the first link between the activity of a microorganism and physical and chemical changes in organic materials. This alerted scientists to the possibility that microorganisms might have similar relationships with plants and animals - specifically that microorganisms might cause disease.

Immunity

The protection from disease provided by vaccination (or by recovery from the disease itself).

Immunology

The study of immunity.

Virology

The study of viruses. Originated during the First Golden Age of Microbiology.

Chemotherapy

Treatment of disease by using chemical substances. The term also commonly refers to chemical treatment for noninfectious diseases, such as cancer. The success of chemotherapy is based on the fact that some chemicals are more poisonous to microorganisms than to the hosts infected by the microbes.

Spontaneous Generation

Until the 2nd half of the 19th century, many scientists & philosophers believed that some forms of life could arise spontaneously from non living matter. Not much more than 100 years ago, people commonly believed that toads, snakes, and mice could be born of moist soil; that flies could emerge from manure; and that maggots (the larvae of flies) could arise from decaying corpses.

Avirulent

When a microorganism loses its ability to cause disease. It loses its virulence. Pasteur discovered why vaccinations work. He found that the bacterium that causes fowl cholera lost its ability to cause disease after it was grown in the lab for long periods. However it, and other microorganisms with decreased virulence, was able to induce immunity against subsequent infections by its virulent counterparts. Pasteur used the term vaccine for cultures of avirulent microorganisms used for preventative inoculation. (The Latin word vaca means cow - this the term vaccine honored Jenner's earlier cowpox inoculation work). Some vaccines are still produced from avirulent microbial strains that stimulate immunity to the related virulent strain. Other vaccines are made from killed virulent microbes, from isolated components of virulent microorganisms, or by genetic engineering techniques.

Interferons

a protein released by animal cells, usually in response to the entry of a virus, which has the property of inhibiting virus replication. Discovered in 1960, interferons inhibit replication of viruses and have triggered considerable research related to the treatment of diseases such as cancer and viral diseases.

Aséptico Techniques

procedures that prevent contamination by unwanted microorganisms, which are now the standard practice in labs and many medical procedures.