microbiology

n.
The branch of biology that deals with microorganisms and their effects on other living organisms.

microbiological mi'cro·bi'o·log'i·cal (-bī'ə-lŏj'ĭ-kəl) or mi'cro·bi'o·log'ic adj.
microbiologically mi'cro·bi'o·log'i·cal·ly adv.
microbiologist mi'cro·bi·ol'o·gist n.

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The multidisciplinary science of microorganisms. The prefix micro generally refers to an object sufficiently small that a microscope is required for visualization. In the seventeenth century, Anton van Leeuwenhoek first documented observations of bacteria by using finely ground lenses. Bacteriology, as a precursor science to microbiology, was based on Louis Pasteur's pioneering studies in the nineteenth century, when it was demonstrated that microbes as minute simple living organisms were an integral part of the biosphere involved in fermentation and disease. Microbiology matured into a scientific discipline when students of Pasteur, Robert Koch, and others sustained microbes on various organic substrates and determined that microbes caused chemical changes in the basal nutrients to derive energy for growth. Modern microbiology continued to evolve from bacteriology by encompassing the identification, classification, and study of the structure and function of a wide range of microorganisms including protozoa, algae, fungi, viruses, rickettsia, and parasites as well as bacteria. The comprehensive range of organisms is reflected in the major subdivisions of microbiology, which include medical, industrial, agricultural, food, and dairy. See also Algae; Bacteriology; Biotechnology; Fungi; Immunology; Industrial microbiology; Medical bacteriology; Medical mycology; Medical parasitology; Microscope; Protozoa; Rickettsioses; Virus.

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n

The branch of biology concerned with the study of microorganisms, including algae, bacteria, viruses, protozoa, fungi, and rickettsiae.

Microbiology is the study of organisms beyond the scope of human vision, particularly bacteria, viruses, algae, fungi, and protozoa. Since its founding in the nineteenth century, the science has largely focused on the isolation, identification, and elimination of pathogens from humans, animals, plants, food, and drinking water. Microbiologists have also examined nonpathogenic forms, seeking to understand their structure, function, and classification in order to control or exploit their activities.

Microbiology Arrives in America, 1878–1899

Microbiology gained a foothold in the United States after the discoveries of European researchers Ferdinand Cohn (1828–1898), Louis Pasteur (1822–1895), and Robert Koch (1843–1910) during the 1870s and early 1880s. While American physicians and biologists followed developments in the germ theory of disease (and the germ theory of fermentations) with great interest, few conducting original studies of their own. One exception was Thomas J. Burrill (1839–1916), a botanist and plant pathologist at the University of Illinois, who identified the etiological agent of pear blight in 1878. Burrill's discovery spawned little interest in bacteria as plant pathogens. Instead, microbiology first appeared in departments of pathology and veterinary medicine. William H. Welch (1850–1934), T. Mitchell Prudden (1894–1924), and Harold C. Ernst (1856–1922) each studied in Europe during the late 1870s, returning to the United States to begin instruction at Bellevue Medical College, Columbia University College of Physicians and Surgeons, Harvard, and Johns Hopkins University. By close of the nineteenth century, more than fifty American medical colleges required formal instruction in bacteriology, mostly intended to impart the techniques for isolating the pathogens responsible for tuberculosis, cholera, diphtheria, anthrax, plague, typhoid fever, and gonorrhea. While American medical colleges actively promoted bacteriological instruction, only William Welch's discovery of the gas-gangrene bacillus (1892) drew attention from European bacteriologists. Instead, American bacteriologists distinguished themselves in their contributions to public health practice and sanitary science.

In response to the global cholera epidemic of 1892, the New York City Health Department founded the first extensive laboratory for public health bacteriology. Under the direction of Hermann M. Biggs (1859–1923), William H. Park (1863–1939), and Anna W. Williams (1863– 1954), the department, in 1894, designed and distributed throat culture kits for diagnosing cases of diphtheria. The next year, Park and Williams refined methods of mass-producing diphtheria antitoxin, supplying it without charge to city physicians, and selling to outside public health departments. By 1899, more than twenty state and city departments of health established similar laboratories, aiding in the diagnoses of tuberculosis, typhoid fever, malaria, and gonorrhea.

Microbiologists also supported the field of sanitary science, helping to eliminate harmful microbes from drinking water, milk, and food. At Massachusetts Institute of Technology and the Lawrence Experiment Station, William T. Sedgwick (1855–1921) and his students designed methods of improving water filtration systems, reducing rates of typhoid fever in American cities by more than 70 percent. Sedgwick's colleagues, Samuel C. Prescott (1872– 1962) and William L. Underwood (1864–1929), studied means of reducing food poisoning in commercially manufactured foods.

American microbiologists achieved their greatest successes in the fields of veterinary medicine, dairying, soil science, and plant pathology, under the aegis of the bureaus of the U.S. Department of Agriculture and the several state agricultural experiment stations. At the Bureau of Animal Industry, Daniel E. Salmon (1850–1914) and Theobald Smith (1859–1934) isolated the bacterial agent of swine plague, and developed the first heat-killed (as opposed to Pasteur's live-attenuated) vaccine. In the early 1890s, Salmon and Smith identified the protozoan responsible for Texas cattle fever, and established that a tick carried the parasite from host to host, the first demonstration of an insect vector in the spread of disease. In the field of dairying, Herbert W. Conn (1859–1917) at the Storrs Agricultural Experiment Station and Harry L. Russell (1866–1954) at the Wisconsin station detailed the function of bacteria in the formation and flavoring of hard cheeses and butter. In the late 1890s, researchers at the New Jersey and Delaware stations advanced the scientific understanding of soil fertility, defining the role of bacteria and fungi in the decomposition of manures, their action upon fertilizers, and their importance in the fixation of atomospheric nitrogen. American plant pathologists, in the 1880s and 1890s, contributed greatly to the understanding and prevention of various wilts, rusts, and blights of agricultural crops. While most plant diseases are fungal in origin, Erwin F. Smith (1854–1927), of the Bureau of Plant Industry, and Harry Russell were the first to identify bacterial diseases of plants.

The Flourishing of American Microbiology, 1900–1924

Microbiology flourished in the first quarter of the twentieth century. The Society of American Bacteriologists and the Laboratory Section of the American Public Health Association formed in 1899. In the first years of the new century, the Rockefeller Institute for Medical Research in New York, the John McCormick Institute in Chicago, and the U.S. Public Health Service Hygienic Laboratory began sponsoring original investigations in medical microbiology. By 1925, American researchers could point to notable advances in the comprehension and control of many infectious diseases, including: Walter Reed (1851– 1902) and James Carroll (1854–1907) for demonstrating that mosquitoes transmitted yellow fever; Simon Flexner (1863–1946) for his discovery of a new variant of dysentery and devising a serum for treating meningitis; Howard T. Ricketts (1871–1910) for his research on Rocky Mountain spotted fever; George W. McCoy (1876–1952) and William B. Wherry (1875–1936) for identifying the bacteria of tularemia; and, F. Peyton Rous (1879–1970) for proposing a viral etiology of some cancers.

In the field of public health, bacteriology occupied an authoritative position. Increasingly, public health leaders shifted their focus from cleanup campaigns and municipal reforms to the bacteriological methods of identifying sick or susceptible individuals, including the control of "health carriers." In 1907, the New York City Health Department detained the immigrant cook Mary Mallon ("Typhoid Mary") for transmitting typhoid fever, even though she showed no signs of the illness herself. Health officials also lobbied for compulsory school vaccinations and mandatory tests for susceptibility to diphtheria and scarlet fever. By 1925, most municipalities distributed filtered or chlorinated water, mandated pasteurized milk, and inspected commercial canneries.

Veterinary microbiologists devised diagnostic tests, vaccines, and treatments for several economically devastating livestock diseases (e.g., hog cholera, blackleg in sheep, pullorum in chickens, and blackhead in turkeys). Regarding bovine tuberculosis and contagious abortion in cattle, these efforts carried implications for human health. In the first years of the new century, Theobald Smith, Harry Russell, and Mazyck P. Ravenel (1861–1946) documented that the dairy products made from tubercular cows could transmit the disease to infants. Similarly, Alice C. Evans (1881–1975) argued, in 1916, that cows suffering from contagious abortion could transmit undulant fever to humans. While Evans's claim drew initial skepticism, her work led to the recognition of a new class of infections, brucellosis. As a result, the Bureau of Animal Industry sponsored a national eradication movement, dramatically decreasing the incidence of both diseases.

The Triumph of Microbiology, 1925–1979

Throughout much of the twentieth century, American microbiologists led an age of scientific triumph. In the battle against infectious disease, researchers and pharmaceutical firms improved vaccines and therapeutic sera to control measles, diphtheria, mumps, rubella, and whooping cough. At Vanderbilt University and the Rockefeller Institute, Ernest W. Goodpasture (1886–1960), Thomas M. Rivers (1888–1962), and Richard E. Shope (1901– 1966) transformed the study of influenza, herpes, and encephalitis, developing methods of culturing these viruses in chick embryos. John F. Enders (1897–1985) and his colleagues at Harvard University devised a technique in 1949 for growing polio virus in cultures of tissue cells. With in a decade, Jonas E. Salk (1914–1995) and Albert B. Sabin (1906–1993) introduced two separate polio vaccines, largely eliminating the scourge of infantile paralysis. While penicillin was introduced as a therapeutic agent in the early 1940s by the British researchers Alexander Fleming, Howard Florey, and Ernst Chain, American scientists also studied the antagonisms between different microbes. In 1939, Rockefeller Institute researcher René Dubos (1901–1981) isolated a crystalline antibiotic, gramicidin, from a soil organism. Unfortunately, gramicidin proved too toxic for internal use. Dubos's former teacher, Selman Waksman (1888–1973), found another group of soil organisms showing anti-germicidal properties. Waksman and his students at Rutgers University identified streptomycin, the first effective antibiotic in the treatment of tuberculosis.

Microbiologists equally contributed to the development of molecular biology. In the 1930s and 1940s, Oswald T. Avery (1877–1955) and his colleagues at the Rockefeller Institute showed that DNA played a role in transforming non-virulent pneumococci into virulent forms, intimating that this substance might be generally involved in heredity. Employing a bacteriophage of E. coli, Max Delbruck (1906–1981) and Salvador Luria (1912– 1991) revealed that bacteria and viruses followed normal principles of replication and mutation, there by establishing phage as a model organism for genetic research. Joshua Lederberg (1925–) and Edward L. Tatum (1909– 1975) showed that bacteria can exchange genes when cultured in direct contact. In 1952, Lederberg and Norton D. Zinder (1928–) elucidated the phenomenon of bacterial transduction, where a phage carries DNA from one bacterium to another. Their research suggested a mechanism for introducing genes into new cells, a technique now common in genetic engineering. In the 1960s and early 1970s, Matthew S. Meselson (1930–), David Baltimore (1938–), and Howard M. Temin (1934–1994) employed bacteriophages and other viruses to delineate the relationship among DNA, RNA, and protein synthesis.

Emerging Challenges, 1980–2002

In 1979, the World Health Organization declared that one of the most ancient and devastating diseases, smallpox, had been officially eliminated. Scientific optimism proved, however, to be short-lived, as medical researchers soon grappled with the emergence of AIDS. While Robert C. Gallo (1937–), of the National Institutes of Health, co-discovered the human immunodeficiency virus in 1983, and developed an accurate test for HIV infection, no vaccine or cure has been found. Microbiologists have also struggled against new microbial threats, from Rift Valley fever, dengue fever, ebola, and hanta virus abroad, to lyme disease and multiple-drug resistant tuberculosis domestically. Even the class of infectious agents has expanded. In 1982, Stanley Prusiner (1942–) found evidence of infectious protein particles or "prions," and concluded that they were responsible for scrapie, a transmissible spongiform encephalopathy fatal to sheep. In the 1990s, Prusiner and others demonstrated that both mad cow disease in livestock and Creutzfeldt-Jakob disease in humans were likely caused by prions.

Bibliography

American Society for Microbiology. "Celebrating a Century of Leadership in Microbiology." ASM News 65, no. 5 (1999): 258–380.

Clark, Paul F. Pioneer Microbiologists in America. Madison: University of Wisconsin Press, 1962.

Garrett, Laurie. The Coming Plague: Newly Emerging Diseases in a World Out of Balance. New York: Farrar, Straus and Giroux, 1994.

Parascandola, John, ed. The History of Antibiotics: A Symposium. Madison, Wisc.: American Institute of the History of Pharmacy, 1980.

Postgate, John. Microbes and Man. 4thed. Cambridge, Mass.: Cambridge University Press, 2000.

Tomes, Nancy. The Gospel of Germs: Men, Women, and the Microbe in American Life. Cambridge, Mass.: Harvard University Press, 1998.

Microbiology is the study of a diverse group of microscopic organisms, or microorganisms: bacteria, fungi, algae, protozoa, and viruses. Bacteria are prokaryotes; the other microorganisms are eukaryotes. Prokaryote cells lack a nuclear membrane and membrane-bound organelles. Recently, bacteria have been divided into eubacteria and archaebacteria, with the latter more closely related to eukaryote cells. Bacteria are mostly unicellular and range in size from tiny mycoplasmas, 200 nanometers (that is, 200 billionths of a meter, or less than 1/100,000 of an inch) in diameter, to the recently discovered Thiomargarita namibiensis, at one millimeter (or about 1/25 of an inch). E. coli cells are one to two micrometers in length (about five to ten times the diameter of the mycoplasmas). Fungi include yeasts, molds, and mushrooms. The bread, wine, and beer yeast, Saccharomyces cerevisiae, is ten micrometers (about 1/2,500 of an inch) in diameter. Algae are photosynthetic organisms, unicellular or multicellular. Protozoa are microscopic, unicellular, and usually motile. Viruses are not cellular organisms; they are intracellular parasites of animals, plants, or bacteria. They are composed of nucleic acid (DNA or RNA) enclosed in a protein coat. Viruses range from 18 to 450 nanometers (from less than one-millionth to almost 1/50,000 of an inch). Microorganisms, with the exception of viruses, can be observed with a compound light microscope (up to ×,000 magnification). Electron microscopes (up to ×100,000 magnification) are used to visualize viruses.

History of Microbiology Before Pasteur

Microorganisms were first visualized by Antoni van Leeuwenhoek (1632–1723), a Dutch cloth merchant and an expert lens grinder. His simple microscopes magnified up to three hundred diameters. In the eighteenth century, many people still believed that living organisms could arise spontaneously from organic matter—the doctrine of abiogenesis, or spontaneous generation.

Lazzaro Spallanzani (1729–1799), an Italian priest and physiologist, did an experiment that came close to proving that life (in this case, microorganisms) does not arise spontaneously from nonliving matter. He sealed flasks containing broth and then boiled them. No spontaneous generation or growth occurred in the flasks; however, the debate continued, as proponents of the doctrine said that air was needed for spontaneous generation. Opponents of this doctrine had a very difficult task trying to prove a negative, namely that something did not happen.

The ancient Egyptians and Romans were comfortable with the idea that organisms invisible to the naked eye could cause disease. During the Dark Ages and the medieval period of Western history, this idea virtually disappeared. In the sixteenth century, Girolamo Fracastoro (1483–1553) described disease passing from one person to another by "germs." Athanasius Kircher (1602–1680) furthered the "germ theory" by observing bacteria from plague victims.

History from Pasteur Onward

Louis Pasteur (1822–1895) was an intellectual giant who dominated science in the middle of the nineteenth century. In 1861, in the midst of a twenty-year study of microbial fermentation, Pasteur dealt the deathblow to the doctrine of spontaneous generation by demonstrating the presence of microorganisms in the air and then by showing that sterile liquid in a swan-necked flask remained sterile. Air could enter such a flask, but microorganisms could not. In 1875, Ferdinand Cohn (1828–1898) published the first classification of bacteria, and used the genus name, Bacillus, for a spore-forming bacterium. In 1875, Robert Koch (1843–1910), a German bacteriologist, proved that a spore-forming bacterium, Bacillus anthracis, caused anthrax. His experiments demonstrated four principles, now known as Koch's postulates, which are still the hallmark of disease etiology: (1) the microorganism must be present in every diseased animal studied, but not be isolated from healthy animals; (2) the microorganism must be isolated from the animal and cultivated; (3) an animal inoculated with the microorganism must develop the disease; (4) the same microorganism must be isolated from the diseased animal inoculated with the microorganism. Working independently on anthrax, Pasteur and his colleagues confirmed Koch's findings. Koch introduced three practices that allowed bacteriologists to obtain pure cultures simply: (1) a semisolid medium composed of nutrients solidified with gelatin, (2) platinum needles sterilized in a flame to pick up bacteria, (3) streaking of bacteria onto a gelatin surface to obtain single cells that would grow into colonies. In 1881, Fanny Hesse, the wife of German bacteriologist, Walther Hesse, suggested using a seaweed extract, agar, which she used to thicken jam, to solidify media in petri plates. Agar had neither of the disadvantages of gelatin: it was rarely degraded by microorganisms and it stayed solid at temperatures above 28°C (about 82°F). Agar is still the solidifying agent of choice. In 1882, Koch used the pure-culture techniques to isolate the bacterium that causes tuberculosis. In 1884, Charles Chamberland, a collaborator of Pasteur's, developed a porcelain filter that would retain all bacteria. When, in 1892, a young Russian scientist, Dmitri Iwanowski, transmitted tobacco mosaic disease to healthy plants using a porcelain-filtered extract, he postulated the presence of a toxin. In 1898, the Dutch microbiologist, Martinus Beijerinck, reproduced Iwanowski's results, but he postulated the existence of very small infectious agents, "filterable viruses." Thus began the field of virology, although visualization of viruses had to wait until the development of the electron microscope in the 1930s. Medical bacteriology progressed rapidly at the Pasteur Institute in Paris, where Pasteur presided, and the Koch Institute in Berlin, where Koch presided.

History of Food Preservation Microbiology

In 1810, Nicolas Appert (1750–1841) applied Spallanzani's results to develop a system of preserving food by sealing it in airtight cans and heating the cans. Without understanding that the heat treatment, or "appertization," was killing microorganisms in the canned food, Appert established the basis for the modern practice of canning. In 1852, Napoleon III asked Pasteur to study the problem of "wine diseases," particularly wine souring. In 1886, Pasteur proclaimed that the off-flavors in wine were caused by contaminating microorganisms. He suggested heating (pasteurizing) the grape juice to kill the spoilage bacteria. He discovered that some microorganisms could grow in the absence of oxygen. He used the term "anaerobic" to apply to microbial metabolism that occurs only in the absence of oxygen, and "aerobic" for metabolism that occurs under normal atmospheric conditions. Fermentation of grape juice by yeast is one kind of anaerobic metabolism. He also described the anaerobic degradation of protein, or putrefaction, by bacteria. Aerobic bacteria, namely the acetic-acid bacteria, were the cause of wine souring. Some of these bacteria metabolize ethanol to acetic acid; others metabolize the acetic acid to carbon dioxide and water. The process of pasteurization, a mild heat treatment of liquids, originated as a means of preserving the desired flavor of milk, fruit juices, beer, and wine. For example, Pasteur recommended that heating bottled wine for a short time at 122°F (50°C) would kill the lactic-acid and acetic-acid bacteria that can spoil wine. In traditional pasteurization, liquids are heated at about 145°F (63°C) for thirty minutes, then held at 50°F (10°C). Nowadays, flash or high-temperature, short-time (HTST) pasteurization is the preferred method (about 162°F [72°C] for fifteen seconds, followed by rapid cooling to 50°F [10°C]) because it has less effect on the flavor of the food being heated. Currently, milk is pasteurized to eliminate the bacteria responsible for tuberculosis, food poisoning, undulant fever, and Q fever. The treatment does not result in sterilization of milk, which can contain twenty thousand bacteria, such as lactobacilli, per ml post-pasteurization. More common in Europe than other parts of the world, is ultrahigh temperature (UHT) treatment (300°F[148.9°C] for one to two seconds), which sterilizes milk, allowing it to be stored without refrigeration for more than the limit of two to three weeks for pasteurized milk. Many brewing companies pasteurize their bottled or canned beer at 140°F (60°C) for a few minutes. Pasteurization is infrequently used, however, in modern winemaking, as it adversely affects the flavor.

Cohn and John Tyndall (1829–1893) both demonstrated that the endospores of Bacillus subtilis cells were far more resistant to heating than were vegetative bacteria. Tyndall developed a method of sterilizing liquids that contained bacterial spores: a medium was first incubated to allow the spores to germinate, then heated to kill most of the bacteria. This process, later termed "tyndallization," was repeated several times. This was a very important development in food science since the bacteria that form endospores include the food-borne pathogens, Clostridium botulinum, C. perfringens and C. difficile. Today, canned food is subjected to a temperature–time treatment that ensures the death of heat-resistant bacterial endospores, particularly those of C. botulinum.

For hundreds of years, substances that inhibit microbial growth have been added to foods in an attempt to prevent spoilage. One of the oldest practices is the salting of meat and fish as a means of preservation. Growth of most bacteria is inhibited by the high osmotic strength generated by the salt. In a relatively dry climate, salted meat can last up to twelve months. In 1958, the United States government determined that no chemical could be added to food or beverages without having been tested for safety. Three important antifungal preservatives for acidic foods (foods with a pH of 4.6 or less) such as canned drinks, salad dressings, cheese, and wines, are benzoic acid, sorbic acid, and propionic acid (or their salts). Sodium nitrate has been used in meat in China and the Middle East since 1200 B.C.E. A bacterial conversion of nitrate to nitrite results in a reaction with the heme pigment, giving the pink color of ham. Nitrite is antibacterial and prevents the germination of C. botulinum and other anaerobic bacteria in meats like ham, bacon, and frankfurters. Sulfur dioxide in some form, for example as produced by sodium metabisulfite, is used to control yeast and bacteria in wines and bacteria in brewing. Sulfur dioxide or bisulfite is an unusual chemical in that it is also an extremely effective antioxidant. Fermentation is another method of preservation. A commonly held dictum is that pathogenic bacteria do not grow at pH levels below 4.5. Fermented foods are inoculated with microorganisms, which reduce the pH of the food by producing acid during their growth. Acids such as acetic or citric acid are also added to decrease the pH of foods. Heat treatments are more effective at killing microorganisms at lower pH. It appears that low pH does not ensure safety from pathogens: in 1993, E. coli 0157:H7 in fresh-pressed apple juice caused an outbreak of diarrhea and hemolytic uremic syndrome. Yersinia spp. may also be able to survive in low pH foods.

Irradiation is a process that destroys microbial pathogens in food. Gamma rays from cobalt 60 or cesium 137, X rays (five million electron volts [5 MeV] maximum), and electrons (10 MeV maximum) are approved sources in the U.S. Irradiation was first used in the U.S. to ensure safe food for astronauts. Subsequently, the Food and Drug Administration (FDA) approved irradiation for wheat, wheat flour, and potatoes. Currently, irradiation is used mostly for spices, but also to disinfect cured meats, to kill Trichinella spiralis in pork, to control salmonella on chicken carcasses, and to reduce microbial load on fresh fruits and vegetables. There is some public resistance to irradiated foods, as the thought is that the food becomes radioactive. It does not.

Control of Microorganisms in Food

The contemporary food microbiologist has the challenges of a growing number of food pathogens and food spoilage. For example, eighty percent of commercial chickens in the U.S. are contaminated with Campylobacter jejuni. The food microbiologist may be involved in food manufacturing and processing, in retail food, in research in a university or government organization, such as the Agricultural Research Service of the United States Department of Agriculture (USDA), FDA, Centers for Disease Control and Prevention, and National Institutes of Health (NIH); or in food-plant inspection or the USDA's Food Safety Inspection Service (FSIS). In food plants, the food microbiologist is often a food technologist with a thorough training in chemistry as well as microbiology, who establishes a laboratory quality assurance manual (LQAM), a training program, and a statistical quality-control program. The food microbiologist must be versed in good manufacturing practices (GMP's), standard operating procedures (SOP's), sanitation, Hazard Analysis and Critical Control Points (HACCP's), rapid methods for the isolation and identification of microorganisms, as well as assays for toxins. HACCP's are designed to ensure food safety, extending beyond microbiological hazards, to chemical (for example, those from mycotoxins and pesticides) and physical (for example, from glass breakage) dangers. To generate an HACCP, the hazards in the plant's processes must be identified, the risk involved at each Critical Control Point must be established, and the critical levels of pathogens at each step in the process must be determined. The process must be monitored, and the monitoring verified. HACCP's are rapidly being required by government industries for more and more food processors. The USDA now mandates that all meat and poultry processors that are federally inspected have an HACCP in operation. The FDA now requires HACCP's for fruit-juice producers. Sanitation methods and monitoring are an extremely important part of any HACCP and a chief duty of a plant's food microbiologist. Surfaces in food-processing plants, meat carcasses, fruits, and vegetables must be kept pathogen-free. The use of simple rapid ATP detection systems (ATP—adenosine triphosphate—degrades quickly and is only found in living cells) allows a food microbiologist to involve plant workers in the sanitation effort. Workers swab sanitized surfaces, process the swab, and read the printout that has been calibrated to tell them the level of cellular contamination. They can resanitize surfaces until the results are acceptable.

In food-production and retail-food plants and in the home, good hygiene, especially hand washing, is the most effective way to eliminate the transmission of these pathogens. Another important practice is proper refrigeration of foods. Finally, proper cooking of raw meats, fish, and eggs by the consumer will destroy any remaining pathogens.

The explosion in genetic and immunological research in the 1980s resulted in many antibody-based and DNA-based methods for the identification of bacteria and toxins. These methods are rapid, reliable, sensitive, and becoming simpler daily. The time-consuming step in the assays is the necessity of initially growing or in some way enriching for the pathogen of interest. There are DNA-based assays for all the major food-borne pathogens. These assays use either DNA probes (usually of 16S rRNA genes, since there are relatively so many copies of these genes in cells) or PCR (a short DNA sequence is amplified in a thermocycler). There are also antibody-based assays for the major food-borne pathogens and toxins. These assays depend upon an antibody produced to some component of a bacterial cell or toxin. The most commonly used antibody-based assay is an ELISA, an enzyme-linked immunosorbent assay. It is described as a "sandwich assay." The test substance is added to a solid support to which the antibody to a particular pathogen is bound. The cell or toxin binds to the antibody. A secondary antibody, which is conjugated to an enzyme, binds to the primary antibody. Addition of the enzyme's substrate results in activity that can be detected. As the field of diagnostics speeds on, the food microbiologist must devote time to a continuing evaluation of newly emerging technologies aimed at reducing or eliminating pathogens as well as microorganisms that adversely affect the quality of food.

Use of Microorganisms for Various Helpful Ends

Before ancient people had any idea of microorganisms, they were using them to ferment foods. Bacteria, yeast, and molds are now used extensively to preserve foods and improve their aroma and flavor. Beer is probably the oldest fermentation product consumed by humans. Its history has been traced back to the Sumerians in 7500 B.C.E. The basic component of beer is a grain or cereal, for example, malted barley, rice, corn, or millet. The major food source in cereals is starch. Barley is germinated to produce starch-degrading enzymes, or amylases. This mixture, "malt," is used to process the starch in barley or other cereals; starch must be broken down into sugar for fermentation to take place. Strains of Saccharomyces cerevisiae are used for lager-style beers, and strains of S. uvarum for ales. Wine, also an ancient beverage, is made by inoculating fruit juice, usually grape juice, with strains of S. cerevisiae, fermenting the high level of sugar in the juice. Many kinds of lactic-acid bacteria (LAB) are also found during yeast fermentation: Lactobacillus spp., Leuconostoc spp., and Pediococcus spp. Winemakers often inoculate their wines with commercial LAB cultures to reduce overly high acidity of juice (grape juice, for example, has a pH of 3.0 to 3.8) and, through their metabolism, to add flavors or "complexity" to the wine.

The bacteria that Pasteur identified as wine spoilers, the acetic-acid bacteria, are used to make vinegar. Wine or cider is inoculated with Acetobacter spp., which produce acetic acid by oxidizing ethanol.

Basic bread is made by adding water and salt to wheat flour. Yeast is added to "leaven" bread. The Egyptians obtained yeast from beer vats to leaven their bread. The Greeks and Romans used yeast from wine vats. Now, strains of S. cerevisiae are used to ferment the sugars in bread dough. LAB are also used to give special flavors to some breads: for example, Lactobacillus sanfrancisco for sourdough and Lactobacillus plantarum for rye bread.

LAB are most important in dairy products. In 1878, Joseph Lister (1827–1912) isolated, in pure culture, a bacterium that caused milk souring. LAB are used to curdle milk for cheese production, and to ripen certain cheeses (Propionibacterium spp., for instance, for Swiss cheese). LAB are also used in the production of yogurt, buttermilk, and kefir, an alcoholic fermented-milk product. Molds, mainly of the penicillia family, are used to break down the fats in cheese and add distinctive flavors, for example, Penicillium roqueforti in Roquefort cheese.

Plant material is fermented to make pickled vegetables, sauerkraut, Spanish-style olives, and soy sauce. LAB, for example, are used to ferment cabbage into sauerkraut. Several genera of bacteria, including LAB, and fungi are used to ferment olives, which are inedible before this processing.

Many fermented products are made in the Far East, often from soybean meal. A koji, or mixed culture of bacteria, yeast, and molds, is used to inoculate the food. For soy sauce, for example, soybean meal is inoculated with a koji containing Aspergillus oryzae and LAB such as Lactobacillus delbrueckii. Other common fermented-soybean foods are tempeh, miso, and sufu (a traditional Chinese cheeselike product). The acids these microorganisms produce, chiefly acetic, butyric, and lactic, prevent the growth of most other microorganisms. The fermentations not only favorably modify flavors and textures, but also have preservative action.

A bacterium, Xanthomonas campestris, produces a polymer, xanthan gum, which is used as a thickener in such foods as salad dressings, cottage cheese, yogurt, ice cream, and frostings.

Harmful Microorganisms

Bacteria, viruses, and protozoa that cause gastroenteritis are transmitted by the fecal–oral route—that is, by the consumption of food or water fecally contaminated by infected persons. The major bacteria that cause gastroenteritis are Salmonella spp, E. coli, Campylobacter jejuni, Vibrio parahaemolyticus, and Yersinia enterocolotica. Ingesting toxins produced by bacteria that have grown in food can also result in gastroenteritis. Bacteria that cause gastroenteritis by producing toxins are Staphylococcus aureus, Clostridium perfringens, and Bacillus cereus. Rotavirus and the Norwalk virus group are the two major viruses causing gastroenteritis.

Milk is pasteurized to eliminate Mycobacterium tuberculosis, M. bovis, Salmonella spp., Listeria spp., enteric viruses, Brucella spp., Coxiella burnetii, and Campylobacter jejuni.

Food-borne bacteria can cause serious diseases: Salmonella typhi causes typhoid fever; Shigella spp. cause bacillary dysentery; E. coli strains can cause dysentery; M. tuberculosis and M. bovis cause tuberculosis; Vibrio cholerae causes cholera; Brucella spp. cause undulant fever; and Coxiella burnetii causes Q fever. Listeria monocytogenes causes listeriosis in predisposed populations, for example, immune-compromised individuals. Hepatitis is caused by the Hepatitis A virus and the recently discovered Hepatitis E virus, which is common in Africa and India and other Asian countries, but not in Western countries. In meat and poultry products, Salmonella, E. coli, Campylobacter jejuni, Listeria, and Clostridium perfringens are the major pathogens. Listeria monocytogenes is the major cheese pathogen. Unlike other food-borne pathogens, its temperature growth range (from 31 to 122°F [–0.4 to 50°C]) allows it to grow under refrigeration conditions. Hepatitis viruses and Yersinia enterocolitica are major oyster pathogens. Some of the pathogens found on fish are of marine origin, for example, Vibrio vulnificus, V. parahaemolyticus, and V. cholerae, and others are from sewage, for example Salmonella spp. and Campylobacter spp. Nuts and grains can become contaminated with mycotoxins, aflatoxins produced by Aspergillus flavus, being the most dangerous.

Prions are particles, smaller than viruses, and mostly composed of protein. It has recently been proposed that prions are the cause of four diseases: Creutzfeldt-Jacob disease and kuru in humans, bovine spongiform encephalopathy (BSE or mad cow disease) in cows, and scrapie in sheep. It is now thought that several dozen people have gotten a human form of BSE by eating the meat of infected cattle. This disease has been named new variant Creutzfeldt-Jakob disease, or nvCJD.

Yeast Extract

In the United Kingdom, South Africa, and Down Under, people enjoy yeast spreads—that is, spreads made from a dark-brown, extremely salty yeast extract. Oddly enough, one, Marmite, is preferred in Australia, and another, Vegemite, is preferred in New Zealand. Some say Marmite is sweeter than Vegemite; others say that Marmite has more caramel flavor. One of babies' first foods Down Under is toast fingers spread with Vegemite or Marmite. These spreads are rich in niacin, thiamine, and riboflavin. Neither of these spreads is tolerated well by North Americans.

Bacteria As Food

In the pre-European Aztec culture, people harvested the cyanobacterium, Spirulina, from lakes for food, and still do so in Chad. Cyanobacteria are capable of photosynthesis, and so some lakes in Chad and in Mexico develop a deep green color. Spirulina may be the only bacterium directly consumed by people. Today, about nine hundred tons a year of Spirulina is produced, mainly by the United States and Thailand. The spirulina product is 65 percent protein and amino acids, 20 percent carbohydrates, and 5 percent fats. Spirulina is rich in vitamins A, D, K, and B_12, as well as beta carotene.

Salmon Color

Farmed salmon are pale in color. The color of wild salmon comes from their consumption of crustaceans in the ocean. A red yeast, Phaffia rhodozyma, is now fed to farmed salmon to color them red. The red pigment in the yeast, astaxanthin, is a carotenoid similar to that found in lobsters.

Bibliography

Bozoglu, T. Faruk, and Bibek Ray, eds. Lactic Acid Bacteria: Current Advances in Metabolism, Genetics and Applications. Berlin: NATO ASI series, Springer-Verlag, 1996.

De Kruif, Paul. Microbe Hunters. New York: Pocket Books, 1964.

Harrigan, Wilkie F. Laboratory Methods in Food Microbiology. 3d ed. London: Harcourt Brace, 1998.

Lechevalier, Hubert A., and Morris Solotorovsky. Three Centuries of Microbiology. New York: McGraw-Hill, 1965.

Mortimore, Sara, and Carol Wallace. HACCP: A Practical Approach. 2d ed. Gaithersburg, Md.: Aspen, 1998.

Postgate, John. Microbes and Man. 3d ed. Cambridge: Cambridge University Press, 1992.

Reed, Gerald, ed. Prescott and Dunn's Industrial Microbiology. 4th ed. Westport, Conn.: AVI Publishing, 1982.

Stanier, Roger Y., John L. Ingraham, Mark L. Wheelis, and Page R. Painter. The Microbial World. 5th ed. Englewood Cliffs, N.J.: Prentice-Hall, 1990.

U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Bacteriological Analytical Manual Online. Available at http:/vm.cfsan.fda.gov/ebam/bam-toc.html.

U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Foodborne Pathogenic Microorganisms and Natural Toxins Handbook. Available at http://vm.cfsan.fda.gov/mow/badbug.zip.

Vanderzant, C., and D. Splittstoesser, eds. Compendium of Methods for the Microbiological Examination of Foods. Washington, D.C.: American Public Health Association, 1992.

Wood, Brian J. B., ed. Microbiology of Fermented Foods. 2d ed., 2 vols. London: Blackie Academic and Professional, Thomson Science, 1998.

—Susan Rodriguez Roy Thornton

A specialist in microbiology.

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