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1 and 10: 

1 and 10 The Microbial World and You Classification of Microorganisms

Brief History of Microbiology: 

Brief History of Microbiology Before Pasteur, effective treatments for diseases were discovered by trial and error, but the cause of the diseases were unknown. The discovery that yeast play a crucial role in fermentation lead scientist to belief that microbes might be involved in causing disease. This idea was known as the Germ Theory of Disease.

The Germ Theory of Disease: 

The Germ Theory of Disease 1835: Agostino Bassi showed that a silkworm disease was caused by a fungus. 1865: Pasteur believed that another silkworm disease was caused by a protozoan. Father of Microbiology 1840s: Ignaz Semmelwise advocated hand washing to prevent transmission of puerperal fever from one OB patient to another.

The Germ Theory of Disease: 

The Germ Theory of Disease 1860s: Joseph Lister used a chemical disinfectant (Phenol) to prevent surgical wound infections after looking at Pasteur’s work showing microbes are in the air, can spoil food, and cause animal diseases. the founder of antiseptic surgery and the use of antiseptics in health care Applies Germ theory to medical procedures One of the earliest medical attempts to control infection

The Germ Theory of Disease: 

The Germ Theory of Disease 1876: Robert Koch proved that a bacterium causes anthrax and provided the experimental steps, Koch’s postulates, to prove that a specific microbe causes a specific disease. Firs proof that bacteria cause disease Father of Microbiology Laboratory Koch’s Postulates


Koch’s Postulates – a method of determining the etiologic (causative) agent of infectious diseases 1. the suspected etiologic agent must be found in every case of the disease and be absent in healthy hosts 2. the suspected etiologic agent must be isolated in pure culture and identified 3. the suspected etiologic agent is inoculated into a healthy, susceptible host and that host must come down with the same disease 4. the same etiologic agent as in step 2 must be isolated and identified in the second diseased animal


Koch and his colleagues also contributed other advances in the microbiology laboratory including: a) simple staining techniques were developed to see bacteria b) the first photographs of bacteria in diseased tissue were taken c) the use of steam to sterilize media d) the use of agar was first used to solidify bacterial growth media e) aseptic transfer of bacteria using platinum wires was first proposed f) the use of Petri dishes was started

Road to Vaccination: 

Road to Vaccination With the proof of the Germ Theory of Disease, the next step in the study of microbiology was to understand how this information could be used to prevent disease in clinical settings. Edward Jenner tried to find a way to protect people from smallpox. It all started with a milkmaid…


Vaccination 1796: Edward Jenner inoculated an 8 year old boy with cowpox virus. The boy was then protected from smallpox. The process used by Jenner is known today as vaccination. It is derived from vacca for cow. The protection provided by vaccination is called immunity.

The Birth of Modern Chemotherapy: 

The Birth of Modern Chemotherapy After the relationship between organisms and disease was established, medical microbiologists focused on the search for substances that could destroy pathogenic microorganisms without damaging the organism. Treatment with chemicals is chemotherapy. Chemotherapeutic agents used to treat infectious disease can be synthetic drugs or antibiotics.

The Birth of Modern Chemotherapy: 

The Birth of Modern Chemotherapy Antibiotics are chemicals produced by bacteria and fungi that inhibit or kill other microbes. Quinine from tree bark was long used to treat malaria. 1910: Paul Ehrlich developed a synthetic arsenic drug, salvarsan, to treat syphilis. 1930s: Sulfonamides were synthesized.

The Birth of Modern Chemotherapy: 

The Birth of Modern Chemotherapy 1928: Alexander Fleming discovered the first antibiotic. He observed that Penicillium fungus made an antibiotic, penicillin, that killed S. aureus. The enormous usefulness of penicillin wasn’t apparent until the 1940s when Penicillin was tested clinically and mass produced. Figure 1.5 Penicillum chrysogenum

The Birth of Modern Chemotherapy: 

The Birth of Modern Chemotherapy Although there have been thousands of antibiotics and other chemotherapeutic drugs, some are too toxic for human use. Examples: antiviral drugs Some interfere with viral reproduction but it would also affect uninfected cells.

The Birth of Modern Chemotherapy: 

The Birth of Modern Chemotherapy Another major problem associated with antimicrobial drugs is the emergence and spread of new varieties of microorganisms that are resistant to antibiotics. Example: vancomycin-resistant Staphylococcus aureus has alarmed healthcare professionals.

Modern Developments in Microbiology: 

Modern Developments in Microbiology The discoveries achieved during the Golden Age of Microbiology lead to new branches of microbiology including immunology and virology. Bacteriology is the study of bacteria. It began with van Leeuwenhoek. It also deals with discoveries and roles of bacteria.

Modern Developments in Microbiology: 

Modern Developments in Microbiology Mycology is the study of fungi. Include medical, agricultural and ecological branches Hospital fungal acquired infections have rise 10%. Parasitology is the study of protozoa and parasitic worms. Recent advances in genomics, the study of an organism’s genes, have provided new tools for classifying microorganisms.

Modern Developments in Microbiology: 

Modern Developments in Microbiology Immunology is the study of immunity. Vaccines and interferons are being investigated to prevent and cure viral diseases. The use of immunology to identify some bacteria according to serotypes (variants within a species) was proposed by Rebecca Lancefield in 1933. Major advance in immunology. Permits rapid identification of specific pathogenic Streptococci based on immunological techniques. Figure 1.4 (3 of 3)

Modern Developments in Microbiology: 

Modern Developments in Microbiology Virology is the study of viruses. Originated during the Golden Age of Microbiology Dmitri Iwanowski reported that an organism that caused tobacco mosaic disease was so small that it passed through filters fine enough to stop all known bacteria. Wendell Stanley was able to crystallized viruses His work facilitated the study of viral structure and chemistry.

Modern Developments in Microbiology: 

Modern Developments in Microbiology Recombinant DNA is DNA made from two different sources. In the 1960s, Paul Berg inserted animal DNA into bacterial DNA and the bacteria produced an animal protein. Recombinant DNA technology, or genetic engineering, involves microbial genetics and molecular biology. Microbial genetics = studies the mechanisms by which microbes inherit traits. Molecular biology = how genetic information is carried in molecules of DNA snd how DNA direcs the synthesis of proteins.

Modern Developments in Microbiology: 

Modern Developments in Microbiology Using microbes George Beadle and Edward Tatum showed that genes encode a cell’s enzymes (1942). Oswald Avery, Colin MacLeod, and Maclyn McCarty showed that DNA was the hereditary material (1944). 1946 -Joshua Lederberg and Edward Tatum discovered that genetic material can be transferred from one bacterium to another by a process called conjugation.

Modern Developments in Microbiology: 

Modern Developments in Microbiology 1953 - James Watson and Francis Crick proposed a model for the structure and replication of DNA. Francois Jacob and Jacques Monod discovered the role of mRNA in protein synthesis (1961).

Selected Novel Prizes in Physiology or Medicine: 

1901* von Behring Diphtheria antitoxin 1902 Ross Malaria transmission 1905 Koch TB bacterium 1908 Metchnikoff Phagocytes 1945 Fleming, Chain, Florey Penicillin 1952 Waksman Streptomycin 1969 Delbrück, Hershey, Luria Viral replication 1987 Tonegawa Antibody genetics 1997 Prusiner Prions Selected Novel Prizes in Physiology or Medicine * The first Nobel Prize in Physiology or Medicine.

Microbes and Human Welfare: 

1880s - Martinus Berjerinck and Sergei Winogradsky First to show how bacteria recycle vital elements between the soil and the atmosphere. Microbial ecology Studies the relationship between microorganisms and the environment. Bacteria recycle carbon, nutrients, sulfur, and phosphorus that can be used by plants and animals. Microbes and Human Welfare


Bioremediation Bacteria degrade organic matter in sewage. Bacteria degrade or detoxify pollutants such as oil and mercury. Toxins can be removed also from chemical spills and toxic waste sites. UN 2.1

Biological Insecticides: 

Biological Insecticides Microbes that are pathogenic to insects are alternatives to chemical pesticides in preventing insect damage to agricultural crops and disease transmission. Bacillus thuringiensis infections are fatal in many insects but harmless to other animals, including humans, and to plants. This toxin is incorporated into a dusting powder that is applied to crops these insects eat. It’s good for alfalfa caterpillars, bollworms, corn borers, cabbageworms, and others.

Modern Biotechnology and Genetic Engineering: 

Modern Biotechnology and Genetic Engineering Biotechnology, the use of microbes to produce foods and chemicals, is centuries old. Genetic engineering is a new technique for biotechnology. Through genetic engineering, bacteria and fungi can produce a variety of proteins including vaccines and enzymes.

Modern Biotechnology and Genetic Engineering (continued): 

Modern Biotechnology and Genetic Engineering (continued) Missing or defective genes in human cells can be replaced in gene therapy. Gene therapy inserts a missing gene or replacing a defective gene Uses harmless viruses to carry the needed gene. Examples: “Bubble boy” - SCID and cystic fibrosis

Modern Biotechnology and Genetic Engineering (continued): 

Modern Biotechnology and Genetic Engineering (continued) Beyond medical applications, recombinant DNA techniques have been also applied to agriculture. Genetically modified bacteria are used to protect crops from insects and from freezing. Bacteria have been used to improve appearance, flavor and shelf life of fruits.

Microbes and Human Disease: 

Microbes and Human Disease Bacteria were once classified as plants giving rise to use of the term flora for microbes. This term has been replaced by microbiota. Microbes normally present in and on the human body are called normal microbiota.

Normal Microbiota: 

Normal Microbiota Normal microbiota prevent growth of pathogens. Normal microbiota produce growth factors such as folic acid and vitamin K.

Normal Microbiota: 

Normal Microbiota There are microbes that want to colonize our bodies (produce disease). Whether our bodies overcome the microbe depends on our resistance. Resistance is the ability of the body to ward off disease. Resistance factors include skin, stomach acid, and antimicrobial chemicals.

Infectious Diseases: 

Infectious Diseases When a pathogen overcomes the host’s resistance, disease results. Emerging infectious diseases (EID): New diseases and diseases increasing in incidence.

Emerging Infectious Diseases: 

Emerging Infectious Diseases West Nile encephalitis West Nile virus First diagnosed in the West Nile region of Uganda in 1937 Appeared in New York City in 1999

Emerging Infectious Diseases: 

Emerging Infectious Diseases Bovine spongiform encephalopathy Also known as Mad Cow Disease Prion (infectious protein) The source of the disease was cattle feed prepare a from sheep infected with their own version of the disease. Proteins from sheep are used to enrich the cattle’s feed.

Emerging Infectious Diseases: 

Emerging Infectious Diseases Escherichia coli O57:H7 Toxin-producing strain of E. coli First seen in 1982 Causes bloody diarrhea Leading cause of diarrhea worldwide It comes from undercook meat and unpasteurized beverages.

Emerging Infectious Diseases: 

Emerging Infectious Diseases Invasive group A Streptococcus Rapidly growing bacteria that cause extensive tissue damage Also known as the flesh-eating bacteria Increased incidence since 1995

Emerging Infectious Diseases: 

Emerging Infectious Diseases Ebola hemorrhagic fever Ebola virus Causes fever, hemorrhaging, and blood clotting Spreads by personal contact with infectious blood or body fluids or tissue. First identified near Ebola River, Congo Outbreaks every few years

Emerging Infectious Diseases: 

Emerging Infectious Diseases Avian influenza A Influenza A virus (H5N2) Primarily in waterfowl and poultry Sustained human-to-human transmission has not occurred yet

Emerging Infectious Diseases: 

Emerging Infectious Diseases Severe acute respiratory syndrome (SARS) SARS-associated Coronavirus Occurred in 2002-2003 Person-to-person transmission

Emerging Infectious Diseases: 

Emerging Infectious Diseases Acquired immunodeficiency syndrome (AIDS) Human immunodeficiency virus (HIV) First identified in 1981 Worldwide epidemic infecting 44 million people; 14,000 new infections every day Sexually transmitted disease affecting males and females In the United States, HIV/AIDS cases: 30% are female and 75% are African American

Emerging Infectious Diseases: 

Emerging Infectious Diseases Cryptosporidiosis Cryptosporidium protozoa First reported in 1976 Causes 30% of diarrhea illness in developing countries In the United States, transmitted via water

Identifying and Classifying Microorganisms: 

Identifying and Classifying Microorganisms A classification scheme provides a list of characteristics and a means for comparison to aid in the identification of an organism. We usually identify microorganisms when it is the cause of an infection. However, they are not necessarily identified by the same techniques they are classified.

Identifying and Classifying Microorganisms: 

Identifying and Classifying Microorganisms Most prokaryotic organisms do not have distinguishing morphological features or even much variation in size and shape. Consequently, microbiologists have developed a variety of methods to test metabolic reactions and other characteristics to identify prokaryotes.

Bergey’s Manual of Determinative Bacteriology: 

Bergey’s Manual of Determinative Bacteriology Widely used reference since its first edition in 1923 It does not classify bacteria according to evolutionary relatedness but instead provides identification schemes based on such criteria as cell wall composition, morphology, differential staining, oxygen requirements, and biochemical testing.

Identification Methods: 

Identification Methods Morphological characteristics: Useful for identifying eukaryotes Differential staining: Gram staining, acid-fast staining 1st step in identifying bacteria Most useful in the clinical environment

Identification Methods: 

Identification Methods Biochemical tests: Determines presence of bacterial enzymes Example: gram-negative bacteria Figure 10.8

Numerical Identification: 

Numerical Identification Figure 10.9


Serology Serology is the science that studies serum and immune responses that are evident in serum. Combine known antiserum plus unknown bacterium Slide agglutination test Figure 10.10


ELISA Enzyme-linked immunosorbent assay Widely used because it is fast and can be read by a computer scanner. Antibodies adhere to the wells of microplate and then unknown bacterium is added to each well. A reaction between antibody and bacterium provides identification of the bacteria.

Western Blot: 

Figure 10.12 Western Blot HIV infection is confirmed by Western blotting and Lyme disease is diagnosed by it.

Phage Typing: 

Figure 10.13 Phage Typing Looks for similarities among bacteria. Determines which phages a bacterium is susceptible to. The tested strain is grown over the entire plate. Plaques, or areas of lysis, indicate the sensitivity of the bacteria to that particular phage.

Flow Cytometry Uses: 

Flow Cytometry Uses Differences in electrical conductivity between species Fluorescence of some species Cells selectively stained with antibody plus fluorescent dye Figure 18.12


Genetics DNA base composition Guanine + cytosine moles% (GC) DNA fingerprinting Electrophoresis of restriction enzyme digests Used to determine the source of hospital-acquired infections. Figure 10.14


Genetics Polymerase chain reaction (PCR)

Nucleic Acid Hybridization: 

Figure 10.15 Nucleic Acid Hybridization Possibility to determine the similarity between two organisms

Nucleic Acid Hybridization: DNA Probe: 

Nucleic Acid Hybridization: DNA Probe Figure 10.16

Nucleic Acid Hybridization: DNA Chip: 

Nucleic Acid Hybridization: DNA Chip Figure 10.17

Ribotyping and rRNA Sequencing: 

Ribotyping and rRNA Sequencing Ribotyping is currently being used to determine the phylogenetic relationships among organisms. This technique is useful for classifying newly discovered organism. There are advantages to use rRNA All organisms have ribosomes Genes have undergone few changes Cells do no have to be culture

Fluorescent In Situ Hybridization (FISH): 

Figure 10.18a–b Add DNA probe for S. aureus Fluorescent In Situ Hybridization (FISH) Fluorescent due-labeled RNA or DNA probes are used to specifically stain microorganisms in place, or in situ. Probe enters the cell and reacts with target ribosome Detection of bacteria without the need of a culture


Table 10.5

Dichotomous Key: 

Dichotomous Key UN 10.2


Figure 10.19, steps 1–2 Cladogram Cladograms are maps that show evolutionary relationships among organisms.


Cladogram Figure 10.19, step 3

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