Chapter One

The Microbial World and You

Microbes in Our Lives

Ø What is microbiology?

l Study of microorganisms and viruses

Ø What are microorganisms?

l Organisms that are too small to be seen with the unaided eye

Ø Have enormous impact

Microbes in Our Lives

¨ A few are pathogenic (disease-causing)

¨ Decompose organic waste

¨ Are producers in the ecosystem by photosynthesis

¨ Produce industrial chemicals such as ethanol and acetone

¨ Produce fermented foods such as vinegar, cheese, and bread

¨ Produce products used in manufacturing
(e.g., cellulase) and treatment (e.g., insulin)

Microbes in Our Lives

¨ Knowledge of microorganisms

¨ Allows humans to

¡ Prevent food spoilage

¡ Prevent disease occurrence

¨ Led to aseptic techniques to prevent contamination in medicine and in microbiology laboratories

Naming and Classifying Microorganisms

Ø Carolus Linnaeus

l Established the system of scientific nomenclature

l Means of communicating to others about specific organisms.

Ø Binomial system

l Each organism has two names:

• Genus (genera): The first name, which is always capitalized and underlined or italicized

• Species (specific epithet): The second name, which is underlined or italicized, but not capitalized.

• Are “Latinized” and used worldwide

• May be descriptive or honor a scientist

Scientific Names

Ø Staphylococcus aureus

l Describes the clustered arrangement of the cells (staphylo-) and the golden color of the colonies (aur-).

Scientific Names

Ø Escherichia coli

l Honors the discoverer, Theodor Escherich, and describes the bacterium’s habitat–the large intestine or colon.

Scientific Names

Ø After the first use, scientific names may be abbreviated with the first letter of the genus and the specific epithet:

l Staphylococcus aureus and Escherichia coli are found in the human body. S. aureus is on skin and E. coli in the large intestine.

Classification of Microorganisms

Ø Three domains (Carl Woese - 1978)

l Bacteria

l Archaea

l Eukarya

• Protists

• Fungi

• Plants

• Animals

Viruses

Bacteria

Ø Prokaryotes

Ø No membrane bound nucleus

Ø Unicellular microorganisms

Ø Different shapes

Ø Peptidoglycan cell walls

Ø Reproduce by binary fission

Ø Some bacteria have flagella for “swimming”

Ø For energy, use organic chemicals, inorganic chemicals, or photosynthesis

Archaea

Ø Prokaryotic

Ø No membrane bound nucleus

Ø Unicellular microorganisms

Ø Lack peptidoglycan

Ø Reproduce by binary fission

Ø Live in extreme environments

Ø Include

l Methanogens

l Extreme halophiles

l Extreme thermophiles

Eukaryotes

Ø Distinct membrane bound nucleus

Ø Membrane bound organelles

Ø Cells are larger than prokaryotes

Ø Moderate environments

Fungi

Ø Eukaryotes

Ø Chitin cell walls

Ø Use organic chemicals for energy.

Ø Molds and mushrooms are multicellular consisting of masses of mycelia, which are composed of filaments called hyphae.

Ø Yeasts are unicellular.

Ø Reproduce sexually or asexually

Protozoa

Ø Eukaryotes

Ø Unicellular

Ø Absorb or ingest
organic chemicals

Ø May be motile via pseudopods, cilia,
or flagella

Ø Reproduce sexually or asexually

Algae

Ø Eukaryotes

Ø Unicellular

Ø Cellulose cell walls

Ø Use photosynthesis for energy (photosynthetic)

Ø Produce molecular oxygen and organic compounds

Ø Sexual and asexual forms

Viruses

Ø Acellular

Ø Consist of DNA or RNA core

Ø Core is surrounded by a protein coat.

Ø Coat may be enclosed in a lipid envelope.

Ø Viruses are replicated only when they are in a living host cell.

Multicellular Animal Parasites

Ø Eukaryote

Ø Multicellular animals

Ø No cell walls

Ø Parasitic flatworms and round worms are called helminths.

Ø Microscopic stages in life cycles.

Ø Sexual reproduction

Ø Motility either absent or reduced

History of Microbiology

Ø Ancestors of bacteria were the first life on Earth.

Ø The first microbes were observed in 1673.

Ø In 1665, Robert Hooke reported that living things were composed of little boxes or cells.

l Led to the Cell Theory

• All living things consist of cells

• All living things are come from preexisting cells.

• Life continues because of growth and division of cells

• Cells are the smallest unit of life maintaining properties of life

The First Observations

Ø 1673-1723, Antoni van Leeuwenhoek described live microorganisms that he observed in teeth scrapings, rain water, and peppercorn infusions.

l Microscopic organisms – “Animalcules”

l Submitted findings to Royal Society of London

l Raised questions – Where did they originate?

The Debate Over Spontaneous Generation

Ø The hypothesis that living organisms arise from nonliving matter is called spontaneous generation. According to spontaneous generation, a “vital force” forms life.

Ø What was the “vital force”?

Ø The alternative hypothesis, that the living organisms arise from preexisting life, is called biogenesis. (Rudolf Virchow, 1858)

Evidence Pro and Con

Ø 1668: Francisco Redi (opponent) filled six jars with decaying meat.

Evidence Pro and Con

Ø 1745: John Needham (pro) put boiled nutrient broth into covered flasks.

Evidence Pro and Con

Ø 1765: Lazzaro Spallanzani boiled nutrient solutions in flasks.

l Spallanzani vs. Lavoisier

Evidence Pro and Con

Ø 1861: Louis Pasteur demonstrated that microorganisms are present in the air.

l Experiments disproving spontaneous generation

l Led to the development of aseptic techniques

The Theory of Biogenesis

Ø Pasteur’s S-shaped flask kept microbes out but let air in.

The Golden Age of Microbiology

Ø 1857-1914

l Period of rapid development

Ø Beginning with Pasteur’s work, discoveries included the relationship between microbes and disease, immunity, and antimicrobial drugs

Fermentation and Pasteurization

Ø Pasteur showed that microbes are responsible for fermentation.

Ø Fermentation is the conversion of sugar to alcohol to make beer and wine.

Ø Microbial growth is also responsible for spoilage of food.

Ø Bacteria that use alcohol and produce acetic acid spoil wine by turning it to vinegar (acetic acid).

Fermentation and Pasteurization

Ø Pasteur demonstrated that these spoilage bacteria could be killed by heat that was not hot enough to evaporate the alcohol in wine.

Ø Pasteruization is the application of a high heat for a short time.

The Germ Theory of Disease

Ø 1835: Agostino Bassi showed that a silkworm disease was caused by a fungus.

Ø 1865: Pasteur believed that another silkworm disease was caused by a protozoan.

Ø 1840s: Ignaz Semmelwise advocated hand washing to prevent transmission of puerperal fever from one OB patient to another.

Ø 1860s: Applying Pasteur’s work showing that microbes are in the air, can spoil food, and cause animal diseases, Joseph Lister used a chemical disinfectant to prevent surgical wound infections

Ø 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.

The Germ Theory of Disease

Ø 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.

Vaccination

Ø 1796: Edward Jenner inoculated a person with cowpox virus. The person was then protected from smallpox.

Ø Vaccination is derived from vacca for cow.

Ø The protection is called immunity.

The Birth of Modern Chemotherapy

¨ Treatment with chemicals is chemotherapy.

¨ Chemotherapeutic agents used to treat infectious disease can be synthetic drugs or antibiotics

¨ Antibiotics are chemicals produced by bacteria and fungi that inhibit or kill other microbes

The First Synthetic Drugs

¨ Quinine from tree bark was long used to treat malaria

¨ Paul Erlich speculated about a “magic bullet” that could destroy a pathogen without harming the host

¨ 1910: Ehrlich developed a synthetic arsenic drug, salvarsan, to treat syphilis

¨ 1930s: Sulfonamides (sulfa drugs) were synthesized

The Birth of Modern Chemotherapy

¨ 1928: Alexander Fleming discovered the first antibiotic.

¨ Fleming observed that Penicillium fungus made an antibiotic, penicillin, that killed S. aureus

¨ 1940s: Penicillin was tested clinically and mass produced.

Modern Developments in Microbiology

¨ Bacteriology is the study of bacteria.

¨ Mycology is the study of fungi.

¨ Parasitology is the study of protozoa and parasitic worms.

¨ Virology is the study of viruses.

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 was proposed by Rebecca Lancefield in 1933.

Modern Developments in Microbiology

¨ Recent advances in genomics, the study of an organism’s genes, have provided new tools for classifying microorganisms.

¡ Microbial genetics: The study of how microbes inherit traits

¡ Genomics: The study of an organism’s genes; has provided new tools for classifying microorganisms

¡ Recombinant DNA: DNA made from two different sources.

ú 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.

Nobel Prizes for Microbiology Research

¨ * The first Nobel Prize 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

2005 Marshall & Warren H. pylori & ulcers

Microbes and Human Welfare

Ø Microbial ecology

Ø Bacteria recycle carbon, nutrients, sulfur, and phosphorus that can be used by plants and animals.

Bioremediation

Ø Bacteria degrade organic matter in sewage.

Ø Bacteria degrade or detoxify pollutants such as oil and mercury.

Biological Insecticides

Ø Microbes that are pathogenic to insects are alternatives to chemical pesticides in preventing insect damage to agricultural crops and disease transmission.

Ø Bacillus thuringiensis infections are fatal in many insects but harmless to other animals, including humans, and to plants.

Modern Biotechnology and Genetic Engineering

Ø Biotechnology, the use of microbes to produce foods and chemicals, is centuries old.

Biotechnology

¨ Recombinant DNA technology, a new technique for biotechnology, enables bacteria and fungi to produce a variety of proteins including vaccines and enzymes

¡ Missing or defective genes in human cells can be replaced in gene therapy

ú Inserting genes for useful enzymes inside bacterial DNA (Ex. E. coli)

ú Efficient and fast production of enzyme by bacteria

Ex. Insulin

¡ Genetically modified bacteria are used to protect crops from insects and from freezing

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

Ø Normal microbiota prevent growth of pathogens.

Ø Normal microbiota produce growth factors such as folic acid and vitamin K.

Ø Resistance is the ability of the body to ward off disease.

Ø Resistance factors include skin, stomach acid, and antimicrobial chemicals.

Biofilms

¨ Microbes attach to solid surfaces and grow into masses

¨ They will grow on rocks, pipes, teeth, and medical implants

Infectious Diseases

Ø When a pathogen overcomes the host’s resistance, disease results.

Ø Emerging infectious diseases (EID): New diseases and diseases increasing in incidence.

Emerging Infectious Diseases

Ø West Nile encephalitis

l West Nile virus

l First diagnosed in the West Nile region of Uganda in 1937

l Appeared in New York City in 1999

Emerging Infectious Diseases

Ø Bovine spongiform encephalopathy

l Prion

l Also causes Creutzfeldt-Jakob disease (CJD)

l New variant CJD in humans is related to cattle fed sheep offal for protein

Emerging Infectious Diseases

Ø Ebola hemorrhagic fever

l Ebola virus

l Causes fever, hemorrhaging, and blood clotting

l First identified near Ebola River, Congo

l Outbreaks every few years

Emerging Infectious Diseases

Ø Avian influenza A

l Influenza A virus (H5N2)

l Primarily in waterfowl and poultry

l Sustained human-to-human transmission has not occurred yet

Emerging Infectious Diseases

Ø So, what do you know about swine flu?

l Influenza A virus (H1N1)

l Detected in April 2009

l Spread person-to-person

• Mimics seasonal flu

Cryptosporidiosis

¨ Cryptosporidium protozoa

¨ First reported in 1976

¨ Causes 30% of diarrheal illness
in developing countries

¨ In the United States, transmitted via water

MRSA

¨ Methicillin-resistant Staphylococcus aureus

¨ 1950s: Penicillin resistance developed

¨ 1980s: Methicillin resistance

¨ 1990s: MRSA resistance to vancomycin reported

¡ VISA: Vancomycin-intermediate-resistant S. aureus

¡ VRSA: Vancomycin-resistant S. aureus

Emerging Infectious Diseases

Chapter One

The Microbial World and You

Microbes in Our Lives

Ø What is microbiology?

l Study of microorganisms and viruses

Ø What are microorganisms?

l Organisms that are too small to be seen with the unaided eye

Ø Have enormous impact

Naming and Classifying Microorganisms

Ø Carolus Linnaeus

l Established the system of scientific nomenclature

l Means of communicating to others about specific organisms.

Ø Binomial system

l Each organism has two names:

• Genus (genera): The first name, which is always capitalized and underlined or italicized

• Species (specific epithet): The second name, which is underlined or italicized, but not capitalized.

• Are “Latinized” and used worldwide

• May be descriptive or honor a scientist

Scientific Names

Ø Staphylococcus aureus

l Describes the clustered arrangement of the cells (staphylo-) and the golden color of the colonies (aur-).

Scientific Names

Ø Escherichia coli

l Honors the discoverer, Theodor Escherich, and describes the bacterium’s habitat–the large intestine or colon.

Scientific Names

Ø After the first use, scientific names may be abbreviated with the first letter of the genus and the specific epithet:

l Staphylococcus aureus and Escherichia coli are found in the human body. S. aureus is on skin and E. coli in the large intestine.

Classification of Microorganisms

Ø Three domains (Carl Woese - 1978)

l Bacteria

l Archaea

l Eukarya

• Protists

• Fungi

• Plants

• Animals

Viruses

Bacteria

Ø Prokaryotes

Ø No membrane bound nucleus

Ø Unicellular microorganisms

Ø Different shapes

Ø Peptidoglycan cell walls

Ø Reproduce by binary fission

Ø Some bacteria have flagella for “swimming”

Ø For energy, use organic chemicals, inorganic chemicals, or photosynthesis

Archaea

Ø Prokaryotic

Ø No membrane bound nucleus

Ø Unicellular microorganisms

Ø Lack peptidoglycan

Ø Reproduce by binary fission

Ø Live in extreme environments

Ø Include

l Methanogens

l Extreme halophiles

l Extreme thermophiles

Eukaryotes

Ø Distinct membrane bound nucleus

Ø Membrane bound organelles

Ø Cells are larger than prokaryotes

Ø Moderate environments

Fungi

Ø Eukaryotes

Ø Chitin cell walls

Ø Use organic chemicals for energy.

Ø Molds and mushrooms are multicellular consisting of masses of mycelia, which are composed of filaments called hyphae.

Ø Yeasts are unicellular.

Ø Reproduce sexually or asexually

Protozoa

Ø Eukaryotes

Ø Unicellular

Ø Absorb or ingest organic chemicals

Ø May be motile via pseudopods, cilia, or flagella

Ø Reproduce sexually or asexually

Algae

Ø Eukaryotes

Ø Unicellular

Ø Cellulose cell walls

Ø Use photosynthesis for energy (photosynthetic)

Ø Absorb or ingest
organic chemicals

Ø May be motile via pseudopods, cilia,
or flagella