Chapter 1: Introduction to Microbiology (Notes)
Course Overview
Welcome to microbiology with instructor Kim Williams.
Topics covered: fundamentals such as replication and metabolism; various fields within microbiology (environmental, food, biotechnology).
The course ends with a medical microbiology theme: immune system interactions, and diseases caused by microorganisms affecting the human host.
There are audio files and PowerPoint slides to reference as you move through the material.
We will not be covering Chapter 2; however, a brush-up of chemistry from Chapter 2 is encouraged if you need to review chemistry concepts since chemistry will be incorporated into the course.
Basic orientation: microorganisms are often associated with disease, but they can also be highly beneficial (e.g., in biotechnology).
Chapter 1 provides foundational terminology and concepts.
What is Microbiology?
Definition: Microbiology is the study of microbes and microorganisms that are too small to see with the unaided eye; magnification is required to view them.
Terms microbe and microorganism are used interchangeably (they are the same).
Examples of microbes/microorganisms:
Bacteria
Viruses
Protozoa
Fungi
Helminths (worms)
Visibility and life cycles:
In most cases, microorganisms require microscopy to be seen.
Some organisms have life-cycle stages that are visible without magnification (e.g., the tapeworm in the adult stage is visible without magnification).
Example: tapeworm is microscopic in the egg stage but visible in the adult stage.
Normal Microbiota and Host Interactions
Normal microbiota: microbes that live in and on our bodies and are beneficial, helping protect against illnesses.
Opportunistic infection: occurs when normal microbiota becomes unbalanced, allowing other microbes to flourish and potentially cause illness.
Pathogen: a disease-causing microbe.
Infectious disease: a disease resulting from a pathogen infecting a susceptible host.
Oxygen and Microbes; Aerobic vs Anaerobic
Aerobic: organisms that require or thrive in the presence of oxygen.
Anaerobic: organisms that do not require oxygen or may be harmed by oxygen.
Facultative anaerobe: defined here as an aerobic organism that can tolerate reduced amounts of oxygen.
Note: The instructor also states a formulation that a facultative aerobe is an anaerobic organism that can tolerate increased amounts of oxygen (this reflects the wording used in the lecture).
Obligates:
Obligate anaerobe: must live in an environment without oxygen.
Obligate aerobe: must live in an environment with oxygen.
Nomenclature and Classification
Scientific name structure: two-part name consisting of genus and species.
Example: extit{Staphylococcus aureus}
Genus: first part, capitalized (e.g., Staphylococcus).
Species: second part, lowercase (e.g., aureus).
The entire name is italicized or underlined when handwritten.
Formatting rules:
Genus: capitalized (first letter of the genus).
Species: lowercase.
Entire scientific name: either underlined or italicized.
Note: The two-part name helps distinguish organisms at a more precise level than genus alone.
Applications of Microbiology
Medical microbiology: investigation of diseases.
Industrial microbiology: production of vaccines, antibiotics, and other products.
Environmental microbiology: bioremediation — using microorganisms to clean up toxic sites.
Four Fields of Study in Microbiology
Bacteriology: study of bacteria.
Mycology: study of fungi.
Virology: study of viruses.
Parasitology: study of parasites, including helminths (worms).
Key Scientific Discoveries and Concepts (Golden Age)
1665: Robert Hooke coined the term "cell" after viewing plant cell compartments; this marked the beginning of cell theory: all living things are composed of cells.
1673: Anton van Leeuwenhoek (spelling as in lecture) discovered motile microbes (motility). The organism studied in his work was Giardia; motility structures and organisms will be discussed later.
1861: Louis Pasteur disproved spontaneous generation; introduced the theory of biogenesis (living things come from living things).
Spontaneous generation background:
Experiments with nutrient broth (e.g., beef broth) in open beakers showed growth after some time, leading to the belief that non-living matter could spontaneously generate life.
Pasteur designed the swan-necked flask to test this: boiled nutrient broth in a flask with a curved neck, exposed to air but with a bend that trapped microorganisms; broth remained sterile, demonstrating microorganisms come from elsewhere (biogenesis).
This work established aseptic technique and supported germ theory.
Additional accomplishments associated with Pasteur’s era: fermentation, pasteurization, germ theory of disease; these advances paved the way for immunizations and antibiotics.
Microscopes: Types and Basic Use
Compound light microscope:
The most basic microscope.
Uses white light.
Staining is often used for better visualization of specimens.
Phase-contrast microscope:
Also uses white light.
Uses light diffraction to enhance contrast, revealing internal structures of living cells through shading patterns.
Fluorescent microscope:
Requires labeling the specimen with a fluorochrome (fluorescent dye).
Specimen is viewed under ultraviolet (UV) light, causing fluorochromes to fluoresce.
Confocal microscope:
Provides three-dimensional imaging.
Also uses fluorochromes; allows for optical sectioning and 3D reconstruction.
Electron microscope:
Uses a beam of electrons instead of light.
Employs electromagnetic lenses for high-resolution imaging.
Scanned probe microscope:
One of the most advanced types currently available.
Uses an electric current to examine the specimen.
Enables examination of molecular and chemical properties of the cell.
Additional Notes
Slides: PowerPoint slides accompany the audio and should be consulted alongside the lecture.
Chapter coverage: Chapter 2 is not formally covered in this course, but review may be beneficial if needed.
Real-world relevance: Microbiology spans disease causation, environmental benefits, industrial applications, and public health implications (e.g., bioremediation, vaccines, antibiotics, aseptic technique, germ theory).
Ethical/practical implications: The discovery of germ theory and aseptic technique underpins modern medical practice, infection control, and antibiotic development; environmental applications like bioremediation demonstrate the societal value of microbiology in addressing pollution and health concerns.
Quick Reference: Key Terms and Concepts
Microbiology = study of microbes/microorganisms too small to see without magnification.
Microbe vs microorganism = interchangeable terms.
Normal microbiota = beneficial microbes living on/in the body.
Opportunistic infection = disease caused by imbalance of normal microbiota.
Pathogen = disease-causing microbe.
Infectious disease = disease caused by a pathogen in a susceptible host.
Aerobic = requires/uses oxygen.
Anaerobic = does not require/uses oxygen.
Facultative anaerobe (per lecture): aerobic organism that can tolerate reduced oxygen.
Facultative aerobe (per lecture): anaerobic organism that can tolerate increased oxygen.
Obligate anaerobe = must live without oxygen.
Obligate aerobe = must live with oxygen.
Binomial nomenclature: two-part name (genus and species) with genus capitalized, species lowercase, and italicized or underlined; example: extit{Staphylococcus aureus} (Genus: Staphylococcus; Species: aureus).
Major fields of microbiology: Bacteriology, Mycology, Virology, Parasitology.
Major applications: Medical microbiology, Industrial microbiology, Environmental microbiology (bioremediation).
Major historical milestones: Hooke (cell theory), Leeuwenhoek (motility), Pasteur (biogenesis, swan-neck flask), fermentation, pasteurization, germ theory, immunizations, antibiotics.
Summary Reminders
Microbiology blends basic science with practical applications across health, industry, and the environment.
Understanding terminology, nomenclature, and the basic tools (microscopes) is foundational for exploring more advanced topics in later chapters.
Recognize the link between historical discoveries and modern practices (aseptic technique, germ theory, vaccines, antibiotics).
Course Overview
Instructor: Kim Williams
Core Topics: Fundamentals (replication, metabolism), various fields (environmental, food, biotechnology).
Medical Microbiology Theme: Immune system interactions, diseases affecting human hosts.
Resources: Audio files and PowerPoint slides are available.
Chapter 2: Not formally covered, but chemistry review is encouraged for foundational concepts.
Basic Concept: Microorganisms can be associated with disease but are also highly beneficial (e.g., biotechnology).
Chapter 1: Provides foundational terminology and concepts.
What is Microbiology?
Definition: The study of microbes and microorganisms that require magnification to be seen (too small for the unaided eye).
Terms: "Microbe" and "microorganism" are used interchangeably.
Examples: Bacteria, Viruses, Protozoa, Fungi, Helminths (worms).
Visibility: Most require microscopy; some, like adult tapeworms, have life-cycle stages visible without magnification (e.g., microscopic in egg stage, visible in adult stage).
Normal Microbiota and Host Interactions
Normal Microbiota: Beneficial microbes living in and on our bodies, protecting against illness.
Opportunistic Infection: Occurs when normal microbiota becomes unbalanced, allowing other microbes to flourish and potentially cause illness.
Pathogen: A disease-causing microbe.
Infectious Disease: A disease resulting from a pathogen infecting a susceptible host.
Oxygen and Microbes: Aerobic vs. Anaerobic
Aerobic: Organisms that require or thrive in the presence of oxygen.
Anaerobic: Organisms that do not require oxygen or may be harmed by it.
Facultative Anaerobe: An aerobic organism that can tolerate reduced amounts of oxygen.
Facultative Aerobe: An anaerobic organism that can tolerate increased amounts of oxygen.
Obligate Anaerobe: Must live in an environment without oxygen.
Obligate Aerobe: Must live in an environment with oxygen.
Nomenclature and Classification
Scientific Name Structure: Two-part name consisting of genus and species.
Example: \textit{Staphylococcus aureus}
Genus: First part, capitalized (e.g., Staphylococcus).
Species: Second part, lowercase (e.g., aureus).
Formatting Rules: The entire name is italicized or underlined when handwritten.
Applications of Microbiology
Medical Microbiology: Investigation of diseases.
Industrial Microbiology: Production of vaccines, antibiotics, and other products.
Environmental Microbiology: Bioremediation (using microorganisms to clean up toxic sites).
Four Fields of Study in Microbiology
Bacteriology: Study of bacteria.
Mycology: Study of fungi.
Virology: Study of viruses.
Parasitology: Study of parasites, including helminths (worms).
Key Scientific Discoveries and Concepts (Golden Age)
1665: Robert Hooke
Coined the term "cell" after viewing plant cells.
Cell Theory: All living things are composed of cells.
1673: Anton van Leeuwenhoek
Discovered motile microbes (e.g., Giardia).
1861: Louis Pasteur
Disproved Spontaneous Generation and introduced Biogenesis (living things come from living things).
Swan-Necked Flask Experiment: Boiled broth in curved-neck flasks remained sterile, demonstrating that microorganisms come from the air, not spontaneously generated.
Established: Aseptic technique and supported germ theory.
Additional Accomplishments: Fermentation, pasteurization, germ theory of disease, paving the way for immunizations and antibiotics.
Microscopes: Types and Basic Use
Compound Light Microscope
Most basic, uses white light.
Staining often used for visualization.
Phase-Contrast Microscope
Uses white light and light diffraction to enhance contrast.
Reveals internal structures of living cells through shading patterns.
Fluorescent Microscope
Requires labeling with a fluorochrome (fluorescent dye).
Specimen viewed under ultraviolet (UV) light, causing fluorescence.
Confocal Microscope
Provides three-dimensional imaging.
Uses fluorochromes, allows optical sectioning and 3D reconstruction.
Electron Microscope
Uses a beam of electrons instead of light.
Employs electromagnetic lenses for high-resolution imaging.
Scanned Probe Microscope
One of the most advanced types.
Uses an electric current to examine the specimen.
Enables examination of molecular and chemical properties of the cell.
Quick Reference: Key Terms and Concepts
Microbiology: Study of microbes/microorganisms too small to see without magnification.
Microbe vs. Microorganism: Interchangeable terms.
Normal Microbiota: Beneficial microbes living on/in the body.
Opportunistic Infection: Disease caused by an imbalance of normal microbiota.
Pathogen: Disease-causing microbe.
Infectious Disease: Disease caused by a pathogen in a susceptible host.
Aerobic: Requires/uses oxygen.
Anaerobic: Does not require/uses oxygen or is harmed by it.
Facultative Anaerobe: Aerobic organism that can tolerate reduced oxygen.
Facultative Aerobe: Anaerobic organism that can tolerate increased oxygen.
Obligate Anaerobe: Must live without oxygen.
Obligate Aerobe: Must live with oxygen.
Binomial Nomenclature: Two-part name (genus and species) with genus capitalized, species lowercase, and italicized or underlined; example: \textit{Staphylococcus aureus} .
Major Fields: Bacteriology, Mycology, Virology, Parasitology.
Major Applications: Medical microbiology, Industrial microbiology, Environmental microbiology (bioremediation).
Historical Milestones: Hooke (cell theory), Leeuwenhoek (motility), Pasteur (biogenesis, swan-neck flask, fermentation, pasteurization, germ theory, immunizations, antibiotics).
Summary Reminders
Microbiology combines basic science with practical applications in health, industry, and the environment.
Understanding terminology, nomenclature, and basic tools (microscopes) is fundamental.
Recognize the link between historical discoveries and modern