CH.1 & 2 Microbiology: Introduction and Microbial Foundations

Course Introduction, Instructor Background, and Syllabus Review

Instructor Profile: Micah Willis, PhD

• Academic Background: Graduated with a PhD in Toxicology from the University of North Carolina at Chapel Hill (UNC-CH).

• Dissertation Title: The Role of Extracellular Vesicles in Burn Injury.

• Postdoctoral Experience: Completed approximately $3$ years as a postdoctoral researcher at the University of Florida (UF).

• Research Focus: Investigated extracellular vesicles within periodontal disease and their potential links to systemic diseases, such as Rheumatoid Arthritis.

• Personal Interests:     * Cooking: Originally considered attending culinary school.     * Video Games: Currently active on PlayStation 5 (PS5) and Xbox One.     * Sports: Enjoys watching sports, including college-level athletics.

Course Overview: MCB2000 Microbiology

• Level: This is a $2000$-level course.

• Target Audience: Science, engineering, biotechnology, and pre-professional majors.

• Scope of Study: Topics include bacterial genetics, metabolism, industrial applications of microbiology, properties of selected organisms, and various microbiological techniques.

• Academic Rigor: This course is challenging and designed to provide a structure similar to courses found in Nursing, Veterinary, and Graduate school programs.

• Course Nature:     * What it is: Structured, concept-based, and focused on understanding biological mechanisms.     * What it is NOT: A memorization-only course, designed to trick students, or a cram-centric environment.

Course Expectations and Mutual Commitments

• Instructor Expectations for Students:     * Regular attendance and active engagement.     * Maintaining progression with weekly work.     * Asking questions early and frequently.     * Acting with academic integrity.     * Effort is prioritized over perfection.

• Student Expectations for Instructor:     * Clarity and organization in material delivery.     * Fairness and consistency in grading and policies.     * Support for the learning process.     * Respect for student time and effort.

Class Structure and Weekly Workflow

The course follows a "Prepare -> Participate -> Practice -> Perform" cycle:

• Before Class ($15-30$ minutes): Students engage with assigned readings or short videos focused on introducing key terms and concepts.

• During Class: Sessions begin with addressal of topic-related questions followed by a $30-45$ minute short lecture to clarify difficult concepts and connect ideas. This includes practice questions, scenarios, and group activities.

• After Class: Homework assignments are designed to reinforce class practice and reflect examples used in the lecture. There are no "surprise" expectations.

Office Hours and Accessibility

• Location: W-$061$.

• Schedule:     * Monday: Appointment only.     * Tuesday: $12:00p$ – $1:00p$.     * Wednesday: $11:30a$ – $2:15p$.     * Thursday: $10:20a$ – $12:45p$ and $2:30-4:30p$.     * Friday: Appointment only.

• Protocols: Appointments must be confirmed at least $24$ hours in advance. Meetings can be conducted via Zoom. Emergency meetings outside these hours may be arranged.

Grading, Policies, and Academic Integrity

Final Grade Calculation

Performance is built over time; no single assignment defines the grade. The system is designed to reward consistency.

Examination and Quiz Policies

• Exams: Closed-book/closed-note. Must be made up within $5$ calendar days if the student initiates contact. Make-up formats may vary.

• Quizzes: Administered at the start of class. Closed-book/closed-note. Make-ups allowed within $3$ calendar days of contact. Late arrival reduces available time. Electronic devices are prohibited.

• Pop Quizzes: Unannounced assessments to encourage attendance. Cannot be made up for any reason. The two lowest scores are dropped at the end of the semester.

General Policies and Important Dates

• Attendance: Not formally graded but strongly expected due to the cumulative nature of the material. Material from absences, including pop quizzes, cannot be made up.

• Late Work: Accepted up to $72$ hours past the deadline with tiered penalties:     * $25\%$ deduction for initial lateness.     * $35\%$ deduction.     * $45\%$ deduction for max lateness.     * After $72$ hours, no work is accepted.

• Artificial Intelligence (AI) Policy: Use of AI to generate text, answers, or data analysis for credit is prohibited and results in a zero. Students may use AI for personal study aids (clarifying terms, generating practice questions).

• Textbook: Rice. Microbiology (OER). OpenStax. ISBN: $9781947172234$. Available for FREE on Canvas.

• Critical Dates (Spring 2026):     * January 14, 2026: Last day to drop/add with refund.     * March 25, 2026: Last day to withdraw for a "W."     * April 25, 2026: End of Spring classes.     * April 27 – May 2, 2026: Final exams.

Student Success Strategies

• From Past Students:     * Take exhaustive notes on everything, including quiz content.     * Do not procrastinate.     * Teach information to others or test each other.     * Utilize YouTube lectures and perform white-board recall from memory.     * Create mind maps to grasp complex concepts.

• Instructor Tips: Attend class, review at least $15$ minutes daily, ask questions immediately when stuck, and put effort into homework.

Introduction to Microbiology: Principles and Diversity

Definition and Importance of Microbiology

• Fundamental Definition: The study of basic life processes for unicellular organisms.

• Areas of Study:     * Cell Structure and Function.     * Microbial Metabolism.     * Microbial Growth.     * Microbial Genetics.

• Benefits to Humanity:     * Medicine: Production of antibiotics like penicillin.     * Agriculture: Use of organisms such as Rhizobia for nitrogen fixation.     * Industry: Production of fermented foods.

• Evolutionary Context: Bacteria-like organisms have existed for approximately $3.5$ billion years. Humans have utilized microbes since before their discovery through visualization.

Groupings of Microorganisms

The six major groups include:

1. Protists: Eukaryotes that are neither plants, animals, nor fungi. Includes Algae (photosynthetic, cellulose wall) and Protozoa (unicellular, use carbon, move via cilia, flagella, or pseudopods).

2. Fungi: Eukaryotes including unicellular yeasts and multicellular molds. They lack chlorophyll and possess cell walls made of Chitin.

3. Bacteria: Prokaryotes (lacking a true nucleus) found in nearly every habitat. They have Peptidoglycan cell walls, reproduce via binary fission, and display high nutritional diversity.

4. Archaea: Prokaryotes often found in extreme environments (hot, acidic, basic). Their cell walls contain Pseudopeptidoglycan rather than Peptidoglycan. They are not known to cause human disease.

5. Viruses: Acellular microorganisms consisting of protein and genetic material (DNA or RNA). A complete particle is a "virion." They are obligate parasites requiring a host to replicate.

6. Helminths: Multicellular parasitic worms (flatworms and roundworms). Life stages include egg, larval (juvenile), and adult. Disease is often caused by the eggs or larvae. 1. **Which of the following characteristics is true about protists?** A) They are always multicellular. B) They have cell walls made of chitin. C) They are primarily photosynthetic eukaryotes. D) They are prokaryotes. **Correct Answer:** C) They are primarily photosynthetic eukaryotes. 2. **What is the primary difference between fungi and plants?** A) Fungi have chlorophyll. B) Fungi lack chlorophyll and have chitin in their cell walls. C) Fungi are always unicellular. D) Fungi can perform photosynthesis. **Correct Answer:** B) Fungi lack chlorophyll and have chitin in their cell walls. 3. **Which of the following is a characteristic of bacteria?** A) They are eukaryotes with a true nucleus. B) They reproduce by mitosis. C) They possess peptidoglycan in their cell walls. D) They cannot be found in extreme environments. **Correct Answer:** C) They possess peptidoglycan in their cell walls. 4. **What distinguishes archaea from bacteria?** A) Archaea have peptidoglycan walls. B) Archaea are not found in extreme environments. C) Archaea have pseudopeptidoglycan in their cell walls. D) Archaea are typically larger than bacteria. **Correct Answer:** C) Archaea have pseudopeptidoglycan in their cell walls. 5. **What is a defining feature of viruses?** A) They contain both DNA and RNA. B) They can independently reproduce. C) They are obligate parasites that require a host to replicate. D) They are considered living organisms. **Correct Answer:** C) They are obligate parasites that require a host to replicate. 6. **Which of the following statements about helminths is accurate?** A) Helminths are unicellular organisms. B) Helminths can cause diseases in humans primarily through their adult form. C) Helminths undergo significant lifecycle stages including egg, larval, and adult stages. D) Helminths are prokaryotic microorganisms. **Correct Answer:** C) Helminths undergo significant lifecycle stages including egg, larval, and adult stages.

Microbial Dimensions and Scale

• Size Range: Most bacteria fall between $1$ and $10\,\mu m$ in size.

• Visualization Thresholds:     * Human Eye Range: Down to approximately $100\,\mu m$ (e.g., Louse).     * Light Microscope Range: $100\,\mu m$ to $200\,nm$ (e.g., mitochondria, bacteria).     * Electron Microscope Range: $200\,nm$ down to $0.1\,nm$ (e.g., viruses, proteins, lipids, atoms).

• Metric Conversions (Log 10 Scale):     * Kilometer ($km$): $10^3\,m$     * Meter ($m$): $10^0\,m$     * Millimeter ($mm$): $10^{-3}\,m$     * Micrometer ($\,\mu m$): $10^{-6}\,m$     * Nanometer ($nm$): $10^{-9}\,m$     * Angstrom ($\unicode{x212B}$): $10^{-10}\,m$

Historical Foundations of Microbiology

Spontaneous Generation vs. Germ Theory

• Spontaneous Generation: An obsolete theory (originating from Aristotle) stating life can arise from inanimate objects (e.g., dust creating fleas, rotting meat creating maggots).

• Germ Theory: States that many diseases are caused by microorganisms (bacteria, viruses, fungi, protozoa). This concept provided the scientific basis for modern medicine.

Key Figures in Microbiology

• Antonie van Leeuwenhoek ($1632-1723$): Known as the "Father of Microbiology." Developed powerful lenses to view "animalcules" in rainwater (likely bacteria and protists).

• Louis Pasteur ($1822-1895$):     * Disproved spontaneous generation using the swan-neck flask experiment ($1862$).     * Showed microbial strains have unique properties.     * Invented pasteurization.     * Developed vaccines for rabies, anthrax, and diphtheria.

• Robert Koch ($1843-1910$):     * Established the direct link between a single microbe and a specific disease (Anthrax via Bacillus anthracis, Cholera via Vibrio cholera, and Tuberculosis via Mycobacterium tuberculosis).     * Developed Koch’s Postulates.

• Joseph Lister ($1827-1912$): Developed procedures for antiseptic surgery including the use of carbolic acid to disinfect wounds and surgical instruments ($1867$).

• Ignaz Philipp Semmelweis (Late $1800$s): Demonstrated that hand washing reduces mortality from puerperal infections in hospitals ($1847$).

• Paul Ehrlich (Late $1800$s): Suggested "magic bullets"—chemicals that could kill microorganisms without harming the patient.

• Girolamo Fracastoro ($1546$): Proposed an early version of the germ theory in De Contagione et Contagiosis Morbis.

• Robert Hooke ($1665$): First to observe "cells" in cork under a microscope.

• John Snow ($1854$): Demonstrated that cholera was transmitted via contaminated drinking water.

Koch’s Postulates

A four-step method to link a specific microbe to a disease:

1. The suspected pathogen must be present in every case of the disease and absent from healthy organisms.

2. The pathogen must be isolated from the diseased host and grown in a pure culture.

3. The isolated pathogen must cause the same disease when inoculated into a healthy, susceptible laboratory animal.

4. The pathogen must be re-isolated from the inoculated animal and shown to be identical to the original isolated pathogen.

Taxonomy and Classification

Evolutionary Principles

• Phylogeny: The study of natural relatedness between groups of organisms.

• Evolution: The process where living things change gradually over long periods. New species originate from pre-existing species. Changes favoring survival are retained, while less beneficial changes are lost.

Three Domains of Life

1. Bacteria: True bacteria (prokaryotic).

2. Archaea: Prokaryotes living in extreme environments (high salt, heat).

3. Eukarya: Organisms with a nucleus and membrane-bound organelles (includes kingdoms: Plantae, Animalia, Fungi, Protista).

Binomial Nomenclature

• Format: Genus species (e.g., Staphylococcus aureus).

• Rules:     * The Genus name must be capitalized.     * The species name must be lowercase.     * The entire name must be italicized (when typed) or underlined (when handwritten).     * After the first mention, the Genus can be abbreviated (e.g., H. sapiens).

Questions & Discussion

Icebreaker Exercise ($8$ minutes):

1. Question: What is your name?

2. Question: What is one food that you could eat every day?

3. Question: What is the last TV show that you binge-watched?

General Questions:

• Prompt: Questions???

• Response: Students are encouraged to use the remaining time to ask clarification questions regarding the syllabus or the introductory lecture material.

Upcoming Deliverables:

• Read Chapters $1$ & $2$.

• Complete Assignment $1$ & $2$.

• Prepare for Pre-Class $2$.

Germ Theory Application Questions

1. Which statement best describes the principle of germ theory?
      A) Diseases are caused by imbalances in body fluids.
      B) Microorganisms are responsible for many diseases.
      C) Diseases arise spontaneously from inanimate matter.
      D) A strong immune system can prevent all infections.
   Correct Answer: B) Microorganisms are responsible for many diseases.

2. In what way did Louis Pasteur's work support germ theory?
      A) He focused on the role of nutrients in bacterial growth.
      B) He introduced antiseptic techniques in surgery.
      C) He disproved spontaneous generation using experiments.
      D) He was the first to classify microorganisms.
   Correct Answer: C) He disproved spontaneous generation using experiments.

Koch’s Postulates Application Questions

3. According to Koch’s Postulates, which of the following must occur in order to establish a causal relationship between a microorganism and a disease?
      A) The microbe must be present in healthy individuals.
      B) The microbe must be isolated and grown in pure culture.
      C) The microbe must produce symptoms in immunized animals.
      D) The microbe must be harmless to laboratory animals.
   Correct Answer: B) The microbe must be isolated and grown in pure culture.

4. Why are Koch’s Postulates still relevant today?
      A) They help determine whether environmental factors cause diseases.
      B) They provide a clear framework for identifying the pathogens of infectious diseases.
      C) They eliminate the need for modern molecular techniques.
      D) They are used solely in agricultural applications.
   Correct Answer: B) They provide a clear framework for identifying the pathogens of infectious diseases.

Binomial Nomenclature Application Questions

5. What is the correct format for writing the scientific name of an organism in binomial nomenclature?
      A) Both names are capitalized and italicized.
      B) The genus is capitalized, and the species is lowercase and italicized.
      C) Both names are lowercase and underlined.
      D) The genus is abbreviated, and the species is written in full.
   Correct Answer: B) The genus is capitalized, and the species is lowercase and italicized.

6. Why is binomial nomenclature important in the classification of living organisms?
      A) It allows for easier communication and reduces confusion among scientists.
      B) It ensures all organisms are named after their discoverers.
      C) It limits species names to three words only.
      D) It dictates how organisms should be genetically modified.
   Correct Answer: A) It allows for easier communication and reduces confusion among scientists.