Course Introduction and Structure

Course Overview

This course, BioMI 2900 - General Microbiology, introduces students to the fundamental principles and modern advances in microbiology. The course covers the diversity, structure, function, and evolution of microorganisms, as well as their roles in health, disease, and the environment.

• Lead Instructors: Dr. Dan Buckley, Dr. Kathleen Hefferon

• Teaching Staff: Daniel Francis (Coordinator), Delia Tota (TA), Evangeline Wang (TA), Mark Watso

• Learning Assistants: Additional support staff for active learning

Course Logistics

• Canvas: Online platform for course materials and announcements

• Textbook: Brock Biology of Microorganisms

• Mastering Microbiology: Online homework and study tool

• Discussion Sections: Begin Monday 1/27, focus on active learning

• Grading: Based on exams, quizzes, homework, and participation

How to Succeed in BIOMI 2900

1. Read the syllabus to understand course expectations.

2. Outline the reading assignments for better comprehension.

3. Take handwritten notes during class to enhance retention.

4. Rewrite notes after class and clarify unclear concepts.

5. Complete homework closed-book; review mistakes and seek help if needed.

6. Practice regularly: join study groups, use eText resources, and attempt practice questions.

7. Utilize office hours and study groups for additional support.

Cornerstones of Modern Microbiology

Key Areas of Microbiology

• Microscopy: Techniques for visualizing microbes and their structures.

• Cultivation & Physiology: Methods for growing microbes and studying their metabolic activities.

• Molecular Biology & Genetics: Investigation of cell structures, molecular functions, inheritance, and regulation.

• Genomics: Study of cellular information, genome sequencing, and evolutionary relationships.

Historical Milestones

• Robert Hooke (1635–1703): First to describe microbes using microscopy.

• Antonie van Leeuwenhoek (1632–1723): First to describe bacteria.

• Louis Pasteur (1822–1895): Disproved spontaneous generation, proposed germ theory, invented pasteurization, developed rabies vaccine.

• Robert Koch (1843–1910): Developed pure culture techniques, proved germ theory of disease (Koch's Postulates).

• Martinus Beijerinck & Sergei Winogradsky: Developed enrichment culture techniques, linked microbes to nutrient cycles.

• Kluyver (1926): Published Unity in Biochemistry, highlighting biochemical similarities across life.

• Watson, Crick, Franklin (1953): Discovered DNA structure.

• Sanger (1977): Developed DNA sequencing methods.

• Woese (1977): Built the first Tree of Life from rRNA sequences, establishing molecular phylogeny.

• Mullis (1985): Invented Polymerase Chain Reaction (PCR).

• Pace (1985): Developed cultivation-independent techniques using rRNA.

Major Concepts and Definitions

Spontaneous Generation vs. Germ Theory

• Spontaneous Generation: Outdated theory that life arises from non-living matter.

• Miasma Theory: Disease caused by 'bad air' from unclean conditions.

• Germ Theory of Disease: Diseases are caused by microorganisms (Pasteur).

Koch's Postulates

1. The suspected pathogen must be present in all cases of the disease and absent from healthy animals.

2. The suspected pathogen must be grown in pure culture.

3. Cells from a pure culture must cause disease in a healthy animal.

4. The pathogen must be reisolated and shown to be the same as the original.

Enrichment Culture

• Definition: Use of defined media to selectively grow specific microbes.

• Application: Studying microbial roles in nutrient cycles and environmental processes.

Microbial Physiological Diversity

• Animals and Fungi: (aerobic respiration; some fungi ferment).

• Plants and Algae: (photosynthesis).

• Microbes: Exhibit aerobic/anaerobic respiration, fermentation, syntrophy, lithotrophy, phototrophy, and respiration of metals, sulfur, and methane.

Modern Molecular Microbiology

Model Organisms

• Escherichia coli (E. coli): Widely used for genetic and biochemical studies due to ease of cultivation and rapid growth.

Universal Phylogenetic Markers

• Ribosomes: Protein synthesis machinery present in all cellular life.

• Ribosomal RNA (rRNA): 16S, 23S, and 5S rRNA genes used for evolutionary studies.

• Molecular Phylogeny: Using gene sequences (especially rRNA) to infer evolutionary relationships and build the Tree of Life.

Genomics and Sequencing

• PCR: Amplifies specific DNA segments for study.

• Genome Sequencing: Determines the complete DNA sequence of an organism's genome.

• Metagenomic Sequencing: Analyzes DNA from entire microbial communities, revealing uncultured diversity.

• Cost of Sequencing: Rapidly decreasing, enabling large-scale genomic studies.

Summary Table: Cornerstones and Key Contributors

Additional info:

• Active learning and discussion sections are shown to improve exam and quiz performance.

• Handwritten notes and active participation are emphasized for success in the course.

• Modern microbiology integrates classical techniques with molecular and genomic approaches to understand microbial diversity and function.