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Medicine & Biology Course Outline

Course: “Introduction to Microbiology” (Biology/Medicine)

Jose Gabriel Nino Barreat, Lic. Biol., DPhil Zoology (2nd year) - July 2020

Course outcomes

  • Students will learn the core principles of modern microbiology with a general overview of the field
  • Students will develop an understanding of the scientific method and the major tools used in microbiology
  • Students will discover the diversity of the microbial world and the role microbes play in human health and disease

Week 1

Day 1. The Science of Microbiology

1.1 The scientific method

1.2 Microbiology: scope and definition

1.3 Importance of microbiology in the modern world

1.4 The microscope and the computer

1.5 The shapes and sizes of microbes

1.6 Activity: scientific thinking in everyday life

Day 2. A brief history of Microbiology

2.1 Antoni van Leeuwenhoek: discovery of bacteria and the “infusoria”

2.2 Louis Pasteur, spontaneous generation and the first vaccines

2.3 Hooke, Schwann, Schleiden, Virchow and cell theory

2.4 Martinus Beijerinck and viruses

2.5 Carl Woese and the third domain

Case study: the infectious agent of mad cow disease

Day 3. The diversity and abundance of microbes

3.1 Microbes: the most abundant organisms on Earth

3.2 Bacteria, archaea and microscopic eukaryotes

3.3 Cell biological and biochemical features

3.4 Viruses, satellite viruses and phages

3.5 The ecology of microbes (free-living, commensal, beneficial or parasitic)

3.6 Video: microbes at home and within the Earth’s crust

Day 4. Genomes, genes and proteins

4.1 Genome size and architecture

4.2 Gene structure and regulation

4.3 The genetic code and the flow of biological information

4.4 The 3-dimensional shape of proteins and their function

4.5 CRISPR-Cas: the adaptive immune systems of bacteria

4.6 Activity: Paper models of proteins, nucleic acids and viruses

Day 5. The evolution of microbes

5.1 Asexual and sexual modes of reproduction

5.2 Horizontal gene transfer and recombination

5.3 Mutation and natural selection

5.4 Strains and the origin of new microbial species

5.5 The global problem of antibiotic/antiviral resistance

5.6 Case study: the rise and fall of penicillin


Week 2

Day 6. Microbes and biotechnology

6.1 The polymerase chain reaction (PCR)

6.2 Gene and genome sequencing

6.3 Gene editing with CRISPR-Cas

6.4 Plasmid vectors and gene expression

6.5 Phage therapy

6.6 Activity: design of a research project

Day 7. The human microbiome

7.1 Microbiota and the microbiome

7.2 Metagenomics

7.3 Variation in microbiome composition

7.4 The microbe-gut-brain axis

7.5 Probiotics, prebiotics and faecal transplants

7.6 Case study: the discovery of Helicobacter pylori

Day 8. Medically relevant microbial diseases

8.1 HIV/AIDS (Human immunodeficiency virus)

8.2 Tuberculosis (Mycobacterium tuberculosis)

8.3 Malaria (Plasmodium spp.)

8.4 Flu (Influenza virus)

8.5 Cholera, typhoid fever and dysentery (Vibrio, Salmonella, Shigella, Entamoeba)

8.6 Discussion: what can we do to lower the burden of infectious disease?

Day 9. Public health and epidemiology

9.1 The dynamics of epidemics

9.2 Herd-immunity and vaccinations

9.3 Zoonoses and anthroponoses

9.4 The social drivers of disease

9.5 One Health

9.6 Case study: the SARS-CoV-2 pandemic

Day 10. Ancient life and astrobiology

10.1 The origin of life on Earth

10.2 Fossil evidence of the first microbes

10.3 Palaeogenomics and palaeovirology

10.4 What can we learn from extremophilic organisms?

10.5 Exoplanets and the inhabitable zone

10.6 Discussion: the search for extra-terrestrial life


Reading list



De Kruif, P. (c1926). Microbe hunters. New York: Harcourt.


Review papers

Gordillo Altamirano, F. L. & Barr, J. J. (2019). Phage therapy in the postantibiotic era.

Clinical Microbiology Reviews 32(2), e00066-18.

Martin, C. R., et al. (2018). The brain-gut-microbiome axis. Cellular and molecular gastroenterology and hepatology 6(2): 133–148.

Schopf, J. W. (2006). Fossil evidence of Archaean life. Philosophical Transactions of the Royal

Society B 361(1470), 869–885.

Schwieterman, E. W., et al. (2018). Exoplanet biosignatures: a review of remotely detectable signs of life. Astrobiology 18(6), 663–708.

Sleator, R. D., Shortall, C. & Hill, C. (2008). Metagenomics. Letters in Applied Microbiology 47, 361–366.

Wolfe, N. P., Dunavan, C. P. & Diamond, J. (2007). Origins of major human infectious diseases. Nature 447, 279–283.



This week in virology

This week in microbiology

Small things considered