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
Books
De Kruif, P. (c1926). Microbe hunters. New York: Harcourt.
https://archive.org/details/in.ernet.dli.2015.221187/page/n67/mode/2up
Review papers
Gordillo Altamirano, F. L. & Barr, J. J. (2019). Phage therapy in the postantibiotic era.
Clinical Microbiology Reviews 32(2), e00066-18.
https://europepmc.org/article/med/30651225
Martin, C. R., et al. (2018). The brain-gut-microbiome axis. Cellular and molecular gastroenterology and hepatology 6(2): 133–148.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6047317/
Schopf, J. W. (2006). Fossil evidence of Archaean life. Philosophical Transactions of the Royal
Society B 361(1470), 869–885.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1578735/
Schwieterman, E. W., et al. (2018). Exoplanet biosignatures: a review of remotely detectable signs of life. Astrobiology 18(6), 663–708.
https://www.liebertpub.com/doi/full/10.1089/ast.2017.1729
Sleator, R. D., Shortall, C. & Hill, C. (2008). Metagenomics. Letters in Applied Microbiology 47, 361–366.
https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1472-765X.2008.02444.x
Wolfe, N. P., Dunavan, C. P. & Diamond, J. (2007). Origins of major human infectious diseases. Nature 447, 279–283.
https://www.ncbi.nlm.nih.gov/books/NBK114494/
Blogs
This week in virology https://www.microbe.tv/twiv/
This week in microbiology https://www.microbe.tv/twim/
Small things considered https://schaechter.asmblog.org/schaechter/