- Course Introduction
Even in ancient times, scholars believed that diseases could be spread by organisms too small to be seen by the naked eye. Before we discovered that bacteria cells were the real culprits, many attributed disease to other sources. Now that scientists have definitively identified the microscopic causes of various infectious diseases, microbiology, or the study of microscopic-sized organisms, has become an increasingly important field in biology and in the larger biomedical community. Most microbes are harmless. Some of them are essential for life on Earth, e.g. through their ability to fix nitrogen. Biotechnology, which is truly the industry of our times, takes advantage of microbes for the production of a variety of complex substances, and it also mass-produces natural and engineered microbes for human use. This course will cover a range of diverse areas of microbiology, including virology, bacteriology, and applied microbiology. This course will focus on the medical aspects of microbiology, as medical research has been the primary motivator in microbiology research.
- Unit 1: Microbes
Microbes are microscopic; thus, we cannot see them by the naked eye. Antoni van Leeuwenhoek crafted the first microscope lenses that magnified over 200 times, and he turned his lenses towards everything. He saw blood cells, sperm, hatching ants, and every cellular microbe groups that we know of today. About 150 years later, Louis Pasteur's meticulously designed swan-necked flask experiments were instrumental in putting off the spontaneous generation hypothesis for microbes. Pasteur showed that microbes arise from microbes, and they are not generated spontaneously from non-living matter. Before any microbe has ever been linked to a disease, the independent death rate analyses of Semmelweis and Nightingale led to the introduction of procedures that we call antiseptic today. Koch was the first to photograph a pathogen in infected tissue; he also laid down guidelines on how to link a microorganism to a disease. These guidelines are Koch's postulates. Only a few microbes cause disease; most microbes are harmless. Microbes are present in all three domains of life: Bacteria, Archaea, and Eukaryota.
Completing this unit should take you approximately 15 hours.
- 1.1: Microscopic Life
- 1.1.1: Magnification Is the Key: Leeuwenhoek Discovers Animalcules
- 1.1.2: The Modern Microscopes
- 1.2: Spontaneous Generation vs. Biogenesis
- 1.3: The Germ Theory
- 1.4: Antiseptic Procedures
- 1.5: General Antimicrobial Methods
- 1.6: Classification System
- 1.6.1: Three Domains of Life
- 1.6.2: Prokaryotes and Eukaryotes
- 1.6.3: Archaea
- 1.6.4: Bacteria
- 1.6.5: Eukaryotic Cells
- 1.7 Viruses
- Unit 2: Microbial Metabolism
Cellular metabolism is the collection of all chemical reaction that takes place in the cell. You have already studied cellular metabolism in BIO101: Introduction to Molecular and Cellular Biology. Take some time to review the cellular metabolism units in these courses before you dive into this unit. In this unit, you will study specifics of microbial metabolism; the most detailed subunit belongs to bacteria. The metabolism in all domains is very divergent; Archaea and Protista are the most divergent. We know most about pathogenic bacteria, because they have medical significance.
Completing this unit should take you approximately 8 hours.
- 2.1: Cellular Metabolism
- 2.2: Bacterial Metabolism
- 2.3: Archaea Metabolism
- 2.4: The Metabolism of Protists
- 2.5: Fungal Metabolism
- Unit 3: Bacterial Growth, Reproduction, and Genetics
This course focuses on bacteria, the most studied type of microorganism. We will begin this unit by learning how bacteria cells obtain their energy and how they grow. Metabolism varies greatly among bacteria; not all share the same kinds of mechanisms. While most require oxygen to survive, for example, some will actually die in the presence of oxygen. As the microbiology field increasingly involves the artificial cultivation of bacteria, it is important to know the methods and concepts behind their growth and cultures as well.
Bacteria divide and multiply at amazing rates. Under the right conditions, the fastest bacteria can divide every 20 minutes! That means that if you cultured just one single bacteria cell before you went to bed, you could wake up 8 hours later with a plate of more than 16 million bacteria! Much of bacterial reproduction is asexual, occurring through binary fission. In binary fission, one cell literally divides in two. We will conclude this unit by learning about horizontal gene transfer, a process by which one bacteria cell incorporates genetic changes from another cell without being its offspring. This unique feature has allowed bacteria to adapt and grow in conditions it would not otherwise be able survive. It has also led to the increase of drug-resistant bacterial infections.
Completing this unit should take you approximately 15 hours.
- 3.1: Bacterial Growth
- 3.1.1: Growth and Nutrition Requirements
- 3.1.2: Generation Time
- 3.1.3: Bacterial Growth
- 3.1.4: Estimation Methods for Population
- 3.1.5: Growth Control
- 3.1.6: Microbial Resistance
- 3.2: Bacterial Reproduction
- 3.2.1: Asexual vs. Sexual Reproduction
- 3.2.2: Binary Fission and Budding
- 3.2.3: Endospore Formation
- 3.3: Bacterial Genetics
- 3.3.1: Bacterial Chromosome
- 3.3.2: Processing Genetic Information
- 3.3.3: Genetic Regulatory Mechanisms
- 3.3.4: Genetic Information Exchange
- 3.3.5: Mutations
- 3.4:Reproduction and Genetics in other Microorganisms
- Unit 4: Microbial Characteristics and Identification
In this unit, we will examine the different shapes and arrangements of bacteria and compare and contrast bacteria with other microorganisms. We will also survey some of the methods (such as plating and staining) used to distinguish between organisms in order to diagnose the causes of infection. When a sample reaches the clinical lab, differential staining enables technicians to identify the shape, arrangement, and gram stain of the organism that the sample contains. This preliminary information, along with cultures, can be used to identify pathogenic microorganisms and isolate them from normal flora.
Completing this unit should take you approximately 3 hours.
- 4.1: Characteristics of Microorganisms
- 4.1.1: Prokaryote Shapes
- 4.1.2: Size of Microorganisms
- 4.1.3: Morphological Characteristics
- 4.2: Identifying Microorganisms
- 4.2.1: Plating and Culturing
- 4.2.2: Differential Staining
- 18.104.22.168: Gram Staining
- 22.214.171.124: Acid Fast Staining
- Unit 5: Bacteria and Human Disease
Ever since Louis Pasteur first theorized that microorganisms were the source of infectious diseases, scientists have labored to learn more about the causes of disease and, more generally, the field of microbiology as a whole. As a result, the majority of microbiology research has focused on human disease and immunology (the study of the immune system). The following unit will discuss microorganisms and the diseases that they cause.
We will begin with bacteria, learning that they are mainly classified as cocci, bacilli, or spiral shaped. They are also differentiated via gram staining procedures, which indicate the amount of peptidoglycan present in a cell wall. If a bacterium contains a lot of peptidoglycan in its cell wall, it will take up the primary gram stain (crystal violet) and will appear purple (gram positive). However, if the bacterium contains a small amount of peptidoglycan and an outer membrane, it will not take up the primary stain. It will instead take up the secondary stain (safranin) and will appear red (gram negative). Each of the classes listed below has been selected for its importance to modern microbiology; take the time to learn all of their names!
Completing this unit should take you approximately 22 hours.
- 5.1: Pathogenesis
- 5.2: Gram Positive and Negative Cocci
- 5.2.1: Staphylococcus
- 5.2.2: Streptococcus
- 5.2.3: Enterococcus
- 5.2.4: Neisseria
- 5.3: Gram-Positive Bacilli
- 5.3.1: Bacillus
- 5.3.2: Clostridium
- 5.3.3: Listeria
- 5.3.4: Mycobacterium and Corynebacterium
- 5.3.5: Actinomyces and Nocardia
- 5.4: Gram-Negative Bacilli
- 5.4.1: Pseudomonas
- 5.4.2: Brucella
- 5.4.3: Bordetella and Legionella
- 5.4.4: Escherichia, Salmonella, Shigella, and Yersinia
- 5.5: Other Bacteria
- 5.5.1: Treponema and Leptospira
- 5.5.2: Vibrio and Campylobacter
- 5.5.3: Chlamydia
- 5.5.4: Mycoplasma
- 5.6: Antibiotics
- Unit 6: Fungi
Mycology, or the study of fungi, focuses on a diverse set of eukaryotic organisms that range from microscopic single-cells to large mushrooms. Fungi include yeasts, molds, and mushrooms. They are decomposers that have chitin in their cell walls. Fungi range from harmless, tasty mushrooms to fatally poisonous toxins. Humans have cultivated fungi not only for food but also for pest control and bioremediation. Penicillin, the first common antibiotic, was derived from the Penicillium mold. Even today, many newly discovered antibiotics have ties to fungi. In this unit, we will look at both those fungi commonly associated with disease as well those that have been cultivated for specialized purposes.
Completing this unit should take you approximately 12 hours.
- 6.1: Fungi and Human Disease
- 6.2: True Pathogenic Fungi
- 6.3: Mycotoxins
- 6.4: Opportunistic Fungi
- 6.4.1: Yeasts
- 6.4.2: Pneumocystis
- 6.4.3: Aspergillus
- 6.5: Specialized Fungi
- 6.5.1: Penicillium
- 6.5.2: Saccharomyces
- 6.6: Antifungals
- Unit 7: Protozoa and Helminths
Pro/Eukaryotes include Fungi, Algae, Protozoa, and Helminths. This unit discusses protozoa and helminths, which are parasites. Parasites are, by definition, organisms that benefit only at the expense of their living hosts. Protozoa are usually single-celled organisms that have highly complex life cycles. Helminths (also known as parasitic worms) live inside their hosts, often in intestinal tracts, where they hijack their host's nutrient absorption pathway. An astounding number of people are believed to be infected with helminths; most estimates claim that at least 1 billion individuals have been affected!
Completing this unit should take you approximately 14 hours.
- 7.1: Protozoa
- 7.1.1: Protozoa Characteristics
- 7.1.2: Types of Protozoa
- 126.96.36.199: Intestinal and Luminal Protozoa
- 188.8.131.52: Blood-Borne Protozoa
- 184.108.40.206: Trichomonas
- 7.2: Helminths
- 7.2.1: Helminths Characteristics
- 7.2.2: Types of Helminths
- 220.127.116.11: Nematodes
- 18.104.22.168: Trematodes
- 22.214.171.124: Cestodes
- 7.3: Antiparasitics
- Unit 8: Viruses
This unit will introduce you to viruses. Viruses are in the grey zone between life and inorganic matter. You have learned that the cell is the smallest unit of life, because it can sustain all life functions including reproduction on its own. Most viruses are smaller than cells. They do not feed or reproduce on their own; instead, they hijack their host's metabolism when they multiply. All viruses are comprised of a nucleic acid core surrounded by a protein coat. Viruses are all categorized into seven groups based on the type of nucleic acid they carry. Viruses, while tiny, have powerful effects on their hosts; they can even cause cancer, birth defects, and death.
Completing this unit should take you approximately 21 hours.
- 8.1: Virus Characteristics
- 8.2: Viral Replication Cycles
- 8.3: dsDNA Viruses
- 8.3.1: Poxviruses
- 8.3.2: Herpesviruses, Adenoviruses, Papillomaviruses, and other Oncogenic Viruses
- 8.4: ssDNA Viruses
- 8.4.1: Parvoviruses
- 8.4.2: Geminiviruses
- 8.5: dsRNA Viruses
- 8.5.1: Arboviruses
- 8.5.2: Birnaviruses
- 8.6: +ssRNA Viruses
- 8.6.1: Coronaviruses
- 8.6.2: Picornaviruses
- 8.6.3: Caliciviruses
- 8.7: -ssRNA Viruses
- 8.7.1: Orthomyxoviruses
- 8.7.2: Paramyxoviruses
- 8.7.3: Rhabdoviruses
- 8.7.4: Filoviruses
- 8.8: DNA and RNA Retroviruses
- 8.8.1: Hepadnaviruses
- 8.8.2: Lentiviruses
- 8.9: Antivirals
- Unit 9: Defense Against Microbes
This unit will discuss the major defenses we have against disease-causing microbes. With all of the microorganisms that threaten to infect and harm an individual, our bodies have evolved sophisticated defenses against these foreign invaders. However, our immune systems can still be overwhelmed; we often need the help of medication to win the battle. In this unit, we will learn about the primary human defenses against disease before discussing the generalized agents that we use outside of the human body to combat different types of microbes.
Completing this unit should take you approximately 7 hours.
- 9.1: Non-Specific Immunity (Skin and Mucous Membrane and Innate Immunity)
- 9.2: Adaptive Immunity
- 9.3: Vaccination
- Unit 10: Applied Microbiology
In this last unit, we will learn about other major sub-fields of microbiology, including environmental microbiology, biotechnology, and microbial food preparation. We briefly touched upon these topics in our introduction, but we will now go through them in more detail. We will also consider some of the many applications of microbiology. Note that bacteria and fungi (yeast) are used to make vitamins, antibiotics, and beer and to clean up petroleum.
Completing this unit should take you approximately 7 hours.
- 10.1: Environmental Microbiology
- 10.1.1: Bioremediation
- 10.1.2: Sewage Treatment
- 10.2: Food Microbiology
- 10.2.1: Aseptic Packaging
- 10.2.2: Fermentation
- 10.3: Industrial Microbiology
- 10.3.1: Industrial Products of Microbes
- 10.3.2: Bioconversion
- 10.3.3: Biofuels