• An infectious disease that can be transmitted from one host to another.
• An infection (colonization on or within the body by a pathogen) that prevents the body form working normally.

3 examples of applied uses of microbes

1. Biotechnology
1. DNA was discovered with the help of bacteria, and almost all molecular biology labs rely on E. Coli bacteria to clone DNA.
2. Insulin: This hormone used to treat diabetes is produced using recombinant DNA technology in bacteria or yeast.
2. Bioremediation: using microbes to destroy or detoxify industrial chemicals like "PERC" at contaminated sites.
3. Food production by fermentation: Synthesis of commercially valuable chemicals (ex. MSG food enhancer), alcohol, yogurt, chocolate, cheese (fermentation).

Two types of microbes (in order from smallest to largest)

• Acellular: nonliving entities
• Prion (misfolded proteins that lead to disease; relatively new)
• Viruses
• Cellular: living organisms
• Bacterium
• Eukaryotes

Why are microbes the oldest and most diverse life forms on earth?

Contrast how organisms were classified historically with how they are today

1. Historically, organisms were classified with a bias towards organisms that could be easily seen, mainly animals and plants because humans like to classify things. DNA technology allowed us to see what else is out there.
2. Today, organisms are classified between living organisms, which are composed of bacteria, archaea, and eukarya, and non-living agents such as viruses, viroids, and prions.

List the three domains and the two domains, according to each model

1. Tree of life based on DNA sequences encoding ribosomal RNA (rRNA): this model is made of 16 subunits of rRNA from each species that is highly conserved to keep a living record. We found that three domains had different sets of s rRNA; bacteria (16s), archaea (16s), and eukarya (18s).
2. Phylogenetic model: Using this model and a more diverse batch of prokaryotes, it was discovered that eukaryotes had evolved from archaea through extensive gene family analysis. This model is a better fit and shows the tree of life having two domains instead.
   1. bacteria and archaea are distinct from one another
   2. archaea and eukarya share a more common ancestor

1. Descendent of bacteria and single-celled archaea
2. Single-celled, no membrane-bound organelles
3. DNA packed in the cytoplasm (nucleoid) -> pre-nucleus
4. Have flagella that differs from eukaryotic flagella (motility)
5. Multiply by binary fission

1. Cells with a "true nucleus"
2. Membrane-bound organelles and nucleus
3. More complex than archaea and bacteria

1. Single-celled
2. No membrane bound organelles
3. DNA – nucleoid
4. Motility – flagella
5. Multiply by binary fission

1. Rigid cell wall made of peptidoglycan
2. Has a variety of shapes
1. Archaea
1. Ribosomes more similar to eukaryotes
2. Transcription more closely resembles eukaryotes
3. Different lipids in membrane
4. rRNA sequence divergence (what mainly differentiates archaea and bacteria)
5. Live in extreme conditions (extremophiles)
6. Hard to identify in nature so little research on them (sampling bias)

1. Microscopic or macroscopic
2. Single-celled, multicellular, have another type of rigid cell wall
3. Degrade organic material and can thus be found in land or food

1. Microscopic
2. Single-celled; larger than prokaryotes
3. Motile with no cell wall
4. Ingest organic material for nutrients and have been referred to as a one-celled animal
5. Found in land and water

1. multicellular parasites descendants of eukaryotes
1. Worm-like organisms: nematods (roundworms), cestodes (tapeworms), trematodes (flukes)
2. Transmission: burrow through skin, consumed (food), insect bite
3. Complex life cycle

1. Obligate intracellular parasite (ex. Inactive outside host)
2. Multiply using host machinery
3. Infected cells - "host"
4. Nucleic acid genome housed by protein coat
5. Infect all life forms

1. Infectious protein
• Consist of protein, no DNA or RNA
2. Causes normal proteins to misfold
3. Misfolded aggregation of proteins - "Fibrils"
• Found in brain
4. Proteins lose normal function
• Cells unable to function
5. Resistant to standard sterilization procedures

1. The first person to see microbes with a microscope
2. Made a microscope that could magnify things 300x
3. Looked at the microbes in his teeth plaque.

Semmelweis

1. Found that silkworms that were infected could infect other worms by proximity, and that diseased worms should isolate to prevent the spread.
2. This idea inspired Pasteur by convincing him that there must be contact between a microbe and a host/food source for it to grow.

Describe Pasteur's experiment to refute spontaneous generation theory

Disproved "spontaneous generation" of microbes: the idea that microbes in the air and a food source (or host) just meet randomly. Microbes grow in liquid when they're introduced from outside.

• The experiment: Broth is sterilized by boiling and air escaped from the open end of a swan-neck flask. As the broth cools, microbes from the air settle in the bend of the flask. As years go by, the microbes do not grow because they can't reach the broth in the flask. When the flask is tilted to allow contact between the broth and microbes, the microbes multiply in the broth.

• The microbes must be found in all organisms suffering from the disease, but should not be found in healthy organisms. *not the case for many viruses (ex. HIV)
• The microbe must be isolated from a diseased organism and grown in pure culture. *viruses need a host to grow
• The cultured microorganism should cause disease when introduced back into a healthy organism. *differing responses between hosts (ex. COVID)
• The microbe must be isolated again from the newly diseased animal and identified as being identical to the original microbe. *animal models of disease

Recombinant DNA

• Inserting the human insulin gene into bacterial DNA allows bacteria to produce insulin for medical use.
• Combining genes from different organisms (like a jellyfish’s fluorescent protein gene into a mouse) creates genetically modified organisms (GMOs).

Their sequences change very slowly over evolutionary time due to their essential role in protein synthesis, making them ideal for comparing distantly related organisms.

- part of the small ribosomal subunit that decodes messenger RNA (mRNA) during protein synthesis

Describe the differences in the "top ten killers" globally in the year 1900 and today

1. In 1900, half of the top ten leading causes of death were infectious diseases.
1. Top three were influenza, tuberculosis, and gastroenteritis
2.  Due to the better understanding of infectious diseases, the top ten leading causes of death today only have 3 communicable diseases.

1. Low-income countries tend to have a high frequency of communicable diseases in their top ten leading causes of death while high-income countries only have 1 communicable disease due to:
1. A lack of public health infrastructure (ex: access to clean water, healthcare, proper housing)
2. Differences in social status, income, ethnicity, gender, disability and/or sexual orientation (social location)
3. Social instability

1. Development of vaccines
2. Discovery of antibiotics
3. Public health infrastructure

1. Microbes strike back by forming an antibiotic resistance to existing treatments of infectious diseases, making new strains of the microbe that can be fatal to public health. Essentially, we're back to the beginning and having to treat diseases we fought were dealt with.

1. Microbiology: the study of organisms that are too small to be seen without a microscope.
2. Pathogens: Microbes that can cause disease. They have shaped human history due to their fatal nature -> led to the collapse of some societies.

1.  Microbes are found everywhere (water, soil, air)
2. Extreme environments (high heat, low temp, high salt etc.)
3. And even human beings (most have a neutral or positive impact on the body)

1. Earth originally had no oxygen and all microbes (earliest forms of life) exercised anaerobic respiration
2. Bacteria (type of microbe) invented photosynthesis before plants in a process that didn't initially 1) produce oxygen, but evolved to do so because it was a 2) more efficient way to extract energy from sunlight.

1. Plants and animals need organic nitrogen for the synthesis of nucleotides and proteins, but the nitrogen in the air (70%) can't be absorbed because they're too complex.
2. Nitrogen fixing bacteria saves the day by converting N2 into ammonia, a form of nitrogen that can be absorbed by plants, animals, and other microbes.
3. Without this bacteria, higher life forms would not have evolved in their current form.

• Most microorganisms are not harmful and therefore don't cause disease.

1. Define the germ theory of disease and the miasma theory of disease

1. Germ theory: The principle that microorganisms can some cause diseases.
2. Miasma theory: Miasmas are poisonous emanations, from putrefying carcasses, rotting vegetation or molds, and invisible dust particles that were thought to enter the body and cause diseases like cholera and malaria.