Microbiology

• The field of microbiology encompasses Bacteria, Archaea, Fungi, Protozoa, and Viruses.
• Microbiologists can be referred to as Bacteriologists, Virologists, Mycologists, Phycologists, and Protozoologists.
• Microorganisms are the first living organisms on the planet, are found everywhere where life is possible, are more numerous than any other kind of organism, and their activities influence human society in many ways.
• Organisms are named according to the Binomial system established by Carolus Linnaeus.
• The naming of microorganisms follows the rules of the Binomial system, which includes italicizing/underlining the Genus, capitalizing the specific epithet, and after the first use, the Genus may be abbreviated.
• Antony van Leeuwenhoek was the first person to observe and accurately describe bacteria “animacules”, observed through a microscope with magnification ranging from 50 to 300X.
• Francesco Redi was the first to oppose the theory of spontaneous generation and experimented with maggots, observing that they arose from the eggs of flies that were attracted to the decaying meat, not by spontaneous generation.
• John Needham hypothesized that spontaneous generation could occur under appropriate conditions and experimented with broth, observing that spontaneous generation occurs.
• Containment level 1 requires no special requirement necessary, work is done on an open bench following good microbiology practice.
• A hand washing sink is necessary and the area must be lockable.
• Containment level 2 requires the additional requirement of biohazard signage being visible, this must be done on the door and where cultures or containers for transport are located.
• An autoclave must be present in or near the area of containment level 2.
• An emergency eyewash and shower are required for containment level 3.
• Containment level 4 requires all Level 1-3 requirements, the lab is isolated in a separate building or isolated zone, dedicated air supply/exhaust, vacuum and decontamination systems are present, clothing change before entering is mandatory, a shower is provided on exit, and all material is decontaminated upon exit from the facility.
• All procedures in containment level 4 are done in a Class III Biological Safety Cabinet (BSC) or in a Class I or II BSC with full-body, air-supplied, positive pressure personnel suit.
• Lazzaro Spallanzani opposed Needham, suggesting that the microorganisms came from the air after broth was boiled, and experimented with a similar set up as Needham but with a control and experimental flask, observing that no growth occurred on the sealed flasks, therefore, spontaneous generation does not occur.
• Louis Pasteur resolved the debate on spontaneous generation and disproved it by conducting the Swan Neck Flask Experiment, placing beef broth in a long-necked flask, bending the neck into an S-shape, boiling the broth, and observing that no growth occurred despite exposure to air, therefore, spontaneous generation does not occur.
• Microorganisms can be found in nonliving materials such as solid, liquids, and air, and can be destroyed by heat and solutions can be kept sterile by blocking access to the solution.
• Joseph Lister, a surgeon, developed a system of surgery designed to prevent microorganisms from entering wounds, showing evidence that microorganisms could cause disease.
• Robert Koch showed the first proof that microorganisms can cause human disease, discovering the causative agent of anthrax and TB, and determining the causative agent of tuberculosis.
• Koch’s Postulates state that if microorganisms cause a disease, then they must be found in the diseased tissue, they must be able to cause the disease in a susceptible host, and they must be isolated from the host.
• ABC Transporter (ATP - Binding Cassette Transporters) has a solute-binding protein, membrane transporter, and ATP-hydrolyzing domain, and is active in bacteria, archaea, and eukaryotes.
• Secondary active transport of molecules is mediated by potential energy of ion gradients, the molecules are not modified, and is mediated by carrier proteins.
• Lactose permease in E. coli is an example of a secondary active transport of molecules mediated by potential energy of ion gradients, the molecules are not modified, and is mediated by carrier proteins.
• Group Translocation is a process where molecules are modified as they cross the membrane.
• Phosphoenolpyruvate: Phosphotransferase System is a process where sugars are phosphorylated as they are transported, PEP is the phosphate donor, and the energy source.
• Siderophores are low molecular weight organic molecules that bind Fe and transport it, as Fe3+ is very insoluble, many bacteria secrete siderophores.
• The three physical forms of culture media are Liquid (broth), semisolid, or solid, solidification requires agar with forms slant, deep, and agar plate.
• A defined medium is a medium where all components and concentrations are known, it is used for identifying the exact nutritional requirements of the organisms in question.
• A complex medium contains ingredients of unknown concentration/composition, useful when nutritional requirements of a particular microorganism are unknown and if you want to grow many different microorganisms.
• Tryptones, Peptones, and Extracts are examples of ingredients used in culture media.
• Agar is a polysaccharide extracted from marine alga, it is not degraded by most organisms, liquefies at 100 o C and can be cooled to 42 - 50 o C before it hardens, providing a huge incubation range to grow bacteria.
• A general purpose medium supports the growth of many microorganisms, an enriched medium is added with blood or other special nutrients, a selective medium allows growth some microorganisms and inhibits the growth of others, and a differential medium allows one to distinguish different groups of microorganisms based on their biological characteristics.
• Blood Agar differentiates hemolytic vs non-hemolytic, EMB Agar differentiates lactose fermenter vs non-lactose fermenter, and MSA Agar differentiates mannitol fermenter vs non-fermenter.
• EMB Agar and Mannitol salt agar can be classified as both a selective and a differential medium.
• Phase Contrast utilizes the differences between thickness and RI of various regions of a cell to increase contrast, with differences converted into alterations in brightness.
• Phase Contrast has an annular diaphragm and phase plate in the objective.
• Phase Contrast is used for looking at live unstained cells.
• Phase Contrast is widely used to study eukaryotic cells to detect bacterial endospores and inclusions.
• Differential Interference Contrast is similar to phase contrast microscopy but more sensitive, using prisms to split up light beams generating colored 3D images.