MICROBIOLOGY LECTURE
MICROORGANISMS
These are organisms that are too small to be seen with the unaided eye. A layperson calls them “germs”, which is a word that is derived from “germinate”, and refers to a rapidly growing cell. Normal microbiota: microorganisms that are normally found on or in the body and do not cause disease. The proper term for a microorganism that causes disease is PATHOGEN. The prefix “patho” means “disease”, and “gen” means “generating”. Types of pathogens include fungi (plant molds and yeasts), protozoa (single celled animals), viruses (the smallest; they can fit inside the nucleus of a bacteria), helminthes (worms), and bacteria. Not all microorganisms are pathogens; many are useful in the environment and to humans.
Bacteriology: a study of bacteria.
Mycology: a study of fungi.
Parasitology: the study of protozoa, parasites, and worms (helminthes).
Immunology: a study of immunity.
Virology: the scientific study of viruses.
BENEFITS OF MICROORGANISMS
1. Decompose organic wastes
2. Are producers in the ecosystem by photosynthesis (algae, cyanobacteria, etc)
3. Produce industrial chemicals such as ethanol and acetone
4. Produce fermented foods such as vinegar, cheese, bread, beer, wine. Fermentation also produces useful products such as solvents to dissolve substances. To be “probiotic” means to add microbes to your diet.
5. Produce products used in manufacturing (e.g. cellulose) and treatment of diseases (e.g. E coli can make insulin).
6. Genetic Engineering (recombinant DNA technology)
7. Normal microbiota: normally found on humans, etc, and do not cause disease except in immunocompromised people (immune system is not strong).
WHY STUDY MICROORGANISMS?
1. Allows humans to prevent food spoilage
2. Prevent disease occurrence and transmission
3. Understanding of aseptic techniques to prevent contamination in medical practice, surgery, laboratories, patient handling, food and medicine preparation.
a. NOSOCOMIAL DISEASES are those acquired in a hospital.
NAMING AND CLASSIFYING MICROORGANISMS
LINNAEUS (a Swedish Botanist) established the system of scientific nomenclature. Each organism has two names: GENUS (from the word “genre”, meaning “more than one”) and an epitaph, also known as the SPECIES (specific name unique to that organism type).
The first letter of the genus name is always capitalized, but never the first letter of the species name. The genus may be abbreviated with the first letter, and the species is written out. The genus and species of an organism is always either underlined OR italicized: E. coli or E. coli are both acceptable.
Escherichia coli is the name of a common bacterium normally found in the large intestine of all humans and animals. If E. coli gets out of that location and into the small intestine or elsewhere, it can cause disease.
Staphylococcus aureus is the name of a common bacterium that is found on human skin. If S. aureus gets inside of an open wound, it can cause disease.
HOW NAMES ARE CHOSEN FOR MICROORGANISMS
Named by location of organism: Enterococcus faecalis (located in feces)
Named by the shape of organism: Bacillus megaterium (rod shaped and large)
Named by the arrangement of organism: Staphylococcus aureus (clusters of circles)
CLASSIFICATION OF MICROORGANISMS
Taxonomy: the science of the classification of organisms.
SUPERKINGDOMS
1. PROKARYA: Prokaryotes have no nucleus
2. EUKARYA: Eukaryotes have a nucleus
KINGDOMS
1. MONERA
a. BACTERIA
i. Prokaryotes: no nucleus
ii. Peptidoglycan cells walls: a substance that makes them strong
iii. Binary fission: reproduce by splitting in two
iv. Diverse energy requirements: For energy, use organic chemicals (contains carbon), inorganic chemicals (no carbon), or photosynthesis (use chlorophyll and sunlight to make food).
v. Normal microbiota are non-pathogenic
vi. Three main types
1. Gram positive
2. Gram negative
3. Acid-fast
vii. Main shapes
1. cocci (ball shaped)
2. vibrio (comma shaped)
3. bacillus (rod shaped)
4. spirochetes (spiral shape)
viii. Arrangements of the cocci
1. staphylococcus (clusters like grapes; example is Staphylococcus aureus)
2. diplococcus (pairs of two)
3. tetrads (groups of four)
4. streptococcus (chains like a bead necklace; example is streptococcus pyogenes = “strep throat”)
b. VIRUSES
i. These are the smallest of all microbes; hundreds of viruses can fit into one bacterium!
ii. They are acellular (no cells)
iii. They consist of a core of a fragment of nucleic acid: either DNA or RNA (not both). The RNA viruses don’t have stable genes and they mutate frequently.
iv. The core is surrounded by a protein coat called a capsid, made up of capsomeres. The capsid may be surrounded by an envelope made up of lipid.
v. Viruses are only replicated when they are living in a host cell.
vi. They don’t have their own metabolism; they use host cells for metabolism.
vii. They are obligate intracellular (must live inside host cell) parasites (live at the expense of the host, which it weakens or kills).
viii. Even when you kill a virus, it can leave behind an active particle.
ix. Examples of viral diseases range from the deadly HIV to the common cold virus. Hepatitis A is a virus that can remain viable (living) even outside of the host for long periods of time; it spreads through fecal contamination (food workers who do not wash their hands after a bowel movement).
x. Vaccines can prevent some viral infections, but antibiotics are ineffective for treatment after infection. Antibiotics work by interfering with cell wall synthesis or metabolism; since viruses don’t have these things, they are not effective. There are medicines that treat but don’t cure viruses, such as acyclovir for Herpes Simplex 1.
c. ARCHAEBACTERIA
i. Prokaryotic
ii. Lack peptidoglycan
iii. Live in extreme environments: deep sea, salt, heat, cold
1. Methanogens: can make methane gas (flatulence!). They can live in animal bodies (cattle, etc), contributes to global warming.
2. Extreme Halophiles: like excess salt
3. Extreme thermophiles: like extreme temperatures (hot and cold)
2. PROTISTA(Protists)
a. ALGAE
i. These are the producers of the ecosystem because they use photosynthesis to make food; other organisms eat them and get their food that way. They are at the bottom of the food chain.
ii. Eukaryotes
iii. Produce oxygen that is needed for all other life forms on earth. Without algae there would not be enough oxygen on earth.
iv. Don’t cause many diseases
b. PROTOZOA
i. Eukaryotes
ii. Larger than bacteria; many bacteria can fit into a protozoa.
iii. Absorb or ingest organic chemicals
iv. Classified according to their motility (movement): by pseudopods (false foot), cilia (hairs) or flagella (tail).
v. Diseases caused by protozoa include malaria (carried by mosquitoes) and ameobiasis (food and water poisoning).
3. FUNGI
a. Eukaryotes: have a nucleus in the cell
b. Larger than protozoa.
c. Chitin cell walls or cellulose
d. Although mushrooms look like plants, they are not because they do not use photosynthesis for food. Fungi are not phototrophic.
e. They are heterotrophic: Use organic chemicals for energy, not photosynthethesis.
f. Not as diverse as bacteria
g. Two types:
i. Yeasts: unicellular, no mycelia
1. Saccharomyces (Baker’s and Brewer’s yeast)
2. Candida albicans (vaginal yeast infections)
ii. Molds and mushrooms: multicellular, consisting of masses of mycelia which are composed of filaments called hyphae.
4. PLANTAE (plants)
a. Plants are photosynthetic (use sunlight to make food).
b. That means they are autotrophs (make their own food)
c. They have roots, stems, and leaves (unlike algae)
d. They do not cause many microbiological diseases; not covered in this course.
5. ANIMALIA (animals): We will just cover multicellular animal parasites.
a. Eukaryotes
b. Multicellular animals
c. Endoparasites (animals that live inside other animals through fecal contamination.
d. Life cycles are seen in stages; they are microscopic.
i. HELMINTHES
1. Flat worms
2. Tapeworms
ii. NEMATODES
1. Roundworms
Taxonomical classification becomes more specific until the organism is uniquely identified:
Kingdom
Phylum
Class
Order
Family
Genus
Species
Dashing
King
Phillip
Came
Over
From
Greece
Singing
MICROBES COMPARISON CHART
BACTERIA / ProkaryoticPeptidoglycan cell walls
Reproduced by binary fission
Uses organic and inorganic chemicals or photosynthesis for energy
Shapes are rod, coccus, spiral
ARCHAEA / Prokaryotic
Lack peptidoglycan
Live in extreme environments
Include methanogens, extreme Halophiles (love salt), extreme thermophiles (love heat and cold)
FUNGI / Eukaryotes
Cell walls have chitin
Heterotrophes: use only organic chemicals for energy
Molds and mushrooms are multicellular; consist of masses of mycelia,
which are composed of filaments hyphae.
Yeasts are unicellular
PROTOZOA / Eukaryotes
Absorb or ingests organic compounds
May be motile via pseudopods, cilia, or flagella
ALGAE / Eukaryotes
Cell wall contain cellulose
Uses photosynthesis for energy
Produces oxygen and organic food for other species
VIRUSES / Non-cellular intracellular parasites; lives at the expense of host
Contain either DNA or RNA surrounded by a protein coat
May have an envelope
Smallest of all microbes
Replicates in living host cell
Antibiotics do not work; requires antiviral agents
HELMINTHES
AND
NEMATODES / Eukaryotes
Helminthes: parasitic flat worms and tapeworms
Nematodes: parasitic roundworms
Endoparasites: animals that live inside other animals through fecal
contamination
Microscopic stages of life cycle
Parasite is in the bite of mosquito or bug; spreads infection in body
MICROBES AND HUMAN WELFARE:
The good things microbes do for us
VOCABULARY
Biotechnology: the industrial application of microorganisms, cells, or cell components to make a useful product.
Microbial ecology: the study of the relationship between microorganisms and their environment; originated from Beijerinck and Windogradskyi.
Microbial genetics: study of the mechanisms by which microorganisms inherit traits.
Microbial physiology: the study of the metabolism of microbes.
Molecular biology: the science of dealing with DNA and protein synthesis of living organisms.
Genomics: the study of an organisms genes; used to classify a microorganisms.
Bio remediation: bacteria degrade organic matter in sewage. Bacteria also degrade or detoxify pollutants such as oil and mercury.
Genetic engineering: a new technique for biotechnology. Bacteria and fungi can produce a variety of proteins including vaccines and enzymes.
Probiotic: adding microbes to your diet.
Nosocomial diseases: acquired in hospitals; an infection that develops during the course of a hospital stay and was not present at the time the patient was admitted.
Neonate: newborn
Immunocompromised: vulnerable to disease caused by normal microbiota.
CONCEPTS
ECOLOGY
Bacteria recycle carbon, nutientss, sulfates, and phosphates that can be used by plants and animals.
BIOREMEDIATION
This is any process that uses microorganisms to return the environment altered by contaminants to its original condition. The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills. Fertilizer was added to some of the beaches in Prince William Sound in an attempt to promote the growth of these naturally occurring bacteria after the infamous 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial toxic wastes.
INSECTICIDES
Bacteria can also be used in the place of pesticides in the biological pest control. This commonly involves Bacillus thuringiensis (also called BT), a Gram-positive, soil dwelling bacterium. Subspecies of this bacteria are used as insecticides under trade names such as Dipel and Thuricide. Because of their specificity, these pesticides are regarded as environmentally friendly, with little or no effect on humans, wildlife, pollinators and most other beneficial insects.
PHARMACOLOGY
In the chemical industry, bacteria are most important in the production of pure chemicals for use as pharmaceuticals. Understanding of bacterial metabolism and genetics allows the use of biotechnology to bioengineer bacteria for the production of therapeutic proteins, such as insulin, growth factors, or antibodies.
FOOD
Bacteria, often Lactobacillus in combination with yeasts and molds, have been used for thousands of years in the preparation of fermented foods such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine and yoghurt. Probiotics: adding bacteria to our diet that are found in milk, yogart, etc. Probiotics are dietary supplements containing potentially beneficial bacteria or yeast, with lactic acid bacteria (LAB) as the most common microbes used. LAB have been used in the food industry for many years, because they are able to convert sugars (including lactose) and other carbohydrates into lactic acid. This not only provides the characteristic sour taste of fermented dairy foods such as yogurt, but acts as a preservative, by lowering the pH and creating fewer opportunities for spoilage organisms to grow. Probiotic bacterial cultures are intended to assist the body's naturally occurring gut flora to reestablish themselves. They are sometimes recommended by doctors, and, more frequently, by nutritionists, after a course of antibiotics, or as part of the treatment for gut related candidiasis. Claims are made that probiotics strengthen the immune system.
BIOTECHNOLOGY
Biotechnology is the manipulation of biological organisms to make products that benefit human beings. Biotechnology contributes to such diverse areas as food production, waste disposal, mining, and medicine. Restriction enzymes in bacteria cut the DNA strands of any organism at precise points. A specific gene can be removed from one bacterium and inserted it into another using restriction enzymes. This event is called genetic engineering. A human gene which codes for a hormone has been transferred to Escherichia coli bacteria. Although the transgenic bacteria (bacteria to which a gene from a different species has been transferred) could not use the human hormone, they produced it along with their own normal chemical compounds. This type of biotechnology is called recombinant DNA technology.
RECOMBINANT DNA TECHNOLOGY
Recombinant DNA is a form of artificial DNA which is engineered through the combination or insertion of one or more DNA strands, thereby combining DNA sequences which would not normally occur together. In terms of genetic modification, recombinant DNA is produced through the addition of relevant DNA into an existing organismal genome, such as the plasmid of bacteria, to code for or alter different traits for a specific purpose, such as immunity. Small circles of DNA exist in bacteria, known as plasmids. These are modified to include the piece of human DNA containing instructions for making proinsulin. Proinsulin is the precursor for insulin. The bacteria then multiply and produce large quantities of human proinsulin for humans to use.