1. Taxonomy

2. Lab Manual…order now!

3. VOCABULARY
Microorganisms: organisms that are too small to be seen with the unaided eye.
Germs: a rapidly growing cell.
Normal microbiota: microorganisms that are normally found on or in the body and do not cause disease.
Pathogen: a microorganism that causes disease

4. VOCABULARY 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.

5. Aseptic
adjective
a: preventing infection b: free or freed from pathogenic microorganisms 
Things cleaned specifically in a way that prevents infection were first described as "aseptic" in the late 19th century. The word combines the prefix "a-," meaning "not," and "septic," from Greek "sēptikos," meaning "putrifying."
"Aseptic" was preceded by more than a century by "antiseptic" (from "anti-," meaning "opposing,").  

6. Appertization
Term of French origin for the process of destroying all the micro-organisms of significance in food, i.e. ‘commercial sterility’; a few organisms remain alive but quiescent. Named after Nicholas Appert (1752–1841), a Paris confectioner who invented the process of canning; he opened the first vacuum-bottling factory in 1804.

7. Fomite
A fomite is an inanimate object, such as a keyboard, that might have microorganisms on it that can be picked up by someone.
"Fomite" is a Latin word for “tinder”.
Much like tinder is a catalyst of fire, a fomite can kindle disease.

8. BENEFITS OF MICROORGANISMS
Decompose organic wastes
Are producers in the ecosystem by photosynthesis (algae, cyanobacteria, etc)
Produce industrial chemicals such as ethanol and acetone
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.
Produce products used in manufacturing (e.g. cellulose) and treatment of diseases (e.g. E coli can make insulin).
Genetic Engineering (recombinant DNA technology)

9. WHY STUDY MICROORGANISMS?
Allows humans to prevent food spoilage
Prevent disease occurrence and transmission
Understanding of aseptic techniques

10. Number of Bacteria
You have more bacterial cells living in and on your body than you have human cells!
If you judge based on cell count or DNA diversity your physical being is more bacteria than human.  (If you go based on weight, human cells still predominate.)

12. LINNAEUS
Established the system of scientific nomenclature: Genus and species.

13. NAMING AND CLASSIFYING MICROORGANISMS
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.

14. NAMING AND CLASSIFYING MICROORGANISMS
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.

15. HOW NAMES ARE CHOSEN FOR MICROORGANISMS
Named by location of organism: Enterococcus faecalis (located in feces)
Named by the shape of organism: Bacillus megaterium (large rod shape)
Named by the arrangement of organism: Staphylococcus aureus (clusters of circles)

16. CLASSIFICATION OF MICROORGANISMS
Taxonomy: the science of the classification of organisms.
SUPERKINGDOMS
PROKARYA: Prokaryotes have no nucleus
EUKARYA: Eukaryotes have a nucleus

17. KINGDOMS: Monera
MONERA
BACTERIA
VIRUSES
ARCHAEBACTERIA

18. Bacteria Prokaryotes (no nucleus) Peptidoglycan cell walls
Reproduce by binary fission
For energy, use organic chemicals, inorganic chemicals, or photosynthesis
Normal microbiota are non-pathogenic
Figure 1.1a

19. BACTERIA
Three main types
Gram positive
Gram negative
Acid fast

20. Main shapes cocci (ball shaped) vibrio (comma shaped)
bacillus (rod shaped)
spirochetes (spiral shape)

21. Arrangements of the cocci
staphylococcus (clusters like grapes)
Example: Staphylococcus aureus
diplococcus (pairs of two)
tetrads (groups of four)
streptococcus (chains like bead necklace)
Example: Streptococcus pyogenes (“strep throat”)

22. Viruses Acellular Consist of DNA or RNA core
Core is surrounded by a protein coat
Coat may be enclosed in a lipid envelope
Viruses are replicated only when they are in a living host cell (obligate intracellular parasites)
Figure 1.1e

23. VIRUSES
HIV
Common cold virus
Hepatitis A

24. VIRUSES
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.

25. ARCHAEBACTERIA Prokaryotic Lack peptidoglycan
Live in extreme environments
Include:
Methanogens
Extreme halophiles
Extreme thermophiles
Figure 4.5b

26. KINGDOMS: Protista PROTISTA ALGAE PROTOZOA FUNGI Molds (multicellular)
Yeasts (single-celled)

27. Algae Eukaryotes Cellulose cell walls Use photosynthesis for energy
Produce molecular oxygen and organic compounds
Figure 1.1d

28. Protozoa Eukaryotes Absorb or ingest organic chemicals
Classified according to their motility (movement) by pseudopods (false foot), cilia (hairs) or flagella (tail).
Diseases caused by protozoa include malaria (carried by mosquitoes) and ameobiasis (food and water poisoning).
Figure 1.1c

29. Fungi FUNGI Eukaryotes: have a nucleus in the cell
Cell walls made of chitin or cellulose
Although mushrooms look like plants, they are not because they do not use photosynthesis for food. Fungi are not phototrophic.
They are heterotrophic: Use organic chemicals for energy, not photosynthethesis.
Not as diverse as bacteria
Two types:
Yeasts: unicellular, no mycelia
Saccharomyces (Baker’s and Brewer’s yeast)
Candida albicans (vaginal yeast infections)
Molds and mushrooms: multicellular, consisting of masses of mycelia which are composed of filaments called hyphae.
Figure 1.1b

30. KINGDOM: Plantae PLANTAE (plants)
Plants are photosynthetic (use sunlight to make food).
That means they are autotrophs (make their own food)
They have roots, stems, and leaves (unlike algae)
They do not cause many microbiological diseases; not covered in this course.

31. Kingdom: Animalia
ANIMALIA (animals): We will just cover multicellular animal parasites.
HELMINTHES
Flat worms
Tapeworms
NEMATODES
Roundworms

32. Multicellular Animal Parasites
Eukaryote
Multicellular animals
Parasitic flatworms and tapeworms are called Helminthes.
Roundworms are called Nematodes.
Microscopic stages in life cycles.
Figure 12.28

33. TAXONOMY
Domain
Kingdom
Phylum
Class
Order
Family
Genus
              Species 

34. TAXONOMY
Dashing
King
Phillip
Came
Over
From
Greece
              Singing 

35. Microorganisms:
Figure 1.1

36. MICROBES COMPARISON CHART
BACTERIA
Prokaryotic
Peptidoglycan cell walls
Reproduced by binary fission
Uses organic (heterotrophs) and inorganic chemicals (chemoheterotrophs) or photosynthesis (autotrophs) for energy
Shapes are rod, coccus, spiral
ARCHAEA
Prokaryotic; these are bacteria that:
Lack peptidoglycan
Live in extreme environments
Include methanogens (love methane gas), extreme Halophiles (love salt), extreme thermophiles (love heat and cold)
FUNGI
Eukaryotes
Cell walls have chitin
Heterotrophs: use only organic chemicals for energy
Molds are multicellular; Yeasts are unicellular

37. MICROBES COMPARISON CHART
PROTOZOA
Eukaryotes
Heterotrophs: use only organic chemicals for energyMay be motile via pseudopods, cilia, or flagella
ALGAE
Cell wall contain cellulose
Uses photosynthesis for energy (autotrophs); Produces oxygen and organic food for other species. They are like plants except they don’t have roots, stems, leaves and can be unicellular.
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
(parasitic worms)
Helminthes: parasitic flat worms and tapeworms
Nematodes: parasitic roundworms
They are endoparasites: animals that live inside other animals through fecal
contamination

38. 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
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.

39. 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 food to cause a benefit.
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.

40. MICROBES AND HUMAN WELFARE

41. ECOLOGY
Bacteria recycle carbon, nutients, sulfates, and phosphates that can be used by plants and animals.

42. BIOREMEDIATION
This is any process that uses microorganisms to return the environment altered by contaminants to its original condition.
Used to clean up oil spills.
Used to clean up industrial toxic wastes.

43. Bioremediation Bacteria degrade organic matter in sewage.
Bacteria degrade or detoxify pollutants such as oil and mercury

44. Oil Spills

45. INSECTICIDES Bacteria can be used in the place of pesticides.
Environmentally friendly
Little or no effect on humans, wildlife, pollinators and most other beneficial insects.

46. PHARMACOLOGY Production of pure chemicals for use as pharmaceuticals.
Insulin
Growth factors
Antibodies

47. FOOD Lactobacillus: fermented foods Cheese Pickles Soy sauce
Sauerkraut
Vinegar
Wine
Yogart

48. FOOD
Probiotics: Live microorganisms which when administered in adequate amounts confer a health benefit on the host. These are bacteria added to milk, yogurt, and other foods.
Lactic acid bacteria (LAB) as the most common microbes used.
provides the characteristic sour taste of fermented dairy foods
acts as a preservative, by lowering the pH and creating fewer opportunities for spoilage organisms to grow.

49. BIOTECHNOLOGY
The manipulation of biological organisms to make products that benefit human beings.
Food production
Waste disposal
Mining
Medicine

50. BIOTECHNOLOGY: Genetic Engineering
Restriction enzymes cut the DNA strands of any organism at precise points.
This is how the sequence of a person’s DNA can be determined.
A specific gene can be removed from one bacterium and inserted it into another using restriction enzymes.

51. BIOTECHNOLOGY: Recombinant DNA Technology
Transgenic bacteria (bacteria to which a gene from a different species has been transferred)
Example: A human gene which codes for a hormone is transferred to Escherichia coli bacteria.
Escherichia coli produces this human hormone along with their own normal chemical compounds.

52. 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.
It is produced through the addition of DNA into an existing organism’s genes to alter traits for a specific purpose, such as immunity.
Bacteria can also be used to produce large quantities of human insulin.

53. NORMAL MICROBIOTA
There are approximately 10 times as many bacterial cells as human cells in the human body.
Three pounds of E. coli live in our intestines, helping to digest food that we cannot digest.
These microbes produce folic acid, biotin, and vitamin K, substances we need to survive but cannot make ourselves.
Useful microbes compete for nutrients in our body, keeping out harmful bacteria.

54. WHY WE HAVE MICROBIAL DISEASES
Mutation leads to evolution of bacteria
Antibiotic use causes resistance and evolution of bacteria
Travel exposes us to microbes we are not used to
Deforestation (removal of trees, especially in the tropics, Africa, Central America) destroys the ecosystem and disturbs natural balance of microbes

55. Lab Soil Project This Thursday, bring a soil sample to lab.
Don’t use really fertile soil…dry is better, but not in an area where no plants are growing. It is best to get soil close to roots of nearby plants, and dig down about 2 inches first.
Fill a 15 ml test tube all the way up with soil.
Record the place of collection, temperature, and any of the below data you can collect
LOCATION
Location 
Latitude
Longitude

56. Lab Soil Project Date and Time Collected * Date Time
Sample Site Descriptors *
SOIL SAMPLE
Air Temperature (°C)
Humidity (%)
Depth (In.)
Type of Soil
Soil Temperature (°C)
pH of Soil
Water Content (%)