1. Introduction to Microbiology
A Historical Perspective
Bio3124
Lecture 1

2. Objectives and reading
Reading: Ch.1
What is microbiology?
History: How it came to be a field of study?
Modern microbiology: day to day impact on society

3. The Scope and Relevance of Microbiology
importance of microorganisms
first living organisms on the planet
How many bugs are out there?
live everywhere life is possible
more numerous than any other kind of organisms
global ecosystem depends on their activities
(possess 50% of earth’s carbon and 90% of nitrogen)
influence human society in many ways

4. Microbes and Microbiology?
Microbes are living organisms
Except for viruses, which are noncellular
Metabolize energy, grow, reproduce
Visualized by a microscope
Unicellular , potentially exist independently
simple in their construction; lack differentiated cells and distinct tissues
Microbiology: study of organisms too small to be seen by the unaided eye (i.e., microorganisms)
How small?

5. Size of Microorganisms
Naked eye
~10 nm to 100 μm
different type of optical system needed to resolve
Where the bugs stand in the universe? Click here

6. Thiomargarita namibiensis
Exceptions to the size rule
Thiomargarita namibiensis
(Pearl of Namibia)
Sulfur Pearl of Namibia was dicovered by Heide Schultz chemolitothrophic G- bacterium
1000X larger than bacteria (0.5-1 mm)

7. Exceptions to the size rule
Mimivirus: DNA virus
1.2 Mbp genome, ds linear
nm in diameter
Infects amoeba
Unique genes
Primitive life form?
Mimivirus
Click to read more

8. The Microbial Tree Difficult to classify
Difficult to distinguish by shape
Often reproduce asexually
Pass DNA to each other horizontally
Use biochemical properties to classify
Gram stain (G- and G+)
Ability to metabolize different substrates (Bergey’s manual determinative bacteriology)
Use DNA sequence to classify
Microbial genomes are sequenced (click to link to database)
Bacterial genomes are relatively small
Genome = organism’s total genetic content
Complete gene sequence known for many species
Over 3000 bacteria, over >100 archaea
thousands of viruses
Microbes have greatest diversity of genomes
Important for understanding evolution

9. The Microbial Family Tree
Carl Woese
16s rRNA gene conserved
Divergence reflects relatedness
Phylogenetic tree
Microbial world in 3 domains
Prokaryotes include 2 domains
Domain of Eubacteria
Domain of Archaea
Eukaryotic domain
Algea
Fungi
Protista

10. Microbes 6 major groups studied by microbiologists Cellular forms:
Prokaryotes
Bacteria
Eukaryotes
Algae
Acellular:
Viruses
Archaea
Protists
Fungi

11. History of Microbiology

12. Old times…
Humans knew how to deal with germs before even knowing about their existence
Storing food in cooler temperatures
Salting, drying, smoking
Use of spices
Cremation of dead
concealing and burying dead beyond a nearest passing river or in a distant area
traditional, mystical and superstitious explanations

13. Discovery of Microorganisms
Antony van Leeuwenhoek ( ), the father of microbiology
a hobbyist microscopist Dutchman
first to observe and describe microorganisms accurately

14. Leeuwenhoek’s microscope
Composed of one lens
Light shines objects at a 45˚ angle
Worked like a dark field microscope
Magnification: fold
bright microorganisms could be seen in a dark bkg

15. Leeuwenhoek’s Observations
Spirillum as seen by Leeuwenhoek’s microscope
Tripartite structure of a human sperm
PMN
RBC
Original blood smear image by Leeuwenhoek
Note the polymorphonuclear cell and RBC
Reported to the Royal Society of London (1673)
Accurate shape, detailed movement
Subjects were most possibly bacteria and protozoa and called them “animalcules“
also reported spermatozoa, blood cells
Check out a paper by Brian J. Ford about Leeuwenhoek

16. Where do microorganism originate from?
Few days of being
exposed to air.
Where do microorganism originate from?
Spontaneous generation??

17. The Conflict over Spontaneous Generation
living organisms can develop from nonliving or decomposing matter
publically a common sense vision with social and cultural roots (almost years ago)
Examples:
flies from rotten meat and animal carcasses
Mice from fungus infested grain barns
Scientific methodology was not established
What was the proof?

18. Jan Baptista Van Helmont (1577-1644)
A Flemish noble man, alchemist and physician
discovered carbon dioxide, introduced the term gas in its present scientific sense
believed in spontaneous generation
Paper by Louis Rosenfeld about Van Helmont

19. Jan Baptista Van Helmont The Origin of life (17th Centuray)
Adult mice

20. Spontaneous Generation

21. Could spontaneous generation be true for microorganisms?

22. Francesco Redi (1626-1697) First blow to spontaneous generation
Laying eggs is required for maggots and flies to come to existence
Supporters of SG: Life is necessary in order to bring about life in certain cases!

23. John Needham ( )
Conclusion: Organic matter had vital force that confers properties of life to non-living matter
BUT: he had left the flasks unsealed after bioling

24. Lazzaro Spallanzani (1729-1799)
Air carries germs to broth and boiling kills the existing ones
Supporters of SG:
Compounds essential for generation of life were destroyed by heating!!
sealing prevents air that is necessary for spontaneous generation

25. Louis Pasteur (1822-1895) Observations:
John Tyndall: Organisms retained on cotton filters resemble microorganisms in contaminated foods
Microorganisms are found in the air
Microorganism in air settle on the surfaces

26. Pateur’s Swan neck flasks could supply air but could also trap ambient germs from entering broth

27. Pasteur Refutes the Spontaneous Generation

28. Pasteur Refutes the Spontaneous Generation
ambient germs are necessary for promoting growth
principle of sterility and aseptic work is important

29. Germ theory: Microorganisms Cause Disease
For over 17 centuries the Galenism (Greek physician B.C.) was predominant view for diseases according to which,
Diseases are due to imbalances in 4 humors: blood, phlegm, yellow bile and black bile

30. Relationship between Microorganisms and Disease
Agostino Bassi ( )
showed that a disease of silkworms was caused by a fungus
M. J. Berkeley (~ )
demonstrated that the great Potato Blight of Ireland was caused by a water mold
Louis Pasteur ( )
showed that the pébrine disease of silkworms was caused by a protozoan Nosema bombycis

31. Other evidence… Joseph Lister (1827-1912) provided indirect evidence
used diluted carbolic acid (phenol) to wash surgical devices and wash wounds
developed the principles of aseptic surgery
his patients had fewer postoperative infections
Disease frequency dropped in his hospital

32. Final proof… Robert Koch (1843-1910)
established the relationship between Bacillus anthracis and anthrax
used criteria developed by his mentor Jacob Henle ( )
these criteria now known as Koch’s postulates
Read more about R. Koch. Check literature section

33. Microorganisms and Diseases Robert Koch
Observations :
The microorganism (Bacillus anthracis) is found only in the infected animals and not in healthy animals.
Infected animals pass the disease to healthy ones
The microorganism found outside of the animal could infect healthy animals

34. Germ theory: Koch’s postulates

35. Questions:
Can Koch’s Postulates be applied to all microorganisms that cause disease?
How can you apply Koch’s postulates to viruses and viral diseases?
How can one apply Koch’s postulates to non-cultivable microorganisms?

36. The Development of Techniques for Studying Microbial Pathogens
Koch’s work led to discovery or development of:
agar
Petri dish
nutrient broth and nutrient agar
methods for isolating microorganisms in pure culture

37. The Pure Cultures and Isolation of Single Colonies
Koch :
Observation: Slices of potato when exposed to air, will generate large number of bacteria (colonies) of different sizes, colours and forms
Colonies

38. Problem: Not all bacteria could grow on potatoes!
Solution :
Koch used gelatin as a means for solidification of rich culture media.
He formulated various culture media

39. Disadvantages of Gelatin
Gelatin liquefaction: It is digested by various microorganisms eg. gelatinase positive enterococci and streptomyces
Low melting temperature: It is in the liquid state above the temperature of 28oC.

40. Agar
Gracilaria (red seaweeds)
Polysaccharide derived from the cell walls of a red algae (Rhodophyta)
A polysaccharide polymer that contains 3,6-anhydrogalactose, 2-O-methyl-α-l-galactopyranose and 6-O-methyl agarobiose
Solid at >37oC.
Melts at 100oC.
Not digested by most bacteria

41. Corollary to Germ Theory
Stop germ transmission, stop disease spread
Kill germ, prevent disease
Antiseptics
1865: Aseptic surgery
Joseph Lister
Antibiotics
1929–1941: Penicillin
Alexander Fleming
Many newer antibiotics
Bacteria become resistant

42. Corollary to Germ Theory
Stop germ transmission, stop disease spread
Stop spread of germs
Epidemiology, public health measures
Resistant individuals prevent spread of germs
1798: Vaccination with cowpox prevents smallpox
Turkish physicians, Lady Montagu, Edward Jenner

43. Other developments… Pasteur and Roux Pasteur and his coworkers
discovered that incubation of cultures for long intervals between transfers caused pathogens to lose their ability to cause disease (attenuation)
Pasteur and his coworkers
developed vaccines for chicken cholera, anthrax, and rabies

44. Modern microbiology: day to day impact on society

45. Microbes Shape Human History
Food & Pharmaceuticals
Bread, wine, cheese, Chocolate
Can also destroy crops
Hormones, antibiotics etc
Microbial diseases change history
14th century: Bubonic plague (Black death) caused by Yersinia pestis in Europe
19th century: Tuberculosis caused by Mycobacterium tuberculosis
today: AIDS by the human immunodeficiency virus (HIV)

46. The golden age of microbiology (1857-1914)
Many pathogens discovered
Microbial metabolism studies undertaken
Microbiological techniques refined
A better understanding of the role of immunity and ways to control and prevent infection by microbes

47. Genetics and DNA Revolution
Molecular genetics depends on bacteria
Concept of “gene” proposed for bacteria
DNA structure
Genetic code
Transcription, translation
Restriction enzymes
Recombinant DNA
Cloning
PCR reaction (watch the interview with Kery Mullis)
E. coli has best understood genome

48. The Future of Microbiology
Challenges and opportunities for future microbiologists
infectious disease
new and improved industrial processes
microbial diversity and microbial ecology
less than 1% of earth’s microbial population has been cultured

49. More challenges and opportunities…
biofilms
genome analysis
microbes as model systems
assessment of implications of new discoveries and technologies
Stephen Jay Gould ( ): “This is truly the "age of bacteria" - as it was in the beginning, is now and ever shall be.”