Microbiology study of organisms too small to be seen by the naked eye. Microbes or Microorganisms commonly referred to as “germs” or “bugs” include bacteria, viruses, fungi, algae, protozoa and helminths. Prions (“infectious proteins”) are recent addition.

1. Themes in Microbiology

2. Various Topics cover:
 Scope of Microbiology
 Importance of Microorganisms
 Characteristics of Microorganisms
 History of Microbiology
 Taxonomy

3. Scope of Microbiology
Microbiology
 study of organisms too small to be seen by the naked eye.
Microbes or Microorganisms
 commonly referred to as “germs” or “bugs”
 include bacteria, viruses, fungi, algae, protozoa and helminths.
 Prions (“infectious proteins”) are recent addition.
(Molecular Biology) A self-propagating misfolded conformer of a protein that
is responsible for a number of diseases that affect the brain and
other neural tissue. Origin From (a reordering of) the initial letters
of proteinaceous infectious particle(s). Coined in 1982 by Stanley B.
Prusiner.

4. Branches of Study
 Bacteriology study of bacteria
 Mycology study of fungi and yeast
 Virology study of viruses
 Parasitology study of parasitic protozoans and
helminths
 Immunology study of the humoral and cellular
immune response to disease
agents and allergens

5.  Epidemiology and Public Health Microbiology
distribution and spread of diseases and their control and prevention
 Food Microbiology
use of microbes in the production of food products and drinks
 Agricultural and Veterinary Microbiology
use of microbes to increase crop and livestock yield and control of
plant pests and animal diseases
 Environmental Microbiology
study of the beneficial and harmful effects of microbes on the
environment
Specializations in Microbiology

6. Importance of Microbiology
 First bacteria*
 Photosynthesis and decomposition
 Human use of microorganisms
 Infectious diseases
 *The ancestors of modern bacteria were unicellular microorganisms that
were the first forms of life to appear on Earth, about 4 billion years ago. For
about 3 billion years, most organisms were microscopic, and bacteria and
archaea were the dominant forms of life.

7. The Progenote*
Evolutionary Timeline: Bacteria appeared 3.5 billion years ago
* A hypothetical simple biological entity or organized system of a kind that could
have included the evolutionary common ancestor of eukaryotes and prokaryotes.

8. Photosynthetic Microbes
Microbes are involved in photosynthesis and accounts for
>50% of earth’s oxygen.
Also involved in decomposition and nutrient recycling.

9. Beneficial Uses of Microbes
Extraction of copper from ore

10. Bioleaching
Bioleaching is the extraction of metals from their ores through the use of living
organisms. This is much cleaner than the traditional leaching using cyanide.
Bioleaching is one of several applications within biohydrometallurgy and
several methods are used to
recover copper, zinc, lead, arsenic, antimony, nickel, molybdenum, gold, silver,
and cobalt.
Process:Bioleaching can involve numerous ferrous iron and sulfur oxidizing
bacteria, including Acidithiobacillus ferrooxidans (formerly known
as Thiobacillus ferrooxidans) and Acidithiobacillus thiooxidans (formerly known
as Thiobacillus thiooxidans).
As a general principle, Fe3+ ions are used to oxidize the ore. This step is
entirely independent of microbes. The role of the bacteria is the further
oxidation of the ore, but also the regeneration of the chemical oxidant Fe3+ from
Fe2+. For example, bacteria catalyse the breakdown of the mineral pyrite (FeS2)
by oxidising the sulfur and metal (in this case ferrous iron, (Fe2+)) using oxygen.
This yields soluble products that can be further purified and refined to yield the
desired metal.

11. Beneficial Uses of Microbes
Synthesis of drugs, hormones and enzymes

12. Beneficial Uses of Microbes
Bioremediation is the use of microbes to degrade organic
matter in sewage and detoxify pollutants such as oil spills.

13. Microbial Biodegradation

14. General overview of microbial biodegradation of petroleum oil by microbial
communities.
Some microorganisms, such as Alcanivorax borkumensis
(marine bacteria), are able to use hydrocarbons as their
source for carbon in metabolism. They are able to oxidize the
environmentally harmful hydrocarbons while producing
harmless products, following the general equation CnHn +
O2 → H2O + CO2. In the figure, carbon is represented as
yellow circles, oxygen as pink circles, and hydrogen as blue
circles. This type of special metabolism allows these microbes
to thrive in areas affected by oil spills and are important in the
elimination of environmental pollutants.

15. Modern Uses of Microbes
 Biotechnology, the use of microbes as miniature
biochemical factories to produce food and chemicals is
centuries old.
 Genetic engineering makes use of molecular biology
and recombinant DNA techniques as new tools for
biotechnology.
 Gene therapy replaces missing or defective genes in
human cells through genetic engineering.
 Genetically modified bacteria are used to protect crops
from pests and freezing.

16. Infectious Diseases
Worldwide infectious disease statistics
United States Public Health Service
(USPHS) - agency where notifiable
diseases are reported
Centers for Disease Control (CDC)-
collects disease data around the U.S.
and publishes the MMWR (Morbidity
and Mortality Weekly Report)
World Health Organization (WHO)-
medical arm of the U.N., monitors
diseases worldwide.

17. Microbial Taxonomy
Traditional Whittaker 5 Kingdom System

18. Microbial Taxonomy
Woese-Fox 3 Domain System

19. A domain is a taxonomic category above
the kingdom level.
The three domains are: Bacteria, Archaea, and Eukarya,
which are the major categories of life.
A kingdom is a taxonomic group that contains one or more
phyla. The four traditional kingdoms of Eukarya include:
Protista, Fungi, Plantae, and Animalia.
Domain & Kingdom

20. Nomenclature
 Linnaeus introduced the binomial system of scientific
nomenclature
 Each organism has two names: the genus and species
epithet
 Italicized or underline
 Genus name is capitalized and species in lower case.

21. Scientific Names
Staphylococcus aureus
describes clustered arrangement of cells and golden
yellow color of colonies
Escherichia coli
Honors the discoverer, Theodor Escherich and
describes its habitat, the colon.
After the first use, scientific names may be abbreviated
with the first letter of the genus and full species
epithet. (Example: E. coli)

22. General Characteristics
 Prokaryotes no nucleus and organelles
 Eukaryotes membrane bound nucleus
and organelles
 Acellular agents genomes contain either
DNA or RNA; newer agent
are regarded proteinaceous

23. Cell Types
Comparative cellular structures of microbes

24. The Microbes
viruses protozoa
bacteria
bacteriophage
algae
spirochaetes
cyanobacteria
fungi

25. Size of Microbes
Microbes vary in size ranging
from 10 nm (nanometers) to
100 mu (micrometers) to the
macroscopic.
Viruses in nm = 10-9 m (meter)
Bacteria in um = 10-6 m
Helminths in mm = 10-3 m

26. Bacteria
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Prokaryotes
Peptidoglycan cell walls
Binary fission
Ex: Escherichia coli

27. Archaea
Prokaryotes
Lack peptidoglycan
Live in extreme environments
(extremophiles)
Include:
 Methanogens
 Extreme halophiles
 Extreme thermophiles

28. Fungi
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Eukaryotes
Chitin cell walls
Molds and mushrooms
are multicellular
Yeasts are unicellular

29. Protozoa
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Eukaryotes
Mostly saprobes* &
commensals**
May be motile by means of
pseudopod, cilia or flagella
*Saprobe sap·robe (sāp'rōb') n. An organism that derives
its nourishment from nonliving or decaying organic matter.
**Commensalism, in ecology, is a class of relationships
between two organisms where one organism benefits
from the other without affecting it.

30. Algae
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Eukaryotes
Cellulose cell walls
Photosynthetic
Produce molecular oxygen
and organic compounds
Part of food chain

31. Helminths
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Eukaryotes
Multicellular animals
Parasitic flatworms and
roundworms called
helminths
Microscopic stages in life
cycles

32. Viruses
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Acellular
Obligate intracellular parasites
Genome consist of DNA or
RNA called Core
Core surrounded by protein
coat called Capsid
Virion may be enclosed in lipid
envelope

33. Prions
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Proteinaceous infectious
agents
Causes Bovine Spongiform
Encephalopathy (BSE)
Also causes Creutzfeldt-
Jacob Disease (CJD)
An Emerging Infectious
Disease (EID)

34. Bovine Spongiform Encephalopathy (BSE), or Mad Cow Disease.
BSE (bovine spongiform encephalopathy) is a progressive
neurological disorder of cattle that results from infection by an unusual
transmissible agent called a prion. ...
Mad Cow Disease is a neurological disorder of cattle.
Creutzfeldt–Jakob disease (CJD) is a universally fatal brain
disorder.[2] Early symptoms include memory problems, behavioral
changes, poor coordination, and visual
disturbances.[2] Later dementia, involuntary movements, blindness,
weakness, and comaoccur.[2] About 90% of people die within a year of
diagnosis.

35. An emerging infectious disease (EID) is an infectious disease whose incidence
has increased in the past 20 years and could increase in the near future.
Emerging infections account for at least 12% of all human pathogens.
EIDs are caused by newly identified species or strains (e.g. Severe acute
respiratory syndrome, HIV/AIDS) that may have evolved from a known infection
(e.g. influenza) or spread to a new population (e.g. West Nile fever) or to an area
undergoing ecologic transformation (e.g. Lyme disease), or be re-
emerging infections, like drug resistant tuberculosis.
Nosocomial (hospital-acquired) infections, such as Methicillin-resistant
Staphylococcus aureus are emerging in hospitals, and extremely problematic in
that they are resistant to many antibiotics.
Of growing concern are adverse synergistic interactions between emerging
diseases and other infectious and non-infectious conditions leading to the
development of novel syndemics.
Many emerging diseases are zoonotic - an animal reservoir incubates the
organism, with only occasional transmission into human populations.
Emerging Infectious Disease (EID)

36. Microbiology As A Science
 Science is a systematized body of knowledge explaining
the occurrence of natural phenomena
 Qualities of a scientist:
curiosity
open-mindedness
skepticism
creativity
objectivity
A syndemic or synergistic epidemic is the aggregation of two or more concurrent
or sequential epidemics or disease clusters in a population with biological
interactions, which exacerbate the prognosis and burden of disease.

37. Scientific Approach
 Deductive reasoning
starts with a general idea that are tested to
prove or disprove it.
 Inductive reasoning
starts with drawing patterns from specific
observations resulting in generalization.

38. Scientific Method
 Hypothesis
 Laboratory experimentation or field Studies
 Data collection and analysis
 Conclusion, either reject or accept hypothesis
 Theory or Law

39. Microbiological Experiment

40. Brief History of Microbiology
 The Microscope
 Spores and Sterilization
 Spontaneous Generation
 Aseptic Technique
 Germ Theory

41. The First Microscope
Microbes were first observed
by Antonie van Leeuwenhoek
using a simple microscope
(ca. 1673)
Reported his “animalcules” to
the Royal Society of London

42. Animalcule ("little animal", from Latin animal + the
diminutive suffix -culum) is an older term for a microscopic
animal or protozoan. ... Some better-
known animalcules include: Actinophrys, and other
heliozoa, called sun animalcules. Amoeba, called
Proteus animalcule.
a minute or microscopic animal, nearly or quite invisible to
the naked eye, as an infusorian or rotifer. ... a tiny animal,
as a mouse or fly. ... "very small animal,“ especially a
microscopic one, 1590s, from Late Latin animalculum

43. Spores and Sterilization
 John Tyndall showed that some microbes in
dust and air were resistant to heat.
 Ferdinand Cohn discovered and described
endospores
 Term “sterile” was introduced to mean the
complete removal of all life forms including
endospores

44. Abiogenesis vs. Biogenesis
 “Spontaneous Generation” was an early belief
that living things can arise from vital forces
present in non-living and decaying matter.
(Ex: maggots from meat or mushrooms from
rotting wood)
 The alternative hypothesis that living organisms
can arise only from pre-existing life forms is
called “Biogenesis”

45. The Pros and Cons
Francisco Redi
(ca. 1668)
A maggot is the larva of a fly (order Diptera); it is applied
in particular to the larvae of Brachycera flies, such as
houseflies, cheese flies, and blowflies, rather than larvae
of the Nematocera, such as mosquitoes and Crane flies.

46. The Pros and Cons
 1745 -John Needham boiled nutrient broth into
covered flasks
Conditions Results
Nutrient broth heated
then placed in sealed
flasks
All showed growth
From where did the microbes come?
Spontaneous generation or biogenesis?

47. The Pros and Cons
LouisJablot

48. The Pros and Cons
Franz Schultze and Theodor Schwann

49. The Pros and Cons
Louis Pasteur put an
end to Abiogenesis
debate with his
Goose Neck Flask
Experiment
He is the father of
Microbiology

50. Louis Pasteur
 Showed microbes caused
fermentation
 Studied spoilage and
introduced “Pasteurization”
to prevent it
 Used cotton plugs in his
cultures to prevent air borne
contamination, devised
Aseptic Technique.

51. Antiseptics and Hand Washing
 1860s - Joseph Lister used, carbolic acid, a
chemical antiseptic to prevent surgical wound
infections
 Ignaz Semmelweis, a Hungarian physician
introduced hand washing as a means of
preventing transfer of puerpueral sepsis in
obstetrical patients

52. Germ Theory of Disease
 1876 - Robert Koch
provided proof that a
bacterium causes anthrax
using experimental steps
now called the Koch’s
Postulates
 He was the first to use agar
as solid culture medium in
bacteriology.

53. Koch’s Postulates
 The microbe must always be present in every
case of the disease
 It must be isolated in pure culture on artificial
media
 When inoculated into healthy animal host it
should produce the same disease
 It must be isolated from the diseased animal
again

54. Infection and Disease
 Infection the entry of a microbe into the host.
 Disease infection followed by the appearance of
signs and symptoms.
 Pathogen an infectious or disease agent.
 Saprobe a microbe that lives on dead or
decaying organic matter.
 Opportunistic pathogen
is a microbe that cause disease in immunocompromised hosts
or when the normal microbiota is altered.

55. Emerging Infectious Diseases
 Occurrence of new diseases and increasing incidence of
old ones (EID)
 Factors:
(a) evolutionary changes in existing organisms
(b) spread of known diseases into new
geographic areas by modern transportation
(c ) ecological changes resulting in introduction of
unusual agents
(d) emergence of antimicrobial resistance

56. Emerging Infectious Diseases
 West Nile Encephalitis, first diagnosed in Uganda in 1937;
appeared in New York City in 1999.
 Invasive Group A Streptococcus, also known as the “flesh eating
bacteria”
 Escherichia coli 0157:H7, causes “bloody diarrhea” and
hemorrhagic uremic syndrome (HUS)
 Bovine Spongiform Encephalopathy (BSE) or “mad cow” disease
caused by prions
 Acquired Immunodeficiency Syndrome (AIDS) caused by HIV and
Africa is hardest hit
 Anthrax caused by Bacillus anthracis was sensationalized in 2001
when spores were disseminated via the mail