At the end of the course the students should be able
Describe the historical development of microbiology and the
natural history of microbial diseases
Explain the rationale for classifying microbes into bacteria, fungi
Classify microorganisms and illustrate their cellular/anatomic
characteristics in general
Discuss the Unique differentiating features of eukaryotes and
Identify the source and spread of microbes
Describe The nature of bacteria
Discuss the morphological differences and Growth requirement of
bacteria, nomenclature and classification of bacteria
Explain biology of protozoa
Describe medically important helminths, ectoparasites
Discuss the nature and properties of viruses
Explain brief appraisal of pathogenicity of viruses
Describe nature of fungi : basic structures and classification
Identify sterilization and disinfection methods
List the different mechanisms of disinfection and sterilization
Is the study of microorganisms
Microorganisms are all single-celled microscopic organisms and include
the viruses, which are microscopic but not cellular
Microbial cells differ in a fundamental way from the cells of plants and
microorganisms are independent entities that carry out their life
processes independently of other cells
The science of microbiology revolves around two
(1) understanding the living world of microscopic
(2) applying our understanding of microbial life processes
for the benefit of humankind and planet Earth
The main types of medically important
Historical development of microbiology and the natural history
of microbial diseases
Microorganisms are visible with the help of magnifying
lenses (ex. Microscope)
→ Microscope is the tool of microbiologist.
Microbiology started after the discovery of magnifying
Microscope has two major roles:
i. Magnification- Enlarging the size
ii. Resolution – showing the fine details
Progress In Microscopy
1590 Hans & Zacharius Janssen: Lense makers
1665 Robert Hooke- views and describes fungi
1676 Anthony van Leeuwenhoek observed
first microscopic organism, blood cells and protists
Robert Hooke and early microscopy
The first descriptions of
Microorganisms by Robert
Hooke in Micrographia in 1665
Microorganisms were first observed by Antonie van
Leeuwenhoek, using a primitive microscope
(a) A replica of Antoni van
Leeuwenhoek’s microscope. (b)
Van Leeuwenhoek’s drawings of
bacteria, published in 1684.
Even from these simple drawings
we can recognize several
shapes of common bacteria: A, C,
F, and G, rods; E, cocci;
H, packets of cocci
Photomicrograph of a human
blood smear taken through a
microscope. Red blood cells
are clearly apparent
Progress in Tools
• 1883 Carl Zeiss and Ernst Abbe make
advancements in microscopy lenses and
• 1931 Ernst Ruska- first electronic
Christian Grham – the use of stains
Summary of types of Microscope
Bright Field Light Microscopy
Dark Field Microscopy
Phase Contrast Microscopy
Transmission Electron Microscopy - TEM
Scanning Electron Microscopy - SEM
Discovery of microorganisms
Discovery of bacteria
Mid- to late
Mechanism of fermentation,
defeat of spontaneous
generation, rabies and other
vaccines, principles of
Methods for preventing
infections during surgeries
Discovery of endospores,
preventing culture media from
Koch’s postulates, pure
discovery of agents of
tuberculosis and cholera
1800s to 1920
Enrichment culture technique,
discovery of many metabolic
groups of bacteria,
concept of a virus
Factors that contributed to the dev’t of
1. Controversy between the supporters of
Abiogenesis (Theory of spontaneous generation) and
2. The Germ Theory of Diseases
things arise from non-living matter
things arise from pre-existing life form
Theory of Spontaneous generation
belief that some forms of life could
arise from vital forces present in nonliving or
ex. flies from manure, etc
Theory of Biogenesis
of the Supporters of Biogenesis
Challenges to spontaneous generation
Spontaneous Generation work?
Francesco Redi’s Experiment (1600’s)
Problem: Did rotting meat produces
Experiment: Used 3 jars:
3.Meshed & closed
Result: No growth in boiled
and closed jar.
Lazaro Spallanzani’s Experiment
Spallanzani's Problem :What causes microbes to
form in decaying broth?
Hypothesis: Microbes come from the air. Boiling will
Experiment: Spallanzani put broth into four flasks
Flask 1 was left open
Flask 2 was sealed
Flask 3 was boiled and then left open
Flask 4 was boiled and then sealed
Result: No growth only in Flask 4.
Conclusion: Life arise from pre-existing form.
Spallanzani is best known for his experiments to
disprove abiogenesis. He showed having boiled a
broth and then sealed the container, no
microorganisms would grow
That is, broth did not spontaneously produce
Louis Pasteur’s Experiment
Louis Pasteur did an experiment to show bacteria do
not arise spontaneously.
He showed microbes caused
fermentation and spoilage,
and disproved spontaneous
Louis Pasteur’s Exp.
Pasteur’s work also led to the development of effective
Food science also owes a debt to Pasteur, as his principles are
applied today in the preservation of milk and many other foods by
heat treatment (pasteurization).
Pasteur’s fame from his rabies research was legendary and led
the French government to establish the Pasteur Institute in Paris
Originally established as a clinical center for the treatment of
rabies and other contagious diseases,
the Pasteur Institute today is a major biomedical research center
focused on antiserum and vaccine research and production
Significances of the controversy
of microorganism in two forms:
Vegetative - heat labile
Spore form – resistance to heat
History of Microbiology cont…
Spores and sterilization
• Some microbes in dust and air were resistant
to high heat.
• Spores were later identified.
• The term “sterile” was introduced which meant
completely eliminating all life forms from
objects or materials.
Microbiology as a science
through accumulation of
knowledge following scientific methods.
Scientific Method involve:
Identification of problem/gap of knowledge
• Conclusion or theory
Natural History of Microbial Diseases
Even as early as the sixteenth century it was thought that
something that induced disease could be transmitted from a
diseased person to a healthy person.
After the discovery of microorganisms, it was widely believed that
they were responsible, but definitive proof was lacking
In sanitation by Ignaz Semmelweis and Joseph Lister provided
indirect evidence for the importance of microorganisms in
causing human diseases
Do Microbes Cause Disease?
• 1546 Girolamo Fracastoro wrote about
“contagion” – communicable disease
Mainly philosophical as the existence of MOs were not known
Proposed that disease are transmitted by:
1. direct contact
2. through air
3. through inanimate objects such as clothes
1835 Agostino Bassi de Lodi linked a fungi with a silkworm disease–
the first recognized contageous agent of animal disease!
but it was the work of a German physician, Robert Koch (1843–1910)
that give experimental support to the concept of infectious disease
Germ theory of disease
Theory is the concept that microorganisms can cause disease, and this theory
is the foundation of modern medicine.
Many diseases are caused by the growth of
microbes in the body and not by sins, bad
character, or poverty, etc.
Robert Koch was a man who dedicated his life
to finding the causes of infectious diseases
Koch was convinced that microbes caused some diseases
However, to test this idea, he needed to isolate the causative agent.
Almost all samples from diseased animals or any natural surface
contained many different microbes and it was impossible to tell which
one was the problem.
A method was needed to separate these different bacteria. The most
common method of isolation was to continually dilute a sample in liquid
broth in hopes only one type of microbe would be found
A major contribution to bacterial techniques was the development of
methods using solid medium for the cultivation of bacteria.
Robert Koch’s Experiment
Koch (1843-1910) verified
(realized)the Germ theory (and formulated
In 1876 Robert Koch – cultivates Anthrax using
blood serum and published postulates:
1. The disease agent must be present in every case, and
absent in healthy individuals.
2. The agent must be isolated and cultured in vitro (i.e.
cultivated in a laboratory environment).
3. Disease must be produced when a pure
culture is inoculated into susceptible host
4. The agent must be recoverable from infected host
Exceptions to Koch’s postulates
1. Many healthy people carry pathogens but do not exhibit
symptoms of the disease.
2. Some microbes are very difficult or impossible to grow in vitro(in
the laboratory) in artificial media. Eg. Treponema pallidum
3. Many species are species specific. Eg. Brucella abortus cause
abortion in animals but no report in humans.
4. Certain diseases develop only when an opportunistic pathogen
invades immunocompromised host
Contribution of Koch discoveries
The establishment of the fact that disease are caused by
Koch's laboratory also developed methods of pure culture
maintenance and aseptic technique.
Aseptic technique involves:
the manipulation of pure cultures in a manner that prevents
their contamination by outside microorganisms.
Equally important, aseptic technique prevents their spread
into the environment
Contribution of Koch disc…
The postulate not only offered a means for linking the cause and
effect of an infectious disease,
but also stressed the importance of laboratory culture of the
putative infectious agent
These discoveries led to the development of successful
treatments for the prevention and cure of many diseases,
thereby greatly improving the scientific basis of clinical medicine
and human health and welfare
Contribution of Koch disc…..
Koch announced his discovery of the cause of tuberculosis M.
tuberculosis in 1882
and published a paper on the subject in 1884 in which his
postulates are most clearly stated.
For his contributions on tuberculosis, Robert Koch was awarded
the 1905 Nobel Prize for Physiology or Medicine.
Koch had many other triumphs in medicine, including discovering
the organism responsible for the disease cholera
and developing methods to diagnose exposure to M. tuberculosis
(the tuberculin test)
Martinus Beijerinck (1851–1931)&Sergei Winogradsky (1856–
1953) greatest contribution to the field of microbiology was their
clear formulation of the enrichment culture technique
In 1929 Alexander Fleming observed that molds can produce a
substance that prevents the growth of bacteria.
His discovery, an antibiotic called penicillin, was later isolated and
produced commercially to protect people against the harmful
effects of certain microorganisms.
The Modern Era of Microbiology
In the 1940s microbiology expanded into the fields of molecular
biology and genetics.
Viruses were found to be simple microbes that could be studied
quantitatively, and they were used to study the nature of DNA
In the early 1970s, genetic researchers discovered recombinant
Scientists found that DNA could be removed from living cells and
spliced together in any combination.
They were able to alter the genetic code dictating the entire
structure and function of cells, tissues, and organs.
The development of early techniques in microbiology
Robert Hooke is the first to use a microscope to describe the fruiting structures of molds. He
also coined the term cell when using a microscope to look at cork, as the dead plant
material in cork reminded him of a jail cell.
Anton van Leeuwenhoek, a Dutch tradesman and skilled lens maker, is the first to
describe microbes in detail.
Ferdinand Julius Cohn publishes landmark paper on bacteria and the cycling of elements.
In it is an early classification scheme that uses the name Bacillus.
Oscar Brefeld reports the growth of fungal colonies from single spores on gelatin and
the German botanist Joseph Schroeter grows pigmented bacterial colonies on slices of
Robert Koch develops methods for staining bacteria, photographing, and preparing
permanent visual records on slides.
Koch develops solid culture media and the methods for obtaining pure cultures of bacteria.
Angelina Fannie and Walther Hesse in Koch's laboratory develop the use of agar as a
support medium for solid culture.
Hans Christian Gram develops a dye system for identifying bacteria [the Gram stain].
First report of the petri plate by Julius R. Petri.
M. H. McCrady establishes a quantitative approach for analyzing water samples using the
most probable number, multiple-tube fermentation test.
Previously living organisms grouped into five kingdoms:
plants, animals, fungi, protists, and bacteria.
DNA sequence-based phylogenetic analysis, on the other hand,
has revealed that the five kingdoms do not represent five primary
Instead, cellular life on Earth has evolved along three primary
lineages, called domains.
Two of these domains, the Bacteria and the Archaea, are
exclusively composed of prokaryotic cells.
The Eukarya contains the eukaryotes, including the plants,
animals, fungi, and protists.
Microbial Taxonomy con…
Definition Taxonomy : is a system for organizing,
classifying & naming of living things.
• Primary concerns of taxonomy are:
Microbial Taxonomy con…
Classification is the organization of organisms into
groups on the basis of either phenotypic similarity or
The hierarchical nature of classification is that species
is made up of one to several strains, and similar
species are grouped into genera (singular, genus).
Similar genera are grouped into families, familiesm
into orders, orders into classes, up to the domain, the
Microbial Taxonomy cont….
– giving a two word name
(Binomial) (Genus and species name)
Identification – assigning to the corresponding
taxa or group using the existing system of
Microbial Taxonomy cont….
• Binomial nomenclature: naming organisms using
the genus and species name together
It is (scientific)
• Genus – always capitalized(Ex. Bacillus, )
• species – use lowercase (ex. subtilis)
• Both italicized or underlined
-Bacillus subtilis, or
- Bacillus subtilis, or
- B. subtilis
Microbial Taxonomy cont…
Levels of Classification:
• Phylum or Division
The polyphasic approach to taxonomy uses three kinds of
methods—phenotypic, genotypic, and phylogenetic—for the
identification and description of bacteria
Phenotypic analysis examines the morphological, metabolic,
physiological, and chemical characteristics of the cell
Genotypic analysis considers characteristics of the genome
These two kinds of analysis group organisms based on
They are complemented by phylogenetic analysis, which seeks
to place organisms within an evolutionary framework
Microbial Taxonomy cont…
►Developed after the five-kingdom system
Eubacteria -true bacteria, with true peptidoglycan
Archaea –odd bacteria that live in extreme
environments, high salt, heat,etc
Eukarya- have a nucleus, & organelles
This domain includes the kingdom of the heterotrophic
eubacteria and includes all human pathogen bacteria.
The other kingdoms, for instance that of the
photosynthetic cyanobacteria, are not pathogenic.
It is estimated that bacterial species on Earth number
in the hundreds of thousands, of which only about
5500 have been discovered and described in detail.
This domain includes all life forms with cell possessing
a genuine nucleus.
The plant and animal kingdoms (animales and
plantales) are all eukaryotic life forms
Pathogenic eukaryotic microorganisms include fungal
and protozoan species
• No membrane bounded organelles
• Cell wall made of Peptidoglycans
• Antibiotic sensitivity
• Reproduction by Binary fission
• DNA with no Histones
• 70S ribosome
Some are parasitc, others are beneficials (food,
antibiotic, industry, agriculture, environment, medical),
some are pathogenic (Salmonella, Shigela), still some
others are toxin producing(Clostridium, S.aurus),
Fungal general characteristics
They are achloropyllus
Without true root, stem, and leaf, no vascular system
Heterotrophic mode of nutrition(they digest and ingest)
They follow both sexual and asexual mode of reproduction
Some are parasitic;(smuts, rust, athletes foot, ringworm);
others are beneficial(antibiotic, food, industry),
some form associations(lichen, Mycorrhiza, termites),
some produce toxins which is potent chemical to human, animal and
Some are still poisonous(Amanita spp.)
Some are still disease causing Mycosis (athletes foot, ring worm,)
Major groups of fungi
• Classification based on:
_Nutrition, Habitat, life cycle, growth
The major Fungal divisions are:
Deutromycetes /fungi imperfecta/ mitosporic