Microbiology

1. Chapter #01
GENERAL MICROBIOLOGY
The Introduction, History and Scope of Microbiology
• Microbiology is the study of microorganisms usually less than 1mm in diameter which
requires some form of magnification
(Microscope) to be seen clearly
– Examples:
• Viruses
• Bacteria
• Fungi
• Algae
• Protozoa's
• Some organisms studies by microbiologists CAN be visualized without the aid of
amplification [bread molds (fungus) and filamentous algae]
– These organisms are included in the discipline of microbiology because of
similarities in properties and techniques used to study them
• Techniques necessary to isolate and culture microorganisms:
– Isolation
– Sterilization
– Culture in artificial media
• Microbiology may be interested in specific types of organisms:
– Virology - viruses
– Bacteriology - bacteria
– Phycology - algae
– Mycology - fungi
– Protozoology - protozoa
• Microbiologists may have a more applied focus:
– Medical microbiology, including immunology
– Food and Dairy microbiology
– Public Health microbiology (Epidemiology)
– Industrial microbiology
– Agricultural microbiology
• Pharmaceutical microbiology
• Pharmaceutical microbiology is the application of microbiology to pharmaceutical and
healthcare environments. The scope of pharmaceutical microbiology is wide ranging.
However, its over-riding function is the safe manufacture of pharmaceutical and
healthcare preparations and medical devices. This involves risk assessment (both
proactive and reactive), together with testing materials and monitoring environments
and utilities.
• Microbiologists may be interested in various characteristics or activities of
microorganisms:
– Microbial morphology
– Microbial cytology
– Microbial physiology
– Microbial ecology
– Microbial genetics and molecular biology
– Microbial taxonomy
• II. Historical Perspectives
• ROBERT HOOKE
One of the most important discoveries of biology occurred in 1665, with the help of a crude
microscope, when Robert Hooke stated that life’s smallest structural units were cells.
• ANTONY VAN LEEUWENHOEK
• First to observe living microbes
• His single-lens magnified 50-300X magnification
• Between 1674-1723 he wrote series of papers describing his observations of bacteria,
algae, protozoa, and fungi (Animalcules)
• ANTONY VAN LEEUWENHOEK
• III. Spontaneous Generation

2. • SPONTANEOUS GENERATION
• Early belief that some forms of life could arise from “vital forces” present in nonliving or
decomposing matter, abiogenesis. In other words, organisms can arise form non-living
matter.
• LOUIS JABLOT
In 1670 Jablot conducted an experiment in which he divided a hay infusion that had been boiled
into two containers: a heated container that was closed to the air and a heated container that
was freely open to the air. Only the open vessel developed microorganisms. This further helped
to disprove abiogenesis.
• REDI’S and JABLOT’S
EXPERIMENTS
• Disproved by:
– Schwann, Friedrich Schroder and von Dusch (1830s) – Air allowed to enter flask
but only after passing through a heated tube or sterile wool
– John Tyndall (1820-1893) – Omission of dust  no growth. Demonstrated heat
resistant forms of bacteria (endospores)
• LOUIS PASTEUR (1822 - 1895)
• Disproved spontaneous generation of microbes by preventing “dust particles” from
reaching the sterile broth
• In 1861 completes experiments that lays to rest spontaneous generation.
• Showed microbes caused fermentation and spoilage
• PASTEUR’S EXPERIMENT
• IV. Role of Micoorganisms in Disease
• Demonstrations that micoorganisms cause disease
• Oliver Holmes (1773 - 1843)
– showed that sepsis could be transmitted by hands of medical student and
may cause disease
– M. J. Berkeley (ca. 1845)
– demonstrated that the Great Potato Blight of Ireland was caused by a Fungus
• Louis Pasteur (1822 - 1895)
– showed that the pébrine disease of silkworms was caused by a protozoan
parasite
• Edward Jenner (ca. 1798): Develop the first Vaccine and used a vaccination procedure
to protect individuals from smallpox
• Louis Pasteur
– developed other vaccines including those for chicken cholera, anthrax, and
rabies
• History
• 1796 – First vaccine (smallpox)
Edward Jenner
• History
• 1885 - Vaccine against Rabies
Louis Pasteur
• Robert Koch (1843 - 1910),
– using criteria developed by his teacher, Jacob Henle (1809-1895), established
the relationship between Bacillus anthracis and anthrax.
– His criteria became known as Koch’s Postulates and are still used to establish
the link between a particular microorganism and a particular disease:
• History
• 1884 Koch’s Postulates of Disease Transmission
Robert Koch
• Koch’s Postulates
• The causative (etiological) agent must be present in all affected organisms but absent
in healthy individuals
• The agent must be capable of being isolated and cultured in pure form
• When the cultured agent is introduced to a healthy organism, the same disease must
occur
• The same causative agent must be isolated again from the affected host
• Development of Culture Media
• Why?
– To enable the isolation of pure cultures (only one type of organism)
• Especially important during Koch’s period

3. • Gelatin not useful as solidifying agent (melts at >28 ºC and some bacteria hydrolyze it
with enzymes)
• Fannie Hesse, the wife of one of Koch’s assistants, proposed using agar
– Not digested by most bacteria
– Melts at 100 ºC
– Used today - ~2% in solid media
• Richard Petri, another of Koch’s assistants, developed the Petri dish
• Development of Vaccines and Antisera
• Edward Jenner in 1796 discovered that cowpox (vaccinia) induced protection against
human smallpox
– Called procedure vaccination
• Vaccination:
– Inoculation of healthy individuals with weakened (or attenuated) forms of
microorganisms, that would otherwise cause disease, to provide protection,
or active immunity from disease upon later exposure.
• Pasteur and Roux reported that incubating cultures longer than normal in the lab
resulted in ATTENUATED bacteria that could no longer cause disease.
– Working with chicken cholera (caused by Pasteurella multocida), they noticed
that animals injected with attenuated cultures were resistant to the disease.
The Introduction, History and Scope of Microbiology
• Microbiology is the study of microorganisms usually less than 1mm in diameter which
requires some form of magnification
• (Microscope) to be seen clearly
– Examples:
• Viruses
• Bacteria
• Fungi
• Algae
• Protozoa's
• Some organisms studies by microbiologists CAN be visualized without the aid of
amplification [bread molds (fungus) and filamentous algae]
– These organisms are included in the discipline of microbiology because of
similarities in properties and techniques used to study them
• Techniques necessary to isolate and culture microorganisms:
– Isolation
– Sterilization
– Culture in artificial media
• Microbiology may be interested in specific types of organisms:
– Virology - viruses
– Bacteriology - bacteria
– Phycology - algae
– Mycology - fungi
– Protozoology - protozoa
• Microbiologists may have a more applied focus:
– Medical microbiology, including immunology
– Food and Dairy microbiology
– Public Health microbiology (Epidemiology)
– Industrial microbiology
– Agricultural microbiology
• Pharmaceutical microbiology
• Pharmaceutical microbiology is the application of microbiology to pharmaceutical and
healthcare environments. The scope of pharmaceutical microbiology is wide ranging.
However, its over-riding function is the safe manufacture of pharmaceutical and
healthcare preparations and medical devices. This involves risk assessment (both
proactive and reactive), together with testing materials and monitoring environments
and utilities.
• Microbiologists may be interested in various characteristics or activities of
microorganisms:
– Microbial morphology

4. – Microbial cytology
– Microbial physiology
– Microbial ecology
– Microbial genetics and molecular biology
– Microbial taxonomy
• II. Historical Perspectives
• ROBERT HOOKE
One of the most important discoveries of biology occurred in 1665, with the help of a crude
microscope, when Robert Hooke stated that life’s smallest structural units were cells.
• ANTONY VAN LEEUWENHOEK
• First to observe living microbes
• His single-lens magnified 50-300X magnification
• Between 1674-1723 he wrote series of papers describing his observations of bacteria,
algae, protozoa, and fungi (Animalcules)
• ANTONY VAN LEEUWENHOEK
• III. Spontaneous Generation
• SPONTANEOUS GENERATION
• Early belief that some forms of life could arise from “vital forces” present in nonliving or
decomposing matter, abiogenesis. In other words, organisms can arise form non-living
matter.
• LOUIS JABLOT
In 1670 Jablot conducted an experiment in which he divided a hay infusion that had been boiled
into two containers: a heated container that was closed to the air and a heated container that
was freely open to the air. Only the open vessel developed microorganisms. This further helped
to disprove abiogenesis.
• REDI’S and JABLOT’S
EXPERIMENTS
• Disproved by:
– Schwann, Friedrich Schroder and von Dusch (1830s) – Air allowed to enter flask
but only after passing through a heated tube or sterile wool
– John Tyndall (1820-1893) – Omission of dust  no growth. Demonstrated heat
resistant forms of bacteria (endospores)
• LOUIS PASTEUR (1822 - 1895)
• Disproved spontaneous generation of microbes by preventing “dust particles” from
reaching the sterile broth
• In 1861 completes experiments that lays to rest spontaneous generation.
• Showed microbes caused fermentation and spoilage
• PASTEUR’S EXPERIMENT
• IV. Role of Micoorganisms in Disease
• Demonstrations that micoorganisms cause disease
• Oliver Holmes (1773 - 1843)
– showed that sepsis could be transmitted by hands of medical student and
may cause disease
– M. J. Berkeley (ca. 1845)
– demonstrated that the Great Potato Blight of Ireland was caused by a Fungus
• Louis Pasteur (1822 - 1895)
– showed that the pébrine disease of silkworms was caused by a protozoan
parasite
• Edward Jenner (ca. 1798): Develop the first Vaccine and used a vaccination procedure
to protect individuals from smallpox
• Louis Pasteur
– developed other vaccines including those for chicken cholera, anthrax, and
rabies
• History
• 1796 – First vaccine (smallpox)
Edward Jenner
• History
• 1885 - Vaccine against Rabies
Louis Pasteur
• Robert Koch (1843 - 1910),

5. – using criteria developed by his teacher, Jacob Henle (1809-1895), established
the relationship between Bacillus anthracis and anthrax.
– His criteria became known as Koch’s Postulates and are still used to establish
the link between a particular microorganism and a particular disease:
• History
• 1884 Koch’s Postulates of Disease Transmission
Robert Koch
• Koch’s Postulates
• The causative (etiological) agent must be present in all affected organisms but absent
in healthy individuals
• The agent must be capable of being isolated and cultured in pure form
• When the cultured agent is introduced to a healthy organism, the same disease must
occur
• The same causative agent must be isolated again from the affected host
• Development of Culture Media
• Why?
– To enable the isolation of pure cultures (only one type of organism)
• Especially important during Koch’s period
• Gelatin not useful as solidifying agent (melts at >28 ºC and some bacteria hydrolyze it
with enzymes)
• Fannie Hesse, the wife of one of Koch’s assistants, proposed using agar
– Not digested by most bacteria
– Melts at 100 ºC
– Used today - ~2% in solid media
• Richard Petri, another of Koch’s assistants, developed the Petri dish
• Development of Vaccines and Antisera
• Edward Jenner in 1796 discovered that cowpox (vaccinia) induced protection against
human smallpox
– Called procedure vaccination
• Vaccination:
– Inoculation of healthy individuals with weakened (or attenuated) forms of
microorganisms, that would otherwise cause disease, to provide protection,
or active immunity from disease upon later exposure.
• Pasteur and Roux reported that incubating cultures longer than normal in the lab
resulted in ATTENUATED bacteria that could no longer cause disease.
– Working with chicken cholera (caused by Pasteurella multocida), they noticed
that animals injected with attenuated cultures were resistant to the disease.
1.1 MICROBIOLOGY; The study of organisms of microscopic size (microorganism), including their
culture, economic importance and pathogenicity etc.
1.2 MICROBES Any microscopic organism; a microorganism e.g. bacteria, fungi, virus, algae and
protozoa.
1.3 MICROSCOPE It is an important scientific tool which is used for studying small objects that
are not visible to naked eyes. The resolution power of a microscope is its extent to which it can
make information or details of an object clearly visible. Different microscopes have different
resolution power.
1.4 HISTORY OF MICROSCOPE Anthony Leeuwenhoek of Holland learned how to make lenses. By
grinding and polishing, he was able to make small lenses with great curvatures. These rounder
lenses produced greater magnification. Anthony Leeuwenhoek (1632-1723) has since been called
the "Father of Microscopy". For his great contributions. Robert Hooke, also spent much of his life
working with microscopes and improved their design and capabilities
1.5 MICROSCOPY TECHNIQUES
Brightfield Microscopy –
the most elementary microscopy technique but important to understand and apply correctly.
Oil Immersion Microscopy - when used properly increases the refractive index of a
sample/specimen. oils increase refraction despite short focal lengths.
Fluorescence Microscope - study the most used microscope in medical/biological fields which
uses high powered light waves to provide unique image viewing options.
Dark Field Microscope - learn more about how when the light source is blocked off, light scatters
as it hits the specimen and is then able to reveal details otherwise difficult to see.

6. Phase Contrast Microscope - learn about an entire new world that has opened up in the field of
microscopy. Once limited to bright field illumination phase contrast observation is now a
standard feature on almost all modern microscopes.
Research Microscope- It is ordinary microscope with vertical and horizontal scale present on the
stage which can be used for research purposes.
1.6 HISTORY OF MICROBIOLOGY
Year Event
1546 Fracastoro suggests that invisible organism cause disease
1590-1608 Jansen develops first useful compound microscope
1676 Leeuwenhoek discover animalcules
1798 Jenner introduces cowpox vaccination
1838-1839 Schwann and Schleiden proposed Cell Theory
1849 Snow studies the epidemiology of cholera epidemic in London
1857 Pasteur shows that lactic acid fermentation is due to microorganism
1861 Pasteur shows that microorganisms do not arise by spontaneous generation
1867 Lister publishes his work on antiseptic surgery
1876-1877 Koch demonstrates that anthrax is caused by Bacillus antracis
1880 Laveran discovers Plasmodium, the cause of malaria
1881 Koch cultures bacteria on gelatin Pasteur develops anthrax vaccine
1882 Koch discovers tubercle bacillus, Mycobacterium tuberculosis
1884 Koch postulates first published Metchnikoff describes phagocytosis Autoclave
developed Gram Stain developed.
1885 Pasteur develops rabies vaccine Escherich discovers Escherichia coli, a cause of
diarrhea
1886 Frankel discovers Streptococus pneumonia, a cause of pneumonia
1887 Petri dish (plate) developed by Richard Petri
1887-1890 Winogradsky studies sulfur and nitrifying bacteria
1890 Von Bering prepares antitoxins for diphtheria and tetnus
1892 Ivanowsky provides evidence for virus causation of tobacco mosaic disease
1894 Kitasato and Yersin discover Yersinia pestis, the cause of plague
1897 Buchner prepare extract of yeast theferments Ross shows that malaria parasite is
carried by mosquito
1902 Landsteniner discovers blood groups
1903 Wright and other discovers antiboides in the blood of immunized animals
1905 Schaudinn and Hoffmann show Treponema pallidum causes syphilis
1906 Wassermann develops complement fixation test for syphilis
1909 Ricketts show that Rocky Mountain spotted fever is transmitted by ticks and
caused y microbe (Rickettsia rickettsia)
1910 Erlich develops chemotherapeutic agent for syphilis
1915-1917 D’Herelle and Twort discover bacterial viruses
1921 Fleming discovers lysozymes
1923 First edition of Bergey’s Manual
1928 Griffith discovers bacterial transformation
1929 Fleming discovers penicillin
1937 Chatton divides living organism into prokaryotes and eukaryotes
1944 Avery shows that DNA carries information during transformation
1946 Lederberg and Tatum describe bacterial conjugation
1949 Enders, Weller and Robbins grow poliovirus in human tissue cultures
1952 Hershey and Chase show that bacteriophages inject DNA into host cells Zinderand
Lederberg discover gernalized transduction
1953 Phase contranst microscope developed Medawar discovers immune tolerance
Watson and Crick propose the double helix structure for DNA
1955 Jacob and Wollman discover the F factor is a plasmid
1962 Porter propes the basic stuructre of immunoglobulin G first quinolone
antimicrobial (nalidixic acid) sunthesized
1975 Kohler and Milstein develops technique for the production of monoclonal
antibodies
1982 Recombinant hepatitis B vaccine developed
1986 First vaccine (hepatitis B vaccine) produced by genetic enginerring approved for
human use
1997 Discovery of Thiomargarita namibiensis, the largest known bacterium Escherichia
coli genome sequenced
2000 Discovery that Vibrio cholerae has two separate chromosomes
2002 Genome of malaria parasite, Plasmodium falicaprum, sequenced
1.7 CHARACTERISTIC OF ALL BIOLOGICAL SYSTEMS
1) the ability to reproduce
2) the ability to ingest or assimilate food substances and metabolize them for energy and growth
3) ability to excrete waste products
4) ability to react to changes in environment – irritability
5) susceptibility to mutation.
1.8 Importance of Microbes Most of the microbes are beneficent
 Escherichia coli is present in all our
 intestines, helps in digestion and also provide us with Vitamins. Minimum one bacterial cell can
produce
 1000 products. E.coli can produce 4000 products and maximum of 10,000 products have been
reported by microbes. Microbes are simply the factories which
 provide us with food. No life is possible without Microbes

7.  Out of all, only few microbes are pathogenic.
• Nomenclature and Classification of Microorganisms
• The Origin of Names
• The Greek philosopher Aristotle attempted to classify all living things as either
Plant or Animal.
1• Land Dwellers
2• Water Dwellers
3• Air Dwellers
Subsequent scientists later tried to classify living creatures by means of locomotion, grouping
butterflies and bats (flying).
• The efforts to classify living things saw great progress in the work of Carl Linnaeus, a
Swedish botanist. He developed his naming system in the middle 1700’s, which
essentially the same one we use today.
Name all known plants, animals, and minerals using Latin and Greek names.
One of his books, Systema Naturae, meaning “The Natural Classification", was published
in1735 and was based on his religious belief that one could understand God by studying his
creation.
• Today, microorganism names originate from four different sources:
• Descriptive – For example Staphylococcus aureus (grape-like cluster of spheres, golden
in color).
• Scientist’s names – e.g., Escherichia coli (Theodor Esherich), Erlichia (Paul Erlich),
Nessieria (Albert Neisser), Listeria (Joseph Lister).
• Geographic places – e.g., Legionella longbeachiae (Long Beach, California),
Pseudomonas fairmontensis (Fairmount Park, Pennsylvania).
• Organizations – e.g., Legionella (American Legion), Afipia felis (Air Force Institute of
Pathology), Cedecea spp. (Centers for Disease Control), Bilophila wadsworthia (VA
Wadsworth Medical Center in Los Angeles)
• TAXONOMY
Kingdom (American system has six: Animalia, Plantae, Fungi, Protista, Archaea, Bacteria)
• Phylum
• Class
• Order
• Family
• Genus
• Species
• Subspecies
• For example, the bacteria used in yogurt
production would be classified as follows
Kingdom: Bacteria
• Phylum: Firmicutes
• Class: Bacilli
• Order: Lactobacillales
• Family: Lactobacillaceae
• Genus: Lactobacillus
• Species: L. delbrueckii
• Subspecies: L. d. bulgaricus
• Rules of nomenclature
• USE BINARY NAMES:

8. Binary names (invented by Linnaeus), consisting of a generic name and a species epithet (e.g.,
Escherichia coli), must be used for all microorganisms. Names of categories at or above
the genus level may be used alone, but species and subspecies names (species names)
may not. In other words…never use a species name alone.
When to Capitalize – The genus name (and above) is always capitalized, the species name is
never capitalized, e.g. Bacillus anthracis.
When to Italicize - Names of all taxa (kingdoms, phyla, classes, orders, families, genera,
species, and subspecies) are printed in italics and should be underlined if handwritten; strain
designations and numbers are not. If all the surrounding text is italic, then the binary name would
be non-italic (Roman typeface) or underlined (e.g. A common cause of diarrhea is E. coli 0157, a
gram negative bacillus).
• When to use Initials
A specific epithet must be preceded by a generic name, written out in full the first time
it is used in a paper. Thereafter, the generic name should be abbreviated to the initial capital
letter (e.g., E. coli), provided there can be no confusion with other genera used in the paper. Be
careful with the “S” words; Salmonella, Shigella, Serratia, Staphylococcus, Streptococcus, etc.
• Common Names
Common names should be in lowercase roman type, non-italic (e.g., streptococcus,
brucella). However when referring to the actual genus name (or above) always capitalize and
italicize.
• Subspecies and Serovars - For Salmonella, genus, species, and subspecies names should
be rendered in standard form: Salmonella enterica at first use, S. enterica thereafter;
Salmonella enterica subsp. arizonae at first use, S. enterica subsp. Arizonae thereafter.
• Abbreviations for Species
use “sp.” for a particular species, “spp.” for several species (“spp” stands for “species plural”).
These abbreviations are not italicized; e.g. Clostridium sp. or Clostridium spp.
• Plural Forms
Plural of genus is genera
Plural of species (sp.) is species (spp.)
Plural of medium is media (never say “this culture media”)
Plural of fungus is fungi
Plural of streptococcus is streptococci (staphylococcus - staphylococci; enterococcus -
enterococci, etc)
Plural of bacillus is bacilli
Plural of bacterium is bacteria
Plural of alga is algae
Plural of protozoan is protozoa
Classification of Microorganism
The agents of human infectious diseases belong to five major groups of organisms:
1 .Bacteria
2 .Fungi,
3 .Protozoa,
4 .Helminths,
5 . viruses.
The bacteria belong to the prokaryote kingdom, the fungi (yeasts and molds) and
protozoa are members of the kingdom of protists, and the helminths (worms) are
classified in the animal kingdom. The protists are distinguished from animals and plants
by being either unicellular or relatively simple multicellular organisms. The helminths
are complex multicellular organisms that are classified as metazoa within the animal
kingdom. Taken together, the helminths and the protozoa are commonly called
parasites. Viruses are quite distinct from other organisms—they are not cells but can
replicate only within cells.

9. Chapter #02
MICRO-ORGANISMS
(A)THE BACTERIA
Bacterial Cell ;Structure & Function
The cellular world is divided into two major groups, based on whether or
not the cells have a nucleus (that is, an internal membrane-enclosed
region that contains the genetic material). Cells that have a well-defined
nucleus are called eukaryotic, whereas cells that lack a nucleus are
called prokaryotic. All bacteria are prokaryotes. In addition, bacterial
DNA is not organized into the elaborate multi chromosomal structures of
the eukaryotes, but typically is a single double-stranded molecule of
DNA. Prokaryotes and eukaryotes employ very similar metabolic pathways
to achieve cell growth and maintain viability. However, prokaryotes
synthesize substances and structures that are unique to bacteria, for
example, peptidoglycon.
Bacteria are single celled or unicellular organism.
Their cell structure is unique in that they don’t have nucleus.
Its nucleic material lies unprotected cytoplasm without the nuclear membrane.
Most organelles of bacteria don’t have organelle membrane.
Their chromosomes composed of a single closed DNA circle.
Most bacteria have cell walls.
Some bacteria survive adverse condition by forming spore a cyst.
Bacteria may occur as single cell, pair or chain of cells.
Some bacteria’s also occur as cluster of 4 or many cells.

10. Definition of “prokaryotic”
 Refers to organisms, typically 1-celled,
having cells which:
 lack a nucleus
 lack membrane-bound organelles
 contain 1 chromosome
 may contain extra-chromosomal DNA
(plasmids)
 contain 70S Ribosomes
 contain peptidoglycan cell walls
Size of Bacteria
⚫ Average bacteria 0.5 ‐ 2.0 um in diam.
⚫ RBC is 7.5 um in diam.
⚫ Surface Area ~12 um^2
⚫ Volume is ~4 um
⚫ Surface Area to Volume is 3:1
⚫ Food enters through SA, quickly reaches all parts of bacteria
⚫ Eukaroytes need structures & organelles
Bacterial cell size, shapes and arrangementsBacterial cell size,
shapes and arrangements
 Shapes of Bacteria
1. Coccus
Chain = Streptoccus
Cluster = Staphylococcus
2. Bacillus
Chain = Streptobacillus

11. Coccobacillus
3. Vibrio = curved Spirillum Spirochete
Prokaryotes – Arrangements of Cells
Prokaryotes – Arrangements of Cells
• Bacteria sometimes occur in
groups, rather than singly.
- pairs (diplococci)
- chains
(streptococ
ci)
- packets (sarcinae)
- clusters (staphylococci).
• Size, shape and arrangement of cells
often first guide in identification of a
bacterium.
Size of Different organisms