Topic A: Organisms that make up the microbial Your introduction to microbes may have been when

world and the development of microbiology your mother warned you about germs (Your mother
pertains germs to microbes that cause diseases.
Topic A
                                                                  1.       Microbes in Our lives

Introduction:  Living things too small to be seen with the

unaided eye are called microorganisms.
                Welcome to the fascinating world of  Microorganisms are important in the
microbiology, where you will learn about creatures maintenance of an ecological balance on
so small that they cannot be seen with the naked earth.
eye. In this topic, you will learn about the meaning  Some microorganisms live in human and
of microbiology and the development of modern other animals and are needed to maintain
microbiology.                good health.
 Some microorganisms are used to produce
Microbiology foods and chemicals.
 Some microorganisms cause disease.
“Micro”
2.       Modern Developments in Microbiology
·         Very small (cannot be seen by the naked or
unaided eye) and
 Bacteriology the study of bacteria,
mycology is the study of fungi and
·         must be viewed by the microscope (an optical
parasitology is the study of parasitic
instrument used to observe very small objects).
protozoa and worms.
 Microbiologists are using genomics, the
“Biology”
study of all of an organism’s genes, to
classify bacteria, fungi and protozoa.
·         “bios” - living organisms
 Immunology is the study of immunity.
·         “logy” - the study of Vaccines and interferons are being
investigated to prevent and cure viral
·         Is the study of living organisms. disease.
 The use of immunology to identify some
Includes the study of: bacteria according to serotypes (variants
within a species) was proposed by Rebecca
Lancefield in 1933.
 nonliving entities as well as
 The study of AIDS, analysis of the action of
 living organism  are called microbes or
interferons, and the development of new
microorganisms
vaccines are among the research interest in
immunology.
MICROBIOLOGY
 New techniques in molecular biology and
electron microscopy have provided tools for
 the study of microbes or microorganisms advancement of our knowledge of virology.
 The branch of biology that studies  Virology is the study of viruses.
microorganisms and their effects on humans.   Recombinant DNA is DNA made from two
different sources. In the 1960s, Paul Berg
 Q: Who introduced you to Microbiology? inserted animal DNA into bacterial DNA
and the bacteria produced an animal
 A: “Don’t touch that, its dirty”. Its full of germs! protein.
 
  Recombinant DNA technology or genetic 3.       Respond to stimuli in the external
engineering involves microbial genetics and environment
molecular biology.
 The development of recombinant DNA 4.       Reproduce and pass on their organization to
technology has helped advance all areas of their offspring
microbiology.
 Using microbes 5.       Evolve and adapt to the environment
 George Beadle and Edward Tatum showed
that genes encode a cell’s enzymes (1942)  Taxonomy: Naming, Classifying and Identifying
 Oswald Avery, Colin MacLeod, and Microorganisms
Maclyn McCarty showed that DNA was the
hereditary material (1944).      Taxonomy
 Francois Jacob and Jacques Monod
discovered the role of mRNA in protein      The science of classifying living beings or
synthesis (1961).
  Latest trend is the study of coronavirus       The systematic classification of living
disease 2019 (Covid-19), previously known organisms
as novel coronavirus 2019.  The Covid - 19
virus AKA Severe Acute Respiratory Nomenclature
Syndrome coronavirus 2 (SARS-CoV 2)
understanding its mode of transmission,  The system of naming things
structures, life span, formulating vaccine
and finding medications to cure the said Naming and Classifying and Identifying
disease Microorganisms

TOPIC B: Microorganisms  The system of nomenclature for organisms

TOPIC B in use today was established in 1735 by:
                                
    - Carolus Linnaeus (Carl Von Linné) 1701-1778
Introduction:
     - Swedish botanist
                Let us all discover the uniqueness of the
microbial world!  In this topic, you will learn about      - Laid down the basic rules for classification
the microorganisms and how they are being
classified.      - Established taxonomic or taxa (singular –
taxon)
Topic Contents:
      - Scientific names are latinized (because Latin
Microorganisms language was traditionally used by scholars)

 Microorganisms are organisms that are too       - Each organism has two names: the genus and
small to be seen with the unaided eye. specific epithet.
 “Germ” refers to a rapidly growing cell.
 Taxonomic Classification
 5. Characteristics of Life
  Man Cat
1.       Cells Kingdom Animalia Animalia
Phylum Chordata Chordate
2.       Maintain structure by taking up chemicals Class Mammalia Mammalia
and energy from the environment Order Primate Carnivora
Family Hominidae Felidae    ·         Staphylococcus aureus and Eshcerichia coli
Genus Homo Felis
species sapien domestica    ·         are found in the human body on skin and E.
coli in the large intestine.
 
 - After the first use, scientific names may be
Scientific names
abbreviated with the first letter of the genus and the
specific epithet:
- The method of assigning scientific or specific
name is called binomial (2-name) system of
    > Staphylococcus aureus - S. aureus
nomenclature
    > Esherichia coli - E. coli
- Each organism has two names:
CLASSIFICATION SYSTEM
   > First name – generic name (genus/genera)
- Five-Kingdom System of Classification
      ·   always capitalized
   > In 1969, Robert H. Whittaker proposed a Five-
   > Second name – species name (specific epithet)
Kingdom System of Classification, in which all
organisms are placed into 5 kingdoms:
     ·   Always not capitalized or
1)      Bacteria and Archaea are in the Kingdom
     ·   Lowercase letter
Procaryote (or Monera)
- Both should be italicized (or underlined if italics
2)      Algae and Protozoa are in the Kingdom of
are not available
Protista (referred to as protists)
- Are “Latinized” and used worldwide.
3)      Fungi are in the Kingdom of Fungi
 May be by:
4)      Plants are in the Kingdom Plantae
- Describes an organism
5)      Animals are in the Kingdom
animalia (humans are in the Kingdom of Animalia)
 Staphylococcus aureus or Staphylococcus
aureus  - Viruses are not included in the Five-Kingdom
 Describes the clustered arrangement of the system of Classification because they are not living
cells (staphylo)- Gr. staphule (bunch of cells; they are acellular.
grapes – describes the clustered arrangement
of the cell);  - Each kingdom consists of divisions or phyla then
 kokkus (berry – indicates that they are divided into classes, orders, genera and species
shaped like spheres) and
 Golden – the color of this bacterium or its  - Popular only for 30 years
colony.
 Three-Domain System of Classification
- Honor a researcher
- In the late 1970s, Carl R. Woese devised a Three-
 Escherichia coli Domain System of Classification
 Honors the discoverer, Theodor
Eshcerich, bacteriologist   ·         2 Domains of procaryotes

- Identify the habitat of a species

  Archaea – archae meaning “ancient”; cell walls, if  2)      Archaea
present, lack peptidoglycan
· Prokaryotic
 2 phyla · Lack peptidoglycan
Bacteria – eubacteria meaning “true”; now · Live in extreme environments
as simply as bacteria; cell walls contain a · Include: Methanogens, Extreme
protein-carbohydrate complex called halophiles, Extreme thermophiles
peptidoglycan)
 23 phyla 3)      Fungi

·         1 Domain · Eukaryotes (having true cellular

cell)
Eucarya – include all eucaryotic organisms · Chitin cell walls
· Use organic chemicals for energy
        Includes: · Molds and mushrooms are
multicellular consisting of
 Protists – slime molds, protozoa, and algae masses of mycelia, which are
 Fungi – unicellular yeasts, multicellular composed of filaments called
molds, and mushrooms hyphae
· Yeasts are unicellular
 Plants – mosses, ferns, conifers and
flowering plants
 4)      Protozoa
 Animals – worms, insects and vertebrates 
· Eukaryotes
  2 Major Categories of Microbes
· Absorb or ingest organic
chemicals
1)      Acellular microbes – also called infectious
· May be motile via pseudopods,
particles. It includes viruses and prions.
cilia, or flagella
2)      Cellular microbes – also called
microorganisms. Include all bacteria, all archaea, 5)      Algae
some algae, all protozoa and some fungi.
· Eukaryotes
    Types of Microorganisms · Cellulose cell walls
· Use photosynthesis for energy
1)      Bacteria · Produce molecular oxygen and
organic compounds
· Unicellular
· No nucleus 6)      Viruses
· Prokaryotes
· Acellular
      3 major basic shapes of bacteria are · Consist of DNA or RNA core
· Core is surrounded by a protein
coat
 Bacillus
· Coat may be enclosed in a lipid
 Coccus envelope
 and spiral · Viruses are replicated only when
· Peptidoglycan cell wall they are in a living host cell
· Divide by Binary fission
· For energy, use organic    Multicellular Animal Parasites
chemicals, inorganic chemicals,
or photosynthesis
 The principal groups of multicellular animal  Part-time bad guys
parasites are flatworms and roundworms,
collectively called helminths. Pathogens
 The microscopic stages in the life cycle of
helminths are identified by traditional  §  Microbes that cause disease
microbiological procedures.  §  Infectious agents
 §  Full-time bad guys
Normal Microbiota
Cause two categories of disease:
 Normal microbiota prevents growth of
pathogens.  Infectious diseases
 Normal microbiota produces growth factors
such as folic acid and vitamin K. Result when a pathogen colonizes (inhabits) the
 Resistance is the ability of the body to ward body and subsequently causes disease; causes more
off disease. illnesses and death
 Resistance factors include skin, stomach
acid, and antimicrobial chemicals.  Microbial intoxications
 Indigenous microflora/microbiota (old
name normal flora) Results when a person ingests a toxin  (poisonous
 The microbes that live on and in the human substance) that has been produced by a microbe in
body are referred to as our indigenous vitro (outside the body).
microflora.
 §  We have, living on and in our bodies (e.g.  
on our skin and in our mouths and intestinal
tract) INFECTIOUS MICROBIAL
DISEASE INTOXICATION
Non-pathogens A pathogen A pathogen
Opportunistic pathogens (or opportunists) colonizes a produces a toxin in
person’s body vitro
 Do not cause disease under ordinary ↓ ↓
conditions, but have the potential to cause
The pathogen A person ingests
disease should the opportunity present itself
causes the toxin.
 Some of the microbes that colonize (inhabit)
our bodies a disease. The toxin causes a
 Although these microbes usually do not disease.
cause us any problems, they have the
↓ ↓
potential to cause infections if they gain
access to a part of our anatomy where they This type of This type of disease
do not belong (e.g. a bacterium disease is is known as
called Escherichia coli (E. coli) lives in our known as an a microbial
intestinal tracts. This microorganism does infectious intoxication
not cause us any harm but can disease if it disease
gains access to our urinary tract infection,  
blood stream or wound.
 Other will strike when a person becomes Emerging Infectious Diseases
run-down, stress-out, or debilitated
(weakened) as a result of some disease or  When a pathogen overcomes the host’s
condition. (e.g. Candida albicans is resistance, disease results.
indigenous microbiota of our genital area
  Emerging Infectious Diseases (EID): New · A new disease involving
diseases and diseases increasing in respiratory symptoms was seen
incidence in the U.S. in 1995
· The U.S. virus, called Hantavirus
West Nile encephalitis Sin Nombre virus, probably
came to the U.S. with rats around
· West Nile Virus 1900
· First diagnosed in the West Nile
region of Uganda in 1937. Acquired immunodeficiency syndrome (AIDS)
· Appeared in New York City in
1999. · Human immunodeficiency virus
(HIV)
Bovine Spongiform Encephalopathy · First identified in 1981.
· Worldwide epidemic infecting 40
· Prion million people; 14,000 new
· Also causes Creutzfeldt-Jakob infections every day.
disease (CJD) · Sexually transmitted disease
· New-variant CJD in humans affecting males and females.
related to cattle fed sheep offal · In the U.S., HIV/AIDS in people
for protein. 13-24 years of age: 44% are
female and 63% are African
Escherichia coli O57:H7 American.

· Toxin-producing strain of E. coli Anthrax

· Fist seen in 1982
· Leading cause of diarrhea · Bacillus anthracis
worldwide. · In 1877, Koch proved B.
anthracis causes anthrax.
 Invasive group A Streptococcus · Veterinarians and agricultural
workers are at risk of cutaneous
· Rapidly growing bacteria cause anthrax.
extensive tissue damage. · In 2001, dissemination of B.
· Increased incidence since 1995 anthracis via mail infected 22
people.
Ebola hemorrhagic fever
SARS (Severe Acute Respiratory Syndrome)
· Ebola virus
· Causes fever, hemorrhaging, and · SARS coronavirus (SARS-CoV
blood clotting or SARS-CoV 1)
· First identified near Ebola River, · virus identified in 2003.
Congo · SARS-CoV is thought to be an
· Outbreak every few years animal virus from an as-yet-
uncertain animal reservoir,
Hantavirus pulmonary syndrome perhaps bats, that spread to other
animals (civet cats)
· first infected humans in the
· Hantavirus
Guangdong province of southern
· Fist identified in 1951 in Korea
China in November 2002.
as cause of hemorrhagic fever
and named for Hantaan River
Other countries/areas in which chains of
human-to-human transmission occurred after early
importation of cases were Toronto in Canada, Hong 4.       Protozoology – the study of protozoa and
Kong Special Administrative Region of China, their activities.
Chinese Taipei, Singapore, and Hanoi in Viet Nam
until end of July 2003 5.       Phycology or Algology – the study of
various types of algae.
MERS (Middle East respiratory syndrome)
 
· Middle East respiratory
syndrome coronavirus, or
MERS‐CoV)
· first identified in Saudi Arabia in FIELDS OF MICROBIOLOGY
2012.
· Although most of human cases of 1.       Agricultural Microbiology
MERS-CoV infections have been
attributed to human-to-human  Agricultural microbiology is an excellent
infections in health care settings career field for individuals with interests in
· Dromedary camel is the major agriculture & microbiology. Included in the
reservoir host for MERS-CoV field of agricultural microbiology are studies
and an animal source of MERS of the:
infection in humans.  beneficial and harmful roles of microbes in
· However, the exact role of soil formation & fertility;
dromedaries in transmission of  in carbon, nitrogen, phosphorus, and sulfur
the virus and the exact route(s) of cycles;
transmission are unknown.  Immunology – the study of complex web of
· Approximately 35% of reported immune responses to infection by
patients with MERS-CoV microorganisms. It also concerns itself with
infection have died. the study of autoimmunity and
· Largest outbreaks seen in Saudi hypersensitivity, inappropriate immune
Arabia, United Arab Emirates, responses that can be harmful to human
and the Republic of Korea. host.

COVID – 19 (Coronavirus disease 2019) In diseases of plants;

·         Newly discovered coronavirus disease · in the digestive processes of
cows and other ruminants; and in
·  the production of crops and
foods.
Topic C: Division of Microbiology
  Many different viruses, bacteria, and fungi
Topic Contents: cause plant diseases.
DIVISION OF MICROBIOLOGY
· A food microbiologist is
concerned:
1.       Bacteriology – the study of the structure,
· with the production,
functions and activities of bacteria
· processing,
· storage,
2.       Virology – the study of viruses and their · cooking,  
effects on living cells of all types. · serving of food,
· as well as the prevention
3.       Mycology – the study of fungi · of food spoilage, food poisoning,
and food toxicity.
 · partially accomplished by bacteria in the
holding tanks of sewage disposal plants, in
A dairy microbiologist oversees the: which feces, garbage, and other organic
materials are collected and reduced to
· grading, harmless waste.
· pasteurization &  Some microorganisms, such as the iron- and
· processing of milk and cheeses sulfur-utilizing bacteria even break down
metals and minerals. Bioremediation
involves the use of microorganisms to clean
up after ourselves—that is, to clean up
To prevent: landfills and industrial and toxic wastes.
 The beneficial activities of microbes affect
 contamination, every part of our environment, including
 Spoilage and soil, water, and air. Environmental
 Transmission of diseases from microbiology and bioremediation are
environmental, animal & human sources. excellent career fields for individuals with
interests in ecology and microbiology.
2.       Biotechnology (Industrial Microbiology)
4.       Microbial Genetics and Genetic
Engineering
 The use of microorganisms in industry—
is an excellent career field for individuals
with interests in industry and  Microbial genetics involves the study of
microbiology.  Many businesses and microbial DNA, chromosomes, plasmids,
industries depend on the proper growth and genes. (Plasmids are small, circular
and maintenance of certain microbes to molecules of extrachromosomal DNA.
produce:  Genetic engineering involves the insertion
 beer, of foreign genes into microorganisms
 wine, (usually into bacteria or yeasts). These
foreign genes may come from any other
 alcohol, and
organism (e.g., another microorganism, an
 organic materials such as enzymes,
animal, or even a plant).
vitamins, and antibiotics.
 The primary purpose of inserting a foreign
gene into a microorganism is to create a
 Industrial microbiologists monitor and
microbe that is capable of either producing a
maintain the microorganisms that are essential for
product of importance to us or
these commercial enterprises. Applied
accomplishing some task of importance to
microbiologists conduct research aimed at
us. Genetically Modified Organisms
producing new products and more effective
(GMOs).
antibiotics.
 Genetic engineering has applications in
agricultural, environmental, industrial, and
3.       Environmental Microbiology and
medical microbiology. The intestinal
Bioremediation
bacterium, Escherichia coli, has been used
extensively in microbial genetics, genetic
 The field of environmental microbiology, or engineering, and microbial physiology.
microbial ecology, has become increasingly  Microbial genetics and genetic engineering
important in recent years because of are excellent career fields for individuals
heightened awareness and concern about with interests in genetics and microbiology.
dangers to the environment.
 Environmental microbiologists are 5.       Microbial Physiology
concerned about water and sewage
treatment. The purification of waste water is
 Research in microbial physiology has microflora—the viruses and bacteria that
contributed immensely to our understanding of the live on or in the human body.
structure and functions of microbial cells. What  §  However, the field of parasitology
microbiologists learn about microbial cells quite involves only the following three categories
often applies to cells, in general. Microbial of parasites: parasitic protozoa, helminths
physiology is an excellent career field for (parasitic worms), and arthropods
individuals with interests in biochemistry and (specifically, certain insects and arachnids).
microbiology. A parasitologist studies these organisms and
their life cycles in an attempt to discover the
best ways to control and treat the diseases
that they cause.

6.       Paleomicrobiology
8.       Sanitary Microbiology
 The field of paleomicrobiology involves the
study of ancient microbes. Although life is  The field of sanitary microbiology includes
thought to have originated between 3.7 and the processing and disposal of garbage and
4 billion years ago, there are no cellular sewage wastes, as well as the purification
fossils available from that time period. But and processing of water supplies to ensure
there are molecular fossils—molecules that no pathogens are carried to the
(usually lipids) known to be made only by consumer by drinking water.
organisms or, in some cases, only by  Sanitary microbiologists also inspect food
particular organisms. Finding such processing installations and eating
molecular fossils in ancient rocks serves as establishments to ensure that proper food
evidence that life existed at that time. handling procedures are being enforced.
 The earliest molecular fossils date back to
between 3.7 and 4 billion years ago. Some 9.       Veterinary Microbiology
paleomicrobiologists examine and study
skeletons and mummified human remains to  A wide variety of microbes—including
determine the infectious diseases that viruses, bacteria, fungi, and protozoa—
occurred in ancient civilizations. Such cause infectious diseases in animals. Control
studies often involve the recovery of of such diseases is the concern of veterinary
microbial DNA from bone and mummified microbiologists.
tissue samples.  The production of food from livestock, the
  For example, finding Mycobacterium raising of other agriculturally important
tuberculosis DNA in Egyptian mummies has animals, the care of pets, and the
revealed that tuberculosis existed as far back transmission of diseases from animals to
as 3000 BC. Paleomicrobiology is an humans are areas of major importance in
excellent career field for individuals with this field. Infectious diseases of humans that
interests in anthropology, archaeology, and are acquired from animal sources are called
microbiology. zoonoses or zoonotic diseases. Veterinary
microbiology is an excellent career field for
7.       Parasitology a person who is fond of animals and
microbiology.
 §  Technically, any organism that lives on or
in another living organism is called a Newest Specialty Profession of Microbiology
parasite. It would seem, then, that the term
parasite would apply to all of the 10.   Geomicrobiology – which focuses on the roles
microorganisms of our indigenous of microbes play in the earth’s crust.
11.   Marine microbiology – a study of oceans and 4.       Some microorganisms are saprophytes
its smallest inhabitant (decomposers of waste products and dead
organisms).
12.   Astromicrobiology – which studies the
potential for microbial life in space. 5.       Microorganisms also play important roles in
certain elemental cycles (e.g. the nitrogen cycles)
and in the breakdown of organic substance to
release plant nutrients like nitrates and phosphates
which are the sources of fertilizers.

6.       Microbes that are pathogenic to insects are

alternatives to chemical pesticides to prevent insect
damage to agricultural crops and disease
transmission.

Topic D: Significance and Practical Applications 7.       Bacillus thuringiensis infections are fatal in
of Microbiology many insects but harmless to other animals
including humans and to plants.
Topic Contents:
8.       Some microorganisms are used in the
SIGNIFICANCE OF MICROBIOLOGY production of useful substances like insulin and
interferon, through the process known as genetic
“Why do we need to study microbiology?” engineering.

Although they are very small, microbes play 9.       Missing or defective genes in human cells can
significant roles in our lives Listed below are few of be replaced in gene therapy.
the many reasons to take a microbiology course and
to learn about microbes: 10.   Genetically modified bacteria are used to
protect crops from insects and freezing.
1.       About a thousand or more species of
microorganisms inhabit the human body and are 11.   Some microorganisms and their products such
collectively referred to as normal flora (microflora as toxins are also potential biological warfare
or indigenous flora) and can be pathogenic (capable agents.
of causing diseases) or non-pathogenic.

2.       Some microorganisms are essential in

biotechnology, e.g. in the production of foods and
beverages.

3.       Some microorganisms, especially bacteria

and fungi are sources of antibiotics.

 Penicillin
 Mold
 Penicillium notatum
 1928 - Alexander Fleming

Beneficial Uses of Microbes