The Science of Microbiology

Eka Jaiani
2024
 Scope of Microbiology
A minor part of microorganisms is pathogenic
(disease-causing)
The practical knowledge of microorganisms is necessary
especially for medicine
Microbiology
 study of organisms too small to be seen by the naked eye.
 Usually requires a magnification tool – the microscope
• Some organisms are large though : Helminths – worms

Microbes or Microorganisms
 commonly referred to as “germs” or “bugs”
 include bacteria, viruses, fungi, algae, protozoa and helminths.
 Prions (“infectious proteins”) are recent addition.
 Microbes in Our Lives
• Microorganisms live in every part of the biosphere
– soil, water, hot springs, deep in the ocean,
"40 miles high" in the atmosphere, inside rocks etc.

• The mass of prokaryote microorganisms (bacteria and

archaea), may be as much as 0.8 trillion tons of carbon

• Viruses are by far the most abundant biological entities

on Earth and they outnumber all the others put together. They
infect all types of cellular life including animals, plants, bacteria
and fungi

“if all the 1 × 1031 viruses on earth were laid end to end, they
would stretch for 100 million light years.”
Microbes in Our Lives
Microorganisms in the environment
Photosynthetic Microbes

 Microbes are involved in photosynthesis and

accounts for >50% of earth’s oxygen.
 Also involved in decomposition and nutrient
recycling.
 Synthesis of drugs,
Beneficial Uses of Microbes hormones and enzymes

Produce industrial chemicals

For example, microbes are used to
produce acetone and butanol, and the
vitamins B2 (riboflavin) and B12
(cobalamin).

 Produce products used in manufacturing

(e.g., cellulase from Trichoderma fungus )
 disease treatment
- insulin
- antibiotics
 Making cheddar cheese
Microbes in Our Lives
 Produce fermented foods
such as vinegar, cheese,
yogurt, beer, vine, ,
sauerkraut, pickles, soy
sauce and bread The curd is chopped into small cubes to
facilitate efficient draining of whey.

 Biotechnology, the use of

microbes to produce foods and
chemicals, is centuries old
The milk has been coagulated by the
action of rennin (forming curd) and is
inoculated with ripening bacteria for
flavor and acidity. Here the workers are The curd is milled to allow even more
cutting the curd into slabs. drainage of whey and is compressed into
(a) blocks for extended ripening. The longer the
ripening, the more acidic (sharper) the
cheese.
 Cell Types

Comparative cellular structures of microbes

 The Classification of Living Things

• Living organisms are assigned to groups based

upon their similarities.

• Systematics is the discipline of identifying and

classifying organisms.
 Taxonomic Classification
Domain - the highest / largest category
3 domains
Domains- Archaea, Bacteria, Eukarya
Kingdom- there are currently five kingdoms (viruses not included)
Phylum
Class Five Kingdoms:

Order 1. Animalia

Family 2. Plantae

Genus 3. Fungi

Species 4. Protista

Subspecies 5. Monera (Archaea,

Bacteria)
 Nomenclature

 Carlous Linnaeus-1735 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.
 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. (Ex: E.
coli)
 Size of Microbes

Microbes vary in size

ranging from 10 nm
(nanometers) to 100 µm
(micrometers) to the
macroscopic.

Viruses in nm = 10-9 m

Bacteria in µm = 10-6 m

Helminths in mm = 10-3 m
 Bacteria Archaea
 Prokaryotes  Prokaryotes
 Lack peptidoglycan
 Peptidoglycan cell walls  Live in extreme
environments (extremophiles)
 Binary fission
Include:
 Ex: Escherichia coli
 Methanogens
 Extreme halophiles
 Extreme thermophiles
 Fungi Protozoa
 Eukaryotes
 Eukaryotes
 Mostly saprobes (An organism that
 Chitin cell walls
derives its nourishment from nonliving or
 Molds and mushrooms decaying organic matter) and commensals
are multicellular (Living in a relationship in which
one organism derives food or other benefits
 Yeasts are unicellular from another organism without hurting or
helping it)

 May be motile by means of pseudopod,

cilia or flagella
 Types of microorganisms

Prey

Pseudopods

(c) An ameba, a protozoan, approaching a food particle.

© 2013 Pearson Education, Inc.
 Algae Helminths
 Eukaryotes  Eukaryotes
 Cellulose cell walls  Multicellular animals
 Photosynthetic  Parasitic flatworms and
roundworms called
 Produce molecular
helminths
oxygen and organic
compounds  Microscopic stages in
life cycles
 Part of food chain
 Viruses
 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
 Prions

 Proteinaceous infectious
agents
 Causes Bovine Spongiform
Encephalopathy (BSE)
 Also causes Creutzfeldt-Jacob QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Disease (CJD)
 Microbiology – Introduction
Historical review of the Science of
Microbiology
Robert Hook – 1665 – Englishman, used a
primitive compound (two magnifying lenses)
microscope
-Reported that life’s smallest units were
little boxes – Cells,
Development of the Cell theory
of life
 Lens
Location of specimen
on pin

Specimen-positioning
Antoni Van screw
Leeuwenhoek Focusing control
1673 - probably the first
person to observe living
cells with a simple Stage-positioning screw
microscope,
-Described what we know Anton van
today as bacteria – rod Leeuwenhoek’s
shaped , spiral shaped , microscopic
observations
etc. “animalcules”
 Spontaneous generation or
biogenesis?
• 1861: Louis Pasteur demonstrated that
microorganisms are present in the air
• Pasteur’s S-shaped flask kept microbes out
but let air in
Conditions Results
Nutrient broth placed in flask, Microbial growth
heated, NOT sealed

Nutrient broth placed in flask, No microbial growth

heated, then sealed

Spontaneous generation or biogenesis?

Disproving the Theory of Spontaneous Generation.
Pasteur first poured Next he heated the neck Microorganisms did not
beef broth into a of the flask and bent it appear in the cooled solution,
long-necked flask. into an S-shape; then he even after long periods.
boiled the broth for
several minutes.

Bend prevented microbes

from entering the flask.

Microorganisms were
present in the broth.

Microorganisms were not

present in the broth after
boiling.
Microorganisms were
not present even after
long periods.
Pasteur proved that fermentation
was caused by a microbe – This killed the spontaneous
yeast generation theory.
 The Golden Age of Microbiology
• 1857–1914
• Beginning with Pasteur’s work, discoveries included immunity,
the relationship between microbes and disease, and
antimicrobial drugs

 He began the revolution in science that led to the

Golden Age of Microbiology

 1880- He discovered why vaccinations works.

avirulent bacteria could be used as a vaccine for
fowl cholera

 Developed vaccines for rabies and anthrax.

 Vaccines led to immunity to diseases that routinely

killed many people
 1840 - Ignaz Semmelweis

1867 – Lister -Aseptic

surgery
 Robert Koch

• Koch identified causative agents of

serious diseases such as anthrax
and tuberculosis
• Introduced pure culture techniques
• The first proof that bacteria actually
cause disease came from Robert
Koch in 1876.
 Flemming and Penicillium - A
Fortunate Accident

• 1928: Alexander Fleming discovered the first antibiotic

• Fleming observed that Penicillium fungus made an
antibiotic, penicillin, that killed S. aureus
• 1940s: Penicillin was tested clinically and mass produced
( Florey and Chain)
 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.
 Emerging Infectious Diseases (EID)

 Occurrence of new diseases and increasing incidence of old ones

 Factors:
- Evolutionary changes in existing organisms
- Spread of known diseases into new geographic
areas by modern transportation
- Ecological changes resulting in introduction of unusual
agents
- Emergence of antimicrobial resistance
 Normal Microbiota
• Microbes normally
present in and on the human
body are called normal
microbiota
( microflora)
• Normal microbiota
prevent growth of
pathogens
• Normal microbiota Several types of bacteria found as part of
the normal microbiota on the surface of
produce growth the human tongue
factors, such as folic
acid and vitamin K
 Relationships of microbiota with the
humans
• Symbiotic - benefits the host
• Commensal – neutral to the host
• Parasitic – injuries the host
The members of the normal flora may stay for a highly variable
periods.
Residents are strains that have an established niche at one of the
many body sites, which they occupy indefinitely.
Transients are acquired from environment and establish themselves
briefly, but tend to be excluded by competition from residents or
by innate or immune defense mechanism.
The term carrier state is used when potentially pathogenic
organism s are involved, however their implication of risk are not
always justified. 30
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A Healthy Microbiome is a Healthy You
• Inside each and every one of us, we actually have our own
microbiome. The human microbiome plays an extremely
important role in the regulation of human bodily function.
• Helps digest food
• Protects against toxins
• Boosts the immune system
• Promotes skin health
• Influences mental health

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 INTERSTING!

• Autistic populations have a unique microbiome

consisting of more clostridial species. Half of all
autistic children with gastrointestinal dysfunction
were found to have the bacteria Sutterella which
was completely absent in non-autistic children
with gastrointestinal dysfunction. There is evidence
that for some children with late-onset autism
antibiotics can alleviate symptoms temporarily.

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 Role of microbiota in defense

• Intestinal mucosal barrier function can be defined as the capacity of the intestine to host the
commensal bacteria and molecules, while preserving the ability to absorb nutrients and prevent the
invasion of host tissues by resident bacteria.
• The dense communities of bacteria in the intestine are separated from body tissues by a monolayer of
intestinal epithelial cells.
• The assembly of the multiple components of the intestinal barrier is initiated during fetal development
and continues during early postnatal life.

• Collectively, the gut microbiota also influences tissue regeneration, permeability of the
epithelium, vascularization of the gut, and tissue homeostasis.

• Pic from: http://journal.frontiersin.org/article/10.3389/fimmu.2012.00310/full 34

Tortora Chapter 1
Funke
Case The Microbial
World and You
Microbiology an
Introduction