Introduction to microbiology.

Classification and nomenclature of

microorganisms.

03.02.16
Course Introduction

Department of Microbiology,
Virology and Immunology

E-mail:
cojocari_daniela@yahoo.com
 Course objectives

List major groups of microorganisms and

their habitats.

Overview and history of Microbiology.

Describe the system of scientific

nomenclature used to name
microorganisms.
 Definition
Microbiology (mikros bios logos
small, live, study) study
microorganisms and their activities.

Microbiology is the study of

microorganisms usually less than
1mm in diameter which requires
some form of magnification to be
seen clearly.

Microbiology - study the organisms

that can exist as single cells, contain
a nucleic acid genome for at least
some part of their life cycle, and are
capable of replicating that genome
themselves or getting replicated with
the help of host cells
 Microbial World
Age(3,5 billion
years).
Abundance and
diversity: 60% of
biomass;
water, soil and air;
Over 4000 species
have been
described
 Microbiology Studies
Shape( morphology);
Structure, nutrition;
Growth and multiplication;
Follow relationships of m\o with host and
environment
 Branches of
Microbiology
Bacteriology: study of bacteria
Mycology: study of fungi
Virology: study of viruses
Beijerinck, NE: discovered intracellular
reproduction of TMV; coined the term
virus (1899)
Parasitology:study of protozoa and
parasitic worms
 Branches of
Microbiology
Immunology: study of immunity
Edward Jenner, UK: developed vaccination (1798)
Metchnikoff, RU: discovered phagocytes (1884)
Paul Ehrlich, DE: theory of immunity (1890)
Chemotherapy
Treatment of disease by using chemical means
Antibiotics produced naturally
Synthetic drugs
Paul Ehrlich (1878) used arsenic compounds
to fight disease
 Branches of
Microbiology
Chemotherapy
Alexander Fleming, Scotland (1928) discovered
penicillin
Selman Waksman, Ukraine (1944) discovered
streptomycin
Problems
Toxicity of drugs => Selective toxicity
Resistance of bacteria to drugs
 Microorganisms are
everywhere, but why is so
important to learn about
them?

Affect our lives in many

different ways.
 Microbes are capable of growing in a wide
variety of environments.

Bacteria will grow in frigid glaciers to

boiling volcanic springs, dry sands to the
open ocean.
 IMPORTANCE OF
MICROORGANISMS

Microorganisms are the oldest forms of life.

Nutrient production & energy flow
Production of foods
Decomposition (bioremediation)
Without certain microorganism life could not exist;
produce O2 and N2
Production of drugs & vaccines
Genetic engineering
Causing disease
Microorganisms have killed more people than have ever
been killed in war.
 Why Study Medical
Microbiology?
The majority of serious diseases in humans (especially those of
early childhood) are due to microbial infections.

Prior to the discovery of antibiotics and vaccines, a large

proportion of children died before adulthood because of
infectious disease.

Till 1900, the average life expectancy in the United States was 40
years of age.

In 2000 - 80 years, largely due to the near eradication of most

serious early childhood diseases.

This trend is seen in the gap between developed and developing

countries in terms of causes of death (mortality).
 MICROBES
MICROBES includes all those living
organisms that can not be viewed (seen)
in any detail by the human eye.

Alternatively, a MICROBE is any living

creature that must be examined with a
magnifying lens in order to see its unique
physical characteristics (size, shape,
motility, color).
 Microbes
Pathogen or pathogenic - capable of producing
disease.
Though only a minority of microorganisms are pathogenic,
practical knowledge of microbes is necessary for their treatment
so is highly relevant to medicine and related health sciences.
Normal flora [normal microbiota] - not typically-
disease-causing
microorganisms normally found in and on healthy individuals.
on the skin,
in the eyes,
in the nose,
in the mouth,
in the upper throat,
in the lower urethra,
in the lower intestine.
A, Influenza virus;
B, West Nile
Virus;

C, Staphylococcus aureus;
D, Streptococcus
pneumoniae.
Microbiologists may be interested in
various characteristics or activities of
microbs and may study:

Microbial morphology
Microbial cytology
Microbial physiology
Microbial ecology
Microbial genetics and molecular biology
Microbial taxonomy
Classification of life
 Formany years, living organisms were
divided into two kingdoms:

Animalia (animal) and

Plantae (vegetable).
Classification Schemes
Two kingdoms

Plantae

Plantae Animalia
 But after 1800s, scientists realized that these
two kingdoms could not adequately express the
diversity of life.

Since the 1960s, the most widely used scheme -

five kingdoms.

Viruses are separate group of biological entities,

although not organisms in the same sense as
Eukaryotes, Archaea and Bacteria.
 Classification schemes,
5 kingdoms

Plantae

Monera Protista Plantae Fungi Animalia

Prokaryotes

Domain Domain Eukaryotes

Bacteria Archaea
(Eubacteria) (Archaeabacteria)
 Classification of Life

3 major Domains of
life
Bacteria
Archaea
Eukaryota (Eukarya)
The first two are Prokaryotes
(Bacteria and Archaea)-
without true nucleus, while
the Eukaryotes all have a true
nucleus in each cell.

The 3 Domains. Source:

http://www.ucmp.berkeley.edu/alllife/images/domains_small.gif
 Kingdom Monera

All organisms in the Kingdom Monera are prokaryotes.

lack nuclei and organelles
most of their cell walls are made of peptidoglycan (the exceptions
are the archaebacteria).

The archaebacteria have cell walls that lack peptidoglycan, cell

membranes that utilize different lipids, and ribosomes similar to
those found in eukaryotes.

The bacteria (eubacteria-true bacteria) are characterized by how

they metabolize resources, their means of motility, and their
shape.

Most organisms in the Kingdom Monera reproduce through

binary fission (asexual) or conjugation (sexual).
 Bacteria
Most utilize flagella for movement.

Digestion is extracellular (outside the cell) and

nutrients are absorbed into the cell.

Circulation and digestion in Kingdom Monera is

accomplished through diffusion.
 Taxonomy
Taxonomy is the classification of organisms. The
most common system in use today is the Five
Kingdoms:
Monera (Prokaryota),
Protista,
Fungi,
Plantae, and
Animalia.

Organisms in each kingdom are divided into phyla.

In each phylum, organisms are separated into classes.
In each class, organisms are segregated into orders.
In each order, organisms are divided into families.
In each family, organisms are separated by genus.
And finally, in each genus organisms are divided into species.

Just remember that King Philip Can Order For Genial Students.
 Prokaryotes
Kingdom - Monera
Domain - Bacteria
Phylum Proteobacteria
Class Gammaproteoba
Order Enterobacteriale
Family Enterobacteriace
Genus Escherichia
Species Escherichia coli
Naming micoorganisms

Binomial (scientific) nomenclature

Gives each microbe 2 names

Genus - noun, always capitalized and may be
abbreviated
species - adjective, lowercase, never abbreviated
A genus name may be used alone to indicate a genus
group; a species name is never used alone
eg: Bacillus subtilis
B. subtilis

Both italicized or underlined

Staphylococcus aureus (S. aureus)
Bacillus subtilis (B. subtilis)
Escherichia coli (E. coli)
 Nomenclature

Common or descriptive names

(trivial names)
Names for organisms that may be in
common usage, but are not taxonomic
names
eg: tubercle bacillus
(Mycobacterium tuberculosis)
meningococcus
(Neiserria meningitidis)
Group A streptococcus
(Streptococcus pyogenes)
Bacterial Classification

by

Metabolism
Morphology (shape)
Staining, etc
According the shapes:
cocci (spherical),

bacillus (rod shaped), and

spirillum (spirals).

polymorph
Classification of bacteria
Cocci
Micrococcus
Staphylococci
Irregular clusters of cocci
Diplococci
Pairs of cocci
Streptococci
Chains of cocci
Classification of bacteria
Bacilli
Rod like
Diplobacilli
Pairs of bacilli
Streptobacilli
Chains of bacilli

Spirochetes
Spiral
 Size of bacteria

Unit of microbial
measurement
micrometers (um)
1 um being 10-6 m or
0.000001 m(1/25,000
inch)
nanometers
1 nm being 10-9 or
0.000000001 m.

Pathogenic bacterial
species vary from
approximately 0.4 to 2
um in size
Eukaryotes
 "The role of the
infinitely small in
nature is infinitely
large"
Louis Pasteur
Historical Perspectives
 Microbiology
Descovery Era (spontaneous generation)
Aristotle(384-322) and other believed that living organisms
could develop from non-living materials.
Antonie van Leeuwenhoek ( 1632-1723) he observed m/o as
animalcules
Transition Era
Francesco Redi (1626-1697),Lazzaro Spallanzai (1729-1799) he
demonsrated that air carried germs to the medium
Golden Era
Louis Pasteur, Lord Josef Lister,Robert Koch,Eduard Jenner,.
Modern Era
Nobel laureates (1900-2014.)
 Historical
YEAR NAME ACHIEVEMENT
1st century BC Varo Concept of Animalia
minuta
1546 Fracostorius Contagion- Cause of
syphilis
1590 Jensen Hand lens
1683 Antony van First Microscope
Leeuwenhoek Animalcules
1678 Robert Hook Compound microscope
1745 Needham (Priest) Abiogenesis
1836 Schulze & Schwan Air contains microbes
1840 Oliver Homes, Poet Contageousness &
physician Puerperal fever
1846 Ignaz Semmelweis Cause, concept &
prophylaxis of child-bed
fever
1853 Augustino Bassi Silk worm disease due to
a fungus
 Pioneers of
Microbiology
Robert Hooke, UK (1665)
Proposed the Cell Theory
Observed cork with crude microscope
All living things are composed of cells
Spontaneous generation
Some forms of life could arise spontaneously from
non-living matter
Francesco Redi, IT (1668)
Redis experiments first to dispprove S.G.
Antonie van Leeuwenhoek

First to observe living

microbes
his single-lens
magnified up to 300X

(1632-1723)
 Louis Pasteur
French chemist
Father/Founder of Modern
Microbiology
Fermentation a
microbiological process
Beer/Wine not produced
without microbes
Showed microbes caused
fermentation & spoilage
Disproved spontaneous
generation of m.o.
Developed aseptic techniques.
Developed a rabies vaccine.

(1822-1895)
 Louis Pasteur 1822-95
Methods & Techniques of cultivation
Introduced sterilization
Tyndalization (Tyndal-1877)
Studied Silkworm disease, anthrax,
chicken cholera, hydrophobia.
Introduced live vaccines Jenner (Cow-
pox vaccine)
Antirabic vaccine
Pasteur Institutes
 Joseph Lister 1867

Prof of Surgery,
Glasgow Royal
Infirmatory
Introduced Antiseptic
Surgery
Called Father of
Antiseptic Surgery
 Robert Koch
German general practitioner
Perfected bacteriological
techniques
Isolated pure cultures of
bacteria for the first time
Discovered Anthrax bacilli,
Cholera vibrio, M. tuberculosis
Father of Medical Microbiology
Hypersensitivity
Established a sequence of
experimental steps to show
that a specific m.o. causes a
particular disease.

(1843-1910)
 Highlights in the History of
Microbiology
1887 1900
Invented Petri Dish Proved mosquitoes carried

(R.J. Petri) the yellow fever agent

(Walter Reed)
1892
Discovered viruses (Dmitri
1910
Iosifovich Ivanovski) Discovered cure for syphilis
1899 (Paul Ehrlich)
Recognized viral 1928
dependence on cells for Discovered Penicillin
reproduction (Martinus (Alexander Fleming)
Beijerinck)
 Highlights in the History of
Microbiology
1977
Developed a method to
sequence DNA (W. Gilbert
& F. Sanger)
1983
Polymerase Chain Reaction
invented (Kary Mullis)
1995
First microbial genomic
sequence published (H.
influenzae) (TIGR)
 Kochs postulates
The organism must be present in every case of the
infectious disease.
It should be possible to isolate the organism in
pure culture from the lesion.
Inoculation of the pure culture into suitable lab
animal should produce a similar disease.
It should be possible to re-isolate the organism in
pure form from the lesions produced in the
experimental animal.
Specific antibodies to the organism should be
demonstrable in patients suffering from the
disease.
 Microbiological methods of
diagnosis
Direct: diagnosis consists in detecting the
pathogen, its components in samples of the patient or
environment.
1) Microscopical-purpose is to study tinctorial
character and shape of m\o.
2) Bacteriological-purpose is isolation and final
identification of m\o.
3) Biological-purpose reproduction of infection in
laboratory animals.
4) Identification of DNA and RNA of m\o using
biological technique.
 Microbiological methods of
dagnosis
Indirect: immunological
1) Serodiagnosis-purpose is to determine Ab
.
2) Allergical-purpose is to determine
hypersensitivity to differents allergens.
 Preparaing a Smear Colonies Isolated from
Agar Surfaces
Place one or two loopfuls of water on the
slide.

Usingan inoculating needle, mix a very

small quantity of the colony with the water
and spread over the slide. It is critical that
microbes are separated from each other
during this step.

Air
drying and heat fixation are performed
as described above.
 Preparaing a Smear from a Liquid Medium
Spread one or two loopfuls of the liquid
over a large area of a clean slide.
Allow the liquid to evaporate ("air dry")
prior to fixation. This attachment process
is accomplished by passing the slide over
the flame of a Bunsen burner two or three
times. Because the slide may become hot,
it is advisable to use a slide holder. Be
careful, however, not to incinerate the
organisms on the slide. Proper fixation
does not require extremely prolonged
exposures to heat.
There are two methods of preparing a
smear, as you may be using organisms
from either a slant or a broth.

If organisms are in broth, you will use a

loop. Put two loopfuls of organisms on
clean slide and skip the next two steps.
 Iforganisms are on a slant, add two
loopfuls of water to clean slide.

Use a needle to transfer organisms from

slant to slide.Note: Do NOT transfer agar!
 Emulsify (mix) organisms with the water
on the slide

A quick way to dry your slide is to lay it on

top of your microscope light.
 Heatfix the slide gently by waving it 4-5
times over a flame.
 Simple stain techniques. Staining can be
performed with basic dyes such as crystal
violet or methylene blue, positively charged
dyes that are attracted to the negatively
charged materials of the microbial cytoplasm.
Such a procedure is the simple stain
procedure. An alternative is to use a dye such
as nigrosin or Congo red, acidic, negatively
charged dyes. They are repelled by the
negatively charged cytoplasm and gather
around the cells, leaving the cells clear and
unstained. This technique is called
the negative stain technique.
 Differential stain
techniques. The differential stain
technique distinguishes two kinds of
organisms. An example is the Gram stain
technique. This differential technique
separates bacteria into two groups,
Grampositive bacteria and Gramnegative
bacteria.
Another differential stain technique is
the acidfast technique. This technique
differentiates species of Mycobacterium from
other bacteria.