Microbiology- I

Omer Ali Hassen

MSc Medical Microbiology, Mekelle University, Ethiopia
Tel: +252-63-4420144
omarh431@gmail.com
 Introduction
DEFINITIONS
Microbiology
 The study of organisms, called microorganisms,
which are too small to be perceived clearly by
the unaided eye
 The study of microscopic organisms.
Three Greek words:
Micros – small
Bios – life
Logos – science
Scope

Direct observation of MOs await the

development of the microscope

Limits for Human eye < 30 μm in Ø (1 μm =10-3 mm)

Very little details perceived Ø < 1 mm.

◦ Any organisms Ø < 1mm microorganism

 Intro…..
Microorganisms included:

Prokaryotes
Bacteria Bacteriology
Diverse group (Rickettsia – Cyanobacteria)
Eukaryotes
Protozoa - Protozoology
Fungi - Mycology
Algae – Phycology
Viruses - Virology
Acellular, Intracellular
Parasites at the genetic level
Intro…..
Two major areas: basic and applied
a) Basic microbiology – fundamental nature of MOs
◦ Morphology – shape, size, chemical composition
◦ Physiology – nutritional requirements, physical conditions
◦ Biochemistry – nutrient breakdown to obtain energy
◦ Genetics – inheritance, variability
◦ Disease causing potential – virulence/pathogenicity
◦ Ecology – natural occurrence, relationships and interactions
◦ Classification – taxonomic relationship among groups
Microbiology as a science…
b) Applied microbiology – employ knowledge of
basic microbiology to control and use
microorganisms in beneficial ways.

◦ Medical and veterinary microbiology

◦ Food and dairy microbiology

◦ Industrial microbiology

◦ Agricultural microbiology

◦ Environmental microbiology
Intro…..
Medical microbiology
A specialty that deals with MOs that only
cause infectious diseases in human beings.

It deals with:
epidemiology, pathogenesis, clinical features,
laboratory diagnosis, treatment, prevention and
control of the diseases caused by the infectious
microbes.
Intro…..
MOs & Society -Why do we study microbiology?
Beneficial OR Harmful?
a) Causative agents of infectious diseases
Important in understanding:
Cxcs of causative agent,
Means of transmission,
Pathogenesis of the disease,
Clinical manifestations,
Diagnosis,
Treatment & mechanisms of action of drugs,
Prevention and control of infections, etc.
Why….
b) Normal flora
◦ Beneficial metabolic functions
◦ Antagonistic effect
c) Environmental importance
◦ Environmental clean-up
◦ Produce oxygen
◦ Food chain
◦ Sewage treatment
Why…..
d) Industrial importance
◦ Food industry & Brewing industry (fermentation)
◦ Pharmaceutical industry (E.g. human insulin)
◦ Genetic engineering
e) Models of choice for research
◦ Simple cell structure
◦ Rapid rate of growth
◦ Inexpensive to culture
◦ Wide range of biochemical activities (biochemical diversity)
Historical developments
Microorganisms ancient by any standards
Microbiology comparatively young
i) Invention of the microscope
Antony Van Leeuwenhoock (1632 – 1723) –Dutch- biologist
◦ Mad simple microscope
◦ Reported his observations with accurate description and
drawings (Discoverer of the microbial world)
◦ Observed bacteria (rods, spheres, and spiral), protozoa,
filamentous fungi, and yeasts.
◦ Described them as “Animaciles”
Historical developments

The theory of spontaneous generation

from where did Organisms come?
Two Schools of Thoughts
1. Spontaneous generation (Abiogenesis)
MOs formed spontaneously from non-living materials
2. Living cells came from pre-existing living cells (Biogenesis)
Dates back at least to the ancient Greeks:
◦ Mud of ponds and streams → frogs, worms
◦ Decaying meat → maggots and flies
◦
Historical developments

Francesco Redi (1626 – 1697)

Italian physician
Refused the idea of SG (rotting meat carefully kept from
flies will not spontaneously produce maggots)
He preformed experiments:
Utilized jars containing meat (covered/uncovered)
Maggots appeared in uncovered jars
Results were not accepted for microscopic organisms
Introduced experimental procedure for disproof of S.G.
Historical developments
John Needham (1745) -English biologist
An advocate for SG
Experiments similar to Redi’s
Introduced the first culture medium (Infusion
broth: meat, grain, etc.)
Briefly boiled chicken broth, put it into a flask
sealed it after cooling, and waited
microorganisms grew.
Conclude – support SG
Historical developments
Lazzaro Spallanzani (1729 – 1799)- Italia biologist/physiologist
Suggested MO had entered from the air after the
broth was boiled, but before it was sealed
Boiled beef broth in flasks for an hour (longer
boiling); sealed the flasks by melting necks
Observation: no growth
Conclude – against SG
Needham Air, important to all life & SG, excluded
from the flasks
Historical developments
Louis Pasteur (1861)- proof - End of SG
i) Filtered air through cotton plug
◦ Placed plug in infusion broth
◦ broth became turbid– presence of MOs in the air
proved
ii) Placed boiled broth in “swan-necked” flasks
◦ Flasks remained sterile unless tilted or neck broken
Historical developments
( Germ theory of fermentation)
Louis Pasteur: disproved the idea of SG
1850’s problem in the French wine industry
Discovered the microbial basis of fermentation
Developed:
◦ Techniques to prevent the spoilage of wine and milk
("Pasteurization") using heat grape juice
L. Pasteur answered a call
◦ The first modern vaccines (for rabies and anthrax).
◦ The idea of using attenuated (weakened) strains of
MOs as the basis for vaccines.
Historical developments

The germ theory of disease

Diseases caused by vague factors
◦ E.g. Bad air, bad blood, super natural force
Historical developments

Joseph Lister (1864) – British Surgeon

Provided a powerful indirect evidence for the
germ theory of disease
Hypothesis: the very bias for surgical infection
might be microbial in nature
devise/develop antiseptic surgery (application of phenol)
Historical developments
Robert Koch (1843 – 1910)
German, physician
Studied the anthrax bacillus
◦ Rod-shaped bacteria in the blood of sheep
◦ Realized spore production
◦ The first to cultivate these bacteria outside the body using blood
serum at body temperature
Eventually led to the development of pure culture techniques, stains,
agar, culture media, petri dishes. Forwarded Koch’s
postulates
Historical developments
Koch’s Postulates (1884) – German physician and microbiologist
1. The organism must always be found in the diseased
animal, but not in healthy individuals
2. The organism must be isolated from diseased animals
and grow in pure culture away from the animal
3. The organism isolated in pure culture must initiate
and produce the disease when re-inoculated into
susceptible animals
4. The organism should be isolated from the experimentally infected
animals
Historical developments
Problems of the postulates:
A disease can be caused by more than one causative
agent, and a MO can cause more than one disease entity
All pathogenic organisms may not be cultured on
laboratory media (Mycobacterium leprae requires animal
host)
Some infectious agents are species specific (Neisseria
gonorrheae only human host)
Certain diseases develop only when an opportunistic
pathogen invades immunocompromized host
Historical developments
Golden Age of Microbiology
Period of rapid development [The 20 – 50 years period
following Koch’s work]
By 1900 almost all major bacterial disease organisms had been
described
Examples:
◦ Anthrax – Bacillus anthracis
◦ Diphtheria – Corynbacterium diphtheriae
◦ Typhoid fever – Salmonella typhi
◦ Gas gangrene -Clostridium perfirngens
Historical developments

The era of antimicrobial chemotherapy

Paul Ehrlich (1910) – German physician and Scientist
◦ Introduced concept of chemotherapy
◦ Use of salvarsan (Arsphenamine)-for the treatment of syphilis.

Alexander Fleming (1928) – Scottish – biologist, pharm

◦ Discovered the first antibiotic – penicillin
◦ Produced by mold that contaminated bacterial culture
plate
Taxonomy and Classification of
Microorganisms
Taxonomy
Definition
“The science that studies organisms in order to
arrange them into groups; those organisms with
similar properties are grouped together and
separated from those that are different.”
Taxonomy

Can be viewed as three separate but interrelated

areas:
◦ Identification-the process of characterizing organisms
to determine its classification
◦ Classification-the process of arranging organisms into
similar or related groups, primarily to provide easy
identification and study
◦ Nomenclature-the system of assigning names to
organisms
Classification

The orderly arrangement of organisms into groups

Taxonomic hierarchy (general):
◦ Phylum/Division Class Order Family Genus Species

◦ Species: the smallest and most definitive level of

division
Taxonomy…..
Example - Bacterial
 Domain – Bacteria
 Phylum – Proteobacteria
 Class - Gamma-proteobacteria
 Order - Enterobacteriales
 Family – Enterobacteriaciae
 Genus - Escherichia
 Species – E. coli
Identification

The process of characterizing a MO to determine its classification

- assigning a name to the organism

Properties compared with pre-characterized “type species”

Type species - the species that is designated as representative of the

genus to which it belongs the species of a genus that is
regarded as the best example of the generic characters of the
genus; the species from which a genus was orig. named.
Nomenclature

Naming- The means by which the characteristics of species are

defined and communicate Governed by international rules
(Inter-Code of Nomenclature of Bacteria)
Rules of Nomenclature

Only one name for an organism

All names are in Latin/Latinized
◦ First word (genus) - capitalized
◦ Second word (species or specific epithet) - not capitalized
◦ Genus and species name (species)- either underlined or
italicized
◦ E. g. Enterobacter cloacae (Enterobacter cloacae)
◦ Species may be further subdivided into sub-species called
strains (eg. Escherichia coli strain 0157-H7)
1. Numerical Taxonomy

Computer or phenetic taxonomy

Many (50 to 200) phenotypic characters
biochemical, morphological, cultural, susceptibilities
Equal weight is used for each character
Names are based by % similarity
FIGURE (Example of dendrogram)
Phylogenetic

Genetic basis of similarity (DNA relatedness)

a) Genome size
b) Guanine-plus-cytosine (G+C) content
c) Thermal stability of related DNA sequences
Polyphasic
Cell theories
History
Robert Hook (1665) - first described cells
AntonieVan Leeuwenhook - Observed the first
living cells
Mathias Schleiden (1838) - “all plants are aggregates
of fully individualized, independent, separate beings”
Theoder Schwann (1839) - “all animal tissues are
composed of individual cells”
Rudolf Virchow (1855) - “All cells arise from
preexisting cells”.
Modern cell theory

1. Every living organism is made up of one or more cells; within

which the life processes of metabolism and heredity occur.

2. Cells are the functional and organizational units of all living

things.

3. All cells arise from pre-existing cells.

Prokaryotic Vs Eukaryotic Cells
All organisms other than viruses and prions are made up of cells

Two general classes of cells:

◦ prokaryotic
◦ eukaryotic.
The evolution of prokaryotic cells preceded that of eukaryotic cells
by 2 billion years
Major similarities b/n prokaryotes and eukaryotes

1. Have DNA genome

3. Have ribosomes
4. Have similar basic metabolism
4. Both are amazingly diverse in forms
 Prokaryotes:
 No distinct nucleus
 DNA is in the form of a single
circular chromosome
 Additional DNA is carried in
plasmids.
 Transcription and translation
can be carried out
simultaneously
 Ribosome size 70S
Eukaryotes:
 Several chromosomes within a
nucleus (linear).
 Nucleus bounded by a nuclear
membrane.
 Transcription requires formation of
mRNA and movement of mRNA out of
the nucleus into the cytoplasm.
 Membrane-bound organelles
 Ribosome size 80S (cytoplasmic)