Introduction to

Microbiology

Classification of Microorganisms

Sisira Kumara
AMRAK Institute of Medical Sciences
 The study of microorganisms,
which are tiny living things that
are not visible to the naked eye.

Microbiology

Includes bacteria, viruses, fungi,

protozoa, and algae.

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Phylogeny: The Study of
Evolutionary Relationships
of Living Organisms
• Over 1.5 million different
organisms have been
identified to date.
• Many similarities among
living organisms:
• Made up of cells
surrounded by a plasma
membrane.
• Use ATP as energy
source.
• Store genetic
information as DNA.
• Ribosomes are the site
of protein synthesis.
Phylogeny: The Study of
Evolutionary Relationships of
Living Organisms

• Both differences and

similarities among
organisms are caused by
natural selection (Darwin,
1858).
• Organisms can be classified
into taxonomic categories
(taxa), based on the
differences and similarities
among them.
Phylogeny: The Study of
Evolutionary Relationships of
Living Organisms

Ancient Greeks classified

all living organisms into two
groups

• Kingdom Plantae
• Kingdom Animalia
Phylogeny: The Study of Evolutionary Relationships of Living Organisms

• In 1850s bacteria and fungi were

incorrectly placed in the Plant Kingdom.
• In 1860s Kingdom Protista was
proposed to include bacteria, fungi,
algae, and protozoa, but many scientists
still classified bacteria and fungi as
plants.
• Intense disagreement over classification
of bacteria and fungi persisted over 100
years.
Phylogeny: The Study of
Evolutionary Relationships of
Living Organisms

• In 1930s electron
microscopy made it clear
that bacterial cells lacked
a nucleus. The term
procaryote was
introduced in 1937.
• In 1959 Kingdom Fungi
was established.
Phylogeny: The Study of Evolutionary Relationships of Living Organisms

• In 1961 the current definition of the

term procaryote was established.
• In 1968 the Kingdom Procaryotae
was accepted by biologists.
• In 1969 Robert Whitaker proposed a
five-kingdom system of biological
classification for all living organisms.
Five-Kingdom System of Biological Classification
• Proposed in 1969 by Robert Whitaker

1. Kingdom Procaryotae (Monera): Oldest known cells. Lived over 3.5 billion years ago. Lack a
nucleus and membrane bound organelles.

The other four kingdoms are eucaryotes. Have a true nucleus and membrane bound organelles.
• 2. Kingdom Protista: Mostly unicellular, lack tissue organization. Most have flagella during life.
• 3. Kingdom Fungi: May be unicellular (yeasts) or multicellular (molds). Many are saprotrophs.
• 4. Kingdom Plantae: Multicellular, photosynthetic.
• 5. Kingdom Animalia: Multicellular, heterotrophs that ingest food through a mouth or oral cavity.
Five-Kingdom Classification System
 Differences Between Eucaryotic and
Procaryotic Cells
Procaryotes Eucaryotes

Cell size 0.2-2 um in diameter 10-100 um in diameter

Nucleus Absent Present
Membranous Organells Absent Present
Cell Wall Chemically Complex Simple when present
Ribosomes Smaller - 70S Larger – 80S / 70S in
organells
DNA Single-circular Multiple - linear
Cell Division Binary Fission Mitosis
Procaryotic cell Eucaryotic cell
(Bacterial cell) (Animal cell)
 • Domain: In 1978 Carl Woese
proposed this level of
classification above kingdom.
The Three
Domain • The three domains are based
on the following distinguishing
System criteria:
▪ Cell wall composition
▪ Membrane lipids
▪ RNA sequence
▪ Protein synthesis
▪ Antibiotic sensitivity
The Three Domain System

• I. Domain Eubacteria: “True bacteria”.

• II. Domain Archaeabacteria: “Ancient bacteria”
• III. Domain Eucarya: All eucaryotes: Protista, Fungi, Plantae, and
Animalia.
The tree of life: A phylogenetic system. A system for representing the origins of cell lines and major taxonomic
groups. There are three distinct cell lines placed in superkingdoms called domains. The first primitive cells, were
ancestors of both lines of “prokaryotes” (Domains Bacteria and Archaea), and the Archaea emerged from the
same cell line as eukaryotes (Domain Eukarya)
Scientific nomenclature
Universal system for naming and classifying living organisms.
Initially developed in the 18th century by Carl Linnaeus.
Binomial nomenclature: Each organism (species) has a two part
name. Names are either italicized or underlined.
• Genus name: Always capitalized, always a noun. May use
initial.
• species name: Always lower case, usually an adjective.

Names are usually derived from Latin (or Greek) or may have
latinized endings. Examples:
• Homo sapiens (H. sapiens): Human
• Penicillium notatum (P. notatum): Mold that produces
penicillin
• Canis familiaris (C. familiaris): Domestic dog
 ⚫ DOMAIN
Classification of
Organisms ⚫ Kingdom
Hierarchy of Taxonomic Categories
⚫ Phylum or Division (Bacteria)
• Class
• Order
• Family
• Genus
• species
Taxonomic Categories
Example
Bacteria
• Characteristics:
o Single-celled organisms.
o Can be spherical (cocci),
rod-shaped (bacilli), or
spiral (spirilla).
o Reproduce by binary
fission.

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Structure of
Bacteria

• Outer layer (Cell

envelope): cell wall of
bacteria + plasma
membrane
• Cell interior: cytoplasm,
cytoplasmic inclusions
(mesosome, ribosomes,
inclusion granules), and
single circular DNA.
• Additional
structures: capsule,
flagella, fimbriae, and
spores.
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Classification of Bacteria

• Bacteria are classified and

identified to distinguish one
organism from another and
to group similar organisms
by criteria of interest to
microbiologists or other
scientists.
We can classify Bacteria on the basis of

1. Morphologic Characteristics
o Cell wall composition – Gram + / Gram -
o Availability of – Flagella / Spores / Capsules / Inclusion Bodies
o Shape

2. Growth Characteristics
o Aerobic / Anerobic / Microaerobic
o Ability to grow under different growth conditions – Temperature / pH
/ Salinity

3. Antigens and Phage Susceptibility

4. Biochemical Characteristics
• Let’s Classify
 gram-positive and gram-negative cell walls

• Discovered by H.C. Gram in

• Classify bacteria as
either Gram positive or
negative based on their
morphology and differential
staining properties.
• The Process - Slides are
sequentially stained with
crystal violet, iodine, then
destained with alcohol and
counter-stained with safranin.
• Gram positive bacteria stain
blue-purple and Gram negative
bacteria stain red.
10/9/2024 27
Classification
of Bacteria on
the Basis of
Shape
Significance of bacteria in
Healthcare:

• Bacteria are a major cause

of hospital-acquired infections
(HAIs). Effective infection
control measures are essential
to prevent the spread of
bacterial infections in
healthcare settings.
• Understanding bacterial
structure and function helps
diagnose infections and select
appropriate antimicrobial
therapies (Damani, 2019).

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Viruses

• Structure: Viruses are acellular

entities with genetic material (DNA or
RNA) enclosed in a capsid protein
coat. Some viruses have an outer lipid
envelope. They lack cellular structures
and cannot carry out metabolic
processes independently (Ward,
2016).

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 Significance of
Viruses in
Healthcare

Viruses are responsible for numerous

infections in healthcare settings,
affecting patients and healthcare
workers.
Measures such as vaccination, hand
hygiene, and isolation are crucial to
prevent the spread of viral infections.
Understanding viral structure and
replication helps develop antiviral drugs
and vaccines (Damani, 2019).

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 FUNGI
Characteristics:
• Eukaryotic organisms.
• Can be unicellular (yeasts)
or multicellular (molds).
• Obtain nutrients by
decomposing organic
material.

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Structure of Fungi

• Eukaryotic Cells: Fungi are

eukaryotic organisms with a true
nucleus and membrane-bound
organelles.
• Cell Wall: Composed of chitin, which
provides rigidity and structural support.
• Cell Membrane: Contains
ergosterol, a target for many antifungal
drugs.
• Reproductive Structures: Fungi
reproduce through spore formation,
which can be sexual or asexual (Ward,
2016).

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 Types of Fungi

Candida albicans: A yeast that causes

candidiasis, affecting the mouth, throat,
and genital areas. It commonly occurs in
immunocompromised individuals (Fraise &
Bradley, 2009).
Aspergillus species: Molds that cause
aspergillosis, a condition that affects the
respiratory system. It is particularly
dangerous for people with weakened
immune systems (Damani, 2019).
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 Significance in Healthcare

• Infections: Fungal infections range from superficial (e.g., athlete's foot)

to systemic (e.g., invasive candidiasis), especially in
immunocompromised individuals (Elliott, Storr, & Jeanes, 2016).
• Diagnosis and Treatment: Requires understanding fungal biology.
Common treatments include antifungal medications such as azoles and
echinocandins.
• Infection Control: Preventing the spread of fungal infections in
healthcare settings involves environmental control measures, such as
maintaining clean, dry environments and using air filtration systems
(Damani, 2019).

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Parasites
• Parasites are complex
eukaryotic organisms that
can be unicellular
(protozoa) or multicellular
(helminths).
• Many parasites have
complex life cycles
involving multiple hosts
and stages of
development (Ward, 2016).

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Examples –
Eukaryotic
microbial parasites

• Plasmodium species: Protozoa that cause

malaria. Transmitted by the bite of infected
Anopheles mosquitoes. Life cycle stages
include sporozoites, merozoites, and
gametocytes (Fraise & Bradley, 2009).
• Giardia lamblia: Causes giardiasis, a
diarrheal illness. Transmitted through
contaminated water and food. Exists in two
forms: trophozoites and cysts (Elliott, Storr,
& Jeanes, 2016).

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Parasites - Significance in Healthcare

Parasitic infections can cause significant morbidity and mortality,

particularly in developing countries.

Diagnosis and treatment require specific diagnostic tests such as

microscopy, antigen detection, and molecular methods.

Treatment includes antiparasitic medications like metronidazole and

chloroquine.

Infection control measures include proper sanitation, vector control,

and education about transmission prevention (Damani, 2019).
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Prions -
Proteinaceous
Infectious Particles

• Prions are misfolded proteins

that can induce other proteins
to misfold, leading to disease.
• They lack nucleic acids (DNA or
RNA), which differentiates them
from other microorganisms
(Ward, 2016).

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 Prions-Significance in Healthcare
Infections:
• Prion diseases are fatal and currently untreatable. They cause spongiform changes in
brain tissue, leading to severe neurological symptoms and death.
Diagnosis and Treatment:
• Diagnosis is challenging and often involves clinical examination, MRI, EEG, and
cerebrospinal fluid tests. There is no effective treatment; management focuses on
supportive care.
Infection Control:
• Strict protocols are necessary to prevent prion transmission in healthcare settings. This
includes using disposable instruments, stringent sterilization procedures, and quarantine
of infected individuals (Damani, 2019).

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 References
• Damani, N. (2019). Manual of Infection Prevention and Control (4th ed.). Oxford: Oxford University Press.

• Elliott, P., Storr, J., & Jeanes, A. (Eds.). (2016). Infection Prevention and Control: Perceptions and Perspectives. Boca Raton: CRC Press.

• Fraise, A., & Bradley, C. (2009). Ayliffe’s Control of Healthcare Associated Infection: A Practical Handbook (5th ed.). Hod der Arnold.

• Ward, D. (2016). Microbiology and Infection Prevention and Control for Nursing Students. London: Learning Matters.

• American Journal of Infection Control (AJIC)

• Journal of Hospital Infection (HIS)

Web Resources:

• The Cochrane Library: http://www.nelh.nhs.uk/cochrane.asp

• Centers for Disease Control and Prevention: http://www.cdc.gov/

• Evidence-based Practice in Infection Control Website (EPIC): http://www.epic.tvu.ac.uk/index.html

• Infection Prevention Society: http://www.ips.uk.net/

• National Institute for Health and Care Excellence: http://www.nice.org.uk/

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