Medical Microbiology I

Lecture 5
Evolution of Bacterial Taxonomy

Taxonomy

Taxonomy
TAXONOMY - hierarchical system for classifying
and identifying organisms (the science of
classification of living organisms)
Developed by Swedish scientist Carolus
Linnaeus in the 18th century - book Systema
naturae (translates as System of Nature) meaning a classification of all known natural life
Each species is assigned a two-part LATINISED
name, or BINOMIAL

Taxonomy
Linnaeus's taxonomy system has TWO main
features that contribute to its ease of use in
naming and grouping organisms.
1. The FIRST is the use of binomial nomenclature.
An organism's scientific name is comprised of a
combination of two terms.
These terms are the genus name and the
species epithet.
Both of these terms are ITALICISED and the
genus name is also CAPITALISED.

Taxonomy
E.g., the scientific name for human is Homo
sapiens - meaning wise man
The genus name is Homo and the species is
sapiens.
These terms are unique and no other species
can have this same name.

Taxonomy
e.g. Escherichia coli - Escherichia is the genus
name and coli is the species epithet
Sometimes the genus is designated by a single
letter abbreviation e.g. E. coli
The abbreviation sp. is used to designate a
single species, whereas the abbreviation spp.
is used to designate more than one species

Taxonomy
2. The SECOND feature of Linnaeus's
taxonomy system that simplifies organism
classification is the ordering of species into
broad categories.
There are seven major categories: Kingdom,
Phylum, Class, Order, Family, Genus, and
Species.

Taxonomy

Taxonomy
A good aid for remembering
these categories is the
mnemonic device:
Keep Plates Clean Or Family
Gets Sick

Taxonomy
Some of these categories can be further
divided into intermediate categories such as
subphyla, suborders, superfamilies, and
superclasses.
An example of this taxonomy scheme is:

Taxonomy
Kingdom
Phylum
Subphylum
Superclass
Class
Subclass
Superorder
Order
Suborder
Superfamily

Family
Subfamily
Genus
Subgenus
Species
Subspecies

Taxonomy
Classification
Brown bear

House cat

Dog

Killer whale

Wolf

Kingdom

Animalia

Animalia

Animalia

Animalia

Animalia

Phylum

Chordata

Chordata

Chordata

Chordata

Chordata

Class

Mammalia

Mammalia

Mammalia

Mammalia

Mammalia

Order

Carnivora

Carnivora

Carnivora

Cetacea

Carnivora

Family

Ursidae

Felidae

Canidae

Delphinidae

Canidae

Genus

Ursus

Felis

Canis

Orcinus

Canis

Species

Ursus arctos

Felis catus

Canis familiaris

Orcinus orca

Canis lupus

Taxonomy
The first step of hierarchical classification is
built into the binomial for a species
Species that are closely related are grouped
into the same genus (plural: genera)
Beyond the grouping of species within genera,
taxonomy extends to progressively broader
categories of classification

Taxonomy
It places related genera in the same family,
puts families into orders, orders into classes,
classes into phyla (singular: phylum), phyla
into kingdoms, and kingdoms into domains
Each taxonomic level is more comprehensive
than the previous one
The named taxonomic unit at any level is
called a taxon (plural: taxa)

Taxonomy
Only the genus name and specific epithet are
italicised, and all taxa at the genus level and
beyond are capitalised

Major Lineages of Life

Previously, there were only two kingdom:
Animalia and Plantae (according to Linnaeus)
Even with the discovery of the diverse
microbial world, the two-kingdom system
persisted
Bacteria were placed in the plant kingdom
using their rigid cell wall as a justification
Eukaryotic unicellular organisms with
chloroplasts were also considered plants

Major Lineages of Life

Major Lineages of Life

Fungi were classified under plant kingdom
partly because they are sedentary, even though
fungi are not photosynthetic and have little in
common structurally with green plants
In the two-kingdom system, unicellular
creatures that move and ingest food e.g.
protozoa were called animals
Microbes such as Euglena that move but are
photosynthetic were placed in both the animal
and plant kingdom by the different researchers

Major Lineages of Life

Robert H. Whittaker, of Cornell University
introduced the five-kingdom system in 1969 Monera, Protista, Plantae, Fungi, and Animalia
The five-kingdom system recognises the two
fundamentally different types of cell types,
prokaryotic and eukaryotic
It sets the prokaryotes apart from all
eukaryotes by placing them in their own
kingdom, Monera

Major Lineages of Life

Major Lineages of Life

Whittaker distinguished 3 kingdoms of
multicellular eukaryotes partly on their nutrition
- Plantae, Fungi, and Animalia
Plants are autotrophic in nutritional mode,
making their food by photosynthesis
Fungi are heterotrophic organisms that are
absorptive in nutritional mode
Most fungi are decomposers that live embedded
in their food source, secreting digestive enzymes
and absorbing the small organic molecules that
are the products of digestion

Major Lineages of Life

Most animals live by ingesting food and
digesting it within specialised cavities
In Whittakers five-kingdom system, Protista
consisted of all eukaryotes that did not fit the
definition of plants, fungi, or animals
Most protists are unicellular forms
The five-kingdom system was used in biology
for over 20 years

Major Lineages of Life

In the late 1970s, Carl R. Woese devised a new
system on evidences that there are 2 distinct
lineages of prokaryotes based on molecular
data (differences in their rRNA sequences)
These new data led to a three-domain system
The three domains - Bacteria, Archaea, and
Eukaryota (Eukarya), are essentially
superkingdoms, a taxonomic level even higher
than the kingdom level

Major Lineages of Life

Major Lineages of Life

Woese considered other conserved molecules in
cells including certain proteins, and conserved
genes (DNA), but settled for the ssrRNA for a
number of reasons.
1. rRNA is found in all cells.
2. rRNA is present in thousands of copies and is
easy to isolate from cells
3. rRNA can be analyzed to determine the exact
sequence of nucleotide bases in its makeup.

Major Lineages of Life

4. The sequence of bases in RNA is a
complementary COPY of the sequence of
bases in the gene (DNA) that encodes for
RNA.
5. Base sequences in different rRNA molecules
can be compared by computer analyses and
statistical methods to reveal precise
similarities and differences in cellular
genomes.

Major Lineages of Life

In this three-domain system, there are two
domains of prokaryotes (Archaea and
Bacteria) and one domain (Eukarya), which
includes all eukaryotic organisms
Archaea comes from the word archae,
meaning ancient
Domain Archaea contains 2 phyla and domain
Bacteria contains 23 phyla

Major Lineages of Life

Determining Relatedness Among

Organisms
The most widely used technique for
determining diversity or relatedness is called
rRNA sequencing
Ribosomes are made up of two subunits: a
small subunit and a large subunit
The small subunit contains only one RNA
molecule - small subunit rRNA or SSU rRNA

Determining Relatedness Among

Organisms
The SSU rRNA in prokaryotic ribosomes is a 16S
rRNA molecule, whereas the SSU rRNA in
eukaryotes is an 18S rRNA (S refers to
Svedberg unit)
The gene that codes for the 16S rRNA molecule
contains about 1500 DNA nucleotides, whereas
the gene that codes for the 18S rRNA molecule
contains about 2000 nucleotides

Determining Relatedness Among

Organisms
The sequence of nucleotides in the gene that
codes for the 16S rRNA molecule is called the
16S rDNA sequence
In order, to determine relatedness, researchers
compare the sequence of nucleotide base pairs
in the gene rather than comparing the actual
SSU rRNA molecules

Determining Relatedness Among

Organisms
If the 16S rDNA sequence of one prokaryotic
organism is quite similar to the 16S rDNA
sequence of another prokaryotic organism,
then the organisms are closely related
The less similar the 16S rDNA sequences in
prokaryotes (or the 18S rDNA sequences in
eukaryotes), the less related are the organisms

Determining Relatedness Among

Organisms
For example, the 18S rDNA sequence of a
human is much more similar to the 18S rDNA
sequence of a chimpanzee than to the 18S
rDNA sequence of fungus

Determining Relatedness Among

Organisms
Perhaps taxonomists will some day combine
the three-domain system and the five-kingdom
system, producing either a six-kingdom system
(Bacteria, Archaea, Protista, Fungi, Plantae, and
Animalia) or a seven-kingdom system (Bacteria,
Archaea, Algae, Protozoa, Fungi, Plantae, and
Animalia)