Microbial Classification
LECTURE 5
Prepared
by
Paul Makocho (PhD)
Malawi University of Science &
Technology
Introduction to Microbiology
Objectives:
By the end of this unit you should be able to:
1. Define taxonomy.
2.Differentiate the three constituents of
taxonomy.
3.Explain the meaning of natural classification.
4.Show the limitations of natural classification.
5.Give advantages of polyphasic taxonomy over
natural classification.
6.Differentiate the three categories of polyphasic
taxonomy.
7.Define a prokaryotic species.
8.Show three different ways in which strains can
be described.
9.Differentiate the classical from the Molecular
Microbial Taxonomy
Taxonomy (Greek taxis, arrangement or order, and
nomos, law or nemein, to distribute or govern) is
defined as the science of biological classification.
It consists of three separate but interrelated parts:
classification, nomenclature, and identification.
Classification is the arrangement of organisms into
groups called taxa(s, taxon) based on mutual
similarity.
Nomenclature is concerned with the assignment of
names to taxonomic groups in agreement with
published rules.
Identification is the practical side of taxonomy-the
process of determining if a particular isolate belongs
to a recognized taxon, and, if so, which one.
The term systematics is often used for taxonomy to
mean the scientific study of organisms with the
ultimate object of characterizing and arranging
Microbial Taxonomy
Systematics encompasses disciplines such as
morphology, ecology, epidemiology, biochemistry,
molecular biology, and Physiology.
One of the oldest classification systems, called
natural classification, arranges organisms into
groups whose members share many characteristics
proposed by the botanists Carl von Linne, or
Carolus Linnaeus.
It was based largely on anatomical characteristics
and was a great improvement over previously
employed artificial systems because knowledge of
an organism’s position in the scheme provided
information about many of its properties.
For example, classification of humans as mammals
denotes that they have hair, self-regulating body
Microbial Taxonomy
When Natural classification is applied to higher
organisms, evolutionary relationships become apparent
simply because the morphology of a given structure (e.g.
wings) in a variety of organisms (ducks, song birds,
hawks)suggest how that structure might have been
modified to adapt to specific environments or
behaviours.
Traditional taxonomic assignment of microbes was
however not necessarily rooted in evolutionary
relatedness. For instance, bacterial pathogens and
microbes of industrial importance were historically given
names that described the diseases they cause or the
processes they perform (e.g. Vibrio chorelae, Clostridium
tetani, and Lactococcus lactis).
Although these labels are of practical use, they do little
to guide the taxonomist concerned with the vast
majority of microbes that are neither pathogenic nor of
industrial consequence.
Microbial Taxonomy
Our recent understanding of the
evolutionary relationships among
microbes now serves as the theoretical
underpinning for taxonomic classification.
In practice, determination of the genus
and species of a newly discovered
prokaryote is based on Polyphasic
taxonomy.
This approach includes phenotypic,
phylogenetic and genotypic features.
To understand how all of these data are
incorporated into a coherent profile of
taxonomic criteria, we must first consider
the individual components.
Microbial Taxonomy
Phenetic system organizes organisms according to
mutual similarity of their phenotypic characteristics.
This classification system succeeded in bringing order
to biological diversity and clarified the function of
morphological structures.
Although phenetic studies can reveal possible
evolutionary relationships, they do not depend on
phylogenetic analysis.
Phenetic compare many traits without assuming that
any features are more phylogenetically important than
others-that is, unweighted traits are employed in
estimating general similarity.
The best phenetic classification is one constructed by
comparing as many attributes as possible. Organisms
sharing many characteristics make up a single group or
taxon.
Microbial Taxonomy
Biologists began developing phylogenetic or
phyletic classification systems that sought to
compare organisms on the basis of evolutionary
relationships.
Scientists realized that when they observed
differences and similarities between organisms as
a result of evolutionary processes, they also
gained insight into the history of life on Earth.
Microbiologists could however not effectively
employ phylogenetic classification systems,
primarily because of the lack of a good fossil
record.
Woese and Fox proposed using rRNA nucleotide
sequence to assess evolutionary relationships
among microorganisms.
Microbial Taxonomy
The validity of this approach is now
widely accepted, and there are currently
over 200,000 different small ribosomal
subunits (16S and 18S) rRNA sequences in
the international databases Genbank and
the Ribosomal Database Project (RDP-II).
Genotypic Classification
The genotypic classification compares
genetic similarity of genes or whole
genomes. Organisms that show 70%
genetic similarity would be said to belong
to the same species.
Microbial Taxonomy
The classification of microbes involves placing
them within hierarchical taxonomic levels.
Microbes in each level or rank share a common
set of specific features.
The ranks are arranged in a non overlapping
hierarchy so that each level includes not only
the traits that define the rank above it but also
a new set of restrictive traits.
The highest rank is the domain, and all
prokaryotes belong to either Bacteria or
Achaea.
Within each domain, each microbe is assigned
(in descending order) to a phylum, class, order,
family, genus, and species.
Microbial Taxonomy
Some prokaryotes are given a subspecies
designation. Microbial groups at each level
have a specific suffix indicative of that
rank or level.
Microbiologists often use informal names
in place of formal, hierarchical ones.
Typical examples of such names include
Purple bacteria, Spirochetes.
These informal names may not have
taxonomic significance as they can include
species from several phyla.
Microbial Taxonomy
Taxonomic ranks
Microbial Taxonomy
The basic taxonomic group is the species.
Taxonomists working with higher organisms define the
term species differently than do microbiologists.
Species of higher organisms are groups of interbreeding or
potentially interbreeding populations that are isolated
from other groups. This is a satisfactory definition for
organisms capable of sexual reproduction but fails with
prokaryotes.
Prokaryotes are characterized by phenotypic, genetic and
phylogenetic criteria.
A prokaryote species is a collection of strains that share
many stable properties and differ significantly from other
groups of strains.
Microbial Taxonomy
A strain consists of the descendants of a single, pure
microbial culture.
With an increasing amount of genome sequence
data, some have argued that the definition of a
prokaryotic species needs further revision.
Perhaps species should be a collection of organisms
that share the same sequence in their core
housekeeping genes (genes coding for products that
are required by all cells and which are continually
expressed).
It will take much more work to resolve this complex
issue.
Whatever the definition, ideally a species also
should be phenotypically distinguishable from other
similar species.
Microbial Taxonomy
Strain within the species may be described in a number of
different ways.
Biovars are variant strains characterized by biochemical or
physiological differences. Morphovars vary morphologically,
and Serovars have distinctive antigenic properties.
For each species, one strain is designated as the Type Strain. It
is usually one of the first strains studied and is more fully
characterized than other strains; however, it does not have to
be the most representative member.
The type strain for the species is the called the Type species and
is the nomenclatural type or holder of the species name.
A nomenclatural type is a way of ensuring permanence of
names when taxonomic rearrangements take place.
When nomenclature revisions occur, the type or type species
must remain intact within the genus of which it is
nomenclatural type. Only those strains very similar to the type
strain or type species are included in the species.
Microbial Taxonomy
Each species is assigned a genus, the next rank in the
taxonomic hierarchy.
A genus is a well defined group of one or more
species that is clearly separate from other genera.
Microbiologists name microorganisms by using the
binomial system of Linneaus.
The Latinized name consists of two parts. The first
part, which is capitalized is the generic name, and
the second is the uncapitalized species name or
specific epithet (e.g. Yersinia pestis, the causative
agent of plague).
The species name is stable i.e. the oldest epithet for
a particular organism takes precedence and must be
used.
Microbial Taxonomy
In contrast, the generic name of an organism can
change if the organism is assigned to another genus
because of new information.
For example some members of the genus
Streptococcus were placed into two new genera,
Enterococcus and Lactococcus, based on rRNA analysis
and other characteristics. Thus Streptococcus faecalis, is
now Enteroococcus faecalis.
Often the name will be shortened by abbreviating the
genus with a single capital letter, for example Y. pestis.
A new prokaryotic species cannot be recognized until
it has been published in the International Journal of
Systematic and Evolutionary Microbiology; until that
time, the new species name will appear in quotation
Microbial Taxonomy
Approaches used in classifying and
identifying microorganisms are mainly
divided into two groups for clarity: Classical
and Molecular.
Classical characteristics
Classical approaches to taxonomy make use
of morphological, physiological,
biochemical, ecological, and genetic
characteristics.
These characteristics have been employed in
microbial taxonomy for many years.
They are quite useful in routine identification
and may provide phylogenetic information
as well.
Microbial Taxonomy
Classical characteristics: Morphological characteristics.
Morphological features are important in microbial
taxonomy for many reasons.
a. Morphology is easy to study and analyse,
particularly in eukaryotic organisms and the more
complex prokaryotes.
b. Morphological comparisons are valuable because
structural features depend on the expression of
many genes, are usually genetically stable, and
normally (at least in eukaryotes) do not vary
greatly with environmental changes.
c. Thus morphological similarity often is a good
indication of phylogenetic relatedness.
Microbial Taxonomy
Classical characteristics: Morphological characteristics.
Microbial Taxonomy
Classical characteristics: Physiological and
metabolic characteristics
Physiological and metabolic characteristics
are very useful because they are directly
related to the nature and the activity of
microbial enzymes and transport proteins.
Because proteins are gene products,
analysis of these characteristics provides
an indirect comparison of microbial
genomes.
Microbial Taxonomy
Classical characteristics: Physiological and metabolic
characteristics
Microbial Taxonomy
Classical characteristics: Ecological characteristics
The ability of a microorganism to colonize a specific
environment is of taxonomic value.
Some microbes may be very similar in many other
respects but inhabit different ecological niches,
suggesting that they may not be as closely related as first
suspected.
Some examples of taxonomically important ecological
properties include life cycle patterns, the nature of
symbiotic relationships, the ability to cause disease in a
particular host, and habitat preferences such as
requirements for temperature, pH, oxygen, and osmotic
concentration.
Many growth requirements are considered physiological
characteristics as well.
Microbial Taxonomy
Classical characteristics: Genetic Analyses
Because most eukaryotes are able to reproduce
sexually, classical genetic analysis has been quite
useful in the classification of these organisms.
Although prokaryotes do not reproduce sexually,
the study of chromosomal gene exchange through
transformation, conjugation, and transduction is
sometimes useful in their classification.
– In transformation, a bacterium takes up a piece
of DNA floating in its environment.
– In transduction, DNA is accidentally moved from
one bacterium to another by a virus.
– In conjugation, DNA is transferred between
Microbial Taxonomy
Classical characteristics: Genetic Analyses
The demonstration of transformation between
two strains therefore provides evidence of a close
relationship.
Transformation studies have been carried out with
several genera including Bacillus, Micrococcus,
Haemophilus, and Rhizobium.
Despite the usefulness of transformation, its results
are sometimes hard to interpret because an
absence of transformation may result from factors
other than major differences in DNA sequence.
Conjugation studies also yield taxonomically useful
data, particularly with the enteric bacteria
Microbial Taxonomy
Classical characteristics: Genetic Analyses
Escherichia can undergo conjugation
with Salmonella and Shigella but not
with Proteus or Enterobacter.
These observations fit with other data
showing that the first three of these
genera are more closely related to one
another than to Proteus and
Enterobacter.
Plasmids are important taxonomically
because they can confound the analysis
Microbial Taxonomy
Classical characteristics: Genetic Analyses
When such plasmids encode a phenotypic trait (or
traits) that are being used to develop a taxonomic
scheme, the investigator may assume that the trait
is encoded by chromosomal genes.
Thus a microbe’s phenetic characteristics are
misunderstood and its relative degree of
relatedness to another microbe may be
overestimated.
For example, Hydrogen sulphide production and
lactose fermentation are very important in the
taxonomy of enteric bacteria, yet genes for both
traits can be borne on plasmids as well as on
bacterial chromosomes.
