Microbial Classification

The science of classification, especially the classification of living forms, is

called taxonomy (from the Greek for orderly arrangement). The objective of
taxonomy is to classify living organisms—that is, to establish the relationships
between one group of organisms and another and to differentiate them.
There may be as many as 100 million different living organisms, but fewer
than 10% have been discovered, much less identified and classified. Taxonomy
also provides a common reference for identifying organisms already classified.
Taxonomy is a basic and necessary tool for scientists, providing a universal
language of communication. Modern taxonomy is an exciting and dynamic
field. The ability to rapidly sequence DNA, even entire genomes, has led to
new insights into classification and evolution and has given rise to the current
Third Golden Age of Microbiology.

In 2001, an international project called the All Species Inventory was

launched. The project’s purpose is to identify and record every species of life
on Earth in the next 25 years. These researchers have undertaken a
challenging goal: whereas biologists have identified more than 1.7 million
different organisms thus far, it is estimated that the number of living species
ranges from 10 to 100 million.
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In 1859, the English naturalist Charles Darwin proposed that natural selection
was responsible for the similarities as well as the differences among
organisms. To facilitate research, scholarship, and communication, we use
taxonomy—that is, we put organisms into categories, or taxa (singular: taxon),
to show degrees of similarities among organisms. These similarities are due to
relatedness—all organisms are related through evolution. Systematics, or
phylogeny, is the study of the evolutionary history of organisms, and the
hierarchy of taxa reflects their evolutionary, or phylogenetic, relationships.

The Three Domains

The discovery of three cell types was based on the observations that
ribosomes are not the same in all cells, from different kinds of cells shows that
there are three distinctly different cell groups: the eukaryotes and two
different types of prokaryotes—the bacteria and the archaea. In 1978, Carl R.
Woese proposed elevating the three cell types to a level above kingdom, called
domain. Woese believed that the archaea and the bacteria, although similar in
appearance, should form their own separate domains on the evolutionary
tree. In addition to differences in rRNA, the three domains differ in membrane
lipid structure, transfer RNA molecules, and sensitivity to antibiotics.

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In this widely accepted scheme, animals, plants, and fungi are kingdoms in the
Domain Eukarya. The Domain Bacteria includes all of the pathogenic
prokaryotes as well as many of the nonpathogenic prokaryotes found in soil
and water. The photoautotrophic prokaryotes are also in this domain. The
Domain Archaea includes prokaryotes that do not have peptidoglycan in their
cell walls. They often live in extreme environments and carry out unusual
metabolic processes.

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 Classification of Organisms
Scientific Nomenclature

In a world inhabited by millions of living organisms, biologists must be sure

they know exactly which organism is being discussed. We cannot use common
names, because the same name is often used for many different organisms in
different locales.

Every organism is assigned two names, or a binomial. These names are the
genus name and specific epithet (species), and both names are printed
underlined or italicized. The genus name is always capitalized and is always a
noun. The species name is lowercase and is usually an adjective. Because this
system gives two names to each organism, the system is called binomial
nomenclature.

Binomials are used by scientists worldwide, regardless of their native language.

This nomenclature enables them to share knowledge efficiently and accurately.
Several scientific entities are responsible for establishing rules governing the
naming of organisms. Scientific names are taken from Latin (a genus name can
be taken from Greek) or latinized by the addition of the appropriate suffix.
Suffixes for order and family are -ales and -aceae, respectively.
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Just as a number of species make up a genus, related genera make up a
family. A group of similar families constitutes an order, and a group of
similar orders makes up a class. Related classes, in turn, make up a phylum.
Thus, a particular organism (or species) has a genus name and specific
epithet and belongs to a family, order, class, and phylum. All phyla that are
related to each other make up a kingdom, and related kingdoms are
grouped into a domain.

Classification of Prokaryotes

The taxonomic classification scheme for prokaryotes is found in Bergey’s

Manual of Systematic Bacteriology. In Bergey’s Manual, prokaryotes are
divided into two domains: Bacteria and Archaea. Each domain is divided into
phyla. Remember, the classification is based on similarities in rRNA
nucleotide sequences. Classes are divided into orders; orders, into families;
families, into genera; and genera, into species.

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The taxonomic hierarchy. Organisms are grouped according to relatedness. Species that
are closely related are grouped into a genus

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Phylogenetic relationships of prokaryotes

Arrows indicate major lines of descent of bacterial groups. Selected phyla are
indicated.

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Classification of Eukaryotes

Most of unicellular, were grouped as the kingdom Protista, a catchall kingdom

for a variety of organisms. Historically, eukaryotic organisms that didn’t fit into
other kingdoms were placed in the Protista. Approximately 200,000 species of
protists have been identified thus far, and these organisms are nutritionally
quite diverse—from photosynthetic to obligate intracellular parasite.
Ribosomal RNA sequencing is making it possible to divide protists into groups
based on their descent from common ancestors. Consequently, the organisms
once classified as protists are being divided into clades, or genetically related
groups.

The Kingdom Fungi includes the unicellular yeasts, multicellular molds, and
macroscopic species such as mushrooms. A fungus absorbs dissolved organic
matter through its plasma membrane to obtain raw materials for vital
functions. The cells of a multicellular fungus are commonly joined to form thin
tubes called hyphae. Fungi develop from spores or from fragments of hyphae.

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Classification of Viruses

Viruses aren’t classified as part of any of the three domains. They aren’t
composed of cells, and they use the anabolic machinery within living host cells
to multiply. A viral genome can direct biosynthesis inside a host cell, and some
viral genomes can be incorporated into the host genome. The ecological niche
of a virus is its specific host cell, so viruses may be more closely related to their
hosts than to other viruses. The International Committee on Taxonomy of
Viruses defines a viral species as a population of viruses with similar
characteristics (including morphology, genes, and enzymes) that occupies a
particular ecological niche.

Viruses are obligatory intracellular parasites. Viral genes carried in the genomes
of other organisms provide a record of viral evolution. There are three
hypotheses on the origin of viruses: (1) They arose from independently
replicating strands of nucleic acids (such as plasmids). (2) They developed from
degenerative cells that, through many generations, gradually lost the ability to
survive independently but could survive when associated with another cell. (3)
They coevolved with host cells.

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 Methods of Classifying and Identifying Microorganisms

Microbiologists have developed a variety of methods to test metabolic

reactions and other characteristics to identify prokaryotes. Bergey’s Manual
of Determinative Bacteriology provides identification (determinative)
schemes based on such criteria as cell wall composition, morphology,
differential staining, oxygen requirements, and biochemical testing.

Morphological Characteristics
Morphological (structural) characteristics have helped taxonomists classify
organisms. Higher organisms are frequently classified according to observed
anatomical detail. But many microorganisms look too similar to be classified
by their structures alone. Organisms that might differ in metabolic or
physiological properties may look alike under a microscope.

Differential Staining
One of the first steps in identifying bacteria is differential staining. Most
bacteria are either gram-positive or gram-negative. Other differential stains,
such as the acid-fast stain, can be useful for a more limited group of
microorganisms.
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Biochemical Tests
Enzymatic activities are widely used to differentiate bacteria. Even closely
related bacteria can usually be separated into distinct species by subjecting
them to biochemical tests. . A number of tests have been developed so
technicians can quickly identify the pathogens, a clinician can then provide
appropriate treatment, and epidemiologists can locate the source of an
illness. All members of the family Enterobacteriaceae are oxidase-negative.
Among the enteric bacteria are members of the genera Escherichia,
Enterobacter, Shigella, Citrobacter, and Salmonella. Escherichia,
Enterobacter, and Citrobacter, which ferment lactose to produce acid and
gas, can be distinguished from Salmonella and Shigella. The time needed to
identify bacteria can be reduced considerably by the use of selective and
differential media or by rapid identification methods.

Rapid identification
methods are manufactured for groups of medically important bacteria, such
as the enterics. Such tools are designed to perform several biochemical tests
simultaneously and can identify bacteria within 4 to 24 hours. This is
sometimes called numerical identification because the results of each test
are assigned a number. In the simplest form, a positive test would be
assigned a value of 1, and a negative is assigned a value of 0.
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The use of metabolic characteristics to identify selected
genera of enteric bacteria

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One type of rapid identification method for bacteria:
EnteroPluri test from BD Diagnostics.

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Serology
Serology is the science that studies serum and immune responses that are
evident in serum. Microorganisms are antigenic; that is, microorganisms that
enter an animal’s body stimulate it to form antibodies. Antibodies are
proteins that circulate in the blood and combine in a highly specific way with
the bacteria that caused their production. In a procedure called a slide
agglutination test, samples of an unknown bacterium are placed in a drop of
saline on each of several slides. Then a different known antiserum is added to
each sample. The bacteria agglutinate (clump) when mixed with antibodies
that were produced in response to that species or strain of bacterium; a
positive test is indicated by the presence of agglutination.

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A test called the enzyme-linked immunosorbent assay (ELISA) is widely used
because it is fast and can be read by a computer scanner. In a direct ELISA,
known antibodies are placed in (and adhere to) the wells of a microplate,
and an unknown type of bacterium is added to each well. A reaction
between the known antibodies and the bacteria provides identification of
the bacteria.

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 Other Methods used of classifying and identifying microorganisms

1. Identification of bacterial species and strains by determining their susceptibility

to various phages and Fatty acid profiles.
2. Flow cytometry measures physical and chemical characteristics of cells.
3. The percentage of GC base pairs in the nucleic acid of cells can be used in the
classification of organisms.
4. The number and sizes of DNA fragments, or DNA fingerprints, produced by
restriction enzymes are used to determine genetic similarities.
5. Single strands of DNA, or and RNA, from related organisms will hydrogen-bond
to form a double-stranded molecule; this bonding is called nucleic acid
hybridization., example: PCR, Southern blotting, DNA chips, and FISH techniqes.
6. Nucleic Acid Amplification Tests (NAATs) can be used to amplify a small amount
of microbial DNA in a sample. The presence or identification of an organism is
indicated by amplified DNA.
7. sequence of bases in ribosomal RNA can be used in the classification of
organisms.
8. Dichotomous keys are used for identifying organisms. Cladograms show
phylogenetic relationships among Prof.
organisms.
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The Western blot. Proteins separated by electrophoresis can be detected by
their reactions with antibodies.

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