• "When written in Chinese the word 'crisis' is
composed of two characters. One represents
danger, and the other represents
The science of biological classification, by
grouping organisms with similar characteristics.
Three Interrelated Parts of
Arrangement into groups
Assignment of Names
• Classification answers questions of the sort:
How is this fungus related to other fungi?
• Identification addresses the more immediate
question: What's the name of the
specimen in front of me?
Three Major Domains
• The three-domain system is a biological
classification introduced by Carl Woese in
1990 that divides cellular life forms into
archaea, bacteria, and eukaryote domains.
• In particular, it emphasizes the separation of
prokaryotes into two groups, originally
called Eubacteria (now Bacteria) and
Archaebacteria (now Archaea).
• Woese argued that, on the basis of
differences in 16S rRNA genes, these two
groups and the eukaryotes each arose
separately from an ancestor with poorly
developed genetic machinery, often called a
progenote. To reflect these primary lines of
descent, he treated each as a domain,
divided into several different kingdoms.
• Prokaryotic, no nuclear membrane, distinct
biochemistry and RNA markers from eubacteria,
possess unique ancient evolutionary history for
which they are considered some of the oldest
species of organisms on Earth; traditionally
classified as archaebacteria; often characterized
by living in extreme environment.
• Kingdom Archaebacteria
• Methanogens – metabolize hydrogen and carbon
• Prokaryotic, no nuclear membrane,
traditionally classified as bacteria, contain
most known pathogenic prokaryotic
organisms, studied far more extensively
• Kingdom Eubacteria
• Cyanobacteria – photosynthesizing bacteria
• Eukaryotes, nuclear membrane present.
• Kingdom Protista or protists
Kingdom Fungi or fungi
Kingdom Plantae or plants
Kingdom Animalia or animals
(Proposed by Aristotle)
Problem with Aristotle’s
If it was green, it was a
plant regardless of other
Five Kingdom System
Six Kingdom System
Three Domain System
(Difference in rRNA and Cell Wall in Procaryotic Organisms)
• Domain Eukaryae
All Eukaryotic Organisms
• Domain Bacteria
True Bacteria and Cyanobacteria
• Domain Archaea
Ancient “Extreme” Bacteria
Modern Taxonomic Hierarchy
• Kingdom Through Species
• Binomial Nomenclature
• Bacillus subtilis
3. Common/Descriptive Names
• Genetic Similarity and Evolutionary Relatedness
Reflects Genetic Similarity and Evolutionary Relatedness
• Based on Observable Characteristics.
Species verses Strain
A specific or defined type of organism
capable of producing young that can
Variation within a species.
• descended from a single organism
• different isolates may be same species but are different strains;
often have slight differences
Bergey’s Manual of Systematic
•First edition published in 1923, now in 9th edition.
•Uses both morphological and Physiological
•Very practical system. Use successive "key"
features to narrow down identification
•Ex. Gram + or -? Then shape? Then motile or
not? etc. Eventually only a few organisms match
the process of elimination.
•Second edition now being published, a major reorganization
•Primary emphasis is phylogenetic, not phenetic
•Example: pathogens are not grouped together, instead they are
scattered in different areas
•Five volumes have instructive titles:
The Archaea, and the Deeply Branching and
The Low G + C Gram-positive Bacteria
The High G + C Gram-positive Bacteria
The Planctomyces, Spirochaetes, Fibrobacters,
Bacterioidetes, and Fusobacteria
American Type Culture
• Algae and Protozoa
• Bacteria and Baceriophages
• Cell Lines
• DNA Materials
• Fungi and Yeasts
• Plant Tissues
• Viruses and Virus Antiserum
• Membrane System
• Membrane Enclosed
Domain Bacteria &
• Few if Any Internal
• Plasma Membrane
• No Membrane Bound
• Either DNA or RNA
• Capsid (Protein Shell)
• Virus Species
A population of viruses with similar
characteristics that occupy a particular
• No Independent Metabolism or
• Requires a Host (Parasitic)
Major Criteria and Methods
Used in the Taxonomy of
Classical Approach Uses These Tools
• Differential Staining
• Biochemical Tests
• Oxygen Requirements
• Phage Typing
Molecular Approach Uses These
• Amino Acid Sequencing
• Total Protein Analysis
• Base Composition
• Nucleic Acid Hybridization
• Numerical Taxonomy
• Fatty Acid Profiles
Describe how staining,
biochemical, immunological, and
molecular tests are used for
(Always Given Two Choices)
1a. Bean round Garbanzo Bean
1b Bean elliptical or oblong Go to 2
2a Bean white White Navy
2b Bean dark Go to 3
3a. Bean evenly pigmented Kidney Bean
3b Bean pigmentation mottled Pinto Bean
• Among the almost infinite varieties of
microorganisms, relatively few cause
disease in otherwise healthy individuals.
• One way of proving that a given disease is
"infectious", is to satisfy Koch's postulates
(first proposed by Robert Koch), which
demands that the infectious agent be
identified only in patients and not in healthy
controls, and that patients who contract the
agent also develop the disease. These
postulates were first used in the discovery
that Mycobacteria species cause
• Diagnosis of infectious disease sometimes
involves identifying an infectious agent
either directly or indirectly.
• Microbiological culture is a principal tool
used to diagnose infectious disease.
• In a microbial culture, a growth medium is
provided for a specific agent.
• A sample taken from potentially diseased
tissue or fluid is then tested for the presence
of an infectious agent able to grow within
• Samples obtained from patients may be
viewed directly under the light microscope,
and can often rapidly lead to identification.
• Microscopy is often also used to observe the
reaction of specific bacteria with specific
stains or dyes.
• Biochemical tests used in the identification
of infectious agents include the detection of
metabolic or enzymatic products
characteristic of a particular infectious
agent. Since bacteria ferment carbohydrates
in patterns characteristic of their genus and
• Immunologic or Serological methods are
highly sensitive, specific and often
extremely rapid tests used to identify
• These tests are based upon the ability of an
antibody to bind specifically to an antigen.
The antigen, usually a protein or
carbohydrate made by an infectious agent,
is bound by the antibody.
• Technologies based upon the polymerase chain
reaction (PCR) method will become nearly
ubiquitous gold standards of diagnostics of the
near future, for several reasons.
• First, the catalog of infectious agents has grown
to the point that virtually all of the significant
infectious agents of the human population have
• Second, an infectious agent must grow within
the human body to cause disease; essentially it
must amplify its own nucleic acids in order to
cause a disease.
• This amplification of nucleic acid in infected
tissue offers an opportunity to detect the
infectious agent by using PCR.
• Third, the essential tools for directing PCR,
primers, are derived from the genomes of
infectious agents, and with time those genomes
will be known, if they are not already.