Quotes
• "When written in Chinese the word 'crisis' is
composed of two characters. One represents
danger, and the other represents
opportunity.“
John Kennedy
Taxonomy (Classification)
Microbiology 2314
Taxonomy
The science of biological classification, by
grouping organisms with similar characteristics.
Three Interrelated Parts of
Taxonomy
• Classification
Arrangement into groups
• Nomenclature
Assignment of Names
• Identification
Determining Identity
Classification Versus
Identification
• 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.
Archaea Domain
• 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
Example:
• Methanogens – metabolize hydrogen and carbon
Bacteria Domain
• Prokaryotic, no nuclear membrane,
traditionally classified as bacteria, contain
most known pathogenic prokaryotic
organisms, studied far more extensively
than Archaea
• Kingdom Eubacteria
Example:
• Cyanobacteria – photosynthesizing bacteria
Eukarya Domain
• Eukaryotes, nuclear membrane present.
• Kingdom Protista or protists
Kingdom Fungi or fungi
Kingdom Plantae or plants
Kingdom Animalia or animals
Two Kingdom
System
(Proposed by Aristotle)
• Plantae
Bacteria
Fungi
Algae
Plants
Two Kingdom
System
• Animalia
Animals
Protozoa
Problem with Aristotle’s
Classification System:
If it was green, it was a
plant regardless of other
features.
Five Kingdom System
•
•
•
•
•
Animalia
Plantae
Fungi
Protista
Procaryotae/Monera
Animalia
1. Multicellular
2. Heterotrophs
Plantae
1. Multicellular
2. Photoautotrophs
Fungi
1. Absorptive
Chemoheterotrophs
2. Decomposers
Protista
1. Unicellular
2. Autotrophic
or
Heterotrophic
Monera
(Bacteria)
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
Domain
(Carl Woese)
Kingdom
Phylum/Division
Class
Order
Family
Genus
Species
Domains
Carolus Linnaeus
1753
1. Kingdom Through Species
2. Binomial Nomenclature
3. Bacillus subtilis
Bacillus subtilis
3. Common/Descriptive Names
Tubercule Bacillus
Mycobacterium tuberculosis
Phylogenetic Classification
• Genetic Similarity and Evolutionary Relatedness
Reflects Genetic Similarity and Evolutionary Relatedness
Charles Darwin
Protista
Phenetic Classification
• Based on Observable Characteristics.
Species verses Strain
• Species
A specific or defined type of organism
capable of producing young that can
also reproduce.
• Strain
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
Bacteriology
•First edition published in 1923, now in 9th edition.
•
•Uses both morphological and Physiological
characteristics
•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
Phototrophic
Bacteria
The Proteobacteria
The Low G + C Gram-positive Bacteria
The High G + C Gram-positive Bacteria
The Planctomyces, Spirochaetes, Fibrobacters,
Bacterioidetes,
and Fusobacteria
American Type Culture
Collection
•
•
•
•
•
•
•
•
Algae and Protozoa
Bacteria and Baceriophages
Cell Lines
DNA Materials
Fungi and Yeasts
Plant Tissues
Seeds
Viruses and Virus Antiserum
Eukaryotic
Cells
Domain Eukaryae
1. Membrane System
2. Compartmentalization
3. Membrane Enclosed
Organelles
4. Nucleus
Prokaryotic
Cells
Domain Bacteria &
Archaea
1. Few if Any Internal
Membranes
2. Plasma Membrane
Mediates Internal
Processes
3. Nucleoid
4. No Membrane Bound
Organelles
Viruses
•
•
•
•
•
Noncellular
Nonliving
Either DNA or RNA
Capsid (Protein Shell)
Envelope
Viruses
• Virus Species
A population of viruses with similar
characteristics that occupy a particular
ecological niche.
• No Independent Metabolism or
Replication
• Requires a Host (Parasitic)
Viral Replication
1.
2.
3.
4.
5.
Attachment
Penetration
Disassembly
Reassembly
Release
Major Criteria and Methods
Used in the Taxonomy of
Microorganisms
Classical Approach Uses These Tools
•
•
•
•
•
•
Morphology
Differential Staining
Biochemical Tests
Oxygen Requirements
Serology
Phage Typing
Molecular Approach Uses These
Tools
•
•
•
•
•
•
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
identification
Dichotomous Keys
(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
Cladogram
Disease Causing
Microorganisms
• Among the almost infinite varieties of
microorganisms, relatively few cause
disease in otherwise healthy individuals.
Koch’s Postulates
• 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
tuberculosis.
Diagnosis
• Diagnosis of infectious disease sometimes
involves identifying an infectious agent
either directly or indirectly.
Culturing Bacteria
• 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
that medium.
Staining Bacteria
• 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
• 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
species.
Immunological Tests
• Immunologic or Serological methods are
highly sensitive, specific and often
extremely rapid tests used to identify
microorganisms.
• 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.
Molecular Diagnostics
• 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
been identified.
• 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.