Taxonomy Micro

Document Sample
Taxonomy Micro Powered By Docstoc
					                  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
•   Multicellular
•   Heterotrophs
    Plantae
•   Multicellular
•   Photoautotrophs
      Fungi

•   Absorptive
    Chemoheterotrophs
•   Decomposers
    Protista

•   Unicellular
•   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
• Kingdom Through Species
• Binomial Nomenclature
• 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


•   Membrane System
•   Compartmentalization
•   Membrane Enclosed
    Organelles
•   Nucleus
    Prokaryotic
    Cells
    Domain Bacteria &
    Archaea

•    Few if Any Internal
     Membranes
•    Plasma Membrane
     Mediates Internal
     Processes
•    Nucleoid
•    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
    •   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.

				
DOCUMENT INFO
Shared By:
Categories:
Tags:
Stats:
views:3
posted:5/9/2014
language:English
pages:81