Taxonomy and Classification

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Taxonomy and Classification

• Classification of Microbes

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Taxonomy

• Science of Classification of organisms
• Hopes to show relationships among organisms
• Is a way to provide universal identification of
  an organism
• Why do we care things are related?

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QA

• Pneumocystis jirovecii was thought to be a
  protozoan until DNA analysis showed it is a
  fungus. Why does it matter whether an organism is
  classified as a protozoan or a fungus?

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Phylogenyor Systematics

• Shows evolutionary relationships and history
  among organisms
• Some obtained from fossil record
• Most bacteria use rRNA sequencing or some other
  sequence information
• A goal is to identify all organisms by 2025

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Hierarchy

• Evolutionary relationships
• Species are groups that interbreed (have
  productive sex)
• How this goes

• Species
• Genus
• Family
• Order
• Class
• Division
• Phylum
• Kingdom (1969)
• Domain (80s)

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The 5 Kingdoms based on nutrient procurement

• Plantae
• Multicellular photoautotrophs
• Animalia
• ingestive
• Fungi
• absorptive
• Protozoa
• Mostly singe celled
• Prokaryotes

• Which of these are microbes?

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The 3 domains

• Eukarya
• Plants, animals fungi and protists
• Bacteria
• (with peptidoglycan)
• Archaea
• With unusual cell walls, and membreanes

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The Three-Domain System
Figure 10.1
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The Three-Domain System
Table 10.1
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Endosymbiotic Theory
Figures 10.2, 10.3
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Table 10.2
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Scientific Nomenclature

• Binomial genus and specific epithet (species).
  Is used world wide
• Is always underlined
• Rules for naming are set by international
  committees
• International Code of Zoological Momenclature
• International Code of Botanical Nomenclature
• Bacteriological Code and Bergeys Manual

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Scientific Names
Scientific Binomial Source of Genus Name Source of Specific Epithet
Klebsiella pneumoniae Honors Edwin Klebs The disease
Pfiesteria piscicida Honors Lois Pfiester Disease in fish
Salmonella typhimurium Honors Daniel Salmon Stupor (typh-) in mice (muri-)
Streptococcus pyogenes Chains of cells (strepto-) Forms pus (pyo-)
Penicillium chrysogenum Tuftlike (penicill-) Produces a yellow (chryso-) pigment
Trypanosoma cruzi Corkscrew-like (trypano-, borer soma-, body) Honors Oswaldo Cruz
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Species Definition

• Eukaryotic species
• A group of closely related organisms that breed
  among themselves
• Prokaryotic species
• A population of cells with similar
  characteristics
• Clone Population of cells derived from a single
  cell
• Strain Genetically different cells within a
  clone
• Culture grown in the lab
• Viral species
• Population of viruses with similar
  characteristics that occupies a particular
  ecological niche

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Is it as easy to classify Microbes as it is
Macrobes?

• How to classify
• What do we have to look at?

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Identifying Bacteria
Applications, p. 283
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Phylogenetic Relationships of Prokaryotes
Figure 10.6
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Of more than 2600 species identified so far

• Only about 250 or 10 are pathogens

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Classification and Identification

• Classification Placing organisms in groups of
  related species. Lists of characteristics of
  known organisms.
• Identification Matching characteristics of an
  unknown organism to lists of known organisms.
• Clinical lab identification

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Bergeys Manual of Systematic Bacteriology

• Morphological characteristics
• Presence of various enzymes
• Serological tests
• Phage typing
• Fatty acid profiles
• DNA finger printing
• Sequence of ribosomal RNA
• Is still very difficult

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Identification Methods

• Morphological characteristics Useful for
  identifying eukaryotes
• Differential staining Gram staining, acid-fast
  staining
• Biochemical tests Determines presence of
  bacterial enzymes

A dichotomous key
Figure 10.8
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A clinical microbiology lab report form
Figure 10.7
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Identifying a Gram Negative, Oxidase Negative
Rod
Figure 10.8
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• Unknown enteri inoculated into tube
• After incubation the 15 tests are observed
• A numerical score is assigned
• The species is assigned
• This may be of is the strain has changed somehow.
  More tests are required

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• Design a rapid test for a Staphylococcus aureus.
  10-14

Figure 6.10
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Serology study of serum and its immune responce

• Combine known antiserum unknown bacterium
• Slide agglutination
• ELISAp288, 514
• Western blotp289
• Southern Blot p292
• DNA chip p293

Figure 10.10
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• Strains with different antigens are called
• Serotypes
• Serovars
• biovars

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DNA Hybridization
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Phage Typing
Determining a strains suceptability to certain
phage or bacterial viruses
Figure 10.13
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The Western Blot
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Flow Cytometry

• Uses differences in electrical conductivity
  between species
• Fluorescence of some species
• Cells selectively stained with antibody plus
  fluorescent dye

Figure 18.12
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A typical dichotomous key See appendix H in
your lab book
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Genetics

• DNA base composition
• Guanine cytosine moles (GC)
• DNA fingerprinting
• Electrophoresis of restriction enzyme digests
• rRNA sequencing
• Polymerase Chain Reaction (PCR)p251

Figure 10.14
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Nucleic Acid Hybridization DNA chip
DNA Chip Technology
Figure 10.17
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Differentiate between classificaiton and
identification
Figure 10.5
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FISH

• Fluorescent in situ hybridization
• Add DNA probe for S. aureus

Figure 10.18
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Differentiate between strain and species?
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Classification of viruses?

• Not currently placed in Domains or Kingdoms
• Why?
• Species are usually a population of viruses with
  similar characteristics that occupies a
  particular ecological niche.

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Dichotomous keys are used for identification of
organisms
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Cladograms show phylogenetic relationships among
organisms
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Differential staining

• Name examples

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The gram stain
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Using Bergies manual

• Used to Identify bacteria not classify
• Features that are used to differentiate various
  organism often have little to do with arranging
  the orgs in taxonomic groups

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4 major groups

• Domain Bacteria
• Gram-negative Eubacteria that have cell walls.
  Proteobacteria
• Non proteobacteria Gram negative bacteria
• Gram positive Eubacteria that have cell walls
• Domain archaeobacteria

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Some groups by identificaiton

• Spirochetes
• Genus Borrelia, Leptospira, Treponema
• Aerobic/microaerophilic, motikle, helical/vibroid
  gram negative bacteria
• Geneus Camphylobacter
• Gram negative aerobic/microaerophilic rods and
  cocci
• Genus Agrobacterium, Alcaligenes, Pseudomonas
• Facultatively anaerobic gram negative rods
• Genus Enterobater, Escherichia, Klebsiella,
  Serratia, Shigella, Yersinia, Eikenella
• Gram positive Cocci
• Genus lactococcus, streptococcus, Staphylococcus
• Endospore forming gram positive rods and cocci
• Genus bacillus, clostridium
• Regular, nonsporing gram positive rods
• Genus Lactobacillus, listeria