KB

Identifying and Classifying Microorganisms

Classification of Organisms

  • Taxonomy - The Science that studies organisms to arrange them into groups
    • Taxa

Three separate but interrelated areas

Identification

      • process of characterizing in order to group

Classification

      • Arranging organisms into similar or related groups

Nomenclature

      • system of assigning names

Previous classification schemes

  • Whittaker (1960's) devised the 5 Kingdom Classification
    • plantae, fungi, animalia, Protista, and monera
    • The first four kingdoms are eukaryotes and the 5th is a prokaryote
  • classification is often based on appearance and physiology

Current Classification Scheme

  • Carl Woese with Kandler and Wheeler (1970s)
  • Based on evolutionary relatedness (phylogeny) as determined by RNA

Domains

    • Eucarya
    • Bacteria (Eubacteria) > Prokaryotes
    • Archaea > Prokaryotes

Three domain system

Bacteria

    • Prokaryotic cell structure, no membrane-bound organelles
    • Ribosomal RNA nucleotide sequences that are unique to the group
    • Unicellular
    • Contains peptidoglycan

Archaea

    • Prokaryotic cell structure, no membrane-bound organelles
    • Ribosomal RNA nucleotide sequences that are unique to the group
    • Unicellular
    • No peptidoglycan

Eukarya

    • Eukaryotic cell structure, including a nucleus and other membrane-bound organelles
    • Ribosomal RNA nucleotide sequences that are unique to the group
    • Unicellular or Multicellular
    • No peptidoglycan

Hierarchical Scheme of Classification

Domain

    • relatively new taxonomy category that reflects the characteristics of the cells that make up the organism

Kingdom

Phylum

    • used in plant classification

Class

Order

    • In prokaryotic nomenclature, the name of the order ends with the suffix -ales

Family

    • In prokaryotic nomenclature, the name of the order ends with the suffix -acene

Genus

Species

    • A group of closely related isolates or strains
    • species can be subdivided into strains
    • not all members are identical

Determining Relatedness

How do we determine phylogeny for microorganisms?

    • more difficult for microorganisms
    • How to determine species with something that doesn't Sexually reproduce?
    • very few differences in Size and Shape
    • Traditionally used phenotypic characteristics but new advancements have allowed us to determine actual phylogeny
    • Informal phenotypic groupings are still a convenient way to categorize organisms and are based on a number of different categories.
      • Both phenotypic and genotypic

Using Phenotype

Microscopic Morphology

    • the first step in identifying a microorganism is to determine its Size, shape, and staining characteristics
    • Size and shape can put the organism into a broad category
    • Stains like gram stain and special Stains

Culture Characteristics

    • How does it grow, color, appearance, smell, growth on differential and selective media

Metabolic Capabilities

    • Biochemical tests, does it ferment, what does the organism react with

Serological Characteristics

    • serologial testing uses antibodies to detect specific proteins and polysaccharides
    • Different bacteria have different characteristics

Proton Profile

    • MALDI-TOF MS ( Matrix-assisted laser desorption ionization on time of flight mass Spectrom)
    • The type of mass spectrometry that determines the chemical composition of a Sample by measuring the masses of the various components
    • very fast

Using Genotype

Detecting Specific Nucleotide sequences

    • methods to detect nucleotide sequences unique to a given species or related group
    • makes it possible to identify organisms that can't be cultured
    • can only detect a single option

Nucleic Acid Amplification Tests (NAATs)

    • collective term including PCR
    • can defect a small amount of microorganisms and identify markers

DNA Probes

    • A tagged piece of single-stranded piece of DNA that is complementary to a sequence of interest is used to identify segments of DNA in the unknown microorganisms
    • fluorescence in situ hybridization (FISH)

Sequencing Ribosomal RNA Genes

    • nucleotide Sequence of ribosomal RNA molecules (RNA) or the DNA that encodes them (rDNA)
      • can be used to identify microbes

Whole Genome Sequencing

    • sequencing the whole genome
    • used to study outbreaks
    • can predict antibiotic resistance

Strains

  • a group of related isolates
  • All Members of a species are not Identical
  • Strains May vary in minor ways
  • has to be decided when an organism is sufficiently different to group as a different species

Binomial Nomenclature (Carl Linnaeus)

  • Each species is identified by 2 names
  • Genus is the first name
    • the first letter capitalized
  • Species is the second name
    • no capitalization
  • must be Italicized

Bacteria

  • Single-celled prokaryotes
  • small
  • no nucleus or other organelles
  • specific shapes
  • most have rigid walls, contain peptidoglycan
  • multiply via binary fission (asexual)
  • Many have appendages (flagella)
  • No introns/splicing
  • 70s ribosomes
  • Domain Bacteria
    • most bacteria are harmless or beneficial

Beneficial Microbes

      • Prevent diseases by competing with pathogens
      • Development of immune system response
      • Aide in digestion
      • Food- Cheese and yogurt
      • Decomposers
      • oxygen production
      • Nitrogen fixation (plants)
      • use as a model organism
      • Genetic engineering
      • Bioremediation - use of organisms to remove or neutralize pollutants from a contaminated site
      • Microbes interact with us in ways we are just beginning to understand-microbiomes
    • Pathogenic microbes
    • some bacteria cause harm, disease, and death
    • Tuberculosis, tenatus, bubonic plague, diphtheria, food poisoning, syphilis, and leprosy

Archaea

common features

    • Prokaryotic and Unicellular
    • Small
    • specific shapes
    • look like bacteria
    • no nucleous or organelles
    • binary fission
    • can have appendages
    • Introns sometimes
    • 70s ribosomes
    • rigid cell walls without peptilogycan
    • Grow in extreme environments
      • high salt and other chemieals
      • extreme temps

Eukarya

common features

    • multicellular or single celled organisms
    • Eukaryotic cell structure
    • contains organelles
    • Large
    • has a nuclear membrane (no loose DNA)
    • Engages in mRNA splicing (mRNA has introns)
    • no peptidoglycan

Includes

Algae

      • diverse group of photosynthetic eukaryotes, single or muti-celled

Fungi

      • diverse group including yeasts and molds, single or multicelled

Protozoans

      • A diverse group of single aquatic or terrestrial organisms. complex and large

Mammals

Helminths

      • Parasitic worms that live at the expense of the host
      • Round worms, tapeworms, and flukes
      • Cause of disease, Particularly in developing countries
      • Adult worms are Macroscopic
      • eggs and larvae are microscopic

Acellular

Viruses

    • nucleic acid surrounded by a protein coat
    • needs host machinery to replicate
    • All forms of life can be infected

Viroids

    • simpler than viruses
    • short RNA without a protective coat
    • can only reproduce in cells
    • cause plant disease
    • some scientists speculate they may cause disease in humans.

Prions

    • only consist of protein
    • Infectious proteins: misfolded versions of normal cellular proteins in the brain
    • Abnormal form can cause fatal neurodegenerative diseases in humans and animals