CLASSIFICATION

• CLASSIFICATION OF MICROORGANISMS

  
• It is estimated that the number of living species rangers from 10 to 100 million. 1.7 million identified.
• Purpose of All Species Inventory

  To identify and record every species of life on Earth in the next 25 years
• All Species Inventory launched

  2001
• Taxonomy


  Putting organisms into categories or taxa, to show degrees of similarities among organisms
• Systematics/Phylogeny


  The study of evolutionary history of organisms

  
• Categorisation of organisms by historical figures

  • Aristotle - categorized organisms in two ways, plants and animals
  • Carolus Linnaeus - introduced a format system of classification with two kingdoms - Plantae and Animalia
  • Carl von Nägeli - proposed that bacteria and fungi be placed in the plant kingdom
  • Ernst Haeckel - proposed the kingdom Protista to include bacteria, protozoa, algae, Fungi
  • Robert G. E. Murray - proposed the Kingdom Prokaryotae

  
• The Three Domains


  • Eukarya - Animals, Plants, Fungi
  • Bacteria - Pathogenic prokaryotes, Non-pathogenic prokaryotes, Photoautotrophic prokaryotes
  • Archea - Prokaryotes that do not have peptidoglycan in their cell walls and carry out unusual metabolic process, often live in extreme environments
• Binomial Nomenclature


  Organisms are given two names - Genus (always capitalize, noun) and Specific epithet (species, lowercase, usually an adjective)
• A scientific name is usually followed by the author's name in an abbreviated form; underlined if handwritten and italicized if typewritten
• The Taxonomic Hierarchy


  • Phyla that related to each other
  • Related kingdoms
  • Related classes
  • Similar orders
  • Similar families
  • Related genera
  • Related species
• Prokaryotic Species


  A population of cells with similar characteristics, members of a bacterial species are nearly indistinguishable from each other but are distinguishable from members of other species usually on the basis of several features
• Types of Bacterial Cultures


  • Culture - bacteria grown in media
  • Mixed Culture - more than one organism
  • Pure Culture - often a clone, a population of cells derived from a single parent cell
  • Strain - pure cultures of the same species that are not identical; subtype of microorganism
• Links to videos on spread plate, pour plate, and streak plate techniques
• Kingdom Fungi


  • Includes unicellular yeasts, multicellular molds, and macroscopic species such as mushrooms
  • Absorbs dissolved organic matter to obtain raw materials for vital functions
  • Fungi develop from spores or from fragments of hyphae
• Kingdom Plantae


  • Mosses, ferns, conifers, and flowering plants
  • All members are multicellular
  • They use photosynthesis, process that converts carbon dioxide and water into organic molecules used by the cell
• Kingdom Animalia


  • Sponges, worms, insects, and animals with backbones (vertebrates)
  • Obtain nutrients and energy by ingesting organic matter through a mouth of some kind
• Viruses


  • Aren't classified as part of any of the three domains
  • Aren't composed of cells, and they use the anabolic machinery within living host cells to multiply
  • Viral genome can direct biosynthesis inside a host cell, and some viral genomes can be incorporated into the host cell
  • The ecological niche of a virus is its specific host cell
  • Viruses may be more closely related to their hosts than to other viruses
  • Viruses are obligatory intracellular parasites
  • Viral genes carried in the genomes of other organisms provide a record of viral evolution
• Viral Species


  A population of viruses with similar characteristics (morphology, genes, enzymes) that occupies a particular ecological niche
• Hypotheses on the origin of viruses

  • They arose from independently replicating strands of nucleic acids (plasmids)
  • They developed from degenerative cells that, through many generations, gradually lost the ability to survive independently but could survive when associated with another cell
  • They coevolved with host cells
• Classification


  Placing organisms in groups of related species, lists of characteristics of known organisms

  
• Identification


  Matching characteristics of an "unknown" to lists of known organisms
• Morphological Characteristics


  • Higher organisms are frequently classified according to observed anatomical detail
  • Many microorganisms look too similar to be classified by their structures alone
  • Morphological characteristics are still useful in identifying bacteria to know the differences in structures such as endospores or flagella

  
• Differential Staining


  • One of the first step in identifying bacteria, includes Gram staining and Acid-fast staining
  • These stains are based on the chemical composition of cell walls and not useful in identifying wall-less bacteria and unusual walls of archaea
  • Microscopic examination of a Gram stain or an acid-fast stain is used to obtain information quickly in the clinical environment

  
• Biochemical Tests


  • Enzymatic activities are widely used to differentiate bacteria
  • Closely related bacteria can usually be separated into distinct species by subjecting them to biochemical tests
  • Biochemical test can provide insight into species' niche in the ecosystem
• Characteristics of Enteric Gram-Negative Bacteria

  • Large heterogenous group of microbes whose natural habitat is the intestinal tract of humans and other animals
  • This family contains several pathogens that cause diarrheal illness
  • All members of the family Enterobacteriaceae are oxidase-negative
  • Lactose Fermenting - Escherichia, Enterobacter, Citrobacter
  • Non-Lactose Fermenting - Salmonella and Shigella
• Selective Media


  Contains ingredients that suppress the growth of competing organisms and encourage the growth of desired ones
• Differential Media


  Contain compounds that allow groups of microorganisms to be visually distinguished by the appearance of the colony or the surrounding media
• Examples of Selective and Differential Media


  • MacConkey Agar - used for the isolation and differentiation of non-fastidious gram-negative rods, particularly members of the family Enterobacteriaceae and the genus Pseudomonas
  • Brilliant Green Agar - selective isolation medium for Salmonella species
  • Eosin Methylene Blue Agar - differential medium that slightly inhibits the growth of Gram-positive bacteria and provides a color indicator distinguishing between organisms that ferment lactose and those that do not
  • Cetrimide Agar - selective medium used for the isolation and identification of Pseudomonas aeruginosa
• A limitation of biochemical testing is that mutations and plasmid acquisition can result in strains with different characteristics, and unless a large number of tests is used, an organism could be incorrectly identified
• Rapid Identification Method


  Manufactured for groups of medically important bacteria, designed to perform several biochemical tests simultaneously and can identify bacteria within 4 to 24 hours
• Serology


  The science that studies serum and immune responses that are evident in serum, microorganisms are antigenic and antibodies are proteins that circulate in the blood and combine in a highly specific way with the bacteria that caused their production
• Antiserum


  Solutions of antibodies, commercially available
• Slide Agglutination Test


  1. Samples of the unknown bacterium are placed in a drop of saline of each of several slides

  2. A different known antiserum is added to each sample

  3. The bacteria agglutinate (clump) when mixed with antibodies that were produced in response to that species or strain of bacterium
• Enzyme-linked immunosorbent assay (ELISA)

  Widely used because it is fast and can be read by computer scanner, known antibodies are placed in the wells of a microplate, an unknown type of bacterium is added to each well, a reaction between the unknown antibodies and the bacteria provides identification of the bacteria
• Western Blotting


  A laboratory technique used to detect a specific protein in a blood or tissue sample, involves using gel electrophoresis to separate the sample's proteins and then transferring the separated proteins out of the gel to the surface of a membrane
• Phage Typing


  Looks for similarities among bacteria, useful in tracing the origin and course of a disease outbreak, is a test for determining to which phages a bacterium is susceptible, bacteriophages (phages) are bacterial viruses that cause lysis of the bacterial cells they infect and are highly specialized, they infect only members of a particular species
• Phage Typing Procedure


  Starts with a plate totally covered with bacteria growing on agar, a drop of each different phage is placed on the plate
• Western Blotting


  A laboratory technique used to detect a specific protein in a blood or tissue sample. The method involves using gel electrophoresis to separate the sample's proteins. The separated proteins are transferred out of the gel to the surface of a membrane.
• HIV infection


  Confirmed by Western blotting