TAXONOMY AND NOMENCLATURE OF BACTERIA by zEmOwYN

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									 TAXONOMY AND
NOMENCLATURE OF
   BACTERIA
                Short history:
   Linné:
     Swedish   biologist / 18th century
     Understood that biologists required an
      internationally recognized scheme: precise
      and concise
     Proposed a latin binominal nomenclature
      consisting of name of genus and species
     Adopted – still in use
     Written in italics
    Historical Perspective of
Bacterial Phylogenetic Analyses:
            Pre-1977

                 1923 - Bacterial
                  Taxonomy:
                 Bergey's Manual of
                  Determinative
                  Bacteriology
                 “Species”
                  description
1925-1965
C.B. van Niel and Roger Stanier
Attempts to classify bacteria
Formulate the prokaryote/eukaryote concept
By the 1960’s express a frustration at the inability of establishing a
satisfactory bacterial phylogeny.


1945 - 1965 Birth and growth of molecular biology based on
studies with bacteria.
Around the 1970’s a whole generation of microbiologists is trained
with “no interest in phylogeny” (and evolution) \
1977 - The “Woesian”
     Revolution
   Carl Woese - a chemist working
    in relative isolation compares
    1977
    16S rRNA sequences and
    discovers that:
   1) “Archaebacteria” represent a
    new kingdom
   2) A universal and quantitative
    phylogeny is possible
                   The taxonomy
   Essential in the practice of medical
    bacteriology
     Isolated   bacteria:
            To predict pathogenic activity (involvement) impossible
             to prove for each isolate “in vivo” models
            To predict epidemiological perspectives
     Predicted    capabilities flows from the work:
            Of many microbiologists
            Over two centuries
            Cumulative efforts
   Current formal nomenclature by identification
    using complex and cumulative methods
       In vitro tests:
                  Reflecting experience
                  Potential pathogenicity
       Are currently used for classification = under
        regulation of the International Committee for
        Systematic Bacteriology – ICBS:
            regularly reviews Bergey’s Manual of Systematic Bacteriology
            Publish 2nd edition /2001/five volumes approved lists of
             bacterial names (over 2300 historical species)
           The trivial classifications
 Are real and valid as those described in Bergey’s
  manual
 Exist because:
          Some workers percieve a new way of dividing bacteria that
           had a practical use and significance
          Other microbiologists recognized the utility of this division –
           have a consensual acceptance
   Sometimes lack mechanisms for a correct
    definition and regulation of any nomenclature.
    Ex. Term of Enterobacteria lack clear taxonomic
    definition.
       The process of classification
   Is based on characterization
         Of selected series of isolates (strains) of recognition of probable
          group
         By selected number of tests – description of group – compare by
          calculation of coefficient of similarity
   New isolates can be identified and named as being
    members of one of postulated taxa on the basis of:
         The similarity to the taxon description
         The similarity to reference strain
   Usually fewer tests are applied in current identification
    than in classification – tests selected for identification:
         That proved reproducible
         Discriminatory
         Convenient in performing
         inexpensive
            Characterization tests –
             Phenotyping methods
(1)   Microscopic morphology
     Cell shape – spheric (cocci), rods, spirillium
     Staining – Gram positive / negative
     Size: 0,1-10μm
     Arrangements – chains
     Capsule: present / absent
     Morphology and flagellar arrangements
     Spore presence, location in the cell
           Characterization tests
           Phenotyping methods
(2) Colony morhology: estimated on solid media
  by pure culture techniques
 Shape – round/oval/irregular
 Size – small/large/tiny
 Surface – rough/smooth
 Edge – thin/regular
 Mucoid
 Adherent/not
 Invading
(3) Growth on liquid media : uniform / in surface
                 Characterization tests
                 Phenotyping methods
(4) Biochemical tests
 Large scale development
 For routine identification (10-20) and for taxonomical
   characterization (>100)
 Based on:
      Metabolic (catabolic) activity on
               Sugars/polysaccharides
               Proteins and derivatives
               Lipids
               Nucleic acids
      Minimal organic growth requirements
               Organic acids
               minerals
      Tolerance to several chemicals
               Survival
               growth
      Growth conditions: pH, temperature, Na+, conc. Aer/anaerobes
              Characterization tests
              Phenotyping methods
(5) Enzymatic activity = enzyme toxin production
(6) Chemotaxonomy
= antigenic structure = serological
  characterization –ex: enterobacteria
= macromolecular structure of cell
The anvelope (murexin peptids, teichuronic
  /teichoic acids, lipids)
(7) Fingerprinting – a classification based on
  chemical composition of bacterial cell
        Complex profiles
        Difficult to perform – usually automate
        Very costly
     Types of media used in medical
              microbiology
   Nutrient media               GENERAL GROWTH

     NUTRIENT MEDIA
                                CONTAIN:
                          PROTEINS/DERIVATIVES
                         •EXTRACTS OF:
         BROTH           MEAT
                         YEAST\CASEIN
                         SOYA
           AGAR          FISH
                         •PEPTONES
                         •AMINOACIDS
        BLOOD AGAR          •SUGARS
                            COMPLEX STARCH
                            MONOSACCHARIDE – GLUCOSE
        CHOCOLATE AGAR      DISACCHARIDE - LACTOSE
                            •MINERALS
     Types of media used in medical
              microbiology
   Enrichment media:
          Always liquid
          Promote the growth of some bacterial groups inhibiting
           commensal organisms
   Selective media
          Inhibit undesirable microorganisms
               Bacteria – groups, species
               fungi
          Contain
             Nutrient complex
             Inhibitory system
             Indicatory system
             minerals
     Types of media used in medical
              microbiology
   Selective media:
     For   Gram-positive
        Cocci
        bacilli
     For   Gram-negative
        Enterobacteriaceae
        Vibrio
        Campylobacter
     For anaerobes
     For fungi
        Types of media used in medical
                 microbiology
   Test media
       For metabolic investigation
       Contain:
            Nutrient complex (not always)
            Substrate
            Indicator system
       Substrates:
            Proteins/ derivatives
            Hydrocarbonates
                  Sugars
                  Organic acids
            lipids
       Indicator of catabolic activity: pH indicator
                Numerical Taxonomy

   Numerical taxonomy is a method which is used
    to differentiate a large number of similar
    bacteria, i.e. species.

   A large number of tests (~100) are carried out
    and the results are scored as positive or
    negative. Several control species are included in
    the analysis.

   All characteristics are given equal weight and a
    computer based analysis is carried out to group
    the bacteria according to shared properties.
    Characterization tests - Genotyping
      methods – molecular genetics
DNA-based bacteria taxonomy
 Assays for guanine-cytosine/adenine-thymidine (GC/AT ratio)
 Detecting G+C content
            Large differences in between genera
            Small varieties inside genera
   DNA-DNA hybridization
            A marker strain/ DNA
            Test DNA extracted from researched strain
            Is recognized as the definitive test for similarity = more than 70% binding with less
             than 5% difference between binding – 96% sequence identity
            Limitations
                        Requires considerable expertise
                        Hampered by technical difficulties
                        Heteroduplex formation decreases markedly at supraspecies levels
   γRNA-16S
            Standard approach
            Various methods are available
            PCR – to amplify gene segment
            Has inevitable errors in proofreadings
                        Sequences for the same species can differ significantly.
         FEATURES DICTATING TAXONOMIC CHARACTERIZATION METHODS

Method           High    Through   Low     automated   Low costs          Differential level
                 speed   put       skill
                                                       capital   roming   genus     species    type

MORPHOLOGICAL    ++      ++        -       -           -         ++       +         -          -

COLONIAL         +++     +++       +       -           +++       +        +         +          -

BIOCHEMICAL      +       ++        ++      Possible    ++        ++       +         +          +

ENZYME           +++     ++        ++      Possible    ++        ++       +         +          +
DETECTION
ANTIGENIC        +++     ++        ++      Possible    ++        -        +         +          +

CHEMOTAXONOMY    -       -         -       -           -         -        +         +          +

FINGERPRINTING   +++     +++       +       Some        -         ++       +         +          +

DNA BASE RATIO   -       -         -       -           +         ++       -         -          -

DNA              -       -         -       -           +         +        +         +          -
HYBRIDIZATION
16SγRNA          -       +         +       -           ++        -        +         +          -
SEQUENCING

								
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