MGY277H1 Lecture 7: Lecture 7

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Unit 7  Microbial Identification and Classification
Classification of Unicellular Microbes
Phylogeny  the evolutionary history of development of a group of organisms (or
even protein or gases)
Phylo clam/tribe in greek
Genesis the origin
Phylogenetic the study of evolutionary relationships between organisms and the
construction of an accurate and complete “tree of life” that faithfully tells us how all
the current species arose is its ultimate goal
Ernst Haeckel’s tree a tree of life in 1866 which include 3 main branches
1. Plants
2. Animal
3. Protista (include bacteria “Moneres”)
Taxonomy the study and creation of hierarchical systems for classifying
and identifying organisms
(Important to phylogeny)
1. How di we build that tree?
2. How did we know where to place each species?
3. What’s a species
Principles of Taxonomy
Taxonomy is the science that studies organisms to arrange them into groups
or tact
3 separate but interrelated areas
1. Classification arranging organisms into similar or related groups and
defining what set of features defines a group/taxa
2. Nomenclature system of assigning name
3. Identification process of characterizing a microbe to determine group
where it belongs (also figure out where an unknown microbe belong)
Strategies to Classify Prokaryotes
Determining phylogeny of prokaryotes is difficult
Higher oragnisms may be morphologically similar and capable of
interbreeding to produce viable offspringthen they are the same species
Prokaryotes are similar in physical characteristics (size, shape) and DO NOT
undergo sexual reproduction difficult to apply same classification criteria
Classically relied heavily on phenotypic characteristic for classification
oHowever, this could be extremely bias and unreliable depending on
the phenotype you choose
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Goal of classifying Prokaryotes
Group according to evolutionary relatedness phylogeny
Classification historically based on phenotypic traits
oSize, shape, staining, metabolic capabilities
oDrawbacks:
Phenotypic differences can be due to few gene products/single
mutations may affect organism’s capabilities
Phenotypically similar organisms may be only distantly related
or closely related organisms may appear dissimilar
NOW molecular techniques are more accurate and less prone to human
bias
oProvide greater insights into evolutionary relatedness
oDNA sequences viewed as evolutionary chronometersrelative
measure of the amount of time that has passed since the last time 2
microbes shared a common evolutionary ancestor (we expect more
diverse as time pass)
DNA sequencing allows construction of phylogenetic tree/chronometers
Current classification system Three Domain System
NO official classification system
System change as new information is discovered
3 Domain system by (Carl Woese et,al), is currently
favoured Compared rRNA nucleotide sequences
rRNA is a universal molecule of cellular life, thus may be used to compare the
evolutionary realtness between cells
This system is almost entirely built upon looking at the 16S rRNA
Three domain
system is
based on
evolutionary relatedness
Replaces 5 Kingdom system
Plantae, Animalia, Fungi, Protista, Prokaryotae
Based on obvious morphological differences
DOES NOT reflect recent genetic insights of ribosomal RNA data indicating
plasnt, animals more closely related than Archaea, Bacteria
The Kingdom os Projaryotes no longer exists
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System to Classify Prokaryotes
Taxonomic Hierarchies
Species is basic unit of taxonomy  a group of
closely related isolates or strains (permits
identification)
The use of “kingdoms” is still in state of flux (NOT
in bacteria/archaea anymore)
Informal groupings also used (phenotype)
May be genetically unrelated but share similar
phenotype
oLactic acid bacteria
oAnoxygenic phototrphs
oEndospore-formers
oSulfate reducesrs
Classifying Prokaryotes
Phylogenetic tree shows evolutionary relatedness
But DNA sequencing also highlight obstacle
Horizontal (lateral) gene transfer complicates
DNA comparisons
oE.g. Bacterium Thermotoga maritime appears
to have acquired ~25% of genes from archaeal
species
Some scientists have proposed a shrub with interwoven
branches
What are strains?
Sub-species and Strains
are level of
categorization
underneath species
Strain typically identify specific isolated of a given species
There may be
considerable variation
between different
strains of a single species
E.coli MGI 655 (aka K12)
most common lab strain of E.coli, 1st isolated in 1922 from a patient with
diaphtheria (e.coli does not cause diphtheria)
E.coli XLI-Blue a manipulated version of MGI655 to make it easier to get
plasmic DNA into and out of
E.coli Sakai (O I57: H7) a cause of severe intestinal/Hamburger disease
E.coli CFT 073 isolated from a urinary tract (bladder) infection
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