Download Classification of microorganisms

Classification of microorganisms
(and everything else for that matter)
•  TAXONOMY - the science of the
classification of organisms
•  Purpose
– to show evolutionary relationships
between groups
– to provide a means of identifying
organisms
Two methods of classification
•  Most scientists favor a PHYLOGENETIC
classification scheme; this reflects the actual
ancestry (evolutionary relationships)
between different organisms
•  Phenetics is an alternative method, in which
classification of organisms is based solely
on observable characteristics, and the goal
is more practical - identification and
common language.
The Five-kingdom System
•  Monera - unicellular prokaryotes (bacteria)
(based upon cellular organization)
•  Protista - unicellular eukaryotes (protozoa, algae)
(based upon cellular organization)
•  Fungi - multicellular heterotrophs with external
digestion (yeasts,molds, mushrooms) (based upon
nutritional pattern)
•  Plantae - multicellular autotrophs (plants) (based
upon nutritional pattern)
•  Animalia - multicellular heterotrophs with
internal digestion (animals) (based upon
nutritional pattern)
The three Domains
•  A domain is considered to be a new level
apart from Kingdom, based on the fact that
cells are really of three fundamental types:
•  Eukarya (eukaryotes)
•  Bacteria (most bacteria)
•  Archaea (archaebacteria) - no peptidoglycan
in cell walls, extreme environments and
strange biochemistry. Molecular studies of
their DNA reveal they are not very related to
eubacteria.
The Linnaean Taxonomic Hierarchy
•  Traditionally has 7 tiers (8 if you count the
domains)
•  Domain, Kingdom, Phylum (Division), Class,
Order, Family, Genus, Species
•  The tiers go from most inclusive to least, until
you reach the species or specific name, usually
denoted as genus and species. This is called a
binomial designation, and MUST BE
underlined or italicized. Also, the genus name
must be capitalized.
•  Examples - Escherichia coli, Homo sapiens
Examples: Classify this!
• 
• 
• 
• 
• 
• 
• 
• 
• 
Human being
Domain - Eukarya
Kingdom - Animalia
Phylum - Chordata
Class - Mammalia
Order - Primates
Family - Hominidae
Genus - Homo
species - sapiens
• 
• 
• 
• 
• 
• 
• 
• 
• 
Dog
Domain - Eukarya
Kingdom - Animalia
Phylum - Chordata
Class - Mammalia
Order - Carnivora
Family - Canidae
Genus - Canis
species - familiaris
Examples: Classify this!
• 
• 
• 
• 
• 
• 
• 
• 
• 
Human being
Domain - Eukarya
Kingdom - Animalia
Phylum - Chordata
Class - Mammalia
Order - Primates
Family - Hominidae
Genus - Homo
species - sapiens
• 
• 
• 
• 
• 
• 
• 
• 
• 
A bacterium like E. coli
Domain - Bacteria
Kingdom - Monera
Phylum - Gracilicutes
Class - Scotobacteria
Order - Enterobacteriales
Family - Enterobacteriacieae
Genus - Escherichia
Species - coli
Bacteria are classified according to...
•  Bergey’s Manual of Bacteriology
•  In 1923, the first edition of the Manual was published
under the auspices of the organization that is today the
American Society for Microbiology (Dr. David H.
Bergey was the Chairman). •  The official title of this publication is “Bergey’s Manual
of DETERMINATIVE Bacteriology.” The latest edition
was published in 1994.
•  It should be clear that through much of its history, the
classification was performed based on “observable
characteristics”, or phenetics, although care was taken to
try to reflect phylogeny as much as was possible.
Characteristics used to classify bacteria
• 
• 
• 
• 
• 
• 
Morphological characteristics (shape, etc.) Differential Staining (Gram stain)
Nutritional Pattern
Relationship with oxygen
Biochemical characteristics (eg, catalase +/-)
Serological analysis - ability of specific antibodies to react
with specific microbe
•  Phage typing - can bacteria be infected by the same phage
•  Protein and DNA sequencing are becoming more popular powerful! (These are not considered “observable
characteristics”, and are the basis for more modern
classification schemes.)
Bacterial classification is changing!
•  Since the advent of sophisticated DNA, RNA and protein
analysis techniques, more data on phylogeny has emerged,
and is continually emerging. •  Therefore, the first edition of “Bergey’s Manual of
SYSTEMATIC Bacteriology” was published during the
1980s to reflect phylogeny - the categories in this book are
quite different, and it is clear that the DETERMINATIVE
Manual has limitations. It is also useful, however, if your
goal is identification, and as the transition to a fully
phylogenetic classification is realized. The second edition
of the SYSTEMATIC Manual was finished in 2003.
•  Another philosophical problem - what is a
species anyway?
•  A species is usually defined as a group of
potentially interbreeding organisms that can
produce viable offspring.
•  Does this work for bacteria?
•  No.
•  Why?
•  Sex again!!
I think you have gathered
•  Bacteria do not have sex!!!!!
•  So, a bacterial species is usually defined as a
population of cells with similar characteristics.
How similar? It's sort of subjective!!!
•  The current convention is that more than 3%
difference in overall genome sequence reflects
membership in a different species.
•  But, remember - both the sexual and non-sexual
definitions are just ways of getting at similarity.
Viral classification
•  Traditionally, as we know, viruses are not
considered alive and thus are not classified in
any of the preceding groups. •  However, we still need to identify types of
viruses for clinical and evolutionary reasons (e.g.
HIV!)
•  So, a viral species is defined as a population of
viruses that have similar characteristics.
•  Some scientists have proposed that viruses get classified
according to whom they can infect - makes sense
evolutionarily, but not in common usage.