Identification and Classification
Living organisms are divided into groups to better understand relationships among species
Taxonomy is the science that studies organisms to order and arrange them
Taxonomy can be viewed in three areas Identification
Process of characterizing in order to group them Classification
Arranging organisms into similar or related groups Nomenclature
System of assigning names
Principles of Taxonomy
Strategies Used to Identify Prokaryotes Wide assortment of technologies used to
identify organisms including Microscopic examination Culture characteristics Biochemical test Nucleic acid analysis
Strategies Used to Classify Prokaryotes Understanding organisms phylogeny assists in
classification Allows for organized classification of newly
recognized organisms Development of molecular techniques for
classification and identification make genetic relatedness possible
Principles of Taxonomy
Taxonomic hierarchies Classification categories arranged in hierarchical order
Species – group of related isolates or strains Most basic unit
Genus – group of related species Family – collection of similar genera Order – collection of similar families Class – collection of similar orders Phylum – collection of similar classes Kingdom – collection of similar phyla Domain – collection similar to kingdoms
New taxonomic category
Principles of Taxonomy
Classification system No such thing as “official” classification system Scheme favored by most microbiologists is
three domain system Before three domain system five kingdom system
was used
Principles of Taxonomy
Principles of Taxonomy
Nomenclature Names given according to International Code
for the Nomenclature of Bacteria
Using Phenotype to Identify Prokaryotes Phenotype can be used in the process
identification of bacteria Methods used include
Microscopic morphology Metabolic capabilities Serology
Microscopic morphology Important initial step in identification
Can be used to determine size, shape and staining characteristics
Size and shape can readily be determined microscopically
Gram stain differentiate Gram + from Gram – Narrows possible identities of organism
Special stains Identifies unique characteristics of organisms
Acid fast stain
Using Phenotype to Identify Prokaryotes
Using Phenotype to Identify Prokaryotes
Metabolic capabilities Identification relies heavily
on analysis of metabolic capabilities
Culture characteristics Colony morphology can
give clues to identity Red pigment of Serratia
marcescens Biochemical tests
More conclusive identification
Most test rely on pH indicators
Commercial biochemical tests allow for series of test with single inoculation
Serology Technique relying on specific interaction
between antibodies and antigens Serological tests are available for rapid
detection of numerous organisms Streptococcus pyogenes the causative agent of
strep throat
Using Phenotype to Identify Prokaryotes
Using Genotype to Identify Prokaryotes Nucleic acid probes can locate unique
nucleotide sequence of a particular species Numerous technologies discussed previously
are being used to identify organisms based on genotype
Advantage Identification of organism that can’t be grown
in culture
Using Genotype to Identify Prokaryotes
Using PCR Used to amplify sequences
that allow for detection of specific sequences for identification
Sequencing ribosomal RNA genes There is little genetic variation
in rRNA Newer technologies are
available to sequence rDNA The DNA that encodes rRNA
Characterizing Stain Differences
Biochemical typing Biochemical tests can be used to identify species
They can also be used to identify strains by tracing specific biochemical characteristics called biovar or biotype
Serological typing Identification made based on differences in
serological molecules Serological characteristics are termed serovar or
serotype
Characterizing Stain Differences
Phage typing Certain strains of given species susceptible to various
bacteriophages a.k.a phage
Virus that infect bacteria
Phage typing identifies organism by phage that infect them Phage type has been largely replaced by molecular
methods
Antibiograms Identifies organism
based on antibiotic susceptibility
Disc impregnated with antimicrobial placed on inoculated plate
Clear are indicates microbial susceptibility
Different strain will have different susceptibility patterns
Characterizing Stain Differences
Classifying Prokaryotes
Classification historically based on phenotype Size, shape, staining characteristics and metabolic
capabilities New molecular techniques make identification more
accurate Allows for accurate construction of phylogenetic tree
Trees show divergence and relationships between organism
Molecular techniques highlighted transfer mechanism of prokaryotic cells
Horizontal or lateral transfer of DNA
Sequencing methods include 16s rDNA sequence analysis
Comparison of 16s rRNA and rDNA sequences revolutionized classification
Lack of mutation allows identification of distant relatedness
DNA hybridization better tool for assessing related ness on species level
Classifying Prokaryotes
DNA hybridization Relatedness of organism can be determined
by similarity of nucleotide sequences Sequence homology is measured by DNA
hybridization Extent of hybridization reflects degree of
similarity If two strain show high percentage of DNA
hybridization they are considered related 70% similarity is considered same species
Classifying Prokaryotes
DNA base ratio Comparison of genomes to determine DNA
base ratio Looking at relative proportion of A:T and G:C
bonding in DNA Base ratio is expressed in G:C content
If GC ratio deviate more than a little organism are not related
Similarity of base composition does not mean relatedness
Classifying Prokaryotes