Identification and Classification of Prokaryotes

Chapter 10

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