Identification and Classification of Prokaryotes

1. Identification and Classification of Prokaryotes Chapter 10

2. 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

3. 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

4. Principles of Taxonomy • 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

5. 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

6. 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

7. Principles of Taxonomy • Nomenclature • Names given according to International Code for the Nomenclature of Bacteria

8. Using Phenotype to Identify Prokaryotes • Phenotype can be used in the process identification of bacteria • Methods used include • Microscopic morphology • Metabolic capabilities • Serology

9. Using Phenotype to Identify Prokaryotes • 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

10. 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

11. Using Phenotype to Identify Prokaryotes • 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

12. 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

13. 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

14. 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

15. 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

16. Characterizing Stain Differences • 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

17. 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

18. Classifying Prokaryotes • 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

19. 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

20. 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