1. Identification and Classification of Prokaryotes
Chapter 10

2. Taxonomy The science of classification
Provides an orderly basis for the naming of organisms
Places organisms into a category or taxon (plural: taxa)
Carolus Linnaeus: 18th century Swedish botanist; the Father of Taxonomy

3. Carolus Linnaeus
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4. 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

5. Binomial Nomenclature
The system used to name all living things
The first name designates the genus (plural: genera) and its first letter is capitalized
The second name is the specific epithet, and it is not capitalized
Together the genus and specific epithet identify the species

6. The Meaning of the Names of Some Microorganisms
Escherichia coli: Named after Theodore Escherich in 1888; found in the colon
Entamoeba histolytica: Ent, intestinal; amoebae, shape/movement; histo, tissue; lytic, lysing or digesting tissue
Strain: A subgroup of a species with one or more characteristics that distinguish it from other members of the same species

7. 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

8. 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

9. Principles of Taxonomy
Taxonomic hierarchies
Classification categories arranged in hierarchical order
Domain – collection similar to kingdoms
Archaea, Prokaryotes, Eukaryotes
Kingdom – collection of similar phyla
Monera, Protista, Fungi, Plantae, Animalia
Phylum – collection of similar classes
Class – collection of similar orders
Order – collection of similar families
Family – collection of similar genera
Genus – group of related species
Species – group of related isolates or strains
Most basic unit

10. Classification of Human Dog Wolf and a Bacterium

11. 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

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

13. Using Phenotype to Identify Prokaryotes
Phenotype can be used in the process identification of bacteria
Methods used include
Microscopic morphology
Gram -. Gram +, cocci, rod, vibro, spirillum, etc.
Metabolic capabilities
Anaerobic, aerobic, Produces SH, Lactose, etc
Serology- do specific antibodies attach

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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

21. 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

22. 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

23. 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 relatedness on species level

24. 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

25. 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

26. Using a Taxonomic Key
Dichotomous Key: A commonly used key to identify organisms.
Has paired statements describing characteristics of organisms.

27. Dichotomous Key for Classifying U.S. Coins

28. Bacterial Identification Tree

29. David H. Bergey
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