This document discusses the classification and identification of prokaryotes. It begins by introducing bacterial taxonomy and classification, which involves grouping organisms with similar properties. Identification involves characterizing organisms using phenotypic characteristics like microscopy, colony morphology, and biochemical tests. It then discusses various classification systems like the Linnaean taxonomy and phylogenetic trees based on 16S ribosomal RNA. Identification can be done using tests on differential and selective media, as well as techniques like PCR, DNA-DNA hybridization, and restriction fragment length polymorphism analysis.

1. Classification
of
Prokaryotes

2. Extreme halophiles

3. Hot springs, home of thermophiles

4. Bacterial Taxonomy
“Taxonomy is the science that studies organisms in
order to arrange them into groups; those organisms
with similar properties are grouped together and
separated from those that are different.”
Classification--the process of arranging organisms
into similar or related groups, primarily to provide
easy identification and study
Identification--the process of characterizing organisms.
Practical use of classification scheme
Nomenclature--the system of assigning names to
organisms.”

5. Identification
 to identify fecally contaminated water.
 to identify organisms associated with food
spoilage or contamination.
 to identify pathogens in the clinical
microbiology laboratory.
 It is important to keep in mind that the appropriate
tests to employ will depend on the organisms likely
present plus time, skills of the tester, and
budgetary concerns.
 In the clinic, patient symptoms help to define what
organisms of interest are likely present.

6. Classification
 Phenotype-based
 Genotype-based

7. Identification vs. Classification

8. Classification of Bacteria (Linnaean)Classification of Bacteria (Linnaean)
 *Kingdom
 Phylum/Division
 Class
 Order
 Family
 *Genus ( 1st
name)
 *Species ( 2nd
name
identifier)

9. King Philip Came Over For Good
Spaghetti
Escherichia coli
 *Kingdom Prokaryotae
 Phylum/Division Gracilicutes
 Class Scotobacteria
 Order Eubacteriales
 Family
Enterobacteriaceae
 *Genus Escherichia
 *Species coli

10. Criterria for Classification
 Growth on Media
 Non selective media
 Selective media
 Differential media
 Bacterial Microscopy
 Gram stain
 Biochemical Tests
 Oxidase, catalase

11. Criterria for Classification
 Immunologic tests.
 Antibody antigen tests
 Genetic instability
 nucleic acid hybridization
 DNA sequence analysis

12. Classification Systems
 Keys
 Numerical Taxonomy (Analytical profile
Index) API
 Phylogenetic Classification (GC content,
DNA sequencing)
 Ribosomal RNA( most conserved throughout
evolution)

13. Phylogenetic Tree
16S ribosomal RNA Line
lengths are based on genetic
distances, i.e., longer lines reflect

14. Identification

15. Phenotypic Characteristics
 Microscopy: Gram stain, acid-fast stain, cell
morphology, cell arrangements.
 Colony morphology: size, color, border shape, etc.
 Growth on Differential media: blood agar, MacConkey
agar, etc.
 Growth on Selective/Differential media: MacConkey
agar, EMB agar, etc.
 Biochemical tests: “Most biochemical tests rely on a
pH indicator or chemical reaction that results in a
color change [or gas production] when a [specific]
compound is degraded.”

17. Catalase
Test

18. Durham Tube: Gas Production

19. Urease
Test

20. Commercial Biochemical Test Kits

21. Dichotomous Key

22. Typing of Strains
Biovar, Biotype (syn)
Serovar, Serotype (syn)
Typing via RFLP analysis
Ribotype (RFLP of rRNA) Also Phage Type

23. Restriction Fragment Length
Polymorphism (RFLP) Analysis
Genomic DNA is
isolated, cut using
specific restriction
enzymes, run out on a
gel, and then Southern
Blotted with specific
DNA probes.
Can you tell me
which lanes contain
bacteria that are
clonally related?
1 2 3 4 5

24. Southern Blotting RFLP generation.
Gels separate DNA
by size.
This is a post-
probe detection
blot.

25. Phage TypingPhages are
viruses of
bacteria.
The clear
spots are due
to bacteria
killing (lysis).
This is a “Soft-Agar
Overlay.”
“Phage” = “Bacteriophage”

26. AntibiogramThe disks are
impregnated
with specific
antibiotics.
The streaks
make up a
bacterial
“lawn”.
These two strains have different
antibiotic-resistance patterns.

27. Numerical Taxonomy
 Numerical Taxonomy is a method of classification that
pools phenotypic characteristics.
 The key to numerical taxonomy is that no one trait (e.g.,
ability to ferment glucose) is elevated in importance above
any other trait (e.g., Gram staining characteristics).
 Instead, all traits are weighted equally.
 Classification in numerical taxonomy is expressed in terms
of a Similarity Coefficient found between two compared
strains.
 Greater similarity coefficient, closer relatedness is inferred.
Greater than ~70% and inference is that two compared
bacteria are of the same species.

28. G-C Content (DNA Base Ratio)
Helix has higher
stability with
greater fraction G-
C vs. A-T pairing.
Higher melting
points therefore
correspond to
greater G-C content

29. DNA-DNA Hybridization
Similarity is in terms of
nucleotide sequence
between the two compared
organisms.