[Micro] classification of prokaryotes
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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.
![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.”](https://image.slidesharecdn.com/6kp4xq4eqt6dbdni5yhj-signature-2127a2ca5368c7fdfd023e8d90dde3fc0b9fe7d91346a4189562c9f63dc0d19d-poli-150819190754-lva1-app6891/85/Micro-classification-of-prokaryotes-15-320.jpg)
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[Micro] classification of prokaryotes
- 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.
- 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.
Editor's Notes
- #2: <10% of pathogen for human disease identified differ in mode of transmission, colonization and pathology
- #5: Taxon: arrangement evolving taxonomy Linaean taxonomy
- #9: Remember: King Philip Came Over For Good Spaghetti
- #10: Remember: King Philip Came Over For Good Spaghetti
- #12: serotype. serovars. serogroups.
- #13: API: 80% to specie level static system ( evolution/ new discovery none possible)