Microbial Taxonomy Flashcards
Taxonomy
The science of identifying, naming, and organizing living organisms into systems of classification
Phylogeny
The study of the evolutionary history of organisms
Limitations of a five-kingdom system
-Monera is not representative of the distinctions within it
Advantages of three-domain system
- Distinguishes between archaea and bacteria
- Fits rRNA sequencing data (Carl Woese)
Characteristics of Bacteria (4)
- Cell wall containing peptidoglycan
- Straight carbon chains on glycerol for membrane lipids
- Formylmethionine is first amino acid in proteins
- Sensitive to antibiotics
Characteristics of Archaea (3)
- Variable cell wall with no peptidoglycan
- Branched carbon chains on glycerol for membrane lipids with ether linkage
- Not sensitive to antibiotics
Characteristics of Eukarya (3)
- Cell wall varies in composition; contains carbohydrates
- Straight carbon chains attached to glycerol
- Not sensitive to antibiotics
Phenotypical Tools for Classification (6)
- Morphology
- Gram Reaction
- Biochemical
- Nutritional
- Physiological
- Others
Morphology
Cell and colony shape, spores, flagella, cell wall pattern
Gram Reaction
Positive, negative, acid fast
Biochemical Tools
Lipid analysis, enzyme protein analysis, serotype
Nutritional Tools
Phototrophic, autotrophic, etc.
Physiological Tools
Aerobic, anaerobic, fermentative, etc.
Other Tools
Storage compounds, temperature optima, pH range, symbioses, antibiotic sensitivity, gaseous needs, phage sensitivity
Genotypic Tools
- Most precise method of classification
- G:C content, DNA hybridization, nucleic acid sequence analysis (whole genome or 16S)
- Plasmid/Chromosomal DNA sequence analysis
Common properties used in phylogeny (3)
- Anatomy
- Fossils
- DNA sequences
Why use 16S rRNA for phylogeny?
- Present in all cells with same function
- Large enough sequence (~1500 residues)
- Contains rapid and slow evolving regions (rapid for closely-related and slow for distantly-related)
- No horizontal transfer of rRNA genes
Ribosomal Database Project (RDP)
Database of about 2 million aligned 16S rRNA sequences
Microbial Diversity Estimates (4)
- 7000 well-characterized
- 10,000 partially identified
- Likely 10^7-10^9 microbial species
- <1% species cultured
