Microbial Taxonomy (classification) - Dr. Lodge Flashcards
What is taxonomy?
- organization of knowledge
- precise names (nomenclature) facilitate communication
- enables accurate identification
- key to a wealth of information
- may reflect evolutionary relationships
What is diagnostic microbiology?
- identify the cause of infectious disease
ex: Salmonella typhimurium
Diagnostic Microbiology:
- Salmonella typhimurium ??
- gram neg
- bacillus (rod shaped)
- member of the enterobacteriaceae
- closely related to E. coli
- will grow on lab media at 37C
- pathogen causing gastroenteritis (food poisoning)
- chromosome of 4, 857, 432 bp
What is phenetic classification?
- grouped according to similar phenotypic characteristics
- use as many attributes as possible
- of practical use in identification (clinical diagnostic )
What is phylogenetic classification?
- a classification that reflects evolutionary relationships
What are the two main characteristics used in classification?
- Morphological
2. Physiological and Metabolic
Morphological characteristics?
- round, rod shaped etc
- size, shape, gram stain, motility, ultrastructure, endospore
Physiological and metabolic characteristics?
- directly related to the activity of e.g. enzymes
- indirectly related to genes
- biochem characteristics are more common in the identification of microbes
ex: what sugars they use if broken down to acid= yellow…not= red
L> as well as gas production
In clinical diagnostics the API strip is used. What is it?
- cupules contai dried reagents
- inoculated with bacterial suspension
- incubated at 37C
- colour changes indicate metabolic properties
- profile can be used to give identification
- works well for a limited set of possible organisms - these do not tell you how well they are related
Phylogeny????
- the evolutionary history of a group of organisms
- often depicted as a phylogenetic tree
- nodes at tips are = species
- nodes at branch points = ancestors
Explain molecular approaches to phylogeny!
- bacteria are all related by descent
- sequence of the genome is a record of the bacterium’s ancestry
- entire genome sequences are now available ( not practical taxonomy )
- use sequences for specific genes/ proteins
What are the assumptions of molecular clocks?
- nucleotide changes accumulate in proportion to time
- changes are random
- changes are usually neutral
aka dont affect structure or function of encoded protein
**mutations and differences ins sequence increase overtime
What are the properties of suitable genes?
- present in all the organisms to be compared
- has the same function in all organisms to be compared
- conserved: will have stable regions that are constant and variable regions
- it must be long enough
Why is 16S rRNA useful in taxonomy?
- present in all the organisms to be compared –> all living things have ribosomes
- has the same function - the function is essential
- highly conserved ( has stable regions and variable regions)
- long (approx 1500 nucleotides)
Explain 16S rRNA sequence analysis. Process and what it revealed
- it was amplified with PCR
- sequence determined
- sequence compared with known sequences
- compare sequence with known sequences int eh data base for identification
- calc relatedness for classifiction and phylogeny
