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
Species concept, Eukaryotic vs bacteria and archaea?
- Euk: interbreeding population, reproductively isolated from other interbreeding populations
- Bacteria and Archaea: haploid , no sexual reproduction
Explain the species concept discussed for prokaryotes!
- a group of strains sharing a high degree of similarity in several independent traits (phenotypic and genetic)
- a group go strains cluster closely phylogenetically and are distinct form other groups of strains ( DNA sequence of multiple genes, 97% or greater 16S rRNA gene sequence identity)
When looking at a phylogeny tree how do we determine closeness?
- line length determines how closely related they are to the next common ancestor
Describe the universal phylogenetic tree!
- Ribosomal RNA is found in all living things
- based on SSU rRNA sequences
- small subunit (SSU) rRNA
- -> bacteria and archaea : 30S subunit, 16S rRNA
- -> Eukaryotes: 40S subunit, 18 S rRNA
- *confirmed by sequencing other genes
Before 16S what was the relationship between archaea and bacteria thought to be?
- they were thought to be more closely related HOWEVER, Eukarya and Archaea have more in common! aka 16S sequence
Universal phylogenetic tree:
- evolutionary history of all living things
- Root =??
- last universal common ancestor (LUCA)
Universal phylogenetic tree:
- what are the three domains??
- Bacteria (eubacteria)
- Archaea (new group)
L> all microorganisms, prokaryotes (no nucleus), many genes not found in bacteria or eukarya - eukarya
**archaea and eukarya have a more recent common ancestor
Explain the Endosymbiotic hypothesis!
- some organelles in eukaryotic cells are descended from bacteria that were engulfed by primitive pre eukaryotic cells
- Aerobic bacteria : mitochondria (developed first)
- photosynthetic bacteria: chloroplasts
Bacteria characteristics go!
- Membrane enclosed nucleus?
- membrane enclosed organelles?
- circular chromosome ?
- paired chromosome ?
- ribosome size?
- introns in genes?
- genes organized in operons?
- growth above 70C?
- microorganisms ?
- No
- rarely
- Almost always
- no
- 70S
- not usually
- Yes
- Yes
- All
Archaea characteristics go!
- Membrane enclosed nucleus?
- membrane enclosed organelles?
- circular chromosome ?
- paired chromosome ?
- ribosome size?
- introns in genes?
- genes organized in operons?
- growth above 70C?
- microorganisms ?
- no
- no
- yes
- no
- 70S
- no
- yes
- yes
- all
Eukarya characteristics go!
- Membrane enclosed nucleus?
- membrane enclosed organelles?
- circular chromosome ?
- paired chromosome ?
- ribosome size?
- introns in genes?
- genes organized in operons?
- growth above 70C?
- microorganisms ?
- yes
- yes
- no
- yes
- 80S
- Yes
- not usually
- no
- many
