Microbial Taxonomy (classification) - Dr. Lodge Flashcards Preview

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Flashcards in Microbial Taxonomy (classification) - Dr. Lodge Deck (26):

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?

1. 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



- 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

1. it was amplified with PCR
2. sequence determined
3. 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
- 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
- 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
- 80S
- Yes
- not usually
- no
- many