Lecture 3. Microbial Systematics

Question 1

What is systematics?

Answer 1

The study of the diversity of organisms and their relationships
Links phylogeny (evolutionary history) with taxonomy

Question 2

What are genus/species names always written in?

Answer 2

Italics

Question 3

What does “staphylo” mean in a bacteria’s name?

Answer 3

“Bunch of grapes” clusters

Question 4

What does “coccus” mean in a bacteria’s name?

Answer 4

Coccus-shaped bacterium

Question 5

What does “epidermis” mean in a bacteria’s name?

Answer 5

Isolated from skin

Question 6

What does “bacillus” mean in a bacteria’s name?

Answer 6

Rod-shaped bacterium

Question 7

What does “thermophilus” mean in a bacteria’s name?

Answer 7

Grows at high temperature

Question 8

What is the current definition of species in higher organisms?

Answer 8

Interbreed and produce viable offspring

Question 9

Why is the definition of species different in microbiology?

Answer 9

Asexual reproduction
Lateral gene transfer
Phenotypic and genotypic plasticity of microorganisms

Question 10

What is the current definition of species in microbiology?

Answer 10

A group of strains that show a high degree of overall similarity and differ considerably from related strain groups with respect to many independent characteristics

Question 11

What do phenotypic analyses analyse?

Answer 11

Observable traits of an organism (results are compared with standard or TYPE cultures)

Question 12

What are the problems with phenotypic analyses?

Answer 12

A single mutation can change apparent definition of a species

Question 13

Where do barophiles grow?

Answer 13

High pressure

Question 14

Where do acidophiles grow?

Answer 14

pH <6

Question 15

Where do alkaliphiles grow?

Answer 15

pH >8

Question 16

Where do halophiles grow?

Answer 16

Very salty conditions

Question 17

Where do microaerophiles grow?

Answer 17

Low oxygen concentration conditions

Question 18

What temperature do psychrophiles grow at?

Answer 18

Low temperature (<15°C)

Question 19

What temperature do mesophiles grow at?

Answer 19

Normal temperature (15-45°C)

Question 20

What temperature do thermophiles grow at?

Answer 20

High temperature (>50°C)

Question 21

What temperature do hyperthermophiles grow at?

Answer 21

Very high temperature (>80°C)

Question 22

What is Fatty Acid Methyl Ester (FAME)?

Answer 22

Determination of fatty acid profile of membrane lipids
Growth under ‘standard’ conditions, extraction of lipids, chemically modify to methyl esters, analysis of FAME products by gas chromatography
Differences in chain length
Presence of double bonds, rings, branched chains or hydroxy groups
Compare chromatograms to database for best match

Question 23

What are the drawbacks of FAME?

Answer 23

Fatty acid profile depends on growth conditions (temp,
medium, growth phase) which need to be standardised
Not all strains can be cultivated under those conditions

Question 24

What is DNA-DNA hybridisation?

Answer 24

Genome wide comparison of sequence similarity
>70% = same species
>25% = same genus

Question 25

What is fatty acid (FA) profiling?

Answer 25

Fame analysis
Pattern membrane Fas; depends on growth media, temp. and incubation time

Question 26

What is DNA profiling?

Answer 26

Ribotyping, rep PCR, AFLP, etc.
Producing DNA fragment patterns for comparative analysis

Question 27

What is multilocus sequence typing?

Answer 27

Characterising strains within a species
Sequence ‘housekeeping’ genes to assign different alleles to strains

Question 28

What is amplified fragment length polymorphism (AFLP)?

Answer 28

PCR targeting repetitive elements in bacterial genome
Used to distinguish closely related strains
Analyses of results is comparison of electrophoretic patterns