Lecture 3 Flashcards
What are systematics?
Study of the diversity of organisms and their relationships
Links phylogeny with taxonomy
Molecular technology to chase evolutionary relationships
How are names given to bacterial species?
Genus/ species names are always written in italics
Name reflects something about the organism
Why is species interbreeding and producing viable offspring problematic in microbiology?
Asexual reproduction
Lateral gene transfer
Phenotypic and genotypic plasticity of microorganisms
What is the definition of no unified species concept?
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
What is phenotypic analysis?
Morphological, metabolic, physiological and chemical characteristics
What is genotypic analysis?
Comparative at the gene and genome level
What is phylogenetic analysis?
Framework of evolutionary relationships
What is the 3 categories of polyphasic bacterial taxonomy?
Phenotypic
Genotypic
Phylogenetic
What is the problem with phenotypic analyses?
A single mutation can change apparent definition of a species
What is motility?
Determination by phase-contrast microscopy
What is nutritional testing in organisms?
Testing for ability to grow on a range of compounds as sole sources of carbon, energy and nitrogen
What is the gram staining procedure?
Using stained cells to visualise them
- Spread culture thinly
- Dry slowly
- Place slide through flame
- Stain cells and add iodine solution
- Wash slide with alcohol
- Gram +ve stays purple, Gram -ve stain washes off
What are phenotypic biochemical tests?
Decomposition of simple carbohydrates
Acid from glucose in anaerobic or aerobic conditions
Fermentation produces acids and changes pH inducing colour change
What is the DNase test?
Colonies producing DNase hydrolyse DNA
If medium is flooded and acidified with 1 N HCl, DNA precipitated out and clear zones appear around DNase +ve colonies
What are the cultural characteristics looked for in organisms?
Colony shape
Elevation
Surface appearance
Texture
Pigmentation
Odour
What is an acidophile?
pH <6
What is an alkaliphile?
pH > 8
What is a barophile?
Requires high pressure
What is a halophile?
Requires very salty conditions
What is a microaerophile?
Requires low oxygen concentration
What is a psychrophile?
Requires low temperature (<15)
Inhabit permanently cold environments
Adapted to low temperatures: proteins more flexible, membranes more fluid
What is a mesophile?
Requires normal temperature (15-45)
What is a thermophile?
Requires high temperature (>50)
What is a hyperthermophile?
Very high temperature (>80)
What is molecular analysis using Fatty Acid Methyl Ester (FAME)?
Determines fatty acid profile of membrane lipids
Growth under ‘standard’ conditions
Extract lipids and chemically modify to methyl esters – analyse using gas chromatography
How is the fatty acid profile of membrane lipids determined?
Differences in chain length
Presence of double bonds, ring, branched chains of hydroxyl groups
Compare chromatograms to database for best match
What are the drawbacks of determining the fatty acid profile of membrane lipids?
Fatty acid profile on growth conditions which need to be standardised
Not all strains can be cultivated under those conditions
What is DNA hybridisation for genotyping analysis?
Genome wide comparison of sequence similarity
Useful for discrimination of strains of a species
What is AFLP for genotyping analysis?
Amplified fragment length polymorphism
PCR targeting repetitive elements in bacterial genome
Used to distinguish closely related strains
Analyses of results is comparison of electrophoretic patterns
What is MLST for genotyping analysis?
Multilocus sequence typing
Characterising strains within a species
Amplify target gene, sequence, determine alleles and compare with other strains of same species
What is GC base ratio for genotyping analysis?
Percentage of GC bases in genome
Similar organisms have close GC content
What is DNA sequencing with genotyping analysis?
Using fluorescent dyes and a capillary column
Read sequence and compare actual sequence
Amplify a specific section of DNA, can target specific populations or functional groups
Can build genomes rapidly using NGS
