19 - Modern uses of microbial genetics

Question 1

Why is bacterial variation important

Answer 1

allows organisms to sustain themselves in multiple different environments e.g. hosts, soils, etc.

Question 2

Bacterial strains

Answer 2

single isolates that are genetically related

Question 3

Bacterial species

Answer 3

collection of related strains

Question 4

Pan (supra) genome

Answer 4

the global gene repertoire of a bacterial species that is comprised of the core and the dispensable (accessory) genome

Question 5

Core genome

Answer 5

the pool of genes that is shared by all the strains of the same bacterial species

Question 6

Dispensable (accessory) genome

Answer 6

the genes shared by some but not all strains in a species

Question 7

Unique genome

Answer 7

Only found in that one strain

Question 8

Problems with sequencing on an as needed bases (pre 2000)

Answer 8

• Genes were repeatedly rediscovered (multiple roles)
• Phenotypes involve many genes, so not all of the genes associated with a phenotype were known
• Expression of genes is conditional on how the bacteria are grown

Question 9

Steps of automated sanger DNA sequencing using chain termination method

Answer 9

1. Microorganisms are isolated in pure culture
2. Genomic DNA is extracted and sheared into fragments to make template DNA
3. Four PCR reactions are set up, each containing template DNA, primers, taq polymerase, dNTPs and ddNTPs (labelled with flourophore)
4. PCR is ran
5. Mixtures separated 1bp at a time by capillary electrophoresis.
6. Excitation of flourophore bp is detected by laser

Question 10

Mass parallel sequencing to build a genome from raw sequencing data

Answer 10

information is fed into a bioinformatics pipeline that:
1. Removes the primer sequences
2. Fragment alignment (compiles fragments based on overlapping similarity)
3. Gap closure and editing forming contig

Question 11

Homologues

Answer 11

elements that are similar because they share a common ancestor

Question 12

Orthologues

Answer 12

homologues that diverged through speciation

Question 13

Paralogues

Answer 13

homologues that diverged through duplication within the same genome

Question 14

Analogues

Answer 14

elements that are functionally similar, through convergent evolution rather than common ancestry

Question 15

why do not all strains in species cause disease

Answer 15

Different strains may have fewer genes involved in virulence (loss and gain of different genes)

Question 16

Genomics

Answer 16

the study of the molecular organisation of genomes, their information content, and the gene products they encode

Question 17

Metagenomics

Answer 17

Study of genomes recovered from environmental samples without isolation and growth of the members of the microbial community

Question 18

Understand how whole genome sequencing has changed our concept of a species

Answer 18

The use of 16S rna sequencing has allowed for the comparison of a universal genome structure across species to determine relatedness, what was once grouped by appearance can now be grouped on genomic similarity and function