Summary Theme 5 MBY251 study note

THEME 5 -MICROBIAL SYSTEMATICS BIOLOGY

Genomics: (DNA)
Functional and comparative
- Discipline of sequencing, analysing, annotation and comparing genomes.
- Gene knockouts / mutations
Sequencing techniques
- Determining the precise order of nucleotides in
DNA/RNA
- 1st generation:
o Sanger dideoxy method
- 2nd generation:
o 100x faster than 1st
o Massively parallel methods (large #
sequenced together)
o Using increased computer power and
miniaturization
- 3rd generation:
o Sequence single DNA molecules
o HeliScope Single Molecule Sequencer
o Pacific Biosciences SMRT (single molecules real time
sequencing) – carried out in nanocontainers
- 4th generation:
o Oxford Nanopore Technologies system
o Don’t use optical detection
o Ion torrent semiconductor sequencing
Genomics introduction
- Genome = genes, regulatory seq, and noncoding DNA
- Comparative: Sequence similarity to genes in other organisms
- Functional: Predict pathogenicity, virulence factors and transport systems
- Can tell us:
o Size and content (and lifestyle of organism)
 Prokaryotes (ave gene = 1000bp)
 As genome size increases, gene content does
 1Mbp = 1000000 bp
 Smaller = parasitic/endosymbiotic (totally host dependent for
nutrients)
o Predict metabolic pathways

Metagenomics
Metagenome: total gene content of
the organisms in an environment (eg.
In a deep sea sediment)
Metagenomics: total gene content of
microbial community
Metatranscriptomics: gene
expression profiles within a microbial
community
Metaproteomics: protein expression
patterns within a microbial
communities