A presentation to a lay audience at Melbourne Knowledge Week on how bacteria are a part of our life and what we are doing with genomics to manage them.

1. Decoding our
bacterial overlords
Dr Torsten Seemann

2. A bacterium

3. Bacteria are diverse

4. 5,000,000,000,000,000,000,000,000,000,000,000
000,000,000,000,000,000,000,000,000,000,000,
000,000,000,000,000,000,000,000.
Bacteria run the show
100,000,000,000,000
1,000,000
90% microbial

5. Help digest
our food
Essential for human life
Immune system
Synthesize
vitamins

6. “Good” E.coli “Bad”
(colon) (bladder)
Bacteria are not malicious

7. 6,000,000,000
letters
The blueprint of life
Genome
A T G C
4,000,000
letters

8. Extract
the DNA
Reading the genome
Chop it into
small pieces
Read DNA of each piece

9. We had a bunch of nice long DNA
(each 4 million letters long)
We got back millions of short DNA
(each only 200 letters long)
We want our nice long DNA back!
(please)
Can’t always get what you want

10. Reconstruct the DNA of the chromosome(s)
Genome assembly

11. ● No box
● Millions of pieces
● Missing and duplicate pieces
● Broken pieces
● No corner or edge pieces
→ Usually end up with ~200 sequences
Like a jigsaw puzzle, but ...

12. Contains ~4,000 genes
Each gene is ~800 letters long
Genes start and end with special triplets
Finding genes
←ATGCATGATTAGCTTTTAGTCTTATAATGTCTTATATATCGCATTTAAGCCCTGATTCTATGAATG→
Genome is ~4,000,000 letters long

13. ● Identify new species
● Find resistance genes
● Understand evolution
● Trace outbreak origin
Applications

14. 2000 finished genomes
10,000 assembled draft genomes
200,000 downloadable genomes
2,000,000 sitting on USB disks?
Genome assembly is different
- RAM more useful than CPU
Computational challenge