This talk introduces a Linux Professional audience to bacterial genomics and modern sequencing technology. The title is slightly misleading and is a bit of clickbait. The diagrams are good.

1. Sequencing your poo
with a USB stick
Torsten Seemann
Victorian Life Sciences Computation Initiative (VLSCI)
Peter Doherty Institute for Immunity and Infection (PDI)
The University of Melbourne
LCA 2016 B&OS Miniconf - Geelong, AU - Mon 1 Feb 2016 - #LCA2016

2. My journey

3. How did I end up here?
■ Started a Science/Engineering degree
□ Finished computer science
□ Did not finish electrical engineering
■ Did a PhD in Computer Science
□ image processing / data compression
■ Victorian Bioinformatics Consortium @ Monash
□ brought computer and biology people together
■ VLSCI @ UniMelb
□ microbial genomics and bioinformatics

4. Open source
■ Unix command line tools
□ Perl, C, Bash
■ Clean interface, easy installation
■ Prokka (GPL v2)
□ 1000s of international users
□ research, government & commercial

5. Biology of bacteria

6. A single-cell organism

7. Shapes

8. Size
103
nm = 1 μm = 1 micron

9. Bacteria are the oldest life on Earth

10. Gingers are not going extinct !
Homo arubinis

11. Celebrity bacteria sightings
“E.coli”
Escherichia coli
“Golden Staph” / “MRSA”
Staphylococcus aureus
“Black death” / “Plague”
Yersinia pestis

12. Bacterial evolution

13. Small genome
6,000,000,000
letters
30,000 genes
Genome
A T G C
3,000,000
letters
3,000 genes

14. Replicons
Usually 1 big
circular chromosome
(1M to 10M bases)
Sometimes 1-6
“mini” chromosomes
(4k - 300k bases)

15. Fast growers
20 min doubling time

16. Vertical transfer of DNA
Occurs during cell division
Sometimes it makes an
error copying the DNA
eg. A → T

17. Horizontal transfer of DNA
Occurs between bacterial cells
Plasmids: virulence & antibiotic resistance genes!

18. The real tree of life
A mixture of horizontal & vertical transmission.

19. Another tree

20. The microbiome

21. Bacteria are everywhere
5,000,000,000,000,000,000,000,000,000,000,000,
0,000,000,000,000,000,000,000,000,000,000,000,
0,000,000,000,000,000,000,000,000
100,000,000,000,000
1,000,000
50-90% bacteria
Our microbiome

22. We need bacteria to survive
Help digest
our food
Aid immune
system
Synthesize
nutrients

23. False anthropomorphism
“Good” E.coli “Bad”
(colon) (bladder)
probiotic pathogen

24. Bacterial communities
■ They don’t live in isolation
□ clumping, bio-film, extra-cellular matrix
■ They are not clonal
□ sub-populations w/ genetic diversity
■ They communicate & coordinate
□ via quorum sensing

25. The gut microbiome
■ Dynamic
□ diet / health
■ Diverse
□ bacteria
□ fungi
□ viruses
■ An “organ”

26. Dysbiosis ⟶ Disease
A microbial imbalance on or inside the body

27. Fecal transplant or transpootation
Cure Clostridium difficile infection
>90% success w/ healthy donors
Transplant fat ⟷ skinny mice
They lose ⟷ gain weight

28. Logical progression
1 gene
⇢ 1 genome
⇢ 1000 genomes
⇢ 100,000 genomes
⇢ Every person at birth?
⇢ Regularly throughout lifetime?
⇢ Daily microbiome profiles?

29. More technology

30. Current sequencing instruments
■ Expensive
■ Not portable
■ Operate in batch mode
■ Short read length
■ Long run time

31. Oxford Nanopore - MinION

32. Nanopore technology
Signal is measured
from ~5-7 bases
Timing is irregular
It can go fast and long

33. Why is this special?
■ Data provided in real time
■ Long sequences
■ Dynamically adjustable
□ eject molecules
□ pause sequencing
■ Portable
■ No moving parts

34. Applications of real time sequencing

35. Oxford Nanopore - PromethION
■ Large scale
■ 48 x MinION
■ On board ASIC
■ Runs Python
■ 400 Tbp/week

36. Bioinformatics

37. Streaming / real-time analysis
■ We are not going to keep all this data
□ Need to think streaming analyses
■ Extract info we need and discard
□ Cheaper to resequence?
■ Lots of new applications
□ Much scope for method development
□ Even more scope for biological discovery

38. Conclusion

40. Contact
tseemann.github.io
torsten.seemann@gmail.com
@torstenseemann

41. The end.