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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
My journey
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
Open source
■ Unix command line tools□ Perl, C, Bash
■ Clean interface, easy installation
■ Prokka (GPL v2)□ 1000s of international users□ research, government & commercial
Biology of bacteria
A single-cell organism
Shapes
Size
103 nm = 1 μm = 1 micron
Bacteria are the oldest life on Earth
Gingers are not going extinct !
Homo arubinis
Celebrity bacteria sightings
“E.coli”Escherichia coli
“Golden Staph” / “MRSA”Staphylococcus aureus
“Black death” / “Plague”Yersinia pestis
Bacterial evolution
Small genome
6,000,000,000letters
30,000 genes
GenomeA T G C
3,000,000 letters
3,000 genes
Replicons
Usually 1 bigcircular chromosome
(1M to 10M bases)
Sometimes 1-6“mini” chromosomes
(4k - 300k bases)
Fast growers
20 min doubling time
Vertical transfer of DNA
Occurs during cell division
Sometimes it makes an error copying the DNA
eg. A → T
Horizontal transfer of DNA
Occurs between bacterial cells
Plasmids: virulence & antibiotic resistance genes!
The real tree of life
A mixture of horizontal & vertical transmission.
Another tree
The microbiome
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% bacteriaOur microbiome
We need bacteria to survive
Help digest our food
Aid immune system
Synthesize nutrients
False anthropomorphism
“Good” E.coli “Bad” (colon) (bladder) probiotic pathogen
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
The gut microbiome
■ Dynamic□ diet / health
■ Diverse□ bacteria□ fungi□ viruses
■ An “organ”
Dysbiosis ⟶ Disease
A microbial imbalance on or inside the body
Fecal transplant or transpootation
Cure Clostridium difficile infection >90% success w/ healthy donors
Transplant fat ⟷ skinny miceThey lose ⟷ gain weight
Logical progression
1 gene⇢ 1 genome
⇢ 1000 genomes⇢ 100,000 genomes
⇢ Every person at birth?⇢ Regularly throughout lifetime?
⇢ Daily microbiome profiles?
More technology
Current sequencing instruments
■ Expensive
■ Not portable
■ Operate in batch mode
■ Short read length
■ Long run time
Oxford Nanopore - MinION
Nanopore technology
Signal is measured from ~5-7 bases
Timing is irregular
It can go fast and long
Why is this special?
■ Data provided in real time■ Long sequences■ Dynamically adjustable
□ eject molecules□ pause sequencing
■ Portable■ No moving parts
Applications of real time sequencing
Oxford Nanopore - PromethION
■ Large scale
■ 48 x MinION
■ On board ASIC
■ Runs Python
■ 400 Tbp/week
Bioinformatics
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
Conclusion
The end.
