2. Exponential changes in understanding
• About us
• What is the microbiome?
• Next generation sequencing
• What is citizen science?
• New kinds of partnerships between industry,
academia, and the public
• Solving the world’s problems and affecting
the lives of a billion people in a positive way
(Singularity!)
3. $350,000 in crowdfunding
Over 2,500 participants 4,500 samples 40 countries
Largest citizen science crowdfunding project in history
Top 15 on Indiegogo crowdfunding platform
Featured in Wired, Scientific American, MIT Technology
Review, ABC News, MSNBC, dozens of others
4. Jessica Richman
• Started and sold her first company
before university
• Co-founder international online
program for women
• Graduate Fellowship at Oxford
• DPhil in progress, mathematical
sociology at Oxford
• BS, Economics and interdisciplinary
engineering, Stanford
Zachary Apte, PhD
• Founded synthetic biology
company based on microfluidics
invention, funded by DOE
• Inventor of statistical measure of
intracellular organization
• Built international open science
web platform
• PhD, Biophysics, UCSF
• BS, Physics, Hampshire College
Will Ludington, PhD
• NSF Graduate Research
Fellowship
• Extensive work in bioinformatics,
biophysics, ecology and
microecology
• Created Ecological Management
Plan for Palmyra Atoll
• PhD, Biochemistry, UCSF
• BS, Biological Sciences, Stanford
About us
Entrepreneur Mathematical
Sociologist Study Design
Biophysicist Entrepreneur
Inventor Developer Statistics
Biochemist Microbiologist
Ecologist Bioinformatics
6. The end of the germ theory
of the disease
• Microscope as enabling technology
• Culture-based research
• Next generation sequencing changes
EVERYTHING
8. HGP - Research Funding ($mm)
HGP - Company Market Cap ($bn)
HGP and HMP
HGP
1990 – Launch of Human Genome Project
1997 – E Coli genome sequenced
2001 – First draft of human genome
2003 – Human Genome Project completed
HMP
2007 – Launch of Human Microbiome Project
2010 – First microbiome-funded IBD paper
published in Gastroenterology
2012 – Human Microbiome Project completed
The per‐base cost of DNA sequencing
has plummeted by ~100,000‐fold over
the past decade, far outpacing Moore’s
Law of technological advance in the
semiconductor industry.
Eric Lander, MIT Broad Institute
HMP - Research Funding ($mm)
Year 1 Year 20 Year 1 Year 5
HMP – Company
Funding ($mm)
10. What is affected by the microbiome?
Gut microbiome
• Weight loss
• Low carb diet?
• Alcohol, caffeine
• Inflammatory Bowel Disease (IBD)
• Antibiotics
• Cancer, anxiety, depression
Other microbiomes
• Chronic sinusitis
• Penis microbiome and bacterial vaginosis, and HIV
transmission
11. What can we learn from the
microbiome?
• Mouse studies and obesity
• Targeted probiotics
• Fecal transplants and synthetic stool
(RePOOPulate)
• Soil and water
• Commercial products
12. What problems can this solve?
Personalized
Medicine
Clinical
Trials
Weight
Loss
Autism/M
ood/Beha
vior
Crohn’s
and IBD
Quantified
Self
13. What diet will help me lose weight?
I have IBD, what might help me with my symptoms?
How do I know?
What elements of my diet are most important to
maintaining a healthy microbiome?
Sinusitis, vaginosis, smelly feet, smelly people?
15. What do participants have access to?
State of the Art DNA sequencing
Illumina Hi-Seq
Patent-pending quality control and
bioinformatics technologies
WE BUILT A WORLD CLASS LAB FOR
$10,000
$89 easy-to-use collection kit for consumers
Health metadata survey
Five collection sites infinity
16S sequencing full sequencing
Interactive, gamified website
In the lab For the user
18. Who can get involved?
• Aligning incentives with citizen science
• Next generation sequencing is allowing us
to directly connect researchers, industry,
citizens and their microbiome.
• Partnerships with organizations benefit all
19. Questions people ask
• Data ownership
• Privacy
• Regulation
• IRB
Platform for collaboration
20. The future
• DIY clinical trials
• Anecdotes become data
• New ways to do product development
• Bacteria as biosensors
• Personalized medicine
Platform for collaboration
1977, the Commodore PET 2001, including either 4 KB (the 2001-4) for $795 or, later, 8 KB (2001-8) of 8-bit RAM. an iPhone has 8 million times more memory$795 in 1977 is $2800 in 2010 dollarsSo, 3 times as expensive and 8 million times less capacity.After receiving your sample, lab professionals extract DNA from cells in your saliva. Your DNA is then chopped up into shorter strands and copied many times via a process called amplification. Next, your DNA is washed over a small microchip-like device that contains short strands of synthetic DNA. The synthetic DNA fragments latch onto the pieces of your DNA that are a complementary match. Then a laser-scanning step reveals which strands of synthetic DNA are stuck to your DNA to determine your genotype. The chip used in our process is the Illumina HumanHap550+ BeadChip, which reads more than 550,000 SNPs (single nucleotide polymorphisms) plus a 23andMe custom-designed set that analyzes more than 30,000 additional SNPs. What this means is that the laboratory process reads nearly 600,000 data points on your genome. Find out more about our genotyping process.