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Sequencing the human microbiome
with citizen science
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!)
$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
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
What is the microbiome?
The end of the germ theory
of the disease
• Microscope as enabling technology
• Culture-based research
• Next generation sequencing changes
EVERYTHING
$795 in
1977
(=$2,800 in
current $)
Accelerating technology &
plummeting cost
Next
Generation
Sequencing
HGP - Research Funding ($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)
Ecosystem, like the rainforest
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
What can we learn from the
microbiome?
• Mouse studies and obesity
• Targeted probiotics
• Fecal transplants and synthetic stool
(RePOOPulate)
• Soil and water
• Commercial products
What problems can this solve?
Personalized
Medicine
Clinical
Trials
Weight
Loss
Autism/M
ood/Beha
vior
Crohn’s
and IBD
Quantified
Self
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?
Citizen Science
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
What’s in your microbiome?
Metagenomics talk from uBiome's Jessica Richman
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
Questions people ask
• Data ownership
• Privacy
• Regulation
• IRB
Platform for collaboration
The future
• DIY clinical trials
• Anecdotes become data
• New ways to do product development
• Bacteria as biosensors
• Personalized medicine
Platform for collaboration
Contact me
• jessica@ubiome.com
• 415-275-2461
Platform for collaboration

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Metagenomics talk from uBiome's Jessica Richman

  • 1. Sequencing the human microbiome with citizen science
  • 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
  • 5. What is the microbiome?
  • 6. The end of the germ theory of the disease • Microscope as enabling technology • Culture-based research • Next generation sequencing changes EVERYTHING
  • 7. $795 in 1977 (=$2,800 in current $) Accelerating technology & plummeting cost Next Generation Sequencing
  • 8. HGP - Research Funding ($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)
  • 9. Ecosystem, like the rainforest
  • 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
  • 16. What’s in your microbiome?
  • 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
  • 21. Contact me • jessica@ubiome.com • 415-275-2461 Platform for collaboration

Hinweis der Redaktion

  1. 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.
  2. Opportunity