metagenomics talk from ubiome's jessica richman
DESCRIPTION
Jessica Richman addressed the Singularity University Executive Program in May 2013, and talked about the metagenomics work at the new company uBiome.TRANSCRIPT
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 ($bn)
HGP and HMP
HGP1990 – Launch of Human Genome Project1997 – E Coli genome sequenced2001 – First draft of human genome 2003 – Human Genome Project completed
HMP2007 – Launch of Human Microbiome Project2010 – First microbiome-funded IBD paper published in Gastroenterology2012 – Human Microbiome Project completed
The per‐base cost of DNA sequencing has plummeted by
~100,000‐fold over the past decade, far outpacing Moore’s Law
of technological advance in the semiconductor industry.
Eric Lander, MIT Broad Institute
HMP - Research Funding ($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/Mood/
Behavior
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 sequencingIllumina 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 surveyFive collection sites infinity
16S sequencing full sequencingInteractive, gamified website
In the lab For the user
What’s in your microbiome?
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