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

Contact me

• jessica@ubiome.com• 415-275-2461

Platform for collaboration