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The uBiome Project — Interview with Jessica Richman

H+: Hi Jessica, can you briefly say a bit about the uBiome project? What is it?

Jessica: Sure, the microbiome is the community of microbes that live on and within us. It sounds kind of funny, but all of us are actually covered in helpful germs – we probably couldn’t live without them – and are certainly less healthy if they are out of balance. Studies have linked our microbiome to human health in numerous ways. Many conditions – from diabetes to depression, asthma to autism — have been found to relate to the microbiome. And the microbiome also keeps us well; the NIH just spent over $100 million to investigate the healthy human microbiome.

uBiome has launched the world’s first citizen science effort to map the human microbiome. uBiome provides participants with a catalog of their own microbes, detailing the microbial composition of the body and explaining what is known about each genera of microbe.  In addition, uBiome compares participants’ microbiomes with scientific studies on the role of the microbiome in health, diet and lifestyle.  uBiome also provides personal analysis tools and data viewers so that users can anonymously compare their own data with crowd data as well as with the latest scientific research.We are being incubated by the California Institute for Quantitative Biosciences at the University of California, San Francisco (UCSF). Our team consists of myself, a serial entrepreneur and PhD student at Oxford, and Dr. Zachary Apte and Dr. William Ludington, recent PhD graduates from UCSF. We also have an all-star scientific advisory board, including inventor and MacArthur Genius award winner Dr. Joseph DeRisi, Dr. Pablo Valenzuela (biotechnology pioneer and inventor of the recombinant Hepatitis B vaccine), as well as doctors, bioinformaticians, and researchers.

H+: You are looking for funding via Indiegogo. Can you tell me a bit about the project you are looking to fund specifically and describe what funders will receive? Why did you choose Indiegogo over other services, i.e. Kickstarter?

Jessica: We are looking to crowdfund our citizen science project at www.indiegogo.com/ubiome. For $79, you can sequence your GI tract; for $235, you can sequence the GI tract three times; for $272 you can sequence all five sites: mouth, ears, nose, GI tract, and genitals. Here’s how it works: You pledge and we send you a sample kit. You swipe the sample brush across the corresponding sample site. The cells are lysed in solution and sent to our laboratory for processing. Once we’ve sequenced your sample, we’ll send a login to our website where you can visualize and understand your data. As a uBiome community member you find out about our latest discoveries first, participate in ongoing citizen science projects, and suggest new questions that we can address together.We chose Indiegogo because they are international, flexible and have great customer service.  However, we hope that a lot more citizen science projects will come online, on any platform.

 

H+: What about privacy?
Jessica: uBiome is HIPAA compliant. We will never release any of your personal identifying data. We will never even store your data in such a way that anyone could figure out who you are from it. And don’t worry — because your microbiome is constantly changing, it can’t be used to figure out who you are either.We’ve been asked a lot if we are going to open our data to the public and we are still weighing how to handle the issue We are huge fans of open science and would love to open our data to the public. However, it is *your* data, not ours, and we are concerned about protecting your privacy, as well as other issues. We may decide to allow our users to choose open data as an opt-in. We’ll do our very best to balance the need for scientific openness with the imperative for strong individual privacy protections.

 

H+:  I was excited to learn about your project because it shows the very real potential for small groups of citizen scientists to self organize and do meaningful science outside of the usual university laboratory system. Can you say anything more about the DIY and independent aspect of this?
Jessica: Yes! I feel very strongly about the future of citizen science and am passionate about getting everyone involved in science. Science is a field of human endeavor which uplifts us and expands our understanding of the universe. Particularly in the biomedical field, science makes possible a better life for all humans. I’m glad to be part of a movement that brings cutting edge science directly to all of us and allows everyone to be empowered to look at our own data, do our own experiments, and democratize the process of scientific discovery.
H+: What do you expect the results of this project to be? Can we cure diseases by learning more about our microbiome?  What is the existing science here?
We can tell you a number of things. First, can draw correlations between the microbiomes sequenced in our study and various health conditions. For example, we can tell you if you have a profile that correlates with Type 2 diabetes or one that correlates with alcoholism.

 

Second, we can track changes over time. We can tell you how your new diet is affecting your microbiome, whether you’ve recovered from a recent dosage of antibiotics, or whether a health condition like IBD is likely to flare up soon.In the bigger picture, the more people that join the uBiome community, the more statistical power the project will have to investigate connections between the microbiome and human health. For example, with 500 people, uBiome will be able to answer questions about relatively common diseases such as diabetes and hypertension. With 2,500, the project can investigate connections to breast cancer. With 50,000 people, the project can begin to address multiple sclerosis and leukemia. A larger uBiome community has more statistical power and can begin to investigate more and rarer diseases in the context of the microbiome.

 

H+: Since the microbiome is an ecology of sorts, it is not static but rather interacting and changing over time as you mention. Many of my readers are interested in the idea of the “quantified self” where individuals measure and record/analyze data from their bodies to optimize performance, health, longevity and so on. What sort of quantification is possible here and what is the future for individual level real time quantification or ongoing measurement of the microbiome over time like this?
Jessica: Definitely — measuring the microbiome over time is really quite interesting. While sequencing the human genome provides invaluable knowledge, it is very difficult to change our genetic makeup. The microbiome, in contrast, may be more easily changed through lifestyle interventions: diet, probiotics, etc. By joining uBiome, citizen scientists can explore their own microbiome and be partners in the process of scientific discovery.More practically, we sell a Quantified uBiome package that includes three GI kits to use at three different time points, as well as a web app for building experiments. This is great for personal experiments, such as starting a new diet, exercise, or other intervention. Larry Smarr also encouraged us to set up a special kit for Bowel Conditions which includes three GI kits and a special survey about bowel conditions that will enable us to go into more detail.

 

H+: Can we engineer or alter the microbiome? It seems there are already some probiotic products that claim to do this by introducing organisms and I recently read a report about a parasite that seems to cure some intestinal problems. I also understand that what is happening in the microbiome can influence mood and therefore also performance and well being. Will we be curating our own personal microbiomes for optimal health and well being in the future? Feel free to speculate :)
Jessica: Well, this is definitely science in the future, but in my opinion, YES. My belief is that microbiome completely rewrites our understanding of disease it undermines the model that says one germ causes one disease so go kill it to make everything fine. We are a complex ecosystem of human and microbial cells, and the more we know, the more likely we are to be able to design interventions that can make a difference. The gut disorders seem to be the place to start, as there are already microbiome-related interventions that are in use — fecal transplants, for example. But that is just the beginning.
At the most basic level, we are sequencing the 16S ribosomal region of bacterial DNA to reconstruct phylogeny and make correlations. Some good review papers on the microbiome are Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes and The Impact of the Gut Microbiota on Human Health: An Integrative View. Very interesting stuff!  This covers the basics, but we’ve also got some other innovations up our sleeve on the sequencing side which should improve accuracy.

Please sign up and support citizen science at www.indiegogo.com/ubiome! We would really appreciate it. :)

 


Want to learn more about what sort of stuff is growing inside and all over you?

Check out this beautiful interactive graphic at Scientific American.

Human Microbiome Project

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