Tag Archives: ubiome

Richard Sprague: Microbiome Gut Cleanse

2 Richard Sprague - Microbiome GutCleanse.001

 

Richard Sprague has been closely tracking his microbiome and sharing his findings for the last couple of years. He’s even joined our friends at uBiome as their citizen-scientist-in-residence.

In this talk, Richard shares his attempt to improve his sleep quality by increasing the amount of bifidobacterium in his gut through eating potato starch. You’ll learn why he took the extreme step of flushing his digestive tract and rebuilding it from scratch.

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Mark Moschel: Parasites and Gut Repair

Moschel-Gut-Viz2

While traveling in Ecuador, Mark Moschel ate some ceviche from a street cart that he later found contained a parasite called giardia.

Mark's Enemy Within

Giardia lamblia

Experiencing fatigue, light-headedness, and digestive issues, Mark used the Reporter app to track his symptoms and Ubiome to measure his gut flora to help him understand and combat the parasite.

Though a trying experience, Mark brings levity to his show&talk presented at QS15.

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Learning From Your Microbiome: uBiome at QS15

Next week we’re hosting our QS15 Conference and Expo and we’re delighted that so many great toolmakers will be joining us to show off their devices, apps, and services. We’ve  asked each of our toolmakers to give us a bit more background information about their company and what they’re excited about. If you’d like to meet these innovative companies and the amazing people behind them then make sure to register today!

QS15_uBiome

1. How do you describe uBiome?
uBiome is a microbiome sequencing service that lets you explore the populations of bacteria that live on and inside your body. Based in San Francisco, we were founded in 2012, went through Y Combinator and have funding from Andreessen Horowitz.

Here’s how it works: we send you a kit, and you send us back a sample from your mouth, nose, skin, genitals, or gut (just a swab of your toilet paper will do). We sequence it for you at our in-house lab, and you can then login to see visualizations and comparisons of your data.

We want everyone to be able to explore their own microbiome while advancing research on a massive scale at this new frontier of science.

2. What’s the backstory? How did you get started?
In 2012, the NIH-funded Human Microbiome Project (HMP) finished, mapping out many of the bacteria who live intimately with us. uBiome launched an Indiegogo campaign that same year, to see if the public would be interested in being part of a project to use the HMP technology for large-scale microbiome studies. The campaign raised 3.5 times more than the $100,000 we asked for, and uBiome was born.

3. What impact has it had? What have you heard from users?
We’ve sequenced tens of thousands of microbiomes now, and started to release preliminary findings. For example, we don’t see a difference between male and female gut microbiomes, but we do see a difference between gut and mouth microbiome samples.

A flood of individuals and researchers from around the world have approached us about starting studies, on everything from underarm bacteria to inflammatory bowel disease. We even have people testing their koalas and their stream water. The level of excitement about being part of this new field of research is incredible.

You can think of it like a genetic test, except for one major difference. With the microbiome, you can actually DO something to shift the levels of bacteria in your body. So as we learn more about patterns associated with different disease states, people may discover ways to hack their microbiomes to reduce suffering and optimize health.

4. What are you doing next? How do you see it evolving?
We have a strong social mission of enabling citizen science around the microbiome, so that people whose lives could be most affected by new research breakthroughs actually have a chance to be part of the process up front and help set the agenda.

uBiome wants to enable anyone to start a study, share what they’ve learned, and collaboratively add to the world’s knowledge about this emerging and powerful field. In a talk our CEO Jessica Richman gave at TEDMED a couple of years ago, she asked the question, “Could a citizen scientist win the Nobel Prize?” It’s really about leveling the playing field to help science go faster.

5. How can people find out more about you?
Visit http://ubiome.com, or stop by our booth at the upcoming Quantified Self Expo. We look forward to meeting you and your bacteria!

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QS Radio Episode #1

QSradio_iTunes

In our first episode of QS Radio we hit the ground running with a great pair of interviews and some super interesting news and discussion about exciting self-tracking projects.

In our show&tell segment, we hear from Shannon Conners, a self-tracking enthusiast who’s been learning amazing things from tracking her diet, exercise, and weight for over four years. Jessica Richman, CEO and co-founder of uBiome, joins us for a short Toolmaker Talk where we learn about the importance of the microbiome and citizen science. To wrap up, Ernesto and Steven share a few interesting tech and self-tracking stories in a segment we call “What We’re Reading.”

We hope you enjoy this inaugural episode. Make sure to check the show notes below for links to items we discussed.

Download the episode here or subscribe on iTunes.

Show&Tell
You can find out more about Shannon Conners and her self-tracking experience on the JMP blog. We spoke in particular about her excellent diet tree map visualization:
ShannonConnors_4yearsfood

Toolmaker Talk
You can find out more about Jessica Richman and uBiome on their website.

What We’re Reading

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What is in My Gut?

LesDethlefsenPostTop2

This past fall we learned about a unique study, conducted at Stanford University, designed to contribute to the understanding of the human microbiome. This study also has a component not common to academic research — data is being returned to the participants. Intrigued, I contacted the principle investigator, Les Dethlefson, to learn more.

Ernesto: Tell me about the Dynamics of Human Microbiota study.

les_dethlefsen_at_the_benchLes Dethlefsen: Since I joined the Relman Lab at Stanford, I’ve been looking at the human gut microbiota, focusing on what affects it and how it changes over time. In our study, we are looking at three different perturbations, deliberate changes to the gut ecology, to see how the microbiota population is affected.

We are very interested in the patterns that emerge. In people who have very stable gut microbiota, does their microbiota remain that way when they undergo diet shifts, a colon cleanout, or an antibiotic? Or maybe people who have a stable gut microbiota most of the time are the ones who are most affected by something unusual such as taking antibiotics. We just don’t know enough to understand these patterns right now. So, we’re really looking for basic ecological information.

Ernesto: If you look at the popular press, it seems the microbiome is the new golden child of biological life sciences. We’re even seeing companies in Silicon Valley get involved with this kind of work.

Les: It is broader than that. It really is a worldwide interest on the parts of both the scientific community and the public. And unfortunately, we are probably going to see some overhype, just as we did with the Human Genome Project. But I do believe this is a very important area. I think there will be a lot of payoffs and health impacts from this research, although it’s not going to be everything.

The shift that, I think, would be good for us to make intellectually is to get rid of the “us vs. them” thinking, because we are symbiotic organisms.

We have evolved with a native gut microbiota, and native microbiota is pretty much everywhere. We have evolved together, so it’s fallacious — an artifact of our past ignorance — that we don’t think of our microbes as part of our physiology.

Ernesto: It seems like exploring the deep sea, an unknown world that we’re just starting to peek into.

Les: It’s along those lines. You’re not wrong about that. But unlike, let’s say, the deep waters surrounding an undersea hydrothermal vent, we already know a lot about human physiology. There are a lot of molecular details and genetic pathways that we already have worked out. The context is somewhat understood.

And now, we have a reasonable start on the initial research: What microbes are present, and where? What’s the range of what we think is the normal distribution? We certainly don’t know enough, because we only know about people in the developed world. However, this may not represent all of human diversity or a very natural state of the gut microbiota.

Candida albicans

Candida albicans

Ernesto: Let’s get back to your study. You are asking participants to send microbiome data in the form of fecal matter and urine to your lab. What are you doing with those samples?

Les: We ask participants to provide both stool and urine samples. With the stool sample, we apply four different methodologies to turn it into data. One is the very common 16S ribosomal RNA (16S rRNA) gene sequencing approach. It’s relatively standard and inexpensive. It acts like an ID card for microbial taxa — telling us approximately what strains are present and in what relative abundance. We have a lot of data like that already for comparison.

sequencerThe second approach we will be applying is metagenomic sequencing, wherein we will be sequencing a random selection of all the genomes of the microbial types that are present. We can’t take this to completion, even with the dropping cost of sequencing, especially because there are some very, very rare microbes that we barely even have the chance to see at all. But we can get a pretty good swathe of genetic sequence data from all the microbes.

The third approach is even more ambitious. It’s called metatranscriptomics. Genes can be carried by any critter, you and I included, but not expressed. Knowing which genes are turned on, and to what extent they’re turned on is a better measure of the biological activity that is actually happening. The metagenome is a measure of potential activities, what the bugs can do. The metatranscriptome shows what the microbes are actually doing. Metatranscriptomics is even more challenging than metagenomics partly because of the nature of messenger RNA (mRNA). It’s a highly unstable molecule. There are technical challenges, but we’re ambitious enough to try to collect information on gene expression.

The fourth approach is not based on gene sequences, but on chemical composition. Metabolomics is the name given to a number of these approaches that are not directed to a specific chemical. These are techniques that try to measure a broad swathe of chemicals present in the environment and their relative abundance. This is a technology that we, in the Relman Lab, know very little about. We’re collaborating with the Nicholson Lab in Imperial College in London, and they will be doing the metabolomic analyses on the stool samples. That may be even closer to where the rubber meets the road — knowing not just the gene expression but also the resulting chemical changes that are happening in the environment.

MicrobeHeatMapMetabolomics takes us to the other type of sample we’re collecting: the urine samples. We aren’t doing this because we have an interest in the urinary microbiome itself, but because, as the Nicholson Lab suggested, the urine provides a more complete, integrated picture of the co-metabolism between the human host and most of the gut microbiota. So while metabolomics for the stool samples would primarily measure the gut microbial activity and what they contribute to the host’s physiology, the urine provides a more integrated picture about how the host metabolism works in concert with the gut microbiota.

Ernesto: If a participant is going to be contributing all of that data, will they have access to it?

Les: As someone with similar interests, I certainly knew that a huge motivation for people to join the study would be the access to their own data. We offer monetary compensation, but for the amount of time that will be spent in contributing samples, it is probably trivial. We knew we would attract the curious, scientifically inclined, and practising scientists. Of course, they would want to see their data.

The Institutional Review Board (IRB) was quite open to us sharing information with the participants about their own microbiota. It probably helped that there’s publicity  about ways people can get this information. There is the American Gut project, offering an assessment of your microbiota for a donation, and uBiome, a private company offering the same kind of service.

I, or another staff member of the study, are going to share this microbiota data with each participant in a conference call. So in effect, I’m going to be a microbiota counselor. It’s nowhere near as high-stakes as sharing genome information. We don’t know enough to say, for example, that this microbiome is definitively healthy, or that it’s unhealthy, or what the exact risks of diseases are due to this particular composition. So we will be putting this information in context, and we will be available as interpreters of the scientific literature. We may be able to say that there is a statistical association between a particular microbial group that someone may have in their gut and some health-related outcome.

sequence_data3

Microbiome sequence data

Ernesto: Will participants be getting a copy of their data as well?

Les: Yes, we will provide that. I have an open source mentality. Added to that is the fact that there are many practicing scientists signing up for the study and saying they want data, not just a PDF summary. I am happy to provide the data in as raw a format as people want. They can get the raw sequence information, a low-level summary (which is the result of the first pass of data processing), or the final summary. I have permission and full intention to share all the data derived from a person’s samples with that person.

Ernesto: Do you think we will see this happening more in the future?

Les: I think we will probably see more of it in the future. We’re moving in the direction of access to information. The open source movement has reached the health and medical realm from its origins in tech and computing. I think the participatory nature of access to data and scientific information is a good thing. It has started, and I don’t see any way of reversing the trend. I would hope that it becomes the norm that there is some appropriate level of sharing, that research participants have access to their data if they wish, and in a way that lets them interpret that data appropriately.

I believe that people have a right to that level of knowledge about their bodies, and if we, scientists, are generating that knowledge, there’s no reason not to share it with the individuals.


The Dynamics of Human Microbiota study is currenlty recruiting participants. If you’re interested in learning more about the ecosystem within read more about the study and check to see if you’re eligible to participate here.

We invite you to share your data access stories, and this article with the #qsaccess hashtag and follow along on quantifiedself.com and @quantifiedself.

 

 

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What We Are Reading

Another batch of links, examples, and visualizations from our QS community and around the web. Enjoy!

Articles

The phone is a gateway drug to health: what MyFitnessPal knows, and what Under Armour gets by Jane Sarasohn-Kahn. There has been a lot of talk this week about Under Armour’s acquisition of the self-tracking app companies Endomondo and MyFitnessPal. Having read through many reactions, I thought this short post by Jane was one of the best.

The Electronic Health Record: Are we the tools of our tools? [PDF] by K. Patrick Ober and William B. Applegate. This article, written for The Pharos, a quarterly journal covering nontechnical medical subjects, is a very interesting peak into how some physicians are thinking about how they practice medicine in the era of the EHR. The authors make the case that the “EHR in the exam room” is not only degrading the patient-doctor relationship, but may be contributing to a growing lack of understanding and a reduction in the holistic view of patient care.

Introducing the #OpenAPS project by Dana Lewis and Scott Leibrand. Dana and Scott, pioneers in the open medical device data and #WeAreNotWaiting movement, have done it again. Building on their experience with testing an using an Artificial Pancreas System (APS) they’ve decide to release an open reference design for an “overnight closed loop APS system.”

We believe that we can make safe and effective APS technology available more quickly, to more people, rather than just waiting for current APS efforts to complete clinical trials and be FDA-approved and commercialized through traditional processes. And in the process, we believe we can engage the untapped potential of dozens or possibly hundreds of patient innovators and independent researchers and also make APS technology available to hundreds or thousands of people willing to participate as subjects in clinical trials.

Ringly’s Destiny Revealed by Robin Sloan. Too often, the narrative around the impending device-creep, which is invading every aspect of our lived experience, settles into a “look at  how terrible we’re becoming as humans.” I really liked how Robin Sloan spun the idea of networked devices into something that becomes a fun enjoyable hacked experience.

How Data Will Help Me Keep My Resolution by Emmy Ganos. Emmy, who is a program associate at the Robert Wood Johnson Foundation, recently attended a few “Data for Health” events and wrote up her thoughts. It was nice to see her expose some ideas around public/communal data and it’s impact on health as well as a this gem from our own Gary Wolf:

In San Francisco, I was surprised to hear Gary Wolf, the leader of the Quantified Self movement, passionately challenge the idea that historically disempowered groups are less capable of analyzing and understanding data about themselves. He shared the provocative point that we too often underestimate people’s intelligence, and think that we have to interpret data FOR people. Wolf’s point is that everyone deserves access to data about themselves, in whatever format it is available.

Quantified Man by Jedd Cole. A nice piece of of short fiction here. To say more would be to spoil it. (Side note: If you run across other QS-themed works of fiction please do send them in. We love reading them.)

Show&Tell

Using tools to analyze my uBiome results by Richard Sprague. Richard is a member of our great QS Seattle meetup group and recently gave a talk (video coming soon!) about analyzing and understanding his uBiome micorbiota data. In this post he walks us through analyzing his data using R. He also has another great post for analyzing the data in Excel if you’re so inclined.

Visualizations

TobiLehman_standing_histogram
Standing Desk Histogram by Tobi Lehman. Tobi has a standing desk and wanted to track how much he was actually standing. He wrote a simple script to allow him to track the state of his desk and found that he typically stands for less than an hour at a time.

ChristopherPenn_BasisWatson
Marketing Analytics Tools for Non-Marketing Uses by Christopher Penn. Don’t let the title fool you, this is a great Quantified Self post. Christopher accessed his data from his Basis watch, visualized it, and then fed it into IBM’s Watson to see what was actually influencing calorie expenditure.

Music_Qlik
Making Qlik sense of the music that you play by Patrick Tehubijuluw. A nice visualization here of Patrick’s music listening history. Make sure to click through to see how you can make this same visualization.

Access Links
Smart Ways to Manage Health Need Smart Regulation
HHS Changes Incentivize Value Driven Care, But What About Device Interoperability?
BYOD – Bring your own Data. Self-Tracking for Medical Practice and Research
Big Data: Seizing Opportunities, Preserving Values (White House Report, PDF)
Patient-Generated Data Fuels Population Health Management
ONC unveils Interoperability Roadmap for public comment
Medical researchers and health care providers must consider moral as well as legal questions on data use, says bioethics body

From the Forum
Basis Peak
QS for Down Syndrome children
Diagnosed sleep apnea, looking for metrics pre/post treatment
HRV app APIs
Separation of cloud vs local storage?

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