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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QS15 Conference Preview: Stephen Cartwright on 17 Years of Location Tracking

On June 18-20 we’ll be hosting the QS15 Conference & Activate Expo in San Francisco at the beautiful facilities at the Fort Mason Center. This will be a very special year with two days of inspiring talks, demos, and discussion with your fellow self-trackers and toolmakers, plus a third day dedicated to the Activate public expo. As we start to fill out our program we’ll be highlighting speakers, discussion leaders, sponsors, and attendees here.

Steve4bStephen Cartwright has been attending the QS Conferences since 2012, where he first spoke about his ambitious geolocation tracking project. As an associate professor at the School of Art and Design at the University of Illinois at Urbana-Champaign, where he teaches sculpture, digital fabrication, and furniture design, Stephen brings an interesting and welcomed point of view and set of experiences to our show&tell program.

At the QS15 Conference he will be sharing his process and what he’s learned from tracking his location every hour using a GPS for the last 17 years. He will describe how his practice has changed and adapted to new technologies over the years, including how active versus passive tracking techniques have impacted this project.

My tracking informs my life and especially my art, so I will consider my tracking through the lens of my 3D data visualization sculpture. The artistic aspect of my work allows the data visualization to become more than informative graphs, they become new landscapes of data.

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We’re excited to have Stephen joining us and asked him a few questions about himself and what he’s looking forward to at the conference.

QS: What is your favorite self-tracking tool (device, service, app, etc)?

Stephen: This is a difficult question, I use different tools for different stages of my work. My practice would be nowhere without a GPS. It took me a long time to replace my Garmin stand-alone GPS but I now use the MotionX GPS app for my iPhone. My requirements for these apps/devices is that the waypoints have to be saved with the date and time attached.

QS: What are you most looking forward to at the conference?

Stephen: The conference is a great place to be among like-minded people and share ideas and inspiration. Although all the attendees have a lot in common everyone comes to self-tracking from a different angle and seeks different outcomes. I love to see how similar practices result in improvements in performance and health, self-help, and even art.

QS: What should people come talk to you about at the conference?

Stephen: Come talk to me about the intersection of art and science, data-visualization, and GPS/location tracking.

QS: What tools, devices, or apps do you want to see at the conference?

Stephen: I am looking for the best smart phone based step and movement tracker.

QS: What topic do you think that Quantified Self community is not talking enough about?

Stephen: I would like to hear more about the relationship between individual trackers and larger data studies. How well do we know ourselves as compared to what can be inferred about us by our data footprint or studies of people in similar circumstances?

Stephen’s session is just one of the many hands-on, up-to-date, expertly moderated sessions we’re planning for the QS15 Global Conference and Exposition. We’ve made some early bird tickets available for readers of the Quantified Self blog (for a limited time):

Register here!

Bonus Video of Stephen’s Data:

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Gordon Bell: Every Beat of My Heart

Gordon Bell has been involved with self-tracking for over a decade. From his ground-breakign MyLifeBits project to his popular book on the possibilities of a fully digital life he is constantly thinking about new ways we can understand ourselves through the data we collect. We are always excited to see him at our QS events and were especially happy to have him reach out to us about presenting at our last Bay Area QS meetup.

Gordon Bell's HR data from a day he visited with his lawyers. Note the spike during the meeting in the morning.

Gordon Bell’s HR data from a day he visited with his lawyers. Note the spike during the meeting in the morning.

Gordon has experienced two heart attacks, one in 1983 and another in 1996, two double bypasses, and currently is living with his third pacemaker. It probably isn’t surprising given his medical history that he has a keen interest in understanding his heart. In this talk Gordon describes what he’s been learning from the data collected from his pacemaker and the 320 days of heart rate and activity data he has collected with his Basis watch.

We’re also excited to have Gordon joining us at our upcoming QS15 Conference & Activate Expo. We’ve made some early bird tickets available for readers of the Quantified Self blog (for a limited time): Register here!

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Meetups This Week

There will be eight great Quantified Self meetups happening all over the world this week. The group in Stockholm will have show&tell talks on sleep tracking, using the Scanadu Scout and using personal data to identify cause and effect in one’s life. Our exemplary QSXX Boston group will be getting together as well. To learn more on how the QSXX meetup groups create a safe space for discussing women-centric self-tracking topics, click here.

To see when the next meetup in your area is, check the full list of the over 100 QS meetup groups in the right sidebar. Don’t see one near you? Why not start your own! If you organize a QS meetup, please post pictures of your event to the Meetup website. We love seeing them.

Monday, March 2
Manchester, England
Oxford, England
Stockholm, Sweden

Tuesday, March 3
Reno, Nevada

Wednesday, March 4
Pittsburgh, Pennsylvania

Thursday, March 5
Lille, France
Toronto, Canada
QSXX Boston, Massachusetts

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What We Are Reading

We have a great list for you today. Special thanks to all those who are reaching out via Twitter to send us articles, links, and other bits of interestingness. Keep ‘em coming!

Articles
Self-Experimentation: Crossing the Borders Between Science, Art, and Philosophy, 1840–1920 by Katrin Solhdju. This brief essay lays out a great foundation for anyone interesting in the history and philosophy of science, with an obvious focus on the self-experiment. This essay is hosted at the Max Plank Institute for the History of Science, at which I highly recommend spending some time clicking around and reading the wonderful essays and articles.

After the Data Confessional: interview with Ellie Harrison by Stephen Fortune. A very interesting and thought-provoking interview with artist Ellie Harrison. For six years self-tracking data was the core component of Ellie’s work as an artist. Then she decided to stop and reconsider her tracking practices and what it meant to her and her work.

Data is the New “___” by Sara M. Watson. “What do we talk about when we talk about data?” is the question Sara posses here to frame a wonderful piece on how our use of metaphors influences our view of data.

A brief history of big data everyone should read by Bernard Marr. If we’re going to talk about how we talk about data it is probably useful to have some historical context. Great timeline here of data in society.

Baby Lucent: Pitfalls of Applying Quantified Self to Baby Products [PDF] by Kevin Gaunt, Júlia Nacsa, and Marcel Penz. An interesting article here from three Swedish design students that looks at current baby and parenting tracking technology. They also conducted a design process to develop a future tracking concept to better understand parent’s reactions to baby tracking. I thought there were a few interesting finding from their interviews.

Hey, Nate: There Is No ‘Rich Data’ In Women’s Sports by Allison McCann. It only seems fitting that a few days before this weekend’s MIT Sloan Conference on Sports Analytics Conference, the “it” place to learn about and discuss sports data, that we learn about the amazing dearth of data collected and published about women’s sports.

Show&Tell
AustinWaterstop-25-word-frequency
Analyzing Email Data by Austin G. Waters. A great deep dive into the 23,965 emails that Austin has collected in his personal account since 2009. I won’t spoil it, but this post just keeps getting better and better as you scroll. Bonus points to Austin for describing his methods and open-sourcing the code he used to conduct this analysis.

The App That Tricked My Family Into Exercising by Adam Weitz. Not a lot of data in this post, but I enjoyed the personal and social changes Adam described through his use the Human activity tracking app.

Visualizations

Smart Art by Natasha Dzurny. Using IFTTT and a few littleBits modules Natasha created a piece of artwork that reflects how often she goes to the gym. Would love to seem more DIY data reflections like this!

SleepCycle_US-Wake-Up-Mood
How does weather affect U.S. sleep patterns? by Sleep Cycle. Sleep Cycle analyzed 142,272 sleep reports from their users (recorded in January of 2015) to explore mood upon awakening, stress levels before bed, and sleep quality. Fascinating stuff.

Access Links
HHS Expands Its Approach to Making Research Results Freely Available For the Public
Many Patients Would Like To Hide Some Of Their Medical Histories From Their Doctors
Doctors say data fees are blocking health reform

From the Forum
Best ECG/EKG Tool for Exercise
BodyMedia API – Anyone have an active key/application?
Sleep monitor recommendations for research on sleep in hospitals
Simplified nutrition, alertness, mood tracking

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Greg Kroleski: Six Years of Tracking My Time

Greg Kroleski has been tracking his time for the past six years, starting when he was 20-years old. Using a spreadsheet he designed himself he collects how much time he spends in eight different categories: Survival, Labor, Social, Spiritual, Mind, Expression, Body, and Distraction. In this talk, presented at the San Francisco QS meetup group, Greg describes the data he’s collected and what he’s learned about where his time goes. If you’re interested in applying his tracking methodology he’s graciously put his spreadsheet template online here.

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QS Access: Data Donation Part 2

In our Access Channel we’re trying to expose ideas, efforts, and insights about personal data access and it’s role in both generating personal and public insights. The last time we wrote about data donation we mentioned a few different projects that allowed you to collect and/or publish your self-tracking data for others to view and access. Today we’re going to showcase a few research-focused projects that collect personal data, but also allow participants to access the data they contribute. This seemingly minor addition, participant access to data, is actually a process not commonly employed by research studies. We’re very interested in new participatory models of research that respect participant’s rights to fully understand and access the data they contribute. If you know of others please get in touch and we’ll add them to the list.

Personal Genome Project: Harvard
Probably the most well-known of these research projects is the ongoing Personal Genomes Project based at Harvard University (PGP). Led by George Church and an outstanding team, the PGP is an ongoing research project recruiting participants to “share their genetic, health, and trait data in a public and non-anonymous manner. Participation is free.

American Gut
Much like the project above, the American Gut project is an open call for participant to collect and share their data. In this case it is human microbiome data. Although enrollment is not free (they request donations starting at $99 to participate) data is returned to participants. (If you’re interested in participating in microbiome research, but live in Europe see the British Gut project)

Dynamics of the Human Microbiota
This new project, based out of Stanford, is also exploring the human microbiome. This study includes a variety of different perturbations and longitudinal data collection. Participants are compensated for their participation, their data is made accessible to them, and they have the opportunity to discuss their results with the study staff.

For those of you interested in research methods and ethics we recommend reading this brief article by Jeantine E. Lunshof, George M. Church, and Barbara Prainsack: Raw Personal Data: Providing Access

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QS15 Conference Preview: Julie Price on Long-term Weight Tracking

On June 18-20 we’ll be hosting the QS15 Conference & Activate Expo in San Francisco at the beautiful facilities at the Fort Mason Center. This will be a very special year with three days of inspiring talks, demos, and discussion with your fellow self-trackers and toolmakers. As we start to fill out our program we’ll be highlighting speakers, discussion leaders, sponsors, and attendees here.

JuliePhoto2Julie Price is a long time member of our Bay Area QS meetup group and will be attending the QS15 Conference & Activate Expo to share her self-tracking story. Julie has been using and experimenting with a wide range of self-tracking tools and behavioral techniques to understand herself. Previously she’s shared her experiences using commercial tools and self-designed methods to understand and improve her marathon training.

Over the past 4 years, Julie has tracked her weight as it moved within a 30 pound range, varying wildly within each year. In December, Julie shared the factors that influenced her weight the most: family visits, distance road races, and a variety of weight loss tactics. As part of our show&tell program, Julie will share an update that includes her newest insights into her weight fluctuations as well as what interventions have made the greatest impact on her weight.

JP_Weight

We’re excited to have Julie joining us and asked her a few questions about herself and what she’s looking forward to at the conference.

QS: What is your favorite self-tracking tool (device, service, app, etc)?

Julie: Hands-down, I love the Whistle to measure my dog’s activity. I use Basis Peak and my husband uses Jawbone Up. Both seem well-designed for certain scenarios and not for others. Between all the wearables we’ve tried, the Whistle has been the most successful in influencing our behavior.

QS: What are you most looking forward to at the conference?

Julie: I’m looking forward to meeting interesting people, learning from their stories, and learning from their creative experiments and observations. But, I’m most looking forward to exploring new ideas that impact the behavior of people who don’t necessarily enjoy data.

QS: What should people come talk to you about at the conference?

Julie: I’m an expert in UX, interaction design, usability, health behavior change, and fitness. I’d love to talk about creative tactics for eliciting behavior change and a process for ensuring the right product and experience is designed for the right person. I also love to talk about health gaming and the complexities of the space.

QS: What tools, devices, or apps do you want to see at the conference?

Julie: Any product in health and fitness that is truly different or thought through from the perspective of the user. I’d love to see any product built with a process that continually validates their direction with target users.

QS: What topic do you think that Quantified Self community is not talking enough about?

Julie: We should explore more innovative ways to meet people where they are and creatively influence them gradually in a way that is meaningful and lasting. It would be great to talk more about what progressive techniques could be applied in order to create impact over both short and long periods of time.

Julie’s session is just one of the many hands-on, up-to-date, expertly moderated sessions we’re planning for the QS15 Global Conference and Exposition. We’ve made some early bird tickets available for readers of the Quantified Self blog (for a limited time): Register here!

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Meetups This Week

This week will bring four fascinating Quantified Self meetups. St. Louis will have a “quantified romance”-themed meetup including a toolmaker talk with the creator of a service that helps with romantic decisions.  In Ashland, they will be getting together to discuss n=1 study designs. This is the same group that started the Individual Metabolic Research Group (iMeRG) that we featured a couple of days ago.

To see when the next meetup in your area is, check the full list of the over 100 QS meetup groups in the right sidebar. Don’t see one near you? Why not start your own! If you organize a QS meetup, please post pictures of your event to the Meetup website. We love seeing them.

Tuesday, February 24
St. Louis, Missouri

Wednesday, February 25
Cincinnati, Ohio

Thursday, February 26
Ljubljana, Slovenia

Saturday, February 28
Ashland, Oregon

Also, enjoy these photos from last week’s meetup in New York, as well as, last month’s meetup in Vienna.
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What We Are Reading

We hope you enjoy this week’s What We’re Reading list!

Articles
The Wow of Wearables by Joseph Kvedar. An excellent post here in the wake of the “Smartphones vs. Wearables” hype in the past weeks. Favorite part:

“I’d have to say that reports of the death of wearables have been greatly exaggerated. The power of sensor-generated data in personal health and chronic illness management is simply too powerful to ignore.”

Survival of the Fittest: Health Care Accelerators Evolve Toward Specialization by Lisa Suennen. If you’re at all interested in the recent surge in health and healthcare focused accelerators this is for you. Excellent reporting. (Thanks for sharing Maarten!)

Your Brain Is Primed To Reach False Conclusions by Christie Aschwanden. Fascinating piece here about the nature of the “illusion of causality.”

A Few Throughs About Patient Health Data by Emil Chiauzzi. Emil, Research Director at PatientsLikeMe, lays out four point to consider when thinking about how to best use and grow self-collected patient data.

Having Parkinson’s since I was 13 has made me an expert in self-care by Sara Riggare.

I am the only person with the whole picture. To me, self-care is everything I do to stay as healthy as possible with a disease that is a difficult life companion. It entails everything from making sure I take my medication in the optimal way, to eating healthily, getting enough sleep, to making sure I stay physically active. I also make an effort to learn as much as I can about my condition; my neurologist says that I know more about Parkinson’s research than he does. I don’t find that odd, since he needs to try to stay on top of research in probably hundreds of neurological diseases, whereas I focus on just one.

From Bathroom to Healthroom: How Magical Technology will Revolutionize Human Health by Juhan Sonin. A beautifully written and illustrated essay on the design of our  personal healthcare future.

Show&Tell
Experimenting with sprints at the end of exercise routines by Gustavo M. Gustavo is a person with type 1 diabetes. After reading that post-exercise high intensity exertion might have an effect on blood glucose he put it to the test.

On Using RescueTime to Monitor Activity and Increase Productivity by Tamara Hala. Tamara walks us through the last three years of her RescueTime data and how she used that information to understand her work and productivity.

How Do You Find Time to Write? by Jamie Todd Rubin. Jamie has been writing for 576 consecutive days. How does he do it? A mixture of data and insight of course!

Visualizations
ILoveYouMaps Say “I Love You” With Mapping by Daniel Rosner. Wonderful to see CHI papers ending up on Medium. This seems like a fun self-tracking/art project.

ShannonConnors_4yearsfood Cleaning up and visualizing my food log data with JMP 12 by Shannon Conners. Once again, Shannon displays a wonderful ability to wow us with her data analysis and visualization. Above is four years of food tracking data!


Two Trains: Sonification of Income Inequality on the NYC Subway by Brian Foo. Brian created this data-driven musical composition based on income data from neighborhoods the border the 2 train. Beautiful work.

Access Links
Walgreens adds PatientsLikeMe data on medication side effects
How Open Data Can Reveal—And Correct—The Faults In Our Health System
Big Data is our Generation’s Civil Rights Issue, and We Don’t Know It.

From the Forum
Creating Scales for Quantifying Action
Sharing Anonymized Data

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