Spotlight on a Researcher: Alexander Biel

Alex Biel is pursuing graduate education in Obesity Prevention and Management at Arizona State University. As part of his master’s thesis in Eric Hekler’s Designing Health Lab, he created ‘Pokemon Go: A Socio-Technical Exploratory Study’. The aim of this pilot study was to gain a better understanding of how games might influence physical activity.

You can join Alex’s study on Open Humans! The Designing Health Lab might have funding for another round. If it does, Alex will get in touch with you.

I spoke with Alex last week.alex_biel_improved

Hope: What do you think are the most glaring mistakes that society makes regarding obesity prevention and management?

Alex: Our entire environment is pretty great at making us fail to be active. I also think the media does a crappy job of showing what’s realistic. That can be discouraging — it was for me. But we have enough information now on the consequences our built environment have, so we should rethink how we’re doing things. It’s time for us as a society to pivot and come up with healthier strategies. The obesity epidemic didn’t happen because of personal failures.

Hope: Why did you want to study people playing Pokemon Go?

Alex: I wanted to look at whether Pokemon Go impacts physical activity. Since Pokemon Go inadvertently prompted people to walk more, it provided a unique opportunity for research to understand how this game, and other games more generally, can be used for fostering physical activity. Also, it’s considered one of the top games ever in terms of initial downloads.

Hope: What was most challenging about the Pokemon study? What was most interesting?

Alex: I heard from others in the lab that recruitment is difficult.  I didn’t really understand this until I worked on finding people myself. My recruitment strategy wasn’t as fluid as I would have liked. I just walked up to 500-600 random students on the ASU campus and asked them if they play Pokemon Go.

I got ethics board approval on October 1st and the first run of the study was done in less than a month. That’s an incredibly quick turnaround that was made possible partially because of all of the great infrastructure that Open Humans provides.  It allowed me to learn some interesting points, such as what seems to be driving gameplay, relatively quickly.

Hope: Is this the first research study that you designed? If not, what else have you worked on?

Alex: This was my first study. Thankfully, Open Humans made it a lot easier than I expected to get started. It gave me the information about steps, which was my main outcome variable,become easily available via their connection with Health Kit.

Hope: Can you describe what gamification is and how it relates to your research?

Alex: Gamification is using game thinking and game mechanics to solve problems and engage users. In this study, my goal was to explore if PokeMon Go appears to influence steps taken per day (spoiler alert, so far it looks like a small trend, but nothing significant based on our current sample) and then to look at the game mechanics of PokeMon Go.

Going forward, I’d like to explore how to create a more efficient recruitment process. I’d also like to add more validated measures to the protocol. A couple of the questions I’d wanted to ask were excluded because they were too open-ended and there were no definitive way to analyze them.

Hope: You’re currently writing your thesis. How do you see yourself using your degree in the future?

Alex: If all goes according to plan, I will be continuing my education at ASU in Dr. Hekler’s lab. I am hoping to use my degree to specialize in designing programs catered to healthy living and healthy food choices. Dr. Hekler has a couple awesome studies that are currently being reviewed, so I am hoping to dive into one of those just as soon as they get approved. *fingers crossed*

Hope: Besides being a graduate student, you’re also a certified personal trainer. What piece of advice have you repeated most often when working with clients?

Alex: One of my old professors said, “Eat less, move more.” I really think that’s the best advice. I’m a huge advocate for developing a healthy lifestyle. I lost 60 pounds by trial and error. When you put immediate gratification aside, anything is possible. It’s hard to change, but doable — especially if you have the right motivation. Find something that gets you psyched and channel that to find better ways to cope. I think a lot of people who claim to be healthy don’t have very healthy coping behaviors.

Hope: Do you do any personal health-tracking on a regular basis? If so, what have you found most helpful about the data you’ve collected?

Alex: Not really. I’ve used them in the past. Theoretically, health trackers are awesome. But I think they’re a way better tool to get people started on a healthier lifestyle than they are to get people to sustain that lifestyle. They’re more like a wake up call. The first time you use one, you think, “That’s all I’m moving?!” People are bad at guessing how much they move. Using a tracker makes you more realistic about your own behaviors, but it’s not necessarily going to get you to change your habits. For instance, I know I don’t walk a lot – I don’t need a tracker to tell me that. So I try to make up for that by standing and stretching as much as possible. I believe that if you’re not getting one thing, then try to balance it out by doing something else.

Hope: What health-tracking technology do you wish existed?

Alex: There’s only so much you can do with the information given to you by the current trackers. Say I’ve walked 7,000 steps today. I don’t know how that’s impacting me. It would be cool to have a one-stop shop that tracks food quantities, health behaviors, and physical activities. I’m optimistic that this will happen one day, but right now you have to be really dedicated to make use of trackers. Plus, most devices and techniques are not that accurate. Even the calories on the back of a box of food are only as accurate as the FDA requires.

Hope: According to your LinkedIn profile, your interests are fitness, coffee, reading, learning, and writing. Is coffee the fuel that sustains your other interests?

Alex: Pretty much.. A nice cup of coffee is my reward for doing the things that I should be doing.

Want to join Alex’s study?
You can join on Open Humans!
The Designing Health Lab might have funding for another round. If it does, Alex will get in touch with you.

Want to get in touch with Alex?
Reach out to him through his Member Profile or LinkedIn

Want more regular news? Like us on FACEBOOK

An inspiring video, new site features, and a new name!

Check out this inspiring video featuring Open Humans participant Liz Salmi and participant/board member Steven Keating.


Search & filter members.

Looking for someone’s profile? Want to see who else has joined an activity? We’ve upgraded the Member List! You can now search for other participants by name or username. You can also use a drop-down to filter the list according to activity, study, or data source.

Visit our new Member Page


Everything about an activity – all in one page.

Want to join a study? Add a data source? Manage related data? Find new ways to share? We’ve pulled all these features together with pages for each activity.

Here are some activity pages you might want to check out…

  • Open Humans HealthKit Integration
    Got an iPhone? This project and open source app, created by James Turner, enables you to add your iPhone’s Health data to Open Humans.
  • 23andMe
    Are you a 23andMe customer? You can add this data to Open Humans. Already added your data? Visit this page to see your files, and find projects you can share it with!
  • Circles
    Got nipples? (Probably!) Join this study to help Abby Wark at Harvard Medical School learn more about the areola – an understudied & uniquely human anatomy feature.

Activity pages are also easy URLs to send to friends. Feel free to share!


A new name for our nonprofit.

Our nonprofit has a new name: the Open Humans Foundation.

Open Humans is a project of a 501(c)(3) charitable organization. Since its founding in 2008, this organization’s name has been “PersonalGenomes.org”. We’ve now got a new name, but our mission remains the same: to make a wide spectrum of data about humans accessible to increase biological literacy and improve human health.

Check out the new website at: http://openhumansfoundation.org

The Open Humans Foundation continues to support our other programs, including the GET Conference and the Personal Genome Project.


Want more regular news? Like us on FACEBOOK

Spotlight on a Participant – Liz Salmi

Liz Salmi is a “healthcare communications nerd, patient advocate, brain cancer blogger, neuro-geek and all around OK gal.” She has had two brain surgeries, 24 months of chemotherapy, and says it is her duty and honor to tell her story. We spoke a few weeks ago.

Hope: How did you find out about Open Humans and what made you join? 

Liz: I first heard of Open Humans from Steven Keating. I’d been following his story for a couple years since we’re both living with a brain tumor. We met when we were asked to participate in “The Open Patient,” a documentary about applying the “open source” philosophy in health care. He was asked to be featured in the documentary because he has open sourced a lot of his health data, and I was asked to do so because I’ve been open sourcing my healthcare story through my blog. I joined Open Humans because I wanted to share some of my health data, too.

Hope: What is most fulfilling to you about sharing your data? 

Liz: There’s sharing data and then there’s sharing information about an experience. What I find fulfilling about sharing my story is that I’m able to connect with others who are going through a similar experience. So many of the people who read my blog write to me, and I get to learn their stories as well. Fewer than 2% of cancers are brain cancers, which means there aren’t many people living with it. Also, the prognosis for most brain cancers is not very good. But someone diagnosed today could stumble across my blog and learn what it’s like to live with this! That’s why I’ve decided to continue it and write about the survivor stage. I still get brain scans every 6 months, and I take medicine for the side effects of my tumor, such as epileptic seizures. I talk about all of this on my blog. Even if the tumor grows, I will continue to share my story.

I’m getting more into the idea of sharing my health data. I believe this data could be a valuable resource not just now, but also in the future. I sometimes wonder if I’d be this open if I felt stigmatized because of my disease, but I have never felt discriminated against because of it. I know people who have rare diseases who haven’t been as fortunate in this regard. It’s a very personal choice to share health information. What is right for me isn’t necessarily right for everyone.

Hope: Before you started your blog, had you ever shared health data — for example, by participating in traditional research studies? 

Liz: I’d never shared health data before my diagnosis because I’d never been in a position to. I wasn’t on a university campus where students were being recruited for studies, so I never felt I had access to any sort of research. However, one of the places I went for a second opinion on my diagnosis was the University of California, San Francisco, a teaching hospital. They asked me to join a study, and said I’d get $20 for it. I said, “Sign me up!” A year later, they contacted me to see how I was doing, and by that time I was already blogging about my experience. I’m one of those people who likes filling out forms and surveys, so at some point I realized I didn’t need any sort of financial incentive to share my data. I felt I had valuable information, and it was fulfilling to know that researchers were looking at it and some good could come out of it.

Hope: You said that it was a huge decision to change the setting on your blog from private to public. Was the decision to publicly share some of your health data on Open Humans similarly momentous, or a no-brainer?

Liz: It was a no-brainer! Even though I had my blog and various other opportunities to be “out” as someone living with brain cancer, I didn’t have a platform to share my health data. When I learned about Open Humans, I knew it was the just the kind of platform I was looking for.

I’ve learned that there are a lot of people who want to contribute data, but who don’t fit into existing studies. It would be great if Open Humans could become a repository for their data, so researchers could access it now or in the future.

Hope: Tom Delbanco, MD and co-founder of OpenNotes, said in the excellent Open Patient video, “If you’re healthy, you worry about privacy. If you’re sick, or if you’re in the emergency room, you could give a damn about privacy. You just want everyone to have access to everything right away so you can be helped.” Do you think the needle is moving at all on this? Do you get a sense that people you meet – either online or off – generally share a commitment to data sharing?

Liz: I was diagnosed with my brain tumor in 2008, and my instinct was to blog about it because I couldn’t find a lot of the sort of information I wanted online. But my boyfriend (now husband), friends, and health care advocates cautioned me against this. They were concerned that I’d regret it because my feelings about my privacy could change over time. But pretty soon they thought it was really cool how I was reaching people!

I’m a member of a generation that has grown up sharing stuff on the Internet, so – for better or worse – we’re used to sharing what older generations consider too personal to talk about publicly. Sharing is ingrained in us. We’re not judging each other. I know people from certain cultural or religious backgrounds still believe that talking about disease is somehow inviting ill will, but most of us just don’t think it’s a big deal.

Hope: You mentioned in your TEDx talk that friends of yours crowdfunded for your medical bills and that your blog is an effort to redefine the support group. Obviously, you’re also sharing your data online on our site. Do you feel you’ve experienced any drawbacks from this 21-century model for healthcare, or has it all been positive?

Liz: Everything has been really positive. Web communication used to be the wild, wild west, but it’s not anymore. It can be very rewarding.

Hope: What are the biggest misconceptions about people living with rare or serious diseases?

Liz: It depends on the disease. I know people with diseases you’ve never heard of. They often feel left out and as if they have no support. I’ve mostly met them over Twitter — through #RareDisease and #BTSM, which stands for Brain Tumor Social Media. I can relate to what they’re going through because there are about 120 types of brain tumors, but we’re still the black sheep of the cancer world. As with rare diseases, there’s not a lot of money flowing in for treatment.

I’ve become a vocal patient advocate partly because I know what it’s like to not be able to find an appropriate support group. Different diseases require different types of support. For instance, people with brain tumors have neurological issues. People with other cancers can’t relate to this, so a generic cancer support group isn’t right for us. Larger cities have more options, but not everyone lives in large cities.

As a side note, there are a lot of things laypeople can do to impact healthcare — like lobbying for more funding. I’ve done this at the federal level, but calling your local district office can make a difference, too.

Hope: Last question. What health-tracking technology do you wish existed?

Liz: I wish there were more ways to share health data and more partnerships between researchers. Also, that more data sites had an app version and that some health tracking apps already in existence were more user friendly!

Want to get in touch with Liz? Reach out to her through her blog, Facebook, Twitter, or LinkedIn.

Study Update: Keeping Pace

One of our goals at Open Humans is to provide updates on participating studies.

Keeping Pace examines how exercise patterns correlate to the environment. Dr. Rumi Chunara spoke in depth about the study at this year’s Health Data Exploration Network Meeting:

  • Watch her talk on YouTube to learn:

    • Why the ‘built environment’ matters

    • Implications of using personally-generated data for research

    • Specific exercise trends observed so far

Dr. Chunara and her team have proven the efficacy of their data by garnering results consistent with findings from social media research:

  • People are most active on the weekends.

  • People are least active on Fridays.

  • The most popular weekday for exercise is Tuesday. (Feel free to speculate on why this is!)

They use data from the free Runkeeper app* to find out:

  1. Where are people most active?

  2. How does this compare to others who live nearby?

  3. What activities do people choose for recreation?

  4. What activities do people choose for transportation?

*They’re looking into expanding to other sources. Stay tuned!

According to the CDC, 71% of adults in the United States are overweight and 35% are obese. Although diet is a significant factor, there are environmental influences as well. Keeping Pace aspires to help inform urban planning and transportation policy changes that could improve public health.

So keep exercising…
And let your workout data be a resource for the greater good! 

Join KEEPING PACE today

Spotlight on a Participant: James Turner

James Turner is one of our most ‘connected’ members, creator of two Open Humans activities, and an endlessly interesting guy.
james_turner_nyscf (1)
Donating tissue for stem cell creation at the New York Stem Cell Foundation

Hope: What is most fulfilling to you about being a member of open-access data studies?

James: Getting to meet and, in a few cases, form friendships with the researchers involved. When I was a teenager, I was seriously considering going into genetics before I got bit by the computer bug. Through the PGP and Open Humans, I feel like I’ve gotten a chance to reconnect with that early interest. Because the researchers and participants have a much more collaborative attitude than the typical research project, you really feel like you’re a part of the science, not just another anonymized identifier in a database.

Hope: You created the ‘Open Humans HealthKit Integration’ as well as the ‘Cross-Genome Error Check’ activity on our site. We’ve already written a blogpost about the ‘HealthKit Integration’. Can you talk a little about the ‘Cross-Genome Error Check’ activity?

James: The tool, which is still in it’s very early days, allows someone with more than one variant file (such as a PGP WGS or 23andMe data) to compare the files for discrepancies (i.e., calls that aren’t in agreement between the files.) It’s a work in progress, and anyone who participates should expect to get incrementally more interesting reports over time, as I improve the tool. I’m still learning all the nuances of the VCF format, so take the early results with a grain of salt. We’re seeing some early interesting data, mainly around homozygous vs heterozygous calls, although there have been a few calls that just seem to be consistently wrong.

One caveat: If you don’t have at least two independent genetic datasets uploaded to OH, don’t bother signing up, I won’t be able to return anything useful for you.

Hope: What health-tracking technology do you wish existed?

James: Oh my, such a list I’d have. A really reliable sleep monitoring technology that wasn’t intrusive. A non-invasive continuous blood glucose monitoring device (Apple Watch 3.0?) But probably the biggest one would be to be able to get really accurate nutritional information about anything I was able to put into my mouth, be it purchased, cooked or ordered.

Hope: You learned about Open Humans through the Personal Genome Project. How did you find out about the PGP and what made you join?

James: I’ve always been a big science geek, all the way since I was a kid. I’ve been lucky enough to be able to pursue this interest by being a freelance journalist as a side career, and as part of that, I have to keep up on sci-tech news on a regular basis. I don’t remember exactly what article I was reading that lead by to the PGP, but I had always been fascinated by genetics, and the idea of being able to get my own genome for free was immediately appealing to me.

Hope: Had you ever shared your health data before?

James: I had participated in a couple of clinical trials due to health issues, but they had been more “participate in this trial to get early access to some medical goodie” types of things. I hadn’t publicly shared any of my health or genomic data. I had been a 23andMe customer, and participated in the surveys on the site they were using to do GWAS.

Hope: What type of research are you most interested in?

James: Boy, that’s a hard question. I think that learning more about how all of the disparate ‘nomes (microbiome, genome, epigenome, connectome, proteome, immunome) work together and interact with each other to make us who we are, and how they fail, is going to end up being the holy grail of the 21st century. The idea that understanding the genome would give us the entire picture has proven to be naive, and the next decades are going to have as much to do with understanding how all the systems play together as how any one gene or group of genes function in isolation.

Hope: Have you changed any of your habits because of the knowledge you’ve gained from the studies and projects you’ve joined?

James: Not really. There’s not a lot of actionable information in my data. I did find out why I’ve always had an issue with alcohol making me ill, it turns out I have a rare nonsense mutation in one copy of my alcohol dehydrogenase enzyme (that’s the enzyme that is responsible for metabolizing booze…) But, since I was a very occasional drinker anyway (because it tended to make me feel ill), it didn’t really change my lifestyle. The same mutation has been associated with an increased risk of Parkinson’s, however, so that’s definitely something I’m going to keep an eye out for as I get older.

Hope: Do any of your friends and family share your curiosity for health data tracking? Do you ever try to make converts to your way of thinking about health?

James: My son (who is a biochem major at UNH) is also a member of the PGP and Open Humans, and we chat a lot about biotech and biology in general. My wife is much more skeptical of the idea, mainly because of privacy concerns and the potential for her data to be used for things she would object to. I definitely try to spread the word about PGP and OH to people who I think would be interested, or who seem to have health issues that I suspect would be valuable to add to the public dataset.

Hope: What is your impression of Open Humans so far?

James: It’s obviously early days. I’m seeing a lot of the back-end technical side, working with Madeleine and Beau as one of their beta-test guinea pigs for the new data APIs they’re developing for third parties to work with OH. The big challenge, as with the PGP, is going to be to get enough people contributing enough useful data to make it more than just a boutique dataset. Right now, there seems to be a lot of duplicative effort between projects such as OH, Genes for Good, the 1,000 Genome Project, and the new federal programs starting to ramp up. Everyone is trying to skin the same open consent cat, but my concern is that we’re going to end up with a lot of isolated data sets rather than one big one that lets researchers really leverage the power of tools like GWAS. Hopefully, OH will be able to act as a common hub to get all of them sharing their data together.

The other big challenge is how to represent all the diverse types of data that are coming in ways that are going to be useful to researchers. If I want to be able to easily say “give me the allele frequency of variant X for everyone who has ever had a systolic blood pressure reading about 150”, there’s no good way to do it right now. It’s JSON files and text files and VAR files, etc, etc. It’s going to be a lot of manual groveling (or clever scripting) for anyone trying to mine that kind of data. But this is a problem bigger than OH.

Hope: On your Member page, you mention that you run a charity. What does it do?

James: I’m the President and Chairman of the Board of the Brony Thank You Fund, a 501(c)3 public charity that fundraises from fans of the new My Little Pony animated series. We print a yearly calendar and do other fundraising activities, supporting a variety of causes. We’ve raised close to $200,000 in the past four years, and notably endowed an animation scholarship at the California Institute of the Arts. Currently, we’re supporting the Dana Farber Cancer Institute.

Also, have some pony genomics.

Applejack: Now how in thunderation is one of them twins a Pegasus and the other one a unicorn?

Mr. Cake: Easy. My great-great-great-great grandfather was a unicorn, and Cup Cake’s great aunt’s second cousin twice removed was a Pegasus. That makes sense, right?

— Season 2, “Baby Cakes”

Hope: You’re also a certified open water diver and private pilot. Is that because walking around at sea level gets boring?

James: I’d really like to be out exploring space, but given the relatively low chances that’s going to happen in my lifetime, flying or diving are about the closest I’m going to get to exploring a strange new world. Flying has always been a passion of mine, and getting to earn my license has let me have some spectacular experiences, including circling Niagara Falls at 2,000’ and flying over downtown Boston below roof-level (pre-9/11). Unfortunately, the combination of putting a kid through college, the post-9/11 security environment for civil aviation, and the difficulty of keeping up my medical certificate had resulted in me having to walk away from piloting, at least in the short run.

I learned to dive because my girlfriend (now wife) had won a trip for two to Australia, and there was no way I was going to go to the other side of the world and not dive the Great Barrier Reef. I’m glad I did, because the reefs around the world are disappearing rapidly due to climate change, so it may have very much been an example of seeing them while they were still there. I went diving with my family down in St. Martin about 10 years ago, but haven’t had a chance to since.

Hope: What’s your favorite sci-fi story about health and/or medicine?

James: The book that turned me on to biology and genetics was The Andromeda Strain by Michael Crichton. I read it when I was 8, and it had a tremendous impact on my life. I’m much less of a fan of Crichton’s later works, as he got increasingly political and tin-foil-hatty, but the book (and the outstanding Robert Wise movie adaptation) still are among my favorites.

Hope: Finally, would you be willing to chat with other OH members on our forum if they have follow-up questions?

James: Absolutely, I’m pathologically extroverted and would love to chat with anyone who has questions or just want to shoot the breeze about geeky stuff.

Join ‘Circles’ and help study a uniquely human trait!

Circles in Human Biology studies a “sensitive” topic: The human areola!

All mammals have nipples, but only humans have areolas. Areolas are the pigmented circular markings that surround our nipples. How did we get these markings? Why are some areolas large and others small? Can we find the genes that build these circles and discover why we have them?

Anyone – of any gender! – can join. The study is especially interested in participants who have had genetic sequencing.

circles_badge

Participation is easy:

  • Sign up on Open Humans
  • Complete an online survey
  • Use simple measurement tools to share data about your own body
  • Share photos of your areolas with the researchers (helpful but not required)

Almost 400 people have signed up and shared their data so far!

By analyzing participant-reported data, the ‘Circles’ team has already learned that areolas are much more diverse than previously thought. They’ve also discovered that the diameter of a person’s areolas is unrelated to the number of areolar glands they have. In fact, people can have anywhere from 0 to more than 30 of these little bumps. Scientists believe these bumps help protect nipples during nursing and provide an olfactory cue to help newborn infants nurse, but research has yet to confirm this.

Learning about diversity in areola morphology could not only help scientists understand breast health, it could teach us about human genetic diversity in general.

To read a New York Times article about this study, click here.

We vary in all kinds of traits, from physical traits like height and hair color to sensory traits like taste or odor perception. These differences impact our lives in big ways, from what foods we eat to what medicines work for us to how we feed our babies. We are just starting to understand how these traits are built genetically and why they vary. These discoveries are going to give us fascinating new insights into the way our genomes build our bodies and influence our lives.

– Abby Wark, Project Director of ‘Circles’

Join ‘Circles in Human Biology’ today!

Citizen Science for iPhone or Fitbit Users!

Open Humans enables participatory research. Blurring the line between scientist and research participant is part of our mission – because we know that data sharers can become data explorers and tool builders, too!

Our two new activities are prime examples:

  • Open Humans HealthKit Integration
    You can install this member-created app to add ‘Health’ data from your iPhone to Open Humans.
  • Open Pokemon GO GO GO!
    Whether or not you’ve played the game, you can share HealthKit or Fitbit data to create a shared data set that we can explore together!

Read on to learn more…

Open Humans HealthKit Integration
Pasted image at 2016_07_07 02_55 PM_picmonkeyed

Did you know iPhones store health data? You might have data you didn’t know about! Since 2014, iPhones have been tracking your activity (e.g. steps) data through the ‘Health’ app. They can also log lots of health data – from blood glucose to weight!

This data is private on your iPhone, but you can decide to share it. James Turner, one of our most engaged and “connected” participants, has applied his iOS developer skills to create the Open Humans HealthKit Integration app to allow you to export HealthKit data to Open Humans!

In the past few months, Open Humans has expanded our features to allow projects to add data to member accounts. We hope researchers use this to return data, but we’re thrilled to see it used by a community member to create a new, valuable data source!

There’s a ton of health and fitness data being captured by iOS users now, and the HealthKit Export app is an attempt to make that data accessible to researchers in a standardized format. 

– James Turner, app creator and Open Humans member

 

Open Pokemon GO GO GO
open-pokemon-go-go-go

This non-study project allows you to contribute to an open data set of physical activity levels for summer 2016. The inspiration for this project was the Pokemon GO craze, but anyone with an iPhone or Fitbit can participate.

This is mostly a personal project. Pokemon GO has been such a phenomenon, and I wanted to create something fun in response! Sharing data like this can create invaluable resources for students and citizen scientists to explore. I also wanted to provide an open source demo for how to make projects on Open Humans – it’s easier than you think! I’ll be writing up an explanation on how it was set it up, and open sourcing the code used. 

– Madeleine Ball, project creator and Open Humans platform co-founder

Contribute to science.
Join studies, connect and share data today.

Spotlight on a Microbiome Researcher: American Gut’s Embriette Hyde

Interested in what researchers are learning about microbiomes? Embriette Hyde is the Project Manager of American Gut and one of Forbes’ “30 Under 30”. I interviewed her last week.

EmbriettepicHope: I read in your bio that you’ve done some forensics microbiome work. Can you talk a little about that?

Embriette: When I was a grad student, I did research at one of two body farms in Texas where people study human cadavers. I don’t want to get too graphic, but insect activity increases, and then decreases again, as bodies decompose. By analyzing the progression of the microbiome associated with bodies, we identified microbial signatures that seemed to be associated both with insect activity as well as decomposition stages in general. This ‘microbial clock’ enabled us to get a pretty accurate determination of the time of death.

Microbiomes can also be used as a sort of fingerprint. Rob Knight, American Gut’s PI (Principal Investigator), co-led a study in 2010 that showed people can be identified from the microbes they leave behind on surfaces. After this research came out, CSI:Miami did an episode based on it!

Right now, human DNA helps to solve crimes, but research like ours is showing that forensics may one day consider microbial DNA as well.

Hope: What are some of the common effects of closed-space lifestyles on the microbiome of humans and animals?

Embriette: In industrialized nations, we spend a majority of our time indoors and in very hygienic areas. This doesn’t seem like a bad thing at face value, but there’s been an increase in chronic conditions such as asthma and allergies in industrialized nations as compared to non-industrialized nations. As a result, a “hygiene hypothesis” has developed: We think that we’re helping ourselves, but we actually may be doing ourselves a disservice.

I did research in which I looked at the microbiomes of 1. humans and pets compared to their home environments, 2. captive Komodo dragons (the biggest living lizard in the world, found in the wild only in Indonesia) and their enclosures, and 3. wild amphibians and their ponds. Humans, pets, and captive Komodos all share many of their microbes with their environment; wild amphibians do not. We don’t have enough information to make any definitive pronouncements or recommendations for what people might want to do about this in their homes, but a first step might be to alter how we care for animals in captivity.

Hope: Can you describe what a ‘microbiome’ is, and why you’re interested in studying it?

Embriette: A ‘microbiome’ is a community of organisms that live in an environment. These organisms are called microbes. I think most people associate microbes with bacteria, but they also include microscopic fungi, archaea, and viruses. Microbes interact with us in an intimate way, evolve alongside us, and do things for us – like break down nitrates in our oral cavity – that have a snowball effect on our health.

Right now, a lot of people are jaded about the use of synthetic drugs, and I believe microbiomes will soon help us to treat disease more successfully.

They could also alter how we approach diet and dietary interventions. A study of diabetics in Israel recently showed that microbiome analysis can help create an algorithm that determines a personalized diet for blood sugar stabilization. One patient in the study was even found to have a better response to ice cream than to tomatoes! This sounds dubious, but it suggests that microbiome analysis could have a potentially life-changing impact (and also likely explains why one diet works for some but yields no results – or negative results – in others!)

I really believe that, one day, microbiome sampling could be as routine as taking a blood test!

Right now, though, it’s still much easier to study animals than humans since we can control their environment and they tend to be genetically similar. This is why it’s so important for projects like American Gut to study big sample sizes. We need to be able to observe physiologically relevant patterns despite the variability brought to the table by studying the human organism.

I’d like to add that the National Microbiome Initiative has given microbiome research a huge boost in national recognition. This, in turn, is influencing the financial and moral support that we’re garnering. A few years ago, I went to a general microbiology conference – not a microbiome specific conference like I’d been used to – and was surprised at the pushback regarding whether microbiome research is coming to conclusions too quickly. I think the NMI will open the door for more scientists to jump on board and help us to realize the tremendous potential for microbiomes in the coming decade.

Hope: What do you do on a typical day at work?

Embriette: Now that I’m the Project Manager for American Gut, I spend a lot of my time communicating with participants and collaborators. The project is growing, and we have developers working to improve the site, researchers who need help with IRB (Institutional Review Board) documents and sample collection, and students who are doing data analysis. I don’t do as much direct data analysis as I did in the past, but I’m involved in a lot of it.

I also participate in local events that help publicize American Gut, like the recent Rock ‘n’ Roll Marathon Series here in San Diego. In general, people in this area tend to be familiar with the concept of the microbiome, so we’ve received a lot of enthusiasm for the project — both from participants and potential collaborators. We’ve even had doctors who’ve approached us because they believe their patients would be interested in joining. We’re so thankful for the positive word of mouth that we’ve received!

Hope: What changes, if any, did you make to your diet or lifestyle after getting the results of your American Gut kit? How did it feel to be a participant in your own study? Did the experience make you any more likely to join other participatory research or “citizen science” projects?

Embriette: I was already changing my diet – eating less meat, processed foods, and candy – before I participated, so I knew I was on the right track. I just wish I had “before and after” samples so I could compare my current microbiome to what it was like five years ago! I also did 23andMe before I did American Gut, so between that and my research, I didn’t sign up as a participant looking for answers to specific questions. I did it more for curiosity’s sake, and to connect to others and be able to say, “I’ve done this, too.”

I’m definitely more likely to join other projects. I know how important participants are to the success of a study. We need people to sign up or we’ll never find answers to our questions.

Unfortunately, people sometimes forget that “citizen science” projects like American Gut are research studies. We’re not a company providing a service. The funding we collect allows us to gather data. I think it can be hard for people to hear that it takes time for science like this to produce actionable results.

Hope: Have you had the opportunity to compare the microbial communities of different cultures?

Embriette: The name “American Gut” is slightly deceptive since we accept participants from anywhere in the world. To date, we have 9,000 samples representing 28 countries in the cohort — and the majority are from the US, UK, and Australia because of our collaborations with Tim Spector at King’s College London (British Gut) and Phil Hugenholtz at the University of Queensland. We’re currently in the process of setting up a third aggregation site in Singapore with Scott Savage.

Comparing just the US to UK samples, for example, we see greater microbiome diversity in those from the UK. I’m not positive why this is, but I have some hypotheses. I’m not sure about the UK, but in Spain, there is still a big culture where people shop for and prepare food on a daily basis rather than relying on on pre-cooked, instant meals. I don’t think anyone has studied whether that has an effect on the microbiome or not, but I wouldn’t be surprised if it did.

Perhaps another reason is the fact that some medications are often not given as readily in other countries as in the US. We know that antibiotics have a negative impact on microbiomes, yet in the US it’s not unusual to be prescribed one for what may be a viral infection, or when the cause of the presenting infection is undetermined. It’s hard to change healthcare practices, but we might benefit from approaches that allow the body to fight infection without such aggressive intervention. When I was in Spain and had a recurring sinus infection, the doctor recommended that I see if my body could fight it off without drugs (and refused to give me the antibiotics I asked for!). Not only was I able to fight the infection, I’ve never had another sinus infection! That experience had a big impact on how I view medical intervention.

In the US, we also continue to give antibiotics to animals intended for food, which can represent a large source for antibiotic resistant bacteria. Europe has already banned this. Agriculturally, I believe they’re ahead of us in this regard.

As for Eastern countries, people there tend to eat more fermented foods – think of soy sauce, miso soup, kimchi – than we do in the US. Preliminary research shows that these foods have a positive effect on microbiome diversity. I have sauerkraut fermenting on my kitchen counter right now for this very reason!

Hope: On the Research Page of your website, you mention that you’re beginning to explore how vaginal ring drug delivery systems impact the vaginal microbiome of women. Can you explain the potential health outcomes of this research?

Embriette: Our focus is on a ring delivery system for preventative HIV drugs. We know that we can deliver the drugs this way; a few groups have done it. What we’re specifically studying, though, is the impact on the microbiome of wearing a ring like this continually. As of now, we don’t yet have enough data to make a determination, but the study is ongoing.

From reading your bio, I was curious to learn that you enjoy studying the Hebrew roots of Christianity. Do you think your religious knowledge affects your approach to science?

I love science and the more I learn, the more convinced I am that there’s a Creator who has provided this world for us. I don’t think this should be viewed as some sort of disconnect. That being said, I’m able to compartmentalize. At work, my focus is scientific truth. But just as we don’t understand everything in science, we don’t understand everything beyond science. I can believe in evolution, but that doesn’t mean I have to believe it’s the origin of everything.

Hope: What health-tracking technology do you wish existed?

Embriette: Smart toilets and personalized sequencers that give feedback saying “here’s what you can do today to keep your microbiome happy.” Also, portable, real-time sequencers for use in the field because sample preservation is sometimes difficult. Finally, an app with a plug-in that can upload data from samples to the Cloud. I’d definitely use that!

Hope: Last question! This year, you received an incredible honor: You were one of Forbes’ “30 Under 30”. How did you celebrate? Did they give you a trophy, and, if so, do you keep it at work or at home?

Embriette: They didn’t give a trophy, but I had the option to buy a plaque for $100 — which I didn’t do (yet)! But I have a nametag from the Forbes retreat that I went to and keep it at work along with other conference nametags.

I found out about this while I was in Spain. I went out for a celebratory dinner with my fiancé, his sister, and her husband. It was shortly after my fiancé’s sister had designed my personal website specifically for my application to Forbes, so I was really excited to be able to celebrate with her in person! But the honor wasn’t really about me; it was about American Gut. I am so fortunate to be leading the project, but there are lots of people who have helped make American Gut a success, and I hope this recognition helps the project more than it helps me.

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