Embriette Hyde & The American Gut Project

At our May 15 event, we heard from Professor Michael Gillings about the human microbiome – the seething hordes of bacteria that populate our guts and pretty much every other nook and cranny of our bodies. The more people look, the more they are learning about the important role these bacteria play in our health. In fact, I put it to you that it will soon be seen as unenlightened and out of touch to refer to them as seething hordes, and that people will instead be calling them things like warm and fuzzy microfriends or carefree pint-sized collaborators.

I thought the topic would make an excellent subject for a podcast, so I was delighted to come across Dr Embriette Hyde from the American Gut Project. Unfortunately I couldn’t align the timezones, but Dr Hyde was kind enough to answer my questions using her fingertips instead of her vocal chords.


What is the American Gut Project?

The American Gut Project is the largest crowdfunded citizen science research project in existence. the project kicked off November 2012 and since then we’ve raised over $1.6 million through Indiegogo (in the beginning) and Fundrazr (current) and have results from 9012 samples collected from 7510 participants-and the project keeps growing! Humans are incredibly variable-from their genetics to their lifestyles-so in order to identify relevant connections between the microbiome and health and disease states, we need lots of samples from lots of people! The overall goal is to collect microbiome sequence data and associated host metadata, like disease history and lifestyle factors, to create an exhaustive map of the human microbiome. We’d like to identify the “bad” and “good” areas on that map and figure out ways to move humans from the bad to the good areas.

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How did you get involved in the AGP?

I remember hearing about American Gut when I was a PhD student at Baylor College of Medicine in Houston, TX. At that moment in time, I couldn’t have imagined that one day I would be leading such an amazing effort! When I joined the Knight lab in May 2014, the project was being led by Daniel McDonald. I had some interest and the effort, so I attended the twice monthly meetings and contributed to some analyses. After the lab moved from CU Boulder to UCSD, we quickly realized that the collaborations here (current and future) would cause the project to quickly grow. We needed a bit more structure, and an official manager for the project to keep things running smoothly. Rob asked if I’d be up for the task, given that when I joined the lab I told him my career goal was to have some sort of project management role. My opportunity came sooner than I expected it, and it’s been truly awesome.

How did you get involved in science more generally?

I was always good at science and became interested at a young age. I remember my parents bought me a really cheap kids microscope when I was about 8 or 9 years old. My dad let me prick his finger so I could look at his blood. I was fascinated! Not to be dark or anything, but I suffered a bout of serious depression in high school. During that time, I didn’t study or put any effort into my classes. Nevertheless, I remember receiving 103% on a science test-all questions plus the extra credit questions correct. I knew at that point that if science came that naturally to me, it was one of my purposes in life and from that point forward I pursued science as a career.

What is a typical day for you on the job?

It doesn’t sound glamorous, but much of my day involves emailing, meetings, and phone calls. We have a lot of collaborators and a lot of inner project workings that need to be managed on a daily basis. I communicate every day with current and future collaborators. I also work really closely with the wet lab team to ensure samples are being processed when they should be, as well as with our data analysts to make sure data are being analyzed and new project needs are being met.



What do you love about your work and what drives you crazy?

One of the funnest things about my job is getting the general public excited about our work. I’ve represented American Gut at local fermentation/Earth Day festivals, the San Diego Rock n’ Roll Marathon Expo, and local farmer’s markets. I really enjoy talking to people at these events and getting them excited about what we do. It’s easy to excite other scientists about your work-but to get the public excited, that’s not as easy, yet it’s crucial to the success of science and especially American Gut, since it is a citizen science project, after all.


I don’t think there is anything that really drives me crazy. Once thing that I wish we could figure out how to do better is inform participants and future participants what we’re doing. Sometimes people think we are a company and that we are offering microbiome “tests” since they contributing funds. That’s not true at all-we’re just a research project, and by giving us money and samples our participants are helping fund our research. The project is not government funded (though some small cohorts are being run through American Gut by collaborators with grants)-so we really do depend on our citizen science participants. We try to make clear at every step who and what we are, yet there still is a disconnect sometimes, and I really scratch my head trying to figure out what else we can do to prevent that confusion.

Do you have any favourite or inspiring scientists?

This will sound cliche, but Rob really is one of my role models. His mind is impressive-I really believe he is a genius. I don’t know how he does what he does, but it’s impressive watching him in action. On a more close to home note, one of my best friends in graduate school, Erin Honsa, played a huge role in where I am at today. Erin was in the laboratory of Dr. Anthony Maresso working on heme acquisition in Bacillus anthracis (yes, anthrax). She always did sound science, thought about all the potential pitfalls and how to head them off before they happened, and gave fantastic talks. I always tried to model myself after her, and I can tell you without a doubt that she is the reason why I am such a good writer and presenter. Another great woman in science that I look up to is Dr. Mary Estes, who was on my thesis committee in graduate school. She is tenacious and a fantastic scientist, and she truly cared about my success. I’ll never forget her contributions to my success by being on my committee, and I would be honored if I could be half the scientist she is one day.

Would you care to speculate about where the science is heading, in terms of the AGP and similar efforts to understand microbes, human health and modern living?

It’s hard to speculate because there is always the risk that someone will twist your words and put the cart before the horse. I’d love to see information we’re learning from American Gut and other microbiome projects make it to the clinic. We’ve done it with fecal transplants for C. diff infections, but that touches a very specific group of people. What if the microbiome was as common as a blood test when you go to the doctor, and what if instead of prescribing antibiotics or other drugs, dietary changes, probiotics, or some other mechanism that we haven’t even thought of yet could be prescribed-basically, to affect the microbiome and move it to a healthier state and relieve disease symptoms? I am also really interested in the microbiome of the built environment and how our indoor working and living habits are affecting our health by directly affecting the microbiome. Perhaps we could have smarter offices and homes that will promote microbiome health? Treadmill and standing desks are a start-but what else could be made possible? The way we work and live could be revolutionized-and I’m excited to see whether and how that happens!

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I linked to the homepages of Embriette and the American Gut project at the top, and you can also check out their twitter selves here:


Finally, if you still haven’t had a gutful of the microbiome, tune into our podcast with Dr Michaela Blyton on the koala microbiome.



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