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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