What is American Gut?

You’ve probably heard by now that the trillions of microbes living on and in our bodies are changing both the way we think about health and disease and even how we define Self. Ever wonder what’s in your gut? Ever wonder how your diet might shift your gut microbes (for better or worse), or how simple lifestyle decisions may have a dramatic impact on your gut and overall health? Ever wonder which microbes on your husband sometimes make him smell funny?

The gut is our main focus, but it is also interesting to look at oral, skin and even vaginal communities for several reasons. It might be possible to develop biomarkers–canaries in our corporeal coal mines that let us predict aspects of your gut health based on a spit sample or a reading (swabbing) of your palm. We know, for example, that arterial plaque shares microbes with the mouth but not with the gut. Could we use plaque samples to predict features of our hearts? Maybe.

 

The developing gut ecosystem

Different human body habitats like the mouth, the skin, the vagina, and, of course, the gut are very different from one another. However, our gut changes profoundly during the course of our development. This image and the movie linked below show the Human Microbiome Project from the $173 million NIH-funded project (each dot represents one body site from one person), along with the developmental trajectory of one infant’s gut from birth (where it resembles the mother’s vaginal community) over the first 2.5 years of life. At the end, it resembles the adult gut, shown here in a color Crayloa should have called fecal brown.

Does diet matter? If so, who has the best diet from the perspective of your gut microbiome?

Yes, definitely, at least if you are a mouse (though if you are a mouse and can read you have bigger worries). We can completely transform a mouse microbiome in one day by starving them or switching them to a high-fat diet. But people are not mice — researchers are great at curing diseases in mice, but with people it’s a bit harder. In humans, even a year on a different diet has relatively subtle effects on who’s in your gut (but larger effects on their relative abundances). In the elderly, people with better diets also have much better health outcomes, but we don’t know what part of this, if any, is due to microbial activity. Human diets vary to the extreme, from complete herbivory (vegans) to something close to pure carnivory. By reaching out to people with all types of diets, whether voluntary due to personal beliefs or to enhance athletic performance, or required by conditions such as celiac disease, we can reach a much broader range of eaters and potentially a much broader range of microbiomes — but American Gut needs all comers. We will also be able to cross-reference your data with those living traditional lifestyles such as hunter-gatherers and farmers across the globe (see below), from Peru to Namibia. However, to do this, good diet information (and other possible influences from smoking to antibiotics) is critical, and so we’ll ask you to fill in detailed information about these factors in the questionnaire with your kit. Your diet and other health information are essential to the project, so please plan on bringing it along! So how does your diet and lifestyle shape your gut microbiome? And how does it compare to folks following different diets – and does it even matter? Most likely yes. Only one way to find out.

 

American Gut – all the cool kids are doing it

Lots of great and interesting microbiomes are joining the project. We know that Lady Gaga is covered in microbes. Wouldn’t you love to know how your gut compares to hers? Well, Lady Gaga hasn’t agreed to participate (yet. If you and she are buddies, you might give her a nudge), but author Michael Pollan is giving it up for science and will be writing about his participation in American Gut (and his microbiome) for the New York Times in the New Year – so don’t miss it! Also, Dean Karnazes (world’s most famous ultramarathon runner, 50 marathons in 50 days – yeah, that guy!) is joining as well, and along with and Shannon Ford (Mrs. United States 2011,  gluten-free eater and Paleo Diet advocate), will be sharing their results with the community. But most people will participate privately, and your privacy will be protected (see below).

people

On the science side, we have assembled a world-class team of experts on the human genome, microbiome, and microbiome in human disease susceptibility  and evolution, including many of the key players in the Human Microbiome Project, the Earth Microbiome Project, and Yourwildlife.org to do the sequencing, analyze your data, and deliver the results back in a comprehensible way (like the National Geographic Genographic project, we understand how important it is to you to have some information about your information that you can show off to your friends and family). With the number of subjects and diversity of ages, backgrounds and lifestyles we can encompass in American Gut, we will be able to make progress in a way that is difficult with smaller, more targeted studies on individual diseases or diets. Additionally, we are using a truly open model based on the Earth Microbiome Project: all sequence data will be released as soon as it comes off the sequencer so that anyone can look at it (but not, of course, at your personally identifying information, which will be protected), and the data analysis will be performed openly and with everyone invited to participate. Because of our collaborations we will also be able to compare a subset of our results to the microbes living in people’s houses, the genes of the sampled folks (maybe you) and more.

Why it’s important and what we hope to learn

We know that many factors can affect the gut microbiome — how old you are, what you eat, whether you have kids or pets, whether you smoke or drink and how much, where you live and have lived before — but we don’t know which of these is most important or what specific microbes are involved. Nor do we know when these factors are important. Does their importance depend on the climate (maybe), on your genes (almost certainly) or something else (who knows). By enrolling everyone who wants to participate, we can look for people who look unusual and test whether there is anything they share.