The Human Microbiome Project and other microbiome projects worldwide have laid an important foundation for understanding the trillions of microbes that inhabits each of our bodies. However, opportunities for the public to get involved in such research has been limited. Now, American Gut gives you an opportunity to join this research project and to compare the microbes in your gut to those in the guts of thousands of other people in the US and around the world. American Gut is a project built on open-source, open-access principles. Our data are for the good of understanding and will be shared both with participants and with other scientists. Our experience has been that our best ideas and work come when we involve people in as many steps of our work as possible, be they scientists, educators, roofers, ultra-marathon runners or corporate leaders. Everyone has something to offer, whether their sample, their hypotheses, their analyses or their dog (yes, their dog, we will get back to that). The more we can understand the complex microbial ecosystems on which we depend, the more everyone will benefit.
A few important points to remember before participating in this research project:
1. Note your de-identified information will be part of a research study and will be made available in a publicly available research database. That is, any personal information that might easily identify who you are will be removed before being placed in the public database.
2. It’s simple to join: send $99 to the project. Once you receive your kit(s), you will be required to a) sign an online consent form and b) fill out an online questionnaire. If either are not signed or filled out, we cannot perform the microbiome analysis. Your payment will only be refunded if requested explicitly. Remember, the online “consent and questionnaire” forms are part of the American Gut portal NOT something you sign with Fundrazr when you join the research project. If you decide that you no longer wish to continue in this study, you will be requested to contact the American Gut Project helpline to inform us of your intent to withdraw. If your sample has not been processed you may request a refund which will be processed through the site where you contributed to the project (via PayPal).
3. The consent forms are maintained on the participant website; details are included in your kit. To sign the consent form, you must agree to use an electronic format for your signature in accordance with the United States’ eSIGN Act and California’s UETA Act. You have the right to obtain the electronic record in a non-electronic form.
If you live in the UK or anywhere else in Europe, visit our sister site British Gut to join this research project.
1. See how your microbiome compares to others and learn how your diet & lifestyle may shape your gut microbiome. Thousands have enrolled already.
2. International participants welcome. However, please add $25 to your payment for shipping kits. Also be aware that you will need to FEDX your sample back to University of California-San Diego. This could get pricey. So please make note of this before joining the study. (Folks in the UK click here)
3. Our team has sequenced thousands of samples from all over the world
4. Once you sign up, you will receive a swab kit in the mail within 4-6 weeks.
Also note we do not diagnose disease or provide medical advice of any kind. By joining American Gut, your sample and diet and lifestyle data will be merged with thousands of other folks and will allow us to explore population-level patterns that will hopefully lead to a better understanding of why we carry the microbes we carry and what aspects of our behavior and disease state drive these microbial patterns. This is Citizen Science 101 and we need your help!
If you live in the UK or anywhere else in Europe, click here.
If you live outside the US, there are some additional conditions to consider before joining the study. 1) In addition to the standard payment of $99, you will need to contribute an additional $25 to cover our costs to send your kit to an international address (so, $99 + $25 = $124). 2) Unlike participants in the US who can simply send their sample back via regular mail service, you will need to FEDX your sample to us – since the sample cannot languish for weeks in the international mail system. This could get costly for you. So, BEFORE signing up, you need to be aware of additional FEDX charges to send your sample from wherever you live to the University of Colorado-Boulder. Depending on where you live, this could be hundreds of dollars. If you live in the UK, click here.
Click here to see a sample (Michael Pollan’s data actually) of what your frameable results will look like.
Click here for a screen shot of more detailed data that will be provided to you online. You will also be able to download this into excel.
Click here for a tour of what happens to your sample once it reaches the Knight Lab in CA.
Click here to watch Rob Knight’s TED talk on microbes – a must see for anyone joining American Gut!
The Human Microbiome Project and other microbiome projects worldwide have laid an important foundation for understanding the trillions of microbes that inhabits each of our bodies. However, opportunities for the public to get involved in such research has been limited. Now, American Gut gives you an opportunity to participate and to compare the microbes in your gut to those in the guts of thousands of other people in the US and around the world. American Gut is a project built on open-source, open-access principles. Our data are for the good of understanding and will be shared both with participants and with other scientists.
Your sampling kit will be mailed from the Knight Lab. The senior scientists on the project is Dr. Rob Knight. Rob is a leading microbiome researcher who is at the forefront of microbial research. His lab and lab members have and continue to work on some of the most important microbiome studies around the world – their research appears regularly in leading scientific journals such as Science, Nature, PNAS, PLOS and so forth. But this isn’t easy – it takes a village. There are 50+ scientific collaborators on the project.
“By combining the crowd-funding model with the open-access data analysis model that we pioneered with the Earth Microbiome Project, we can finally give anyone with an interest in his or her microbiome an opportunity to participate,” said Knight, a Howard Hughes Medical Institute Early Career Scientist.
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. The movie below shows 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. Michael Pollan has given it up for science and written about his participation in American Gut (and his microbiome – click here to see some of his results) for the New York Times. Also, Dean Karnazes (world’s most famous ultramarathon runner, 50 marathons in 50 days – yeah, that guy!) has joined 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).
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.
How you can help
Because so little is known about the gut microbiota in general — the projects performed to date, although extremely valuable, have generally focused on very carefully chosen groups of people being studied for specific purposes (they reflect our diversity to about the same extent that Congress does…). We want real diversity–your diversity–be it in terms of ethnicity, diet, lifestyle, how often you wash, or something else! And, because this is a crowdfunded project, we also need your financial support. While paying for studies of microbes has become cheaper, money that pays for the time of scientists, reagents and, and you aren’t going to believe this, a robot (more on the robot later). So, you might be asking yourself, if you contribute to see what lives in you what do you get in return? Like other crowdfunded projects, American Gut will give you rewards to say thank you for your support. You will get a list of the dominant microbes in your gut, and several visualizations showing how they compare to the population at large (charts showing the dominant kinds of microbes along with what they are most associated with, and an overall view of the kinds of possible microbial configurations and how they compare to other people, including the Human Microbiome Project). Like the Genographic project, we will also include some visualizations showing where else on earth similar microbes have been found, using the Earth Microbiome Project data.
We started looking at the dog gut microbiota in 2008 to start understanding the role of genetics in influencing microbial communities, and to look at microbe transfer within families. Dogs are also a lot less concerned with privacy than people are, at least based on what they are willing to do in public! They are interesting because they aren’t as artificial as lab animals, and share more of the genetic and diet variation that we see in humans, as well as letting us understand the relationships between our microbiota and that of our non-human companions.
How it works
First thing you need to do is decide on your payment level and join our little project to unravel the microbial diversity that is the American Gut (and mouth and skin). Once you sign up (click here for that), you will receive a swab kit in the mail within 2-4 weeks. Note international participants may take a bit longer. Once you receive your swab/kit, follow the instructions and send back your sample(s). You will be required to sign an online consent form as well. Each kit will be identified with a special ID number that you will also use when you fill out the online questionnaire and to retrieve your results at www.microbio.me/americangut. Please note that everyone that volunteers and receives a swab/kit, will be asked to fill out an online questionnaire with some basics about yourself, diet and lifestyle. Importantly, and this is critical, you will be asked to provide 7 days of detailed dietary information. This will allow us to compare vegetarians to omnivores to junk food eaters to folks with IBD to gluten-free eaters and so on. However, you DO NOT have to fill in any of the questions you do not want to. Up to you – however, the more info we have the more interesting the study.
In order to get accurate dietary info, we strongly urge you to use an online tool (if you do not already do so) to provide us with the 7 days of dietary info we need. We know entering so much information is a pain in the you-know-what, but it will make your sample — and our project — more meaningful. So it never hurts to start practicing before you receive your swab/kit. We recommend the following free sites for data entry and highly recommend you start practicing – but any/many free sites will work:
Below are some images of people and robots in the Knight lab at the University of Colorado at Boulder, one of the (main) labs that will be processing samples from the American Gut project, showing sampling with swabs and one of our liquid-handling robots (and when it comes down to it, who doesn’t get into science for the robots?).
What you get
All kits include pre-labeled tubes and instructions. Samples need to be returned immediately after collection – regular mail is fine, but you might want to spring for priority mail if possible. For international participants, you must use FEDX – so please budget for that as well when considering the study. You are also required to contribute an additional $25 to cover our costs associated with shipping you the kit(s). Depending on what you sign up for, you may get information about the microbes that are present in one sample, in samples collected across your body (skin, oral, gut) or across your family, or over time (e.g., Feces for a Week). You may get a readout of what kinds of microbes were in the sample (the microbiota), or, for PERKs that include functional characterization (shotgun metagenomics, shotgun metatranscriptomics, etc.) you may be able to see what the microbes are doing as well as who they are. Your results come with a downloadable PDF of your data suitable for framing that shows how your samples integrate with the rest of the world, as well as some information about the dominant kinds of microbes found in your sample and what they do. In addition to the PDF of some of your results you will also be able to view online a more detailed taxa report that you can also download into excel. Additionally, all American Gut samples will be entered into a database so you will be able to look up your sample by a unique identifier known only to you and to the Institutional Review Board-approved staff and see how it compares to others as additional samples accumulate.
Click here to see a sample (Michael Pollan’s data actually) of what your frameable results will look like – note your PDF will be available for download (we do not mail out PDFs of your results).
Click here for a screen shot of more detailed data that will be provided to you online. You will also be able to download this into excel.
Open source learning and citizen science – it just has to be
Data from American Gut will be open source and be included as part of the Earth Microbiome Project (EMP), which is a massively collaborative international study aimed at systematically characterizing microbial life on earth. The EMP would like to sample every environment on Earth to catalogue which microbes are there and how abundant are they. The open source nature of our project is important because data should be free, the only way to make best use of data from massive studies is to give it to the world and see what they can do with it. The EMP, for example, uses crowd-sourced analysis to help interpret the data and provide comprehensive exploration of the full breadth of the dataset. But please be assured, your personal data will never be revealed – ever.
Couple of things (please read folks) – once you have reviewed the payment levels, click here and join the study.
- If you send $99, receive 1 swab/kit that can be used for either a stool, skin, or oral sample. Send $180, receive two kits – which can be for two people (stool samples) or just for you – maybe one stool and one oral sample. If you send $260 to the project, you will receive 3 kits and a contribution of $320 gets you four kits. You get the idea. If you are interested in helping out further and would like to get more than four kits, contribute $320 and get four kits and then contribute again for however many kits you would like.
- Please remember you will receive and a postcard in the mail notifying you when your results are available online. You will be able to download a high resolution PDF of some of your results and access a table with more detailed taxa information. The taxa table can be downloaded into excel.
$99 “Find out who’s in your gut” The ribosome is the factory that makes proteins and is found in all cells, and fascinatingly it is mostly made of RNA. One RNA subunit, called the 16S rRNA, is especially effective as a barcode for understanding which microbes (specifically, bacteria and archaea) are found in a given sample. This PERK includes DNA extraction and 16S rRNA sequencing of one stool sample (or an oral or skin sample – the same kit works for any of these), and shows which bacteria and archaea were present in that sample along with how much of each kind.
$180 “Microbes for two: see what you’re sharing” DNA extraction and 16S rRNA sequencing of two stool samples, e.g. couples, father/son, mother/daughter, you and your dog (or, one stool and say an oral sample – is up to you – mix and match how you like).
$260 “Microbes for three” DNA extraction and 16S rRNA sequencing of three stool samples if there are three of you in your home (or, two stools and say an oral sample or one stool, one oral and one skin – is up to you – mix and match how you like).
$320 “Microbes for four” DNA extraction and 16S rRNA sequencing of four stool samples if there are four of you in your home (or, two stools and say two oral samples or two stools and one oral and one skin). It’s up to you – mix and match, you get the idea.
$500 “A week of feces” (you heard us!) DNA extraction and 16S rRNA sequencing of up to 7 samples. Collect a stool sample every day of the week and send to us along with your detailed dietary information etc. See how your New Year’s resolution changed your gut microbes! Or see how much those antibiotics you took for a sniffle affected you. Or your travel to Mexico, where you drank the water. Our microbes change a lot over our lives, but what affects them the most remains largely a mystery.
$1,500 “All in the family” Shallow shotgun metagenomic analysis of up to four fecal samples (furry family members also ok), including mapping to reference genomes and comparing profiles of genetic similarities and differences among different family members. Shallow shotgun metagenomics means instead of using the 16S rRNA as a marker gene, we fragment all the DNA in the sample, grind it up, sequence it in small pieces, and try to figure out what it is afterwards. The bad news is that much of this information is still mysterious because we don’t know the complete genomes of most of the microbes in there, but the good news is that you can get an insight into the gene functions, not just which microbes are there.
$2,500 “Beyond bacteria” Deeper shotgun metagenome and virome characterization of one sample, plus additional marker gene sequencing (16S rRNA, 18S rRNA and ITS, for you sequencing wonks) to characterize not just the bacteria but also the viruses, microbial eukaryotes (like giardia), and fungi in your gut. This PERK allows you to see everything, not just the bacteria, that’s in there. 18S rRNA is similar to 16S rRNA but for eukaryotes (like us); ITS is the internally transcribed spacer, a very fast-evolving region that lets you see very detailed information about the species that are there.
$3,750 “Functional feces” Deeper shotgun metagenomic characterization of up to 7 stool samples, providing an analysis of the variability of functions over time. This could be a great opportunity to see if fasting or extreme diet has an effect on your microbes! We would recommend doing this as a timeseries, either daily, weekly or monthly, to track how you’re doing when you travel or when you change your diet (those New Year’s resolutions again!)
$5,000 “A genome from your gut” Deep characterization of a single stool sample by shotgun metagenomics, includes best-effort attempt to assemble one or more bacterial genomes out of your gut. Only serious need inquire – please email firstname.lastname@example.org to express your interest before signing up for this one.
$15,000 “What are they actually doing” RNA expression profiling of up to five samples, which tells you not only who is in your gut but what genes they have turned on. Ideal for seeing responses to probiotic yogurt or other short-term dietary changes! RNA, or ribonucleic acid, is primarily used as the messenger in the cell transmitting DNA to protein: looking at the RNA therefore tells you which genes are switched on, which often happens at much faster time scales than change in the genes or species that are in your gut but can have huge functional consequences in terms of producing metabolites that could affect health. Only serious need inquire – please email email@example.com to express your interest before signing up for this one.
$25,000 “Hundreds of genomes from your gut” Be among the first in the world to get the most detailed map of your gut microbiome and help us push the state-of-the-art in high-throughput sequence technology of microbial communities. We will perform ultra-deep sequencing of your microbiome sample aimed at generating as many individual bacterial genomes as possible (we can’t tell you how because the details of the technique are still under wraps prior to publication). Only serious need inquire – please email firstname.lastname@example.org to express your interest before signing up for this one.
Privacy is protected by de-identifying the samples on receipt, sending you your unique code, and performing all downstream data analyses only with that code. Information likely to be identifying will be scrubbed from the records before posting. We will not store your personally identifying information in any database or release it on the internet in any way. There is a theoretical possibility that you might be identified by the information you provide (e.g. you might be the only 400-lb vegan of Kazakh descent in Wasilla), but we will take all reasonable precautions to avoid inadvertent identification of participants. All human-subjects aspects of the project have been approved by the Institutional Review Board at the University of Colorado, and all animal aspects by the Institutional Animal Care and Use Committee. Transfer of materials to other sites is covered by code access agreements. Click here for some FAQs. If you join the study, please add email@example.com to your email contacts.
Some videos you might find useful.