Are We What We Eat? Citizen Scientists Team with Genomics Experts for Insights from our Gut Microbes

Are you curious about the microbes living in your gut and what they do? Our microbial partners- trillions of them - outnumber our own cells by as many as 10 to 1 in and on our own bodies.

We are just beginning to understand the many vital roles of these microbial partners – our symbionts – and what they accomplish for us and with us. Scientists once joked about these “microbial hitchhikers” but with the advances of genomic sequencing and our continued genomic exploration, we have seen that their roles range from helping us digest our food to building up our immune system. The microbial communities, in fact, play central roles, even if we don’t yet fully understand the details of their interactions.

Previous genomic research projects, including the five-year, $173-million NIH-funded Human Microbiome Project, have usually focused on highly selected groups of people. If you were a curious person interested in seeing the direct analysis of your own microbiome, there were few, if any, options to participate in a study. Now, researchers at the University of Colorado Boulder involved with the Human Food Project, have introduced the American Gut project, a new long-term research project linking investigators around the world, including those at the Institute for Genome Sciences at the University of Maryland School of Medicine, and connecting them directly with the general public. The American Gut Project is crowd-funded by individuals interested in learning more about their own gut bacteria – or even the microbes of their pets, as animals will also be included in the research.

Two leading scientists involved at UM’s Institute for Genome Sciences (IGS) are Jacques Ravel, PhD, Associate Director Genomics and Owen White, PhD, Associate Director, Bioinformatics, at IGS. Both have been actively involved in longitudinal, multi-institutional studies of the microbiome and the subsequent analysis – or interpretation – of the vast data produced.

“The American Gut Project is opening new scientific doors because it is open to the public and funded through a crowd-sourced revenue model,” explains Dr. Ravel. “Soon our annual health check-up will include a personalized evaluation of our gut microbiome and this citizen science project is the first step to make this possible.”

Ravel, a Professor in Microbiology and Immunology at the University of Maryland School of Medicine, as well as Associate Director for Genomics at the Institute, has led groundbreaking new interdisciplinary research on the microbial communities in women’s health.

Owen White, PhD, is a Professor of Epidemiology and Public Health at the University of Maryland School of Medicine, and an expert in annotating and analyzing the volumes of sequencing data produced in such studies. White’s bioinformatics department at IGS led the management of the Human Microbiome Project’s Data Analysis and Coordination Center (or HMP DACC), which organized and analyzed the volumes of data produced by the participating institutions over the five years of the study.  

“The American Gut is a big data project, which IGS has the expertise and infrastructure to manage, in conjunction with our other research institution partners,” explained White. “Our experiences managing the HMP will guarantee that the data is rapidly available to the scientific community and we can help turn the information into better health management procedures.”

The gut microbiome has been linked to many diseases, including obesity, cancer, and inflammatory bowel disease: interestingly, all these diseases have more in common in Western populations. A key aspect of the project is to integrate studies of Americans of all sizes with studies of people living more simple lifestyles in Africa, South America and elsewhere.

“We should start thinking about diets not only from the perspective of what we should eat, but what we should be feeding our entire supraorganism,' say Jeff Leach, founder of the Human Food Project and co-founder of American Gut. Leach, trained as an anthropologist, has studied hunter-gatherers and hopes to use American Gut to compare Westernized populations with those elsewhere in the world.

Public interest is immense, says the research team. 18,000 people have already signed up to receive more information about the project. “The American Gut project builds on the Human Microbiome Project by allowing anyone to participate, and will let the public join in the excitement of scientific discovery,” said Lita Proctor, PhD, program director for the Human Microbiome Project. “We can expect this to lay the groundwork for all sorts of fascinating studies in the future, that others will in turn expand.”

The American Gut project is an opportunity for “citizen scientists” working with teams of leading genome scientists and labs throughout the U.S. to help shape a new way of understanding about how diet and lifestyle may contribute to human health through each person’s microbial “suite”, or personal arrangement of tiny microbes. Dr. Knight explains that a key aspect of the project is to understand how diet and lifestyle, whether by choice or by necessity, affects people’s microbial makeup. A diet by choice might be those followed by vegetarians or athletes. A diet by necessity would include those affected by autoimmune diseases or people with food allergies.

The steep decline in the cost of DNA sequencing and recent advances in computational techniques allow for the analysis of microbial genomes in orders of magnitude cheaper than was possible only a few years ago, explained Knight. Sequencing is now inexpensive enough that participants can include their families, and even their pets. Participants who donate $99 or more can expect to get tens of thousands of sequences from microbes in their gut. The American Gut website has information about the various options open to the public.

“I am pleased to participate in this pioneering effort that blends the vast interest of the public in science with questions that are worth answering about human health and nutrition,” said Martin Blaser, chair of the Department of Medicine and professor of microbiology at New York University. “Through this consortium, the technical and intellectual resources are there for important new knowledge.”

The project will seek to build on a growing canine and feline database, as well. “The majority of data we currently have on the dog and cat microbiomes has come from a handful of small studies in research or clinically ill animals,” said Associate Professor Kelly Swanson of the Department of Animal Sciences and Division of Nutritional Sciences at the University of Illinois at Urbana-Champaign. “This study will apply the technology to free-living pets, where diet, genetics and living environment are quite different from household to household.”

“This research may identify important trends not possible with lab-based studies, and help guide us on how to feed our pets in the future,” said Swanson.

Scientific participants in the project include many of the key players in the Human Microbiome Project and research facilities around the world. To learn more about participating in or contributing to the project, visit https://www.indiegogo.com/americangut. To see a list of collaborators on the project, including those who are willing to be listed as press contacts, visit http://humanfoodproject.com/the-people/collaborators.