Knight Lab Logo

The American Gut is based out of Rob Knight’s lab at the University of California, San Diego-meaning and samples provided by American Gut citizen science participants are processed by technicians working in the Knight lab.  The Knight lab is one of the largest microbiome research labs in the world, processing samples from hundreds of projects at a rate of nearly 1,000 per week. Notably, the protocols used by the lab to process these samples have been extensively tested and benchmarked and are freely available from the Earth Microbiome Project’s website.

History of American Gut

The American Gut Project, an Earth Microbiome Project study co-founded by Dr. Rob Knight and Jeff Leach, is the world’s largest crowd-funded citizen science project in existence. As of October 2015, the project contributions from over 6,500 participants surpassed $1 million on Fundrazr. American Gut was conceived during the summer of 2012 when co-founder Jeff Leach was in Australia exploring the possibility of mapping the gut microbes of Aboriginal Australians and planning a microbiome project among hunter-gatherers in East Africa. Frustrated with no simple and cost-effective way for a members of the general public to know their own microbes – and the need for large data sets to compare African and possibly aboriginal microbes to those of people living in Westernized cultures – Jeff approached co-founder Rob Knight (then at the University of Colorodao Boulder) about the possibility of using crowd funding as a means to build large, public data sets. At the time, the idea seemed a little bit crazy but with a bit of hard work on the part of Rob and others in his lab, the American Gut Project went live Thanksgiving of 2012.The American Gut Project enables participants to learn about their own body’s microbes while also contributing to the greater scientific effort to learn how the human microbiome is associated with various aspects of our health-from associations with diet to the amount of alcohol someone drinks to whether or not someone has autism or IBD. Because all de-identified data are made freely available, researchers from all over the world can access the data to ask questions about the microbiome and its association with a variety of health and lifestyle factors.

Rob Knight


American Gut co-founder, Rob Knight, is the principal investigator at the Knight Lab and is a professor in the Department of Pediatrics, with an additional appointment in the Department of Computer Science and Engineering, at the University of California San Diego. A New Zealand native, Rob obtained his PhD from Princeton University analyzing the evolution of the genetic code. Rob is also a self-taught computer programmer, and he and students and post-docs in his laboratory are responsible for developing microbiome data analysis tools and pipelines, such as UniFrac, Qiime, and Qiita, which are used by microbiome researchers the world-over.  Rob was chosen as one of 50 Howard Hughes Medical Institute Early Career Scientists in 2009, is a Senior Editor is the ISME Journal, is a member of the Steering Committee of the Earth Microbiome Project, and is the CSO and co-founder of Biota TechnologyTM, a microbial DNA sequencing company targeting the energy market. Rob will also lead a new research-focused Center for Microbiome Innovation, which will be part of the new UCSD campus-wide Microbiome and Microbial Sciences Initiative, announced in October 2015.

Jeff Leach

jeff-leachJeff Leach is the Founder of the not-for-profit Human Food Project and Co-Founder of the American Gut Project – the largest open-source, crowd funded microbiome project in the world. His research has been published in numerous journals including the European Journal of Clinical Nutrition, Nature, Journal of Field Archaeology, Current Research in the Pleistocene, Journal of Archaeological Science, British Journal of Nutrition, and numerous others. His research has been featured in numerous magazine and newspaper articles and he has written opinion pieces about health and nutrition for the New York Times and San Francisco Chronicle. His work among the Hadza was recently profiled in the prestigious journal Science and in several television programs and an upcoming PBS documentary.


American Gut Abroad

Through its collaborator network, the American Gut Project has expanded into Europe through the British Gut Project, led by Dr. Tim Spector,into Australia through an aggregation site spearheaded by Dr. Phil Hugenholtz, and most recently into Asia (Singapore) through an aggregation site spearheaded by Scott Savage. These efforts have facilitated the collection of hundreds of samples from participants outside of North America, which will enable us to characterize geographical differences in the human microbiome-and determine whether associations observed in the US are also seen in other areas of the world.

If you are an individual or research group interested in working with us to start an “X Gut” project in another country, please carefully review our policies for affiliated projects and contact American Gut Project Manager Embriette Hyde at