Center for Microbiome Innovation

We’re surrounded by an invisible microbial world that, through advances in DNA sequencing and chemical readouts we’re just beginning to understand. These complex microbial communities go way beyond what we use to make our beer, yogurt and bread: they’re in our gut helping us digest our food, on our skin determining whether we attract mosquitoes or get sunburn, and everywhere from the soil helping plants grow to the ocean making the bulk of the world’s oxygen. At UC San Diego’s Center for Microbiome Innovation, we are working together to understand, preserve, and where appropriate harness these microbes to benefit humanity and the planet. We imagine a future where you’ll be able to ask intelligent agents like IBM’s Watson to interpret them for you. Just as computing has become pervasive, we see a future where a better understanding of microbiomes can help the health of you, your children, your pets and even make your fermented foods tastier.

Rob Knight, PhD


Rob Knight, PhD, is professor in the Departments of Pediatrics and Computer Science & Engineering at the University of California San Diego, and author of “Follow Your Gut: The Enormous Impact of Tiny Microbes.” He received a B.Sc. in Biochemistry in 1996 from the University of Otago in his native New Zealand, a PhD in 2001 from Princeton University in Ecology and Evolutionary Biology, and performed postdoctoral work at the University of Colorado, Boulder before becoming a faculty member in the interdisciplinary BioFrontiers Institute there in 2004. He moved to UC San Diego in 2015 to launch and direct the UC San Diego Microbiome and Microbial Sciences Initiative, which is now part of the White House’s National Microbiome Initiative.

Knight’s work focuses on using readout technologies such as next-generation sequencing to improve our understanding of the structure, function and dynamics of the human microbiome, contributing to the main data analysis in the NIH-funded Human Microbiome Project. He is co-founder of the Earth Microbiome Project and the American Gut Project. Current research interests include relating the human microbiome to diseases ranging from obesity to mental illness, spatial and temporal mapping of microbial communities on different scales ranging from our bodies to our planet, and developing new data visualization methods that assist in resolving the challenge of microbial “Big Data.”

American Gut Project

Why are over ten thousand people paying to have robots and lasers read out the DNA from the bacteria in their poop? Because the genes in your microbiome can be more important for aspects of health and disease than every gene in your genome. In the American Gut Project we’re working with citizen scientists in the United States and internationally to understand how what we eat, including fermented foods, changes our microbiome for better or for worse. Fascinatingly, the differences between different people’s microbiomes don’t match up to things you’d expect, like whether your a man or a woman, an vegan or an omnivore, but instead are affected by things like how many kinds of plants you eat and whether you’re on specific medications. And some of those medications you’re not taking on purpose, but getting unintentionally from your food. On this panel, you’ll hear about the latest results of the project, how Americans match up to people in other countries, and just how much your microbiome can change if you get sick or have surgery.

Daniel McDonald

Dr. Daniel McDonald is the Scientific Director for the American Gut Project. The American Gut Project is a non-profit crowd-funded citizen science effort to rapidly advance our understanding of the types of microbial configurations associated with humans by allowing anyone in the world to participate in this cutting edge research. Daniel has been involved in the American Gut since its inception in November 2012, and has helped bring the project to over $2,000,000 in funding largely from members of the general public; he holds a PhD in Computer Science, works for the Knight Lab in the Department of Pediatrics at UCSD, and regularly publishes peer-reviewed microbiome papers.

Global FoodOmics

We’ve all heard the old adage you are what you eat- but, do we know what we eat? There is much we don’t yet know about the foods we eat; for example, which different molecules and microbes are found on different foods? We are launching an effort to answer these questions and more. Using advanced analytical tools, we will characterize the molecules and microbes present in and on 1000’s of different foods and beverages.

Julia Gauglitz

Dr. Julia M. Gauglitz is the Project Manager of the Global FoodOmics Project, a new initiative at the University of California, San Diego seeking to understand the metabolites and microbes that make up the foods that we eat. Julia earned her Ph.D. as an NSF awarded graduate research fellow at the University of California, Santa Barbara. Julia is excited to use her expertise in chemistry and microbiology to lead a cutting edge interdisciplinary effort to understand foods. Julia has spoken at international research conferences, was a science fellow for the National Network of Ocean and Climate Change Interpretation and was recently featured in a Smithsonian Magazine article entitled “You are what you eat, and what you eat is millions of microbes.“