About the Center

The UC San Diego Center for Microbiome Innovation leverages the university’s strengths in clinical medicine, bioengineering, computer science, the biological and physical sciences, data sciences and more to coordinate and accelerate microbiome research. We also develop methods for manipulating microbiomes for the benefit of human and environmental health.




Mastering the many laboratory and bioinformatics protocols – as well as the huge volumes of resulting data – are key barriers to leveraging microbiome research to improve therapies, as well as advancing the many other practical applications of this field. To overcome these hurdles, the Center for Microbiome Innovation provides core facilities for data generation. We also assist researchers who have interesting samples but modest expertise in these area. By coordinating with nucleic acid sequencing and mass spectrometry facilities already at UC San Diego, we offer our industry partners expertise with:


  • Sample preparation
  • High-throughput DNA extraction
  • Bioinformatics and data analysis





Our graduate students and postdoctoral researchers work in interdisciplinary teams at the cutting-edge of microbiome research, biomedical engineering, quantitative measurements and modeling, cellular and chemical imaging and drug discovery. These researchers have the skills, interest and drive to apply microbiome research to a wide range of opportunities and challenges facing our industry partners.

Center students draw from the new UC San Diego Microbial Sciences Graduate Research Initiative, in addition to more established graduate programs across the campus, including the interdisciplinary bioinformatics program. Students solve problems together in effective multidisciplinary teams using the latest technologies, giving them the foundations to become research, technology and clinical leaders in the emerging fields springing up around microbiome research.






Over time, the Center aims to develop game-changing technologies to advance and scale this work — from nanotechnology sensors that reach inside single cells to drones that map the global microbiome and connect to climate models.



In addition to the exciting frontiers presented by human microbiome research, all animals, plants and fungi on land, in rivers and lakes, and in the oceans are associated with unique microbial communities. So are the habitats in which they reside. Just as our microbiomes help define human health, environmental microbiomes define the health and wellbeing of our planet.

Researchers at the Scripps Institution of Oceanography, the rest of UC San Diego, and beyond are beginning to unravel the complexities of these microbiomes so we can better understand their involvement in processes ranging from symbioses to global nutrient cycling, how they can be exploited as a resource for natural product drug discovery, and how they can be optimized to benefit humanity and our planet.



Genetically speaking, we’re all 99.9 percent the same. And yet we’ve invested millions of dollars investigating the slight genetic variations that affect our health. While these studies have resulted in a wealth of clinically relevant information, we still have yet to fully appreciate 99 percent of the genes in our body — the microbial genes expressed by the trillions of microbes that live in, on and around us. Those microbes and their genes make up our microbiomes.

Far from the inert freeloaders they were once thought to be, microbes help us digest and process nutrients, producing their own waste and metabolites. They also constantly interact with — and help shape — our immune systems. In a nutshell, our microbiomes help make us who we are, in sickness and in health.

Researchers at UC San Diego and elsewhere are already finding that the makeup of our gut microbiomes is associated with diseases and conditions you might expect, such as food allergies, obesity, inflammatory bowel disease and colon cancer. They’re also discovering that the gut microbiome plays a role in diseases you might not expect, such as rheumatoid arthritis, atherosclerosis and asthma. Even more surprisingly, in mouse models at least, the microbiome in the gut has even been linked to the brain. While human studies are still needed, this could mean that traits like how anxious you are, how outgoing you are, even how depressed you are or whether you have autism, may depend on the tiny microbes in your gut.

And that’s just the gut microbiome. Studies of the microbial communities living on the skin, in the mouth, in your home, in hospitals, and in many other places are revealing new surprises about the roles microbes play in our lives and environment.



CMI Industry Sponsors