UC San Diego Center for Microbiome Innovation (CMI)

UCSD is a world-leader in microbiome research, biomedical engineering, quantitative measurements and modeling, cellular and chemical imaging, drug discovery, "omics" sciences and much more. The CMI draws interdisciplinary teams of these researchers together to push the boundaries of human understanding of microbiomes — the distinct constellations of bacteria, viruses and other microorganisms that live within and around humans, other species and the environment.

CMI Mission and Goals

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. CMI also develop methods for manipulating microbiomes for the benefit of human and environmental health. Over time, CMI aims to develop game changing technologies to advance and scale this work, from nanontechnology sensors that reach inside single cells to drones that map the global microbiome and connect to climate models.


CMI Faculty Investigators


More than 130 UC San Diego professors and research scientists have joined CMI since its launch in 2016. These researchers lead teams working at the leading edge of many interrelated areas, including microbiology, cell and molecular biology, computer science, physical sciences, biomedical engineering, electrical engineering, pharmacology, clinical care, ecology, oceanography, anthropology and more.  Considerable research effort focuses on the interaction of human pathogenic and commensal microbes, how antibiotics impact the microbiome, and the evolution of antibiotic resistance within our bodies, in the foodchain, and in hospital environments. 

CHARM Collaboration Contact:  Rob Knight, PhD  (Director of CMI)

CHARM ⬌ CMI Collaborations

Antibiotics have profound and rapid effects on microbiome composition that can be detrimental to human health, especially on extensive exposure, increasing the risk of obesity, allergy and autoimmune disorders. CHARM and CMI investigators collaborate on targeted therapies (e.g. anti-virulence agents, immune boosters) that spare the healthy microbiome, cultivation of beneficial microbes (e.g. probiotics) to prevent or treat infection, studies of antibiotic resistance genes circulating among the human microflora, and microbiome replacement to cure recurrent C. difficile infection.


Molecular Cartography of Skin

CHARM & CMI Investigators created novel technologies for 3D mapping of mass spectrometry data and microbial 16S rRNA amplicon sequences. The molecular composition of human skin showed diverse distributions modulated by daily routines such as the application of hygiene products. These maps identify spatial relationships of hygiene, the microbiota, and environment, guiding predictive models of skin phenotypes tailored to individual health.

Read Article in Proc Natl Acad of Sci USA