We accelerate microbiome research
and develop new methods for manipulating microbiomes
to improve human health and benefit the environment.
UC San Diego is a world-leader in microbiome research, biomedical engineering, quantitative measurements and modeling, cellular and chemical imaging, drug discovery, "omics" sciences and much more. We draw 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.
Researchers at UC San Diego Unveil New Interactive Web Tool for Visualizing Large-Scale Phylogenetic Trees
March 17, 2021
Born of these needs for advancement, a team of researchers with the Center for Microbiome Innovation (CMI) at the University of California San Diego (UC San Diego), led by Kalen Cantrell and Marcus W. Fedarko, unveiled EMPress, a new interactive visualization tool, in an article published in mSystems on March 16, 2021. The paper, entitled “EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets,” showcases the tool’s functionality, versatility, and scalability, and explores some of the potential applications in visualization and data analysis. Full Story
March 11, 2021
The wastewater sampling initiative began as a pilot program on the UC San Diego campus in the summer of 2020 with only six collection sites but quickly grew as they determined that environmental testing was a key to preventing the spread of COVID-19. However, the manual work involved in concentrating samples was a roadblock to scaling the surveillance program beyond the university. This project marked the first collaboration between the Center for Microbiome Innovation (CMI) and the Center for Machine-Integrated Computing & Security (CMICS), both research centers are part of UC San Diego Jacobs School of Engineering. Full Story
February 16, 2021
Researchers from the Center for Microbiome Innovation at UC San Diego, led by Clarisse Marotz and corresponding author Karsten Zengler, designed a study to measure not just the composition of the oral microbiome, but the microbial load as well, and how it’s affected by daily activities such as eating and brushing one’s teeth. The results, entitled “Quantifying live microbial load in human saliva samples over time reveals stable composition and dynamic load,” were published in mSystems on February 16, 2021. Full Story
Sourcing Viral Surveillance Supplies at the Pharmacy: Understanding Consumer-Grade Materials' Viability as SARS-CoV-2 Testing Media
January 25, 2021
As the COVID-19 pandemic grew and quickly took hold of the world, one of the biggest challenges in the response efforts was determining the most effective approach to monitoring the virus’s spread. That task has become all the more critical as regional and national governments have been tasked with balancing the protection of public health against the reality that society is ill-equipped to handle a prolonged shutdown. Full Story
January 13, 2021
University of California San Diego professor Bernhard O. Palsson has been named the Y.C. Fung Endowed Chair in Bioengineering at the Jacobs School of Engineering. Palsson is also a professor of pediatrics, and Director of the Center for Biosustainability. Palsson’s research focuses on developing experimental and computational models of the red blood cell, E. coli, CHO cells, and several human pathogens to establish their systems biology. His Systems Biology Research Group leverages high-power computing to build interactive databases of biological information and is increasingly focused on Genome Design and Engineering. Full Story