Microbiology and Immunology

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Caltech's version of microbiology and immunology is unique. Over sixteen faculty from four divisions (BBE, CCE, GPS, EAS) work together to train students in how to understand microbial systems at various spatial and temporal scales: from the molecular to the global, from the past to the present, and towards future engineering applications. We utilize microorganisms to explore basic biology and biochemistry problems, understand the physical principles governing biological systems, investigate mechanisms that underpin the robustness, stability, and design of complex networks, and explore the interactions among microbes in communities and between microbes and their environment. We also investigate interactions between microbes (under both pathogenic and non-pathogenic conditions) and the immune system, and we seek to understand how the immune system develops, functions, and can be manipulated to maintain human health.

Environmental Microbial Interactions (EMI)

(Fischer, Hsiao, Ismagilov, Leadbetter, Mazmanian, Newman, Orphan, Phillips, Sessions, Sternberg)

EMI laboratories are focused on understanding how complex microbial communities have co-evolved with Earth and its animal and plant inhabitants. Employing approaches that span analytical chemistry, animal models, genetics, genomics, imaging, immunology, and custom microfluidics, these labs strive to achieve an integrated understanding of the microbial role in ecosystems that are important in human or planetary health and disease.


The immune system is our defense against pathogenic microorganisms. It involves an innate branch that recognizes generic aspects of pathogens and an adaptive branch that recognizes specific molecules on pathogens. Caltech laboratories are using structural biology, molecular biology, and mouse genetics to study how the immune system develops, how the immune system interacts with microbes that naturally reside in our bodies and are not pathogens, and how signals are transduced in both the innate and adaptive branches of the immune system. In addition, there is a strong translational medicine effort, with a focus on pathologies of the immune system including cancer, engineering antibodies to produce more potent vaccines, and engineering immune cells to attack cancer.

Microbial Molecular and Cellular Biology (MMBR)

(Aravin, Cai, Clemons, Elowitz, Hsiao, Jensen, Mazmanian, NewmanRees)

Because they can grow rapidly, have small genomes, and are amenable to many types of molecular analyses, microbes provide outstanding model systems in which to study fundamental cellular processes. MMBR laboratories draw on techniques including cryo-electron and fluorescence microscopy, protein crystallography, genetics, and biochemistry to study the bioenergetics, regulation of gene expression, protein trafficking, lipid-protein interactions, and ultrastructure of diverse organisms.

Synthetic and Quantitative Microbial Biology (SQMB)

(Arnold, Cai, Elowitz, JensenIsmagilovPhillips)

SQMB laboratories are working to understand the quantitative basis for fundamental capabilities of microbes, and to learn how to reprogram microbes both to better understand how they work and to develop novel industrial and biomedical capabilities. Techniques include directed evolution, custom microfluidics, quantitative time-lapse imaging of single cells, and mathematical modeling, and the research involves a variety of model and non-model microbial species.