University of Oregon


Research Areas




Host-Microbe Systems Assembly

We investigate the factors that shape the composition of host-associated microbial communities and assess the relative contributions of selective filtering by the host environment, interactions between microbes, and stochastic processes in community assembly.

Host-Microbe Systems Dynamics

We use light sheet microscopy to characterize the spatial and temporal dynamics of microbial and host cells and genes during the establishment of host-associated microbial communities.


Host-Microbe Systems Evolution

We study the variation of host- associated microbial communities across genetically diverse populations of hosts to uncover the genetic determinants that shape the composition of resident microbial communities.




Cores & Hubs of Innovation


We pioneer methods to rear germ-free or axenic fish as animal models to study host-microbe interactions. In addition we curate collections of host- associated microbes and develop genetic tools and resources to study their biology.


Live Imaging

We are innovating the use of light sheet microscopy to study the dynamics of host-microbe interactions on temporal and spatial scales that are relevant to microbes.



We harness the power of next generation sequencing to explore the diversity of host-associated microbial communities, host transcriptional responses to these communities, and host genetic variation associated with these communities.



We draw on sampling theory, spatial biodiversity theory, and probabilistic approaches to analyze highly complex sequence and image data and to model host-microbe systems.





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The META Center for Systems Biology is a National Center for Systems Biology funded by the National Institute for General Medical Sciences of the National Institutes of Health


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