Biophysics, Imaging, and Soft Materials

Position Announcement

Post-doctoral fellow or Research Associate

Imaging-based studies of microbial community dynamics

We seek applications for a postdoctoral fellow or research associate position focused on applying advanced imaging and analysis techniques to investigate the dynamics of gut microbial communities. The position would be based in the Parthasarathy lab [1] at the University of Oregon and associated with its Microbial Ecology and Theory of Animals (META) Center [2] and a recently awarded five-year Program Project grant from the National Institutes of Health.

Every animal is associated with a diverse community of microbes. Though it is now well appreciated that these microbes contribute significantly to their hosts' functions, the mechanisms underlying these interactions remain mysterious. The biophysical characteristics of gut microbial communities are especially fascinating, as processes of growth, aggregation, motility, and spatial organization must be important for multi-species coexistence and competition, but are notoriously difficult to investigate. Our lab applies light sheet fluorescence microscopy to larval zebrafish, a model vertebrate, to gain insights into gut microbial dynamics, obtaining the only large-scale, high-resolution views of intestinal microbes in any vertebrate to date, and revealing connections between community structure, population dynamics, and disease [e.g. 3-5].

Movie: Live imaging of a single optical plane in the intestinal midgut of a 6 dpf larval zebrafish inoculated with a GFP-labeled Vibrio species. See [3] for details.

The new researcher will build on existing local expertise in light sheet fluorescence microscopy and associated instrumentation, designing and implementing experiments focused both on the internal dynamics of zebrafish gut microbial communities and on the biophysics of transmission of symbiotic microbes between hosts. He/she will interact with a vibrant and highly interdisciplinary community of local research groups, with opportunities for co-mentoring by faculty in Physics, Molecular Biology, Ecology and Evolution, and Neuroscience. He/she will also be encouraged to develop his/her own research projects.

Potential candidates must have a Ph.D. from a relevant discipline such as physics, biophysics, bioengineering, or biology. Expertise in at least one of the following is strongly preferred: microscopy, microbiology, instrument design and construction, optics, biological imaging, and image analysis. We welcome researchers interested in leveraging their experiences to move into a new field.

The University of Oregon is located in Eugene, Oregon, an area noted for its quality of life and natural beauty. Eugene is about two hours' drive from Portland, and an hour's drive from the Pacific Ocean and the Cascade Mountains.

For more information about this position, including how to apply, please email Raghuveer Parthasarathy ( and include (1) a cover letter explaining your background and career interests (2) a CV, and (3) names and contact information of three references. Also, please write with any questions. The position will remain open until filled. Women and members of groups underrepresented in science are encouraged to apply. The University of Oregon is an EO/AA/ADA institution committed to cultural diversity.


[1] Parthasarathy Lab:

[2] META:

[3] T. J. Wiles, M. Jemielita, et al., PLOS Biol. 14, e1002517 (2016). [Link]

[4] S. L. Logan et al., Proc. Natl. Acad. Sci. 115, E3779–E3787 (2018). [Link]

[5] B. H. Schlomann, et al., Biophysical Journal. 115: 1-7 (2018) [Link]