Katherine Xue

Assistant Professor, Molecular Biology and Biochemistry
Charlie Dunlop School of Biological Sciences

human microbiome, microbial ecology, microbial evolution

Xue lab website

Each of us is home to trillions of microbes, and the interactions between these microbes play key roles in shaping human health. The Xue lab at UC Irvine studies how microbes interact and evolve in complex communities like the human gut microbiome. We combine experimental and computational techniques to characterize ecological and evolutionary dynamics in the gut microbiome and to investigate how specific microbial interactions give rise to community-scale dynamics.

Jane Coffin Childs Memorial Fund Postdoctoral Fellowship Award, 2021-2023.
HHMI-Janelia Leading Edge Fellow, 2022.
James S. McDonnell Foundation Postdoctoral Fellowship Award in Understanding Dynamic and Multi-scale Systems, 2019-2021.
Fannie and John Hertz Foundation Fellowship, 2015-2019.
James F. Crow Early Career Researcher Award, Genetics Society of America, 2018.
Harold M. Weintraub Graduate Student Award, 2018.
NSF Graduate Research Fellowship, 2014-2017.

Katherine received her A.B. from Harvard University and her PhD from the University of Washington, where she studied influenza evolution in Jesse Bloom’s lab. As a postdoctoral fellow, she worked with David Relman and Dmitri Petrov at Stanford University to investigate ecological dynamics in the gut microbiome. She started her lab at UC Irvine in 2025.

Full list of publications:
https://scholar.google.com/citations?hl=en&user=F8FIv88AAAAJ

Selected publications:
Xue, K.S.†, Walton, S.J., Goldman, D.A., Morrison, M.L., Verster, A.J., Parrott, A.B., Yu, F.B., Neff, N.F., Rosenberg, N.A., Ross, B.D., Petrov, D.A., Huang, K.C., Good, B.H.†, Relman, D.A.† Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation. Manuscript in revision. bioRxiv (2023). DOI: 10.1101/2023.09.26.559480 †corresponding authors

Goldman, D.A.*, Xue, K.S.*,†, Parrott, A.B., Jeeda, R.R., Lopez, J.G., Vila, J.C.C., Petrov, D.A., Good, B.H., Relman, D.A., Huang, K.C†. Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities. Proceedings of the National Academy of Sciences 122 (11) e2322440122 (2025). DOI: 10.1073/pnas.2322440122 *co-first authors, †corresponding authors

Xue, K.S., Stevens-Ayers, T., Campbell, A.P., Englund, J.A., Pergam, S.A., Boeckh, M., Bloom, J.D. Parallel evolution of influenza across multiple spatiotemporal scales. eLife 6: e26875 (2017). DOI: 10.7554/eLife.26875

Cellular and Molecular Biosciences

Mathematical, Computational and Systems Biology

Link to this profile
https://faculty.uci.edu/profile/?facultyId=7327

Last updated
09/15/2025