University of Oregon




Parthasarathy, R. (2018). Monitoring microbial communities using light sheet fluorescence microscopy. Current Opinion in Microbiology, 43, 31-37. doi:10.1016/j.mib.2017.11.008 PubMed


Jones, T. A., Hernandez, D. Z., Wong, Z. C., Wandler, A. M., & Guillemin, K. (2017). The bacterial virulence factor CagA induces microbial dysbiosis that contributes to excessive epithelial cell proliferation in the Drosophila gut. PLOS Pathogens, 13(10). doi:10.1371/journal.ppat.1006631 PubMed


Burns, A. R., Watral, V., Sichel, S., Spagnoli, S., Banse, A. V., Mittge, E.,  Sharpton T. J., Guillemin K., Kent, M. L. (2017). Transmission of a common intestinal neoplasm in zebrafish by cohabitation. Journal of Fish Diseases. doi:10.1111/jfd.12743 PubMed


Burns, A. R., Miller, E., Agarwal, M., Rolig, A. S., Milligan-Myhre, K., Seredick, S., Guillemin, K., Bohannan, B. J. M. (2017). Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model. Proc Natl Acad Sci U S A. doi:10.1073/pnas.1702511114 PubMed.


Taormina, M. J., Hay, E. A., & Parthasarathy, R. (2017). Passive and Active Microrheology of the Intestinal Fluid of the Larval Zebrafish. Biophys J, 113(4), 957-965. doi:10.1016/j.bpj.2017.06.069 PubMed.


Stagaman, K., Burns, A. R., Guillemin, K., & Bohannan, B. J. (2017). The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish. ISME J, 11(7), 1630-1639. doi:10.1038/ismej.2017.28.  PubMed.


Burns, A. R., & Guillemin, K. (2017). The scales of the zebrafish: host-microbiota interactions from proteins to populations. Curr Opin Microbiol, 38, 137-141. doi:10.1016/j.mib.2017.05.011 PubMed


Guillemin, K. (2017). Reflections on a Decade: With Cat-like Tread. Cell Host Microbe, 22(2), 130-133. doi:10.1016/j.chom.2017.07.014 PubMed


Small, C. M., Milligan-Myhre, K., Bassham, S., Guillemin, K., & Cresko, W. A. (2017). Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut. Genome Biol Evol, 9(3), 504-520. doi:10.1093/gbe/evx014 PubMed.


Rolig, A. S., Mittge, E. K., Ganz, J., Troll, J. V., Melancon, E., Wiles, T. J., Alligood, K., Stephens, W.Z., Eisen, J.S., Guillemin, K. (2017). The enteric nervous system promotes intestinal health by constraining microbiota composition. PLoS Biol, 15(2), e2000689. doi:10.1371/journal.pbio.2000689 PubMed.


Guillemin, K. (2017). What Is the Future of Developmental Biology? Teaming with Microbes. Cell, 170(1), 6-7. doi:10.1016/j.cell.2017.06.019 PubMed


Huang, J. Y., Goers Sweeney, E., Guillemin, K., & Amieva, M. R. (2017). Multiple Acid Sensors Control Helicobacter pylori Colonization of the Stomach. PLoS Pathog, 13(1), e1006118. doi:10.1371/journal.ppat.1006118 PubMed.


Melancon, E., Gomez De La Torre Canny, S., Sichel, S., Kelly, M., Wiles, T. J., Rawls, J. F., Eisen, J.S., Guillemin, K. (2017). Best practices for germ-free derivation and gnotobiotic zebrafish husbandry. Methods Cell Biol, 138, 61-100. doi:10.1016/bs.mcb.2016.11.005 PubMed.


Leve, L. D., Neiderhiser, J. M., Harold, G. T., Natsuaki, M. N., Bohannan, B. J., & Cresko, W. A. (2017). Naturalistic Experimental Designs as Tools for Understanding the Role of Genes and the Environment in Prevention Research. Prev Sci. doi:10.1007/s11121-017-0746-8 PubMed.




Wiles, T. J., Jemielita, M., Baker, R. P., Schlomann, B. H., Logan, S. L., Ganz, J., Melancon, E., Eisen, J.S., Guillemin, K., Parthasarathy, R. (2016). Host Gut Motility Promotes Competitive Exclusion within a Model Intestinal Microbiota. PLoS Biol, 14(7), e1002517. doi:10.1371/journal.pbio.1002517 PubMed.


Stephens, W. Z., Burns, A. R., Stagaman, K., Wong, S., Rawls, J. F., Guillemin, K., & Bohannan, B. J. (2016). The composition of the zebrafish intestinal microbial community varies across development. ISME J, 10(3), 644-654. doi:10.1038/ismej.2015.140 PubMed.


Preston, J. L., Royall, A. E., Randel, M. A., Sikkink, K. L., Phillips, P. C., & Johnson, E. A. (2016). High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq). BMC Genomics, 17, 464. doi:10.1186/s12864-016-2669-3 PubMed.


Milligan-Myhre, K., Small, C. M., Mittge, E. K., Agarwal, M., Currey, M., Cresko, W. A., & Guillemin, K. (2016). Innate immune responses to gut microbiota differ between oceanic and freshwater threespine stickleback populations. Dis Model Mech, 9(2), 187-198. doi:10.1242/dmm.021881 PubMed.


Mason, T., Snell, K., Mittge, E., Melancon, E., Montgomery, R., McFadden, M., Camoriano, J., Kent, M.L., Whipps, C.M., Peirce, J. (2016). Strategies to Mitigate a Mycobacterium marinum Outbreak in a Zebrafish Research Facility. Zebrafish, 13 Suppl 1, S77-87. doi:10.1089/zeb.2015.1218 PubMed.


Klein, A. M., Bohannan, B. J., Jaffe, D. A., Levin, D. A., & Green, J. L. (2016). Molecular Evidence for Metabolically Active Bacteria in the Atmosphere. Front Microbiol, 7, 772. doi:10.3389/fmicb.2016.00772 PubMed.


Hill, J. H., Franzosa, E. A., Huttenhower, C., & Guillemin, K. (2016). A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development. Elife, 5. doi:10.7554/eLife.20145 PubMed.


Burns, A. R., Stephens, W. Z., Stagaman, K., Wong, S., Rawls, J. F., Guillemin, K., & Bohannan, B. J. (2016). Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. ISME J, 10(3), 655-664. doi:10.1038/ismej.2015.142 PubMed.



Wong, S., Stephens, W. Z., Burns, A. R., Stagaman, K., David, L. A., Bohannan, B. J., Guillemin, K., Rawls, J. F. (2015). Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut. MBio, 6(5). doi:10.1128/mBio.00687-15 PubMed.


Stephens, W. Z., Wiles, T. J., Martinez, E. S., Jemielita, M., Burns, A. R., Parthasarathy, R., Bohannan, B.J., Guillemin, K. (2015). Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine. MBio, 6(6). doi:10.1128/mBio.01163-15 PubMed.


Stagaman, K., Martinez, E. S., & Guillemin, K. (2015). Immigrants in immunology: the benefits of lax borders. Trends Immunol, 36(5), 286-289. doi:10.1016/ PubMed.


Rolig, A. S., Parthasarathy, R., Burns, A. R., Bohannan, B. J., & Guillemin, K. (2015). Individual Members of the Microbiota Disproportionately Modulate Host Innate Immune Responses. Cell Host Microbe, 18(5), 613-620. doi:10.1016/j.chom.2015.10.009 PubMed.


Baker, R. P., Taormina, M. J., Jemielita, M., & Parthasarathy, R. (2015). A combined light sheet fluorescence and differential interference contrast microscope for live imaging of multicellular specimens. J Microsc, 258(2), 105-112. doi:10.1111/jmi.12220 PubMed.


Anderson, J. K., Huang, J. Y., Wreden, C., Sweeney, E. G., Goers, J., Remington, S. J., & Guillemin, K. (2015). Chemorepulsion from the Quorum Signal Autoinducer-2 Promotes Helicobacter pylori Biofilm Dispersal. MBio, 6(4). doi:10.1128/mBio.00379-15 PubMed.



Stagaman, K., Guillemin, K., & Milligan-Myhre, K. (2014). Tending a complex microbiota requires major immune complexity. Mol Ecol, 23(19), 4679-4681. doi:10.1111/mec.12895 PubMed.


Jemielita, M., Taormina, M. J., Burns, A. R., Hampton, J. S., Rolig, A. S., Guillemin, K., & Parthasarathy, R. (2014). Spatial and temporal features of the growth of a bacterial species colonizing the zebrafish gut. MBio, 5(6). doi:10.1128/mBio.01751-14 PubMed.



O’Dwyer, J. P., Kembel, S. W., & Green, J. L. (2012). Phylogenetic diversity theory sheds light on the structure of microbial communities. PLoS Comput Biol, 8(12), e1002832. doi:10.1371/journal.pcbi.1002832
PCOMPBIOL-D-12-01226 [pii] PubMed.








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