University of Oregon





Logan SL, Thomas J, Yan J, Baker RP, Shields DS, Xavier JB, Hammer BK, Parthasarathy R. (2018) The Vibrio cholerae type VI secretion system can modulate host intestinal mechanics to displace commensal gut bacteria. Proc. Natl. Acad. Sciences: Epub ahead of print. doi: 10.1073/pnas.1720133115 PubMed


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 TA, Hernandez DZ, Wong ZC, Wandler AM, 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 AR, Watral V, Sichel S, Spagnoli S, Banse AV, Mittge E, Sharpton TJ, Guillemin K, Kent ML. (2017) Transmission of a common intestinal neoplasm in zebrafish by cohabitation. Journal of Fish Diseases. doi:10.1111/jfd.12743 PubMed


Burns AR, Miller E, Agarwal M, Rolig AS, Milligan-Myhre K, Seredick S, Guillemin K, Bohannan BJM. (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 MJ, Hay EA, 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 AR, Guillemin K, Bohannan, BJ. (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 AR, 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 CM, Milligan-Myhre K, Bassham S, Guillemin K, Cresko WA (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 AS, Mittge EK, Ganz J, Troll JV, Melancon E, Wiles TJ, Alligood K, Stephens WZ, Eisen JS, 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 JY, Goers Sweeney E, Guillemin K, Amieva MR. (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 TJ, Rawls JF, Eisen JS, 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 LD, Neiderhiser JM, Harold GT, Natsuaki MN, Bohannan BJ, Cresko WA. (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 TJ, Jemielita M, Baker RP, Schlomann BH, Logan SL, Ganz J, Melancon E, Eisen JS, 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 WZ, Burns AR, Stagaman K, Wong S, Rawls JF, Guillemin K, Bohannan BJ. (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 JL, Royall AE, Randel MA, Sikkink KL, Phillips PC, Johnson EA. (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 CM, Mittge EK, Agarwal M, Currey M, Cresko WA, 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 ML, Whipps CM, 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 AM, Bohannan BJ, Jaffe DA, Levin DA, Green JL. (2016) Molecular evidence for metabolically active bacteria in the atmosphere. Front Microbiol, 7, 772. doi:10.3389/fmicb.2016.00772 PubMed.


Hill JH, Franzosa EA, 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 AR, Stephens WZ, Stagaman K, Wong S, Rawls JF, Guillemin K, Bohannan BJ. (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 WZ, Burns AR, Stagaman K, David LA, Bohannan BJ, Guillemin K, Rawls JF. (2015) Ontogenetic differences in dietary fat influence microbiota assembly in the zebrafish gut. MBio, 6(5). doi:10.1128/mBio.00687-15 PubMed.


Stephens WZ, Wiles TJ, Martinez ES, Jemielita M, Burns AR, Parthasarathy R, Bohannan BJ, 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 ES, Guillemin K. (2015) Immigrants in immunology: the benefits of lax borders. Trends Immunol, 36(5), 286-289. doi:10.1016/ PubMed.


Rolig AS, Parthasarathy R, Burns AR, Bohannan BJ, 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 RP, Taormina MJ, 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 JK, Huang JY, Wreden C, Sweeney EG, Goers J, Remington SJ, 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 MJ, Burns AR, Hampton JS, Rolig AS, 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 JP, Kembel SW, Green, JL. (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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