Michelle Flenniken, Assistant Professor- Ph.D. from Montana State University, 2006.

Office: 215 Plant BioScience Building
Lab: 337 Plant BioScience Building

Phone: 406-994-7229 (office), 406-994-5152 (lab)
Email Dr. Flenniken

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Flenniken Lab Personnel


Research in the Flenniken Lab is aimed at elucidating the molecular mechanisms underlying host-pathogen interactions in agriculturally important systems; including honey bees (Apis mellifera). Projects in the lab focus on five principal aspects of honey bee biology: (1) determining the mechanisms and contributions of RNA-triggered pathways in honey bee antiviral defense, (2) honey bee pathogen monitoring, detection and discovery with an emphasis on pathogens associated with colony losses (including CCD), (3) investigating the pathogenesis of the recently discovered Lake Sinai viruses, (4) understanding the influence of the individual bee microbiome, metabolome, and transcriptome on the immune response and outcome of infections, and (5) examining the sublethal effects of agrochemicals on honey bee health. Honey bees are an excellent model in which to investigate immune mechanisms at both the individual bee and entire colony level. In addition and in collaboration with Dr. Nina Zidak, we are investigating the interactions between Potato virus Y (PVY) and several potato cultivars.


Research focused on host-pathogen interactions (virology, microbiology, immunology) and teaching.


  • B.S. Biology, Chemistry Minor, University of Iowa, Iowa City, IA, 1998
  • Ph.D. Microbiology, Montana State University, Bozeman, MT, 2006
  • Postdoctoral Fellow, Microbiology and Immunology, University of California San Francisco, San Francisco, CA, 2007-2012


  • American Society of Virology  2010 – present
  • Entomological Society of America 2013 – present
  • Society for Invertebrate Pathology 2013 – present
  • American Association of Professional Apiculturists, Board Member, 2012 – present
  • MSU Women’s Faculty Caucus, Steering Committee for College of Agriculture 2012-present


  • General Genetics - BIOB 375
  • Virology - BIOM 435, MB 530                                                                                                          


Research in the Flenniken laboratory is supported by the United States Department of Agriculture National Institute of Food and Agriculture, Agriculture and Food Research Initiative (USDA-NIFA-AFRI) Program, Montana Department of Agriculture Specialty Crop Block Grant Program, the National Institutes of Health IDeA Program COBRE grant GM110732, National Science Foundation EPSCoR NSF-IIA-1443108, Hatch Multistate Funding (NC-11873), Project Apis m., the Montana State Beekeepers Association, Montana State University, and the Montana State University Agricultural Experiment Station.


Glenny#, W.,Cavigli#, I., Daughenbaugh, K.F., Radford, R., Kegeley, S., and Flenniken, M.L., Honey bee (Apis mellifera) colony health and pathogen composition in migratory beekeeping operations involved in California almond pollination, (2017), #equal co-authorship, PLoS ONE 12(8): e0182814  doi.org/10.1371/journal.pone.0182814 .  

Doublet, V., Poeschle, Y., Gogol-Doring, Alaux, C., Annoscia, D., Aurori, C., Barribeau, S.M., Bedoya-Reina, O., Brown, M.J.F., Bull, J.C., Flenniken, M.L, Galbraith, D.A., Genersch, E., Gisder, S., Grosse, I., Holt, H.L., Hultmark, D., Lattorff, H.M.G, Le Conte, Y., Manfredini, F., McMahon, D.P., Moritz, R.F.A., Nazzi, F., Niño, E.L., Nowick, K., van Rij, R.P., Paxton, R.J., and Grozinger, C.M., Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens,(2017), BMC Genomics, 18:207 doi:10.1186/s12864-017-3597-6.

Brutscher, L.M., Daughenbaugh, K.D., and Flenniken, M.L., Virus and dsRNA-triggered transcriptional responses reveal key components of honey bee antiviral defense, (2017), Scientific Reports 7 doi:10.1038/s41598-017-06623-z.

Brutscher, L.M., McMenamin A.J., and Flenniken, M.L., The buzz about bee viruses,(2016), PLoS Pathogens 12(8): e1005757. doi:10.1371/journal.ppat.1005757.

McMenamin A.J., Brutscher, L.M., Glenny, W., and Flenniken, M.L., Environmental factors affecting the replication and pathogenicity of bee viruses,(2016), Current Opinion in Insect Science (16):14-21.

Engel P., et al. Flenniken, M.L., Dainat, B., The bee microbiome: impact on bee health and model for evolution and ecology of host-microbe interactions, (2016), mBio 7(2): e02164-15.

Brutscher, L.M. and Flenniken, M.L., RNAi and Antiviral Defense in the Honey Bee (2015), Journal of Immunology Research, Article ID 941897 doi:10.1155/2015/941897.

Cavigli, I., Daughenbaugh, K.F., Martin, M., Lerch, M., Banner, K., Garcia, E., Brutscher, and Flenniken, M.L., Pathogen Prevalence and Abundance in Honey Bee Colonies Involved in Almond Pollination, (2015), Apidologie; doi:10.1007/s13592-015-0395-5).

Daughenbaugh, K.F., Martin, M., Brutscher, L.M., Cavigli, I., Garcia, E., Lavin, M., and Flenniken, M.L., Honey bee infecting Lake Sinai viruses, (2015), Viruses, 7, 3285-3309; doi:10.3390/v7062772.

Brutscher, L.M., Daughenbaugh, K.F., and Flenniken, M.L., Antiviral Defense Mechanisms in Honey Bees (2015), Current Opinion in Insect Science (in press)..

Runckel, C.,DeRisi, J.L., and Flenniken, M.L.  A draft genome of the honey bee trypanosomatid parasite Crithidia mellificae (2014), PLoS ONE 9(4): e95057.

Flenniken, M.L. and Andino R.Non-specific dsRNA -Mediated Innate Immune Response in the Honey Bee (2013), PLoS ONE 8(10): e77263

Runckel*, C., Flenniken*, M.L., Engel, J.C., Ruby, J.G., Ganem, D., Andino, R., and DeRisi, J.L.(2011). Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema and Crithidia, PLoS ONE 6(6):e20656. *Co-first authors contributed equally to this work.Several media outlets including the PBS NewsHour and This Week in Virology featured this work.

Flenniken, M.L., Kunitomi, M., Tassetto, M. and Andino, R. (2010). Insect Antiviral Defense; the Antiviral Role of RNA Interference. In Insect Virology, Asgari, S. and Johnson, K. (eds.), (Norwich, UK: Horizon Scientific Press).

Flenniken, M.L., Young, M.J., and Douglas, T. (2009). A Library of Protein Cage Architectures as Nanomaterials, Current Topics in Microbiology and Immunology, Vol. 327, Viruses and Nanotechnology, edited by M. Manchester and N.F. Steinmetz, Springer-Verlag, Berlin Heidelberg, Germany.

Kaiser, C.R., Flenniken, M.L., Harmsen, A.G., Harmsen, A.L., Jutila, M.A., Douglas, T., Young, M.J. (2007).  Biodistribution studies of protein cage nanoparticles demonstrate broad tissue distribution and rapid clearance in vivo. Intl. J. Nanomedicine, 2 (4), 713-733.

Wiedenheft, B., Flenniken, M.L., Allen, M.A., Young, M., Douglas, T. (2007). Bioprospecting in high temperature environments; application of thermostable protein cages. Soft Matter, 3, 1091-1098.

Uchida, M., Klem, M., Allen, M., Suci, P., Flenniken, M.L., Gillitzer, E., Varpness, Z., Liepold, L., Young, M., Douglas, T.(2007).Biological Containers: Protein Cages as Multifunctional Nanoplatforms. Adv. Mater. 2007, 19, 1025–1042.

Flenniken, M.L., Willits, D.A., Harmsen, A.L., Liepold, L.O., Harmsen, A.G., Young, M.J., and Douglas, T. (2006). Melanoma and Lymphocyte Cell Specific Targeting Incorporated into a Heat Shock Protein Cage Architecture. Chemistry & Biology 13, 161-170.

Uchida, M., Flenniken, M.L., Allen, M., Willits, D.A., Crowley, B., Brumfield, S., Willis, A.F., Jackiw, L., Jutila, M., Young, M.J., Douglas, T. (2006). Targeting of Cancer Cells with Ferrimagnetic Ferritin Cage Nanoparticles.  Journal of the American Chemical Society,128, 16626-16633.

Carlson, J.C.T, Jena, S.J., Flenniken, M.L., Chou, T., Siegel, Wagner, C.R. (2006). Chemically Controlled Self-Assembly of Protein Nanorings. Journal of the American Chemical Society, 128 (23), 7630-7638.

Flenniken, M.L., Liepold, L.O., Crowley, B., Willits, D.A., Young, M.J., and Douglas, T. (2005). Selective attachment and release of a chemotherapeutic agent from the interior of a protein cage architecture. Chemical Communications (Camb.), 447-449.

Granger, B.L., Flenniken, M.L., Davis, D.A., Mitchell, A.P., and Cutler, J.E. (2005). Yeast wall protein 1 of Candida albicans. Microbiology151, 1631-1644.

Flenniken, M., Allen, M., and Douglas, T. (2004). Microbe manufacturers of semiconductors. Chemistry & Biology,11, 1478-1480.

Flenniken, M.L., Allen, M., Douglas, T. (2004). Phage Display Libraries: A Technique for Peptide-Mineral Discovery. Chemtracts-Inorganic Chemistry, 17, 1-11.

Flenniken, M., Allen, M., Young, M., Douglas, T. (2004). Viruses as Host Assemblies. In Encyclopedia of Supramolecular Chemistry, Volume 2, A.J. Steed W, ed. (New York City: Marcel Dekker, Inc.), 1563-1568.

Flenniken, M.L., Willits, D.A., Brumfield S., Young, M.J., Douglas, T. (2003). The Small Heat Shock Protein Cage from Methanococcus jannaschii Is a Versatile Nanoscale Platform for Genetic and Chemical Modification. NanoLetters, 3, 1573-1576.

Graff, J.W., Mitzel, D.N., Weisend, C.M., Flenniken, M.L., and Hardy, M.E. (2002). Interferon regulatory factor 3 is a cellular partner of rotavirus NSP1. Journal of Virology 76, 9545-9550.