Kerwin, A. H., McAnulty, S. J., Nyholm, S. V. (2021) Development of the Accessory Nidamental Gland and Associated Bacterial Community in the Hawaiian Bobtail Squid, Euprymna scolopes. Biological Bulletin

Nyholm, S. V. (2020) In the beginning: egg–microbe interactions and consequences for animal hosts. Phil. Trans. R. Soc

Kerwin, A. H., Gromek, S. M., Suria, A. M., Samples, R. M., Deoss, D. J., O’Donnell, K., Frasca Jr., S., Sutton, D. A. Wiederhold, N. P., Balunas, M. J., Nyholm, S. V. (2019) Shielding the Next Generation: Symbtiontic Bacteria from a Reproductive Organ Protective Bobtail Squid Eggs from Fungal Fouling. mBio

Lynch, J. B., Schwartzman, J. A., Bennett, B. D., McAnulty, S. J., Knop, M. Nyholm, S. V., Ruby, E. G. (2019) Ambient pH Alters the Protein Content of Outer Membrane Vesicles, Driving Host Development in a Beneficial Symbiosis. Journal of Bacteriology 

Baker, L. J., Freed, L. L., Easson, C. G., Lopez, J. V., Fenolio, D., Sutton, T. T., Nyholm, S. V., Hendry, T. A. (2019) Diverse deep-sea anglerfishes share a geneticall reduced luminous symbtion that is acquired from the environment. eLife

Rader, B., McAnulty S. J., Nyholm, S. V. (2019) Persistent symbiont colonization leads to a maturation of hemocyte response in the Euprymna sclolopes / Vibrio fischeri symbiosis. Microbiology Open

Belcaid, M., Casaburi, C., McAnulty M. J., Schmidbaur, H., Suria, A. M., Moriano-Gutierrez, S., Pankey, M. S., Oakley, T. H., Kremer, N., Koch, E.J., Collins, A. J., Nguyen, H., Lek, S., Goncharenko-Foster, I., Minx, P., Sodergren, E., Weinstock, G., Rokhsar, D., McFall-Ngai, M., Simakov, O., Foster, J. S., Nyholm, S. V. (2019) Symbiotic organs shaped by distinct modes of genome evolution in cephalopods. PNAS

Kerwin, A. H., Nyholm S.V. (2018). Reproductive System Symbiotic Bacteria Are Conserved between Two Distinct Populations of Euprymna scolopes from Oahu, Hawaii. mSphere

Kerwin, A. H., Nyholm S. V., (2017). Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and in eggs throughout development. Environmental microbiology

McAnulty, S. J., Nyholm, S. V., (2017) The Role of Hemocytes in the Hawaiian Bobtail squid, Euprymna scolopes: A Model Organism for Studying Beneficial Host-Microbe Interactions. Front. Microbiol.

Gromek, S. M., Suria A. M., Fullmer M.S., Garcia, J.L., Gogarten, J.P., Nyholm S. V., Balunas, M.J. (2016). Leisingera sp. JC1, a Bacterial isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios. Front. Microbiol.

Collins, A. J., Fullmer S. M. , Gogarten, J. P., Nyholm, S. V. Comparative genomics of Roseobacter clase bacteria isolated from the accessory nidamental gland of Euprymna scolopes. Frontiers Microbiology. 6:123.

Schleicher, T. R., VerBerkmoes, N. C., Shah, M., & Nyholm, S. V. (2014). Colonization state influences the hemocyte proteome in a beneficial squid-vibrio symbiosis. Molecular & Cellular Proteomics : MCP, 1–46.

Beinart, R. A., Nyholm, S. V, Dubilier, N., & Girguis, P. R. (2014). Intracellular Oceanospirillales inhabit the gills of the hydrothermal vent snail Alviniconcha with chemosynthetic , γ -Proteobacterial symbionts. doi:10.1111/1758-2229.12183

Albertin, C. B., Bonnaud, L., Brown, C. T., Crookes-Goodson, W. J., da Fonseca, R. R., Di Cristo, C., … Ragsdale, C. W. (2012). Cephalopod genomics: A plan of strategies and organization. Standards in Genomic Sciences, 7(1), 175–88. doi:10.4056/sigs.3136559

Rader, B. A., & Nyholm, S. V. (2012). Host/microbe interactions revealed through “omics” in the symbiosis between the Hawaiian bobtail squid Euprymna scolopes and the bioluminescent bacterium Vibrio fischeri. The Biological Bulletin, 223(1), 103–11. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/22983036

Nyholm, S. V, & Graf, J. (2012). Knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses. Nature Reviews. Microbiology, 10(12), 815–27. doi:10.1038/nrmicro2894

Nyholm, S. V, Song, P., Dang, J., Bunce, C., & Girguis, P. R. (2012). Expression and putative function of innate immunity genes under in situ conditions in the symbiotic hydrothermal vent tubeworm Ridgeia piscesae. PloS One, 7(6), e38267. doi:10.1371/journal.pone.0038267

Collins, A. J., LaBarre, B. a, Won, B. S. W., Shah, M. V, Heng, S., Choudhury, M. H., Nyholm, S. V. (2012). Diversity and partitioning of bacterial populations within the accessory nidamental gland of the squid Euprymna scolopes. Applied and Environmental Microbiology, 78(12), 4200–8. doi:10.1128/AEM.07437-11

Fidopiastis, P. M., Rader, B. a, Gerling, D. G., Gutierrez, N. a, Watkins, K. H., Frey, M. W., S.V. Nyholm Whistler, C. a. (2012). Characterization of a Vibrio fischeri aminopeptidase and evidence for its influence on an early stage of squid colonization. Journal of Bacteriology, 194(15), 3995–4002. doi:10.1128/JB.00108-12

Collins, A. J., Schleicher, T. R., Rader, B. a, & Nyholm, S. V. (2012). Understanding the role of host hemocytes in a squid/vibrio symbiosis using transcriptomics and proteomics. Frontiers in Immunology, 3(May), 91. doi:10.3389/fimmu.2012.00091

Collins AJ, Nyholm SV (2011) Draft genome of Phaeobacter gallaeciensis ANG1; a dominant member of the accessory nidamental gland of Euprymna scolopes. J. Bacteriol. 193:3397-3398.

Schleicher, T. R., & Nyholm, S. V. (2011). Characterizing the host and symbiont proteomes in the association between the Bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri. PloS One, 6(10), e25649. doi:10.1371/journal.pone.0025649

Collins AJ, Nyholm SV (2010) Obtaining Hemocytes from the Hawaiian Bobtail Squid Euprymna scolopes and Observing their Adherence to Symbiotic and Non-Symbiotic Bacteria.JoVE. 36. http://www.jove.com/index/details.stp?id=1714, doi: 10.3791/1714

Wier AM, Nyholm SV, Mandel MJ, Massengo-Tiassé RP, Schaefer AL, Koroleva I, Splinter-Bondurant S, Brown B, Manzella L, Snir E, Almabrazi H, Scheetz TE, Bonaldo Mde F,Casavant TL, Soares MB, Cronan JE, Reed JL, Ruby EG, McFall-Ngai MJ. (2010) Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis. Proc. Nat. Acad. Sci., USA, 107, 2259-64

McFall-Ngai MJ, Nyholm SV, Castillo MG (2009) The role of the immune system in the initiation and persistence of the Euprymna scolopes-Vibrio fischeri symbiosis. Semin.Immunol. 22: 48-53.

Nyholm SV, Stewart JJ, Ruby EG, McFall-Ngai MJ (2009) Recognition between symbiotic Vibrio fischeri and the haemocytes of Euprymna scolopes. Environ. Microbiol. 11:483-93.

Nyholm, SV (2009) Peptidoglycan monomer release and Vibrio fischeri. J. Bacteriol. 191:1997-1999.

Nyholm SV, Nishiguchi MK (2008) The evolutionary ecology of a sepiolid squid-Vibrio association: from cell to environment. Vie et Milieu 58: 175-184.

Spencer V. Nyholm, Julie Robidart and Peter R. Girguis. 2008. Coupling metabolite flux to transcriptomics: insights into the molecular mechanisms underlying primary productivity by the hydrothermal vent tubeworm Ridgeia piscesae. Biol. Bull. 214: 255-265. Symbiosis

Nyholm, S.V. and M. J. McFall-Ngai. 2004. The Winnowing: Establishing the Squid-Vibrio Symbiosis. Nature Rev. Microbiol. 2: 632-642.

Nyholm, S. V. and M. J. McFall-Ngai. 2003. Dominance of Vibrio fischeri in secreted mucus outside the light organ of Euprymna scolopes: the first site of symbiont specificity. Appl. Environ. Microbiol. 69: 3932-7.

Nyholm, S. V., B. Deplancke, H. R. Gaskins, M. A. Apicella, and M. J. McFall-Ngai. 2002. Roles of nonsymbiotic and symbiotic bacteria in the dynamics of mucus secretion during symbiont colonization of the Euprymna scolopes light organ. Appl. Environ. Microbiol. 68:5113-5122.

Nyholm, S. V., E. V. Stabb, E. G. Ruby, and M. J. McFall-Ngai. 2000 Establishment of an animal-bacterial association: recruiting symbiotic vibrios from the environment. Proc. Nat. Acad. Sci., USA 97:10231-10235.

Nyholm, S. V. and M. J. McFall-Ngai. 1998. Sampling the light-organ microenvironment of Euprymna scolopes: description of a population of host cells in association with the bacterial symbiont Vibrio fischeri. Biol. Bull. 195: 89-97.