Publications

Below is a list of publications from research supported by GEMS. You can also view these publications on our Google Scholar page.

GEMS Institute profile on Google Scholar

2025

  • Ganote et al., 2025

    Ganote, C., Caesar, L., Rice, D. W., Whitaker, R. J., & Newton, I. L. G. (2025). Evolutionary trends in Bombella apis CRISPR-Cas systems. bioRxiv.

    https://doi.org/10.1101/2025.02.05.636693

  • Hughes et al., 2025

    Hughes, A. G., Cullum, J. E., Fredericks, M. J., Wilson, P. J., Schwarzenberger, A., & Cáceres, C. E. (2025). Influence of melatonin on the successful infection of Daphnia dentifera by Metschnikowia bicuspidata. Ecosphere, 16 (2), e70192.

    https://doi.org/10.1002/ecs2.70192

  • Li et al., 2025

    Li, S., Laderman, E., Markle, H., Yang, Y., Bergelson, J., & Pascual, M. (2025). Negative frequency-dependent selection contributes to modular structure of effector repertoires in Pseudomonas syringae. bioRxiv.

    https://doi.org/10.1101/2025.01.16.632277

  • Payne et al., 2025

    Payne, A.N., Prayugo, V., & Dolezal, A. G. (2025). A honey bee-associated virus remains infectious and quantifiable in postmortem hosts. Journal of Invertebrate Pathology, 209, 108258.

    https://doi.org/10.1016/j.jip.2024.108258

  • Robinson et al., 2025

    Robinson, C. R. P., Dolezal, A. G., Liachko, I., & Newton, I. L. G. (2025). Mobile genetic elements exhibit associated patterns of host range variation and sequence diversity within the gut microbiome of the European honey bee. bioRxiv.

    https://doi.org/10.1101/2025.01.31.635958

  • Sanath-Kumar et al, 2025

    Sanath-Kumar, R., Rahman, A., Ren, Z., Reynolds, I. P., Augusta, L., Fuqua, C., Weisberg, A. J., & Wang, X. (2025). Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion. bioRxiv.

    https://doi.org/10.1101/2025.02.23.639760

  • Schakel et al., 2025

    Schakel, O. F., Fritts, R. K., Zmuda, A. J., Setayeshgar, S., & McKinlay, J. B. (2025). Microbial cross-feeding is stabilized when a dependent mutant is segregated from its independent ancestor. bioRxiv.

    https://doi.org/10.1101/2025.01.23.634601

2024

  • Baglivo et al., 2024

    Baglivo, I., Malgieri, G., Roop, R. M. 2nd, Barton, I. S., Wang, X., Russo, V., Pirone, L., Pedone, E. M., & Pedone, P. V. (2024). MucR protein: Three decades of studies have led to the identification of a new H-NS-like protein. Molecular Microbiology, 00, 1-14.

    https://doi.org/10.1111/mmi.15261

  • Basu et al., 2024

    Basu, A., Adams, A. N. D., Degnan, P. H., & Vanderpool, C. K. (2024). Determinants of raffinose family oligosaccharide use in Bacteroides species. Journal of Bacteriology, 206 (10), e0023524.

    https://doi.org/10.1128/jb.00235-24

  • Boehm Vock et al., 2024

    Boehm Vock, L. F., Mossman, L. M., Rapti, Z., Dolezal, A. G., & Clifton, S. M. (2024). Spatiotemporal, environmental, and behavioral predictors of Varroa mite intensity in managed honey bee apiaries. bioRxiv.

    https://doi.org/10.1101/2024.09.23.614412

  • Caesar et al., 2024

    Caesar, L., Rice, D. W., McAfee, A., Underwood, R., Ganote, C., Tarpy, D. R., Foster, L. J., & Newton, I. R. L. (2024). Metagenomic analysis of the honey bee queen microbiome reveals low bacterial diversity and Caudoviricetes phage. mSystems, 9:e01182-23.

    https://doi.org/10.1128/msystems.01182-23

  • Farley et al., 2024

    Farley, K. R., Buechler, A. K., Bianco, C. M., & Vanderpool, C. K. (2024). Small RNAs positively and negatively control transcription elongation through modulation of Rho utilization site accessibility. bioRxiv.

    https://doi.org/10.1101/2024.02.02.578684

  • Kosmopoulos et al., 2024

    Kosmopoulos, J. C., Batsone-Doyle, R. T., & Heath, K. D. (2024). Co-inoculation with novel nodule-inhabiting bacteria reduces the benefits of legume-rhizobium symbiosis. Canadian Journal of Microbiology, 70, 275-288.

    https://doi.org/10.1139/cjm-2023-0209

  • Liaghat et al., 2024

    Liaghat, A., Yang, J., Whitaker, R., & Pascual, M. (2024). Punctuated virus-driven succession generates dynamical alternations in CRISPR-mediated microbe-virus coevolution. Journal of The Royal Society Interface, 21(217), 20240195.

    https://doi.org/10.1098/rsif.2024.0195

  • Mishra et al., 2024

    Mishra, A., Hughes, A. C.. Amon, J. D., Rudner, D. Z., Wang, X., & Kearns, D. B. (2024). SwrA-mediated multimerization of DegU and an upstream activation sequence enhance flagellar gene expression in Bacillus subtilis. Journal of Molecular Biology, 436 (4), 168419.

    https://doi.org/10.1016/j.jmb.2023.168419

  • Robinson et al., 2024

    Robinson, C. R. P., Dolezal, A. G., & Newton, I. L. G. (2024). Host species and geography impact bee-associated RNA virus communities with evidence for isolation by distance in viral populations. ISME Communications, 4(1), 1-14.

    https://doi.org/10.1093/ismeco/ycad003

  • St. Clair et al., 2024

    St. Clair, A. L., Dwyer, B., Shapiro, M., & Dolezal, A. G. (2024). Adult honey bee queens consume pollen and nectar. bioRxiv.

    https://doi.org/10.1101/2024.12.04.626851

  • Suttenfield et al., 2024

    Suttenfield, L. C., Rapti, Z., Chandrashekhar, J. H., Steinlein, A. C., Vera, J. C., Kim, T., & Whitaker, R. J. (2024). Phage-mediated resolution of genetic conflict alters the evolutionary trajectory of Pseudomonas aeruginosa lysogens. mSystems, 9:e00801-24.

    https://doi.org/10.1128/msystems.00801-24

  • Vereau Gorbitz et al., 2024

    Vereau Gorbitz, D., Schwarz, C., McMullen, J. G., Cerón-Romero, M., Doyle, R. T., Lau, J. A., Whitaker, R. J., Vanderpool, C. K., & Heath, K. (2024). Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum. bioRxiv.

    https://doi.org/10.1101/2024.10.17.618979

2023

  • Barton et al., 2023

    Barton, I. S., Ren, Z., Cribb, C. B., Pitzer, P. E., Baglivo, I., Martin, D. W., Wang, X., & Roop, R. M. (2023). Brucella MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid. mBio, 14(6), Article e02201-23.

    https://doi.org/10.1128/mbio.02201-23

  • Cáceres & Stewart Merrill, 2023

    Cáceres, C. E., & Stewart Merrill, T. E. (2023). The role of varying resources on Daphnia dentifera immune responses. Fundamental and Applied Limnology, 196(3-4), 217-228.

    https://doi.org/10.1127/fal/2022/1458

  • Collins & Whitaker, 2023

    Collins, A. J., & Whitaker, R. J. (2023). CRISPR Comparison Toolkit: Rapid identification, visualization, and analysis of CRISPR array diversity. The CRISPR Journal, 6(4), 386–400.

    https://doi.org/10.1089/crispr.2022.0080

  • Fishman et al., 2023

    Fishman, F. J., & Lennon, J. T. (2023). Macroevolutionary constraints on global microbial diversity. Ecology and Evolution, 13(8), e10403.

    https://doi.org/10.1002/ece3.10403

  • Măgălie et al., 2023

    Măgălie, A., Schwartz, D. A., Lennon, J. T., & Weitz, J. S. (2023). Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching. Journal of Theoretical Biology, 561, Article 111413.

    https://doi.org/10.1016/j.jtbi.2023.111413

  • Ren et al., 2023

    Ren, Z., Takacs, C. N., Brandão, H. B., Jacobs-Wagner, C., & Wang, X. (2023). Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi. PLoS Genetics, 19(7), Article e1010857.

    https://doi.org/10.1371/journal.pgen.1010857

  • Ricks & Yannarell, 2023

    Ricks, K. D., & Yannarell, A. C. (2023). Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response. Proceedings of the Royal Society B: Biological Sciences, 290(2001).

    https://doi.org/10.1098/rspb.2023.0469

  • Ricks et al., 2023

    Ricks, K. D., Ricks, N. J., & Yannarell, A. C. (2023). Patterns of plant salinity adaptation depend on interactions with soil microbes. The American Naturalist, 202(3), 276-287.

    https://doi.org/10.1086/725393

  • Schwartz et al., 2023

    Schwartz, D. A., Rodríguez-Ramos, J. A., Shaffer, M., Flynn, R. M., Daly, R. A., Wrighton, K. C., & Lennon, J. T. (2023). Human-gut phages harbor sporulation genes. mBio, 14(3).

    https://doi.org/10.1128/mbio.00182-23

  • Terrill Sondag et al., 2023

    Terrill Sondag, E. E., Stuart Merrill, T. E., Drnevich, J., Holmes, J. R., Fischer, E. K., Cáceres, C. E., & Strickland, L. R. (2023). Differential gene expression in response to fungal pathogen exposure in the aquatic invertebrate, Daphnia dentifera. Ecology and Evolution, 13(8).

    https://doi.org/10.1002/ece3.10354

  • Wisnoski & Lennon, 2023

    Wisnoski, N. I., & Lennon, J. T. (2023). Scaling up and down: Movement ecology for microorganisms. Trends in Microbiology, 31(3), 242-253.

    https://doi.org/10.1016/j.tim.2022.09.016

2022

  • Bolin et al., 2022

    Bolin, L. G., Lennon, J. T., & Lau, J. A. (2022). Traits of soil bacteria predict plant responses to soil moisture. Ecology, 104(2).

    https://doi.org/10.1002/ecy.3893

  • Halloway et al., 2022

    Halloway, A. H., Heath, K. D., & McNickle, G. G. (2022). When does mutualism offer a competitive advantage? A game-theoretic analysis of host–host competition in mutualism. AoB Plants, 14(2), 1-9.

    https://doi.org/10.1093/aobpla/plac010

  • Heath et al., 2022

    Heath, K. D., Batstone, R. T., Cerón Romero, M., & McMullen, J. G. (2022). MGEs as the MVPs of partner quality variation in legume-Rhizobium symbiosis. mBio, 13(4).

    https://doi.org/10.1128/mbio.00888-22

  • Massey & Newton, 2022

    Massey, J. H., & Newton, I. L. G. (2022). Diversity and function of arthropod endosymbiont toxins. Trends in Microbiology, 30(2), 185–198.

    https://doi.org/10.1016/j.tim.2021.06.008

  • McMullen & Lennon, 2022

    McMullen, II, J. G., & Lennon, J. T. (2022). Mark‐recapture of microorganisms. Environmental Microbiology, 25(1), 150-157.

    https://doi.org/10.1111/1462-2920.16267

  • Parish et al., 2022

    Parish, A. J., Rice, D. W., Tanquary, V. M., Tennessen, J. M., & Newton, I. L. G. (2022). Honey bee symbiont buffers larvae against nutritional stress and supplements lysine. ISME Journal, 16(9), 2160–2168.

    https://doi.org/10.1038/s41396-022-01268-x

  • Schwartz et al., 2022

    Schwartz, D. A., Lehmkuhl, B. K., & Lennon, J. T. (2022). Phage-encoded sigma factors alter bacterial dormancy. mSphere, 7(4).

    https://doi.org/10.1128/msphere.00297-22