Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711
Shoemaker, W.R., M.E. Muscarella, & J.T. Lennon. Genome Sequence of the Soil Bacterium Jantinobacterium sp. KBS0711. Genome Announcements 3, e00689-15 (2015).
Posts by Collection
publications
Horizontal and Pseudo-environmental Transmission of the Antifungal Probiotic Bacterium Janthinobacterium lividum on Green Frog (Lithobates clamitans) Tadpoles
Rebollar, E.A., S.J. Simonetti, W.R. Shoemaker, & R.N Harris. Horizontal and Pseudo-environmental Transmission of the Antifungal Probiotic Bacterium Janthinobacterium lividum on Green Frog (Lithobates clamitans) Tadpoles. Applied and Environmental Microbiology 82, 2457-2466 (2016).
A macroecological theory of microbial biodiversity
Shoemaker, W.R.*, K.J. Locey*, & J.T. Lennon. A macroecological theory of microbial biodiversity. Nature Ecology and Evolution 1, 0107 (2017).
Whole genome sequence of the soil bacterium Micrococcus
Kuo, V., W.R Shoemaker, M.E. Muscarella, & J.T. Lennon. Whole genome sequence of the soil bacterium Micrococcus* sp. KBS0714. Genome Announcements 5, e00697-17 (2017).
Evolution with a seed bank: the population genetic consequences of microbial dormancy
Shoemaker, W.R., & J.T. Lennon. Evolution with a seed bank: the population genetic consequences of microbial dormancy. Evolutionary Applications 11, 60–75 (2018).
Evolutionary determinants of genome-wide nucleotide composition
Long, H., W. Sung, S. Kucukyildirim, E. Williams, S. Miller, W. Guo, C. Patterson, C. Gregory, C. Strauss, C. Stone, C. Berne, D. Kysela, W.R. Shoemaker, M. Muscarella, H. Luo, J.T. Lennon, Y.V. Brun, & M. Lynch Evolutionary determinants of genome-wide nucleotide composition. Nature Ecology and Evolution 2, 237-240 (2018).
Microbial population dynamics and evolutionary outcomes under extreme energy-limitation
Shoemaker, W.R., S.E. Jones, M.E. Muscarella, M.G. Behringer, B.K. Lehmkuhl, and J.T. Lennon. Microbial population dynamics and evolutionary outcomes under extreme energy-limitation. Proceedings of the National Academy of Sciences of the United States of America 118, 33 (2021).
Molecular evolutionary dynamics of energy-limited microorganisms
Shoemaker, W.R., E. Polezhaeva, K.B. Givens, & J.T. Lennon. Molecular evolutionary dynamics of energy-limited microorganisms. Molecular Biology and Evolution 38, 4532–45 (2021).
Comparative Population Genetics in the Human Gut Microbiome
Shoemaker, W.R., D. Chen, and N.R. Garud. Comparative Population Genetics in the Human Gut Microbiome. Genome Biology and Evolution 14, evab116 (2022).
An experimental test of disease resistance function in the skin-associated bacterial symbiont communities of three tropical amphibian species
Hughey, M.C., E.A. Rebollar, R.N. Harris, R. Ibáñez, S.C. Loftus, L.L. House, M.C. Bletz, D. Medina, M.K. Riley, W.R. Shoemaker, M.C. Swartwout, and L.K. Belden. An experimental test of disease resistance function in the skin-associated bacterial symbiont communities of three tropical amphibian species. FEMS Microbiology Ecology 98, fiac023 (2022).
Predicting Parallelism and Quantifying Divergence in Microbial Evolution Experiments
Shoemaker, W.R. & J.T. Lennon. Predicting Parallelism and Quantifying Divergence in Microbial Evolution Experiments. mSphere. e00672-21 (2022).
Seed Banks Alter the Rate and Direction of Molecular Evolution in Bacillus subtilis
Shoemaker, W.R., E. Polezhaeva, K.B. Givens, and J.T. Lennon. Seed Banks Alter the Rate and Direction of Molecular Evolution in Bacillus subtilis. Genetics iyac071 (2022).
Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome
Wolff, R., W.R. Shoemaker, and N.R. Garud. Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome. mBio e02502-22 (2023).
Bacteria-phage coevolution with a seed bank
Schwartz, D.A., W.R. Shoemaker, Magalie, A., Weitz, J., and J.T. Lennon. Bacteria-phage coevolution with a seed bank. ISME J. 17, 1315–25 (2023).
A macroecological perspective on genetic diversity in the human gut microbiome
Shoemaker, W.R. A macroecological perspective on genetic diversity in the human gut microbiome. Plos One 18, 7 (2023).
Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth
Shoemaker, William R., and Jacopo Grilli. Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth. eLife 12 (2024): RP89650.
Eco-evolutionary dynamics: The repeatability of diversification in an experimental microbial community
Shoemaker, William R. Eco-evolutionary dynamics: The repeatability of diversification in an experimental microbial community. Current Biology34.4 (2024): R140-R143.
Macroecological patterns in experimental microbial communities
Shoemaker, William R., Álvaro Sánchez, and Jacopo Grilli."Macroecological patterns in experimental microbial communities. PLOS Computational Biology 21.5 (2025): e1013044.
Macroecological patterns in experimental microbial communities
Shoemaker, William R., and Jacopo Grilli. "The macroecological dynamics of sojourn trajectories in the human gut microbiome." bioRxiv (2025): 2025-06.
Longitudinal dynamics of ethanol-resistant microbes and sporulation in the human gut
Miklavcic, Ursa, Aleksander Mahnic, William R. Shoemaker, Jacopo Grilli, Sandra Janezic, and Maja Rupnik. "Longitudinal dynamics of ethanol-resistant microbes and sporulation in the human gut." bioRxiv (2025): 2025-07.
Evolutionary bioenergetics of sporulation
Karakoç, Canan, William R. Shoemaker, and Jay T. Lennon. Evolutionary bioenergetics of sporulation. bioRxiv (2025): 2025-08.