Publications, preprints, and commentaries

Evolutionary bioenergetics of sporulation

Karakoç, Canan, William R. Shoemaker, and Jay T. Lennon. Evolutionary bioenergetics of sporulation. bioRxiv (2025): 2025-08.

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.

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.

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.

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.

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.

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).

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).

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).

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).

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).

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).

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).

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).

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).

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).

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).

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).

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).

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).

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).

^* Equal authorship