Publications

2026

• An Interpretation, Survey, and Outlook on Microbial Macroecology

  Shoemaker, W.R.

  Environmental Microbiology, 28(6):e70314

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• The macroecological dynamics of sojourn trajectories in the human gut microbiome

  Shoemaker, W.R., and J. Grilli

  mSystems, 11(3):e01221-25

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• Leveraging DNA and RNA oscillatory dynamics to investigate the ecology and physiology of a freshwater microbial community

  Shoemaker, W.R., M. Dal Bello, and J. Grilli

  bioRxiv, 2026.02.24.707719

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• Evolutionary bioenergetics of sporulation

  Karakoç, C., W.R. Shoemaker, and J.T. Lennon

  Proceedings of the National Academy of Sciences, 123(6):e2524274123

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2025

• A balance between environmental filtering and competitive exclusion modulates the macroecology of alternative stable states in microbial communities

  Bupu, A., W.R. Shoemaker, O. Mazzarisi, and J. Grilli

  bioRxiv, 2025.12.19.695337

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• Longitudinal dynamics of ethanol-resistant microbes and sporulation in the human gut

  Miklavcic, U., A. Mahnic, W.R. Shoemaker, J. Grilli, S. Janezic, and M. Rupnik

  bioRxiv, 2025.07.08.663423

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• Macroecological patterns in experimental microbial communities

  Shoemaker, W.R., Á. Sánchez, and J. Grilli

  PLOS Computational Biology, 21(5):e1013044

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2024

• Eco-evolutionary dynamics: The repeatability of diversification in an experimental microbial community

  Shoemaker, W.R.

  Current Biology, 34(4):R140–R143

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• Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth

  Shoemaker, W.R., and J. Grilli

  eLife, 12:RP89650

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2023

• A macroecological perspective on genetic diversity in the human gut microbiome

  Shoemaker, W.R.

  PLOS ONE, 18(7):e0288926

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• Bacteria-phage coevolution with a seed bank

  Schwartz, D.A., W.R. Shoemaker, A. Măgălie, J.S. Weitz, and J.T. Lennon

  The ISME Journal, 17(8):1315–1325

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• Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome

  Wolff, R., W.R. Shoemaker, and N.R. Garud

  mBio, 14(2):e02502-22

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2022

• Seed banks alter the molecular evolutionary dynamics of Bacillus subtilis

  Shoemaker, W.R., E. Polezhaeva, K.B. Givens, and J.T. Lennon

  Genetics, 221(2):iyac071

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• Predicting Parallelism and Quantifying Divergence in Microbial Evolution Experiments

  Shoemaker, W.R., and J.T. Lennon

  mSphere, 7(1):e00672-21

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• Comparative Population Genetics in the Human Gut Microbiome

  Shoemaker, W.R., D. Chen, and N.R. Garud

  Genome Biology and Evolution, 14(1):evab116

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• An experimental test of disease resistance function in the skin-associated bacterial 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

  FEMS Microbiology Ecology, 98(3):fiac023

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2021

• Molecular Evolutionary Dynamics of Energy Limited Microorganisms

  Shoemaker, W.R., E. Polezhaeva, K.B. Givens, and J.T. Lennon

  Molecular Biology and Evolution, 38(10):4532–4545

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• 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

  Proceedings of the National Academy of Sciences, 118(33):e2101691118

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2018

• Evolutionary determinants of genome-wide nucleotide composition

  Long, H., W. Sung, S. Kucukyildirim, E. Williams, S.F. Miller, W. Guo, C. Patterson, C. Gregory, C. Strauss, C. Stone, C. Berne, D. Kysela, W.R. Shoemaker, M.E. Muscarella, H. Luo, J.T. Lennon, Y.V. Brun, and M. Lynch

  Nature Ecology & Evolution, 2(2):237–240

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• Evolution with a seed bank: The population genetic consequences of microbial dormancy

  Shoemaker, W.R., and J.T. Lennon

  Evolutionary Applications, 11(1):60–75

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2017

• A macroecological theory of microbial biodiversity

  Shoemaker, W.R.*, K.J. Locey*, and J.T. Lennon  *equal contribution

  Nature Ecology & Evolution, 1(5):0107

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• Whole-Genome Sequence of the Soil Bacterium Micrococcus sp. KBS0714

  Kuo, V., W.R. Shoemaker, M.E. Muscarella, and J.T. Lennon

  Genome Announcements, 5(32):e00697-17

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2016 & earlier

• Direct and Indirect Horizontal Transmission of the Antifungal Probiotic Bacterium Janthinobacterium lividum on Green Frog (Lithobates clamitans) Tadpoles

  Rebollar, E.A., S.J. Simonetti, W.R. Shoemaker, and R.N. Harris

  Applied and Environmental Microbiology, 82(8):2457–2466 (2016)

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• Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711

  Shoemaker, W.R., M.E. Muscarella, and J.T. Lennon

  Genome Announcements, 3(3):e00689-15 (2015)

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