Microbial Ecology and Evolution

Microbial communities form the foundation of our planetary life support system. We study how bacterial populations coalesce to form complex ecological communities in dynamic environments. We are particularly interested in how these evolving communities maintain stability and functional resilience in the face of environmental fluctuations. We focus on microbial communities residing in the mammalian gut. These gut microbes provide crucial services to their hosts. Loss of key bacterial diversity, changes in community structure, and undesirable evolutionary trajectories can result in disease states.

Selected Publications

  • Poyet, M., Groussin, M., Gibbons, S.M., Avila-Pacheco, J., Jiang, X., Kearney, S.M., Perrotta, A.R., Berdy, B., Zhao, S., Lieberman, T., Swanson, P.K., Smith, M., Roesemann, S., Alexander, J.E., Rich, S.A., Livny, J., Vlamakis, H., Clish, C., Bullock, K., Deik, A., Scott, J., Pierce, K.A., Xavier, R., and Alm, E.J. 2019. A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research. Nature Medicinehttps://doi.org/10.1038/s41591-019-0559-3
  • Zhao, S., Lieberman, T.D., Poyet, M., Groussin, M., Gibbons, S.M., Xavier, R.J., Alm, E.J. 2019. Adaptive evolution within gut microbiomes of healthy people. Cell Host & Microbe. https://doi.org/10.1016/j.chom.2019.03.007
  • Kearney, S.M., Gibbons, S.M., Erdman, S., Alm, E.J. 2018. Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal. Cell Reports, https://doi.org/10.1016/j.celrep.2018.07.032
  • Kearney, S.M., Gibbons, S.M., Poyet, M., Gurry, T., Bullock, K., Allegretti, J.R., Clish, C.B., Alm, E.J. 2018. Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota. ISME Journal, https://doi.org/10.1038/s41396-018-0192-z
  • Gibbons, S.M., Kearney, S.M., Smillie, C.S., and Alm, E.J. 2017. Two dynamic regimes in the human gut microbiome. PloS Computational Biology, http://dx.doi.org/10.1371/journal.pcbi.1005364
  • Gibbons, S.M., Scholz, M., Hutchison, A.L., Dinner, A.R., Gilbert, J.A., and Coleman, M.L. 2016. Disturbance regimes predictably alter diversity in an ecologically complex bacterial system. mBio 7(6):e01372-16. doi:10.1128/mBio.01372-16
  • Leone, V., Gibbons, S.M., Martinez, K., Hutchison, A.L., Huang, E.Y., Cham, C.M., Pierre, J.F., Heneghan, A.F., Nadimpalli, A., Hubert, N. and Zale, E. 2015. Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Cell Host & Microbe, 17(5), pp.681-689
  • Gibbons, S.M., Schwartz, T., Fouquier, J., Mitchell, M., Sangwan, N., Gilbert, J.A. and Kelley, S.T. 2015. Ecological succession and viability of human-associated microbiota on restroom surfaces. Applied and Environmental Microbiology, 81(2), pp.765-773
  • Lax, S., Smith, D.P., Hampton-Marcell, J., Owens, S.M., Handley, K.M., Scott, N.M., Gibbons, S.M., Larsen, P., Shogan, B.D., Weiss, S. and Metcalf, J.L., 2014. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science, 345(6200), pp.1048-1052
  • Gibbons, S.M., Caporaso, J.G., Pirrung, M., Field, D., Knight, R. and Gilbert, J.A. 2013. Evidence for a persistent microbial seed bank throughout the global ocean. Proceedings of the National Academy of Sciences USA, 110(12), pp.4651-4655

Selected Preprints

  • Diener, C., Hoge, A.C.H., Kearney, S.M., Erdman, S.E., Gibbons, S.M. 2019. Non-responder phenotype reveals microbiome-wide antibiotic resistance in the murine gut. in review

Featured Projects

  • Microbiome Stress Project

    We have joined researchers at Duke University, the University of New Hampshire, and Montana State University to conduct a large-scale meta-analysis of how environmental stressors impact microbial communities. Prior surveys, like the Earth and Human Microbiome Projects, have established a baseline for healthy ecosystems across the planet. The Microbiome Stress Project will focus on ecological resistance and resilience of natural microbial communities to disturbances. The meta-analysis encompasses hundreds of studies…

  • The Macaque Microbiome

    The Gibbons Lab has established a collaboration with Dr. Adam Ericson at Emory University and the Yerkes National Primate Research Center to study how the macaque microbiome develops from birth to adulthood. We will track hundreds of animals from the first few days of life into adulthood. This is an exciting opportunity to watch how individual microbiomes develop and establish across many individuals over time. We will have two main…