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

  • Levy, R., Magis, A.T., Earls, J.C., Manor, O., Wilmanski, T., Lovejoy, J., Gibbons, S.M., Omenn, G.S., Hood, L., Price, N.D. 2020. Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome. Proceedings of the National Academy of Sciences USA, https://doi.org/10.1073/pnas.1922498117
  • 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. bioRxiv, in review, https://www.biorxiv.org/content/10.1101/566190v1
  • Groussin, M., Poyet, M,. Sistiaga, A., Kearney, S.M., Moniz, K., Noel, M., Hooker, J., Gibbons, S.M., Segurel, L., Froment, A., Mohamed, R.S., Fezeu, A., Juimo, V.A., Girard, C., Nguyen, L.T.T., Shapiro, B.J., Lehtimäki, J.M.S., Ruokolainen, L., Kettunen, P.P., Vatanen, T., Sigwazi, S., Mabulla, A., Domínguez-Rodrigo, M., Summons, R.E., Xavier, R.J., and Alm, E.J. 2020. Industrialization is associated with elevated rates of horizontal gene transfer in the human microbiome. bioRxiv, in review, https://doi.org/10.1101/2020.01.28.922104

Featured Projects

  • Near-Causal Inference in Multi-omic Data

    Many diseases are associated with changes of the microbial composition in our gut. However, we are just beginning to understand the relationships between the bacteria living in our intestinal system and the physiology and health of our bodies. One of the particular challenges we face is determining the causal direction for host-microbial associations. For instance, we may observe that individuals with diabetes have a greater abundance of a particular bacterium…

  • 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…