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

• Lim, J.J., Diener, C., Wilson, J., Valenzuela, J.J., Baliga, N.S., Gibbons, S.M. 2023. Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes. Nature Communications, https://www.nature.com/articles/s41467-023-41424-1
• Diener, C., Gibbons, S.M. 2023. More is different: metabolic modeling of diverse microbial communities. mSystems, https://doi.org/10.1128/msystems.01270-22
• Diener, C., Hoge, A.C.H., Kearney, S.M., Kusebauch, U., Patwardhan, S., Moritz, R.L., Erdman, S.E., Gibbons, S.M. 2021. Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut. Communications Biology, 4(316), https://doi.org/10.1038/s42003-021-01841-8
• 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., Lafosse, S., Tabe, F.E., Girard, C., Iqaluk, D., 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., Nartey, Y.A., Agyei-Nkansah, A., Duah, A., Awuku, Y.A., Valles, K.A., Asibey, S.O., Afihene, M.Y., Roberts, L.R., Plymoth, A., Onyekwere, C.A., Summons, R.E., Xavier, R.J., and Alm, E.J. 2021. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell, https://doi.org/10.1016/j.cell.2021.02.052
• Otwell, A.E., Carr, A.V., Majumder, E.L.W., Ruiz, M.K., Wilpiszeski, R.L., Hoang, L.T., Webb, B., Turkarslan, S., Gibbons, S.M., Elias, D.A., Stahl, D.A., Siuzdak, G., Baliga, N.S. 2021. Sulfur metabolites play key system-level roles in modulating denitrification. mSystems 6:e01025-20. https://doi.org/10.1128/mSystems.01025-20
• Gibbons. S.M. 2020. Keystone taxa indispensable for microbiome recovery. Nature Microbiology, https://doi.org/10.1038/s41564-020-0783-0
• 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 Medicine, https://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