Gut Microbiome and Health

The gut microbiome is an integral component of the human body – almost like an organ. Dozens of inflammatory conditions (e.g. inflammatory bowel disease, obesity, and rheumatoid arthritis) have been associated with the microbiome, in addition to several cancers and cognitive disorders. We mine large multi-omic human data sets to identify promising associations (directed and undirected) between microbial communities and human health. These associations serve as hypotheses for in vivo, ex vivo, and in silico testing. We use these data, along with existing knowledge bases, to build mechanistic models that map ecological structure to community phenotypes. Our goal is to establish causality for a subset of microbe-host associations and to build tools for designing ecosystem interventions, which will allow for the translation of these insights into novel treatments for complex diseases. Ultimately, we want to develop ‘ecological therapeutics’ to treat complex conditions that emerge from many interacting factors and often require a personalized intervention (i.e. there will never be a single ‘pill’ that can be deployed to treat the disease). The microbiome is quickly becoming a new branch of medical science. Just as we all have our own unique genomes, we also have unique microbiomes. Understanding the composition and function of our unique gut communities will be crucial in the development of personalized, preventative, and predictive medicine.

Selected Publications

  • Quinn-Bohmann, N., Freixas-Coutin, J.A., Seo, J., Simmons, R., Diener, C., Gibbons, S.M. 2024. Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease. BMC Biology,
  • Diener, C.#, Dai, C.L.#, Wilmanski, T., Baloni, P., Smith, B., Rappaport, N., Hood, L., Magis, A.T.*, Gibbons, S.M.* 2022. Genome-microbiome interplay provides insight into the determinants of the human blood metabolome. Nature Metabolism,
  • Wilmanski, T., Kornilov, S.A., Diener, C., Conomos, M.P., Lovejoy, J.C., Sebastiani, P., Orwoll, E.S., Hood, L., Price, N.D., Rappaport, N., Magis, A.T., Gibbons, S.M. 2022. Heterogeneity in statin responses explained by variation in the human gut microbiome. Med,
  • Diener, C., Qin, S., Zhou, Y., Patwardhan, S., Tang, L., Lovejoy, J. Magis, A.T., Price, N.D., Hood, L., Gibbons, S.M. 2021. Baseline gut metagenomic functional gene signature associated with variable weight loss responses following a healthy lifestyle intervention in humans. mSystems, e009624-21,
  • 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),
  • Wilmanski, T., Diener, C., Rappaport, N., Patwardhan, S., Wiedrick, J., Lapidus, J., Earls, J.C., Zimmer, A., Glusman, G., Robinson, M., Yurkovich, J.T., Kado, D.M., Cauley, J.A., Zmuda, J., Lane, N.E., Magis, A.T., Lovejoy, J.C., Hood, L., Gibbons, S.M., Orwoll, E., Price, N.D. 2021. Gut microbiome pattern reflects healthy ageing and predicts survival in humans. Nature Metabolism,
  • 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,
  • Patwardhan, S., Diener, C., Swegle, S., Howsmon, B., Gibbons, S.M. 2021. What are poop transplants and how do they work? Frontiers for Young Minds, 9:571389. doi:10.3389/frym.571389
  • Manor, O., Dai, C.L., Kornilov, S., Smith, B., Price, N.D., Lovejoy, J.C., Gibbons, S.M., Magis, A.T. 2020. Health and disease markers correlate with gut microbiome composition across thousands of people. Nature Communications, 11, 5206,
  • Gibbons. S.M. 2020. Keystone taxa indispensable for microbiome recovery. Nature Microbiology,
  • 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,
  • Diener, C., Gibbons, S.M., Resendis-Antonio, O. 2020. MICOM: metagenome-scale modeling to infer metabolic interactions in the gut microbiota. mSystems,
  • 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
  • Wilmanski, T., Rappaport, N., Earls, J.C., Magis, A.T., Manor, O., Lovejoy, J., Omenn, G.S., Hood, L., Gibbons, S.M., Price, N.D. 2019. Blood metabolome signature predicts gut microbiome alpha-diversity in humans. Nature Biotechnology,
  • 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.
  • Gurry, T., HST Microbiome Consortium, Gibbons, S.M., Nguyen, L.T.T., Kearney, S.M., Ananthakrishnan, A., Jiang, X., Duvallet, C., Kassam, Z., Alm, E.J. 2018. Predictability and persistence of probiotic dietary supplementation in a healthy human cohort. Scientific Reports,
  • Kearney, S.M., Gibbons, S.M., 2018. Designing synbiotics for improved human health. Microbial Biotechnology, 11(1), 141-144
  • Pakpour, S., Bhanvadia, A., Zhu, R., Amarnani, A., Gibbons, S.M., Gurry, T., Alm, E.J., Martello, L.A. 2017. Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment. Microbiome, 5:148, doi:10.1186/s40168-017-0368-1.
  • Duvallet, C., Gibbons, S.M., Gurry, T., Irizarry, R. and Alm, E.J. 2017. Meta-analysis of microbiome studies reveals disease-specific and shared responses. Nature Communications, 1784 (2017), doi:10.1038/s41467-017-01973-8

  • Califf, K.J., Schwarzberg-Lipson, K., Garg, N., Gibbons, S.M., Caporaso, J.G., Slots, J., Cohen, C., Dorrestein, P.C., and Kelley, S.T. 2017. Multi-omics analysis of periodontal pocket microbial communities pre-and post-treatment. mSystems, 2(3), pp.e00017-17
  • 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,
  • 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
  • Fuller, M., Priyadarshini, M., Gibbons, S.M., Angueira, A.R., Brodsky, M., Hayes, M.G., Kovatcheva-Datchary, P., Bäckhed, F., Gilbert, J.A., Lowe, W.L. and Layden, B.T. 2015. The short-chain fatty acid receptor, FFA2, contributes to gestational glucose homeostasis. American Journal of Physiology-Endocrinology and Metabolism, 309(10), pp.E840-E851
  • Torres, P.J., Fletcher, E.M., Gibbons, S.M., Bouvet, M., Doran, K.S. and Kelley, S.T. 2015. Characterization of the salivary microbiome in patients with pancreatic cancer. PeerJ, 3, p.e1373.
  • Vitaglione, P., Mennella, I., Ferracane, R., Rivellese, A.A., Giacco, R., Ercolini, D., Gibbons, S.M., La Storia, A., Gilbert, J.A., Jonnalagadda, S. and Thielecke, F. 2015. Whole-grain wheat consumption reduces inflammation in a randomized controlled trial on overweight and obese subjects with unhealthy dietary and lifestyle behaviors: role of polyphenols bound to cereal dietary fiber. The American Journal of Clinical Nutrition, 101(2), pp.251-26