Gut Microbiome and Health

The gut microbiome is now being recognized as a new organ of the human body. It is not an essential organ, like the liver or the heart, but we have found that proper functioning of the gut microbiome is necessary for long-term wellness and quality of life. 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 databases, like the Wellness 100K Project, to identify promising associations between microbial communities and human health. These associations serve as hypotheses for in vivo and ex vivo testing. Our goal is to establish causality for a subset of these associations, which will then 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 of our unique gut communities will be crucial in the development of personalized, preventative, and predictive medicine.

Selected Publications

  • 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


  • 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
  • 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 health and disease. in review
  • Zhao, S., Lieberman, T.D., Poyet, M., Groussin, M., Gibbons, S.M., Xavier, R.J., Alm, E.J. 2018. Adaptive evolution within the gut microbiome of individual people. in review

Related Projects

  • 100K Wellness Project

    We are partnering with Arivale to collect dense, dynamic data clouds from 100,000 people over the next several years. This large cross-disciplinary endeavor, called the 100K Wellness Project, spans multiple labs at ISB. We will integrate measurements of human physiology, immune function, and diet with measurements of the composition and functional potential of the gut microbiome. By tracking people undergoing wellness-coaching, we will build a set of hypotheses for how shifts…

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