Google Scholar

Bold Underscorred Text = Gibbons Lab members (starting in 2019); * = corresponding author; # = co-first author


  • 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,
  • Day, J.A.#, Diener, C.#, Otwell, A.E.#, Tams, K.E., Bebout, B., Detweiler, A.M., Lee, M,D., Scott, M.T., Ta, W., Ha, M., Carreon, S.A., Tong, K., Ali, A.A., Gibbons, S.M.*, Baliga, N.S.* 2021. Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics. PLoS ONE 16(2): e0247534.
  • Vangay, P., Burgin, J., Johnston, A., Beck, K.L., Berrios, D.C., Blumberg, K., Canon, S., Chain, P., Chandonia, J.M., Christianson, D., Costes, S.V., Damerow, J., Duncan, W.D., Dundore-Arias, J.P., Fagnan, K., Galazka, J.M. Gibbons, S.M., Hays, D., Hervey, J., Hu, B., Hurwitz, B.L., Jaiswal, P., Joachimiak, M.P., Kinkel, L., Ladau, J., Martin, S.L., McCue, L.A., Miller, K., Mouncey, N., Mungall, C., Pafilis, E., Reddy, T.B.K., Richardson, L., Roux, S., Shaffer, J.P., Sundaramurthi, J.C., Thompson, L.R., Timme, R.E., Zheng, J., Wood-Charlson, E.M., and Eloe-Fadrosh, E.A. 2021. Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities. mSystems, 6:e01194-20; doi:10.1128/mSystems.01194-20
  • 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.
  • 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, 5, 1067–1068.
  • 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,


  • Gibbons, S.M.* 2019. Defining microbiome health through a host lens. mSystems.
  • 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 predicts gut microbiome alpha-diversity in humans. Nature Biotechnology,
  • 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
  • Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C.C., Al-Ghalith, G.A., Alexander, H., Alm, E.J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J.E., Bittinger, K., Brejnrod, A., Brislawn, C.J.,Brown, C.T., Callahan, B.J., Caraballo-Rodríguez, A.M., Chase, J., Cope, E.K., Da Silva, R., Diener, C., Dorrestein, P.C., Douglas, G.M., Durall, D.M., Duvallet, C., Edwardson, C.F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J.M., Gibbons, S.M., Gibson, D.L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G.A., Janssen, S., Jarmusch, A.K., Jiang, L., Kaehler, B.D., Kang, K.B., Keefe, C.R., Keim, P., Kelley, S.T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M.G. I., Lee, J., Ley, R., Liu, Y., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B.D., McDonald, D., McIver, L.J., Melnik, A.V., Metcalf, J.L., Morgan, S.C., Morton, J.T., Naimey, A.T., Navas-Molina, J.A., Nothias, L.F., Orchanian, S.B.,Pearson, T., Peoples, S.L., Petras, D., Preuss, M.L., Pruesse, E., Rasmussen, L.B., Rivers, A., Robeson, M.S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S.J., Spear, J.R., Swafford, A.D., Thompson, L.R., Torres, P.J., Trinh, P., Tripathi, A., Turnbaugh, P.J., Ul-Hasan, S., van der Hooft, J.J.J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K.C., Williamson, C.H.D., Willis, A.D., Xu, Z.Z., Zaneveld, J.R., Zhang, Y., Zhu, Q., Knight, R., and Caporaso, J.G.* 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology,
  • Xiang, X., Gibbons, S.M., Li, H., Shen, H., and Chu, H.* 2019. Proximate grassland and shrub-encroached sites show dramatic restructuring of soil bacterial communities. PeerJ, doi 10.7717/peerj.7304
  • Carr, A., Diener, C., Baliga, N.S.*, and Gibbons, S.M.* 2019. Use and abuse of correlation analyses in microbial ecology. ISME Journal
  • 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.
  • Rocca, J.D.*, Simonin, M.*, Blaszczak, J.R., Ernakovich, J.G., Gibbons, S.M., Midani, F.S., Washburne, A.D. 2019. The Microbiome Stress Project: towards a global meta-analysis of environmental stressors and their effects on microbial communities. Frontiers in Microbiology. doi: 10.3389/fmicb.2018.03272


  • 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 prebiotic dietary supplementation in a healthy human cohort. Scientific Reports.
  • Otwell, A.E., García de Lomana, A.L., Gibbons, S.M., Orellana, M.V., Baliga, N.S.* 2018. Systems biology approaches towards predictive microbial ecology. Environmental Microbiology.
  • 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,
  • 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,
  • Gibbons, S.M., Duvallet, C., Alm, E.J.* 2018. Correcting for batch effects in case-control microbiome studies. PloS Computational Biology,
  • Xiang, X., Gibbons, S.M., Li, H., Shen, H., Fang, J., and Chu, H.* 2018. Shrub encroachment is associated with changes in soil bacterial community composition in a temperate grassland ecosystem. Plant and Soil, 1-13, doi: 10.1007/s11104-018-3605-x
  • Kearney, S.M.*, Gibbons, S.M., 2018. Designing synbiotics for improved human health. Microbial Biotechnology, 11(1), 141-144


  • Gibbons, S.M.*, 2017. Metapopulation theory provides new insight into microbial biogeography. Environmental Microbiology, doi: 1111/1462-2920.13702
  • Gibbons, S.M.*, 2017. Microbial community ecology: function over phylogeny. Nature Ecology & Evolution, 1(1), doi:10.1038/s41559-016-0032
  • 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.
  • Thompson L.R., Sanders J.G., McDonald D., Ladau J., Locey K., Navas-Molina J.A., Prill R.J., Gibbons S.M., Gonzalez A., Amir A., et al. 2017. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, doi:10.1038/nature24621
  • 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., Lekberg, Y., Mummey, D.L., Sangwan, N., Ramsey, R.W., and Gilbert, J.A.* 2017. Invasive plants rapidly reshape soil properties in a grassland ecosystem. mSystems, 2:e00178-16.
  • 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,


  • Gibbons, S.M.*, 2016. The Built Environment Is a Microbial Wasteland. mSystems, 1(2), pp.e00033-16
  • 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
  • Xiang, X., Gibbons, S.M., He, J.S., Wang, C., He, D., Li, Q., Ni, Y. and Chu, H.* 2016. Rapid response of arbuscular mycorrhizal fungal communities to short-term fertilization in an alpine grassland on the Qinghai-Tibet Plateau. PeerJ, 4, p.e2226
  • O’Brien, S.L., Gibbons, S.M., Owens, S.M., Hampton‐Marcell, J., Johnston, E.R., Jastrow, J.D., Gilbert, J.A., Meyer, F. and Antonopoulos, D.A.* 2016. Spatial scale drives patterns in soil bacterial diversity. Environmental Microbiology, 18(6), pp.2039-2051


  • Gibbons, S.M. and Gilbert, J.A. 2015.* Microbial diversity—exploration of natural ecosystems and microbiomes. Current Opinion in Genetics & Development, 35, pp.66-72
  • Xiang, X., Gibbons, S.M., Yang, J., Kong, J., Sun, R. and Chu, H.* 2015. Arbuscular mycorrhizal fungal communities show low resistance and high resilience to wildfire disturbance. Plant and Soil, 397(1-2), pp.347-356
  • Wood, M., Gibbons, S.M., Lax, S., Eshoo-Anton, T.W., Owens, S.M., Kennedy, S., Gilbert, J.A. and Hampton-Marcell, J.T.* 2015. Athletic equipment microbiota are shaped by interactions with human skin. Microbiome, 3(1), p.1
  • 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
  • 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.
  • Van Bonn, W.*, LaPointe, A., Gibbons, S.M., Frazier, A., Hampton‐Marcell, J. and Gilbert, J.A.* 2015. Aquarium microbiome response to ninety‐percent system water change: Clues to microbiome management. Zoo Biology, 34(4), pp.360-367
  • Lax, S., Hampton-Marcell, J.T., Gibbons, S.M., Colares, G.B., Smith, D., Eisen, J.A. and Gilbert, J.A.* 2015. Forensic analysis of the microbiome of phones and shoes. Microbiome, 3(1), p.1.
  • 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.251-261
  • Gibbons, S.M.*, 2015. Statistical Tools for Data Analysis. Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks, Humana Press


  • 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
  • Pfister, C.A., Gilbert, J.A. and Gibbons, S.M. 2014. The role of macrobiota in structuring microbial communities along rocky shores. PeerJ, 2, p.e631
  • Winston, M.E.*, Hampton-Marcell, J., Zarraonaindia, I., Owens, S.M., Moreau, C.S., Gilbert, J.A., Hartsel, J., Kennedy, S.J. and Gibbons, S.M. 2014. Understanding cultivar-specificity and soil determinants of the cannabis microbiome. PloS One, 9(6), p.e99641
  • Lekberg, Y.*, Gibbons, S.M. and Rosendahl, S. 2014. Will different OTU delineation methods change interpretation of arbuscular mycorrhizal fungal community patterns? New Phytologist, 202(4), pp.1101-1104
  • Gibbons, S.M., Jones, E., Bearquiver, A., Blackwolf, F., Roundstone, W., Scott, N., Hooker, J., Madsen, R., Coleman, M.L.* and Gilbert, J.A.* 2014. Human and environmental impacts on river sediment microbial communities. PLoS One, 9(5), p.e97435
  • Rideout, J.R., He, Y., Navas-Molina, J.A., Walters, W.A., Ursell, L.K., Gibbons, S.M., Chase, J., McDonald, D., Gonzalez, A., Robbins-Pianka, A. and Clemente, J.C. 2014. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ, 2, p.e545
  • Xiong, J., Sun, H., Peng, F., Zhang, H., Xue, X., Gibbons, S.M., Gilbert, J.A. and Chu, H.* 2014. Characterizing changes in soil bacterial community structure in response to short-term warming. FEMS Microbiology Ecology, 89(2), pp.281-292


  • McTee, M.R., Gibbons, S.M., Feris, K., Gordon, N.S., Gannon, J.E. and Ramsey, P.W.* 2013. Heavy metal tolerance genes alter cellular thermodynamics in Pseudomonas putida and river Pseudomonas spp. and influence amebal predation. FEMS Microbiology Letters, 347(2), pp.97-106
  • Rubin, B.E.*, Gibbons, S.M., Kennedy, S., Hampton-Marcell, J., Owens, S. and Gilbert, J.A. 2013. Investigating the impact of storage conditions on microbial community composition in soil samples. PloS One, 8(7), p.e70460
  • Lekberg, Y., Gibbons, S.M., Rosendahl, S. and Ramsey, P.W.* 2013. Severe plant invasions can increase mycorrhizal fungal abundance and diversity. The ISME Journal, 7(7), pp.1424-1433.
  • 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
  • Roy, A.S., Gibbons, S.M., Schunck, H., Owens, S., Caporaso, J.G., Sperling, M., Nissimov, J.I., Romac, S., Bittner, L., Mühling, M. and Riebesell, U. 2013. Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms. Biogeosciences, 10(1), pp.555-566


  • Larsen, P.E., Gibbons, S.M. and Gilbert, J.A.* 2012. Modeling microbial community structure and functional diversity across time and space. FEMS Microbiology Letters, 332(2), pp.91-98
  • Ramsey, P.W., Gibbons, S.M., Rice, P., Mummey, D.L., Feris, K.P., Moore, J.N., Rillig, M.C. and Gannon, J.E.* 2012. Relative strengths of relationships between plant, microbial, and environmental parameters in heavy-metal contaminated floodplain soil. Pedobiologia, 55(1), pp.15-23
  • Lekberg, Y., Schnoor, T., Kjøller, R., Gibbons, S.M., Hansen, L.H., Al‐Soud, W.A., Sørensen, S.J. and Rosendahl, S.* 2012. 454‐sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities. Journal of Ecology, 100(1), pp.151-160


  • Gibbons, S.M., Feris, K., McGuirl, M.A., Morales, S.E., Hynninen, A., Ramsey, P.W. and Gannon, J.E.* 2011. Use of microcalorimetry to determine the costs and benefits to Pseudomonas putida strain kt2440 of harboring cadmium efflux genes. Applied and Environmental Microbiology, 77(1), pp.108-113


  • Feris, K.P., Ramsey, P.W., Gibbons, S.M., Frazar, C., Rillig, M.C., Moore, J.N., Gannon, J.E. and Holben, W.E.* 2009. Hyporheic microbial community development is a sensitive indicator of metal contamination. Environmental Science & Technology, 43(16), pp.6158-6163

Preprints in Review

  • Diener, C.*, Qin, S., Zhou, Y., Patwardhan, S., Tang, L., Lovejoy, J. Magis, A.T., Price, N.D., Hood, L., Gibbons, S.M.* 2021. Weight loss response following lifestyle intervention associated with baseline gut metagenomic signature in humans. bioRxiv, in review,
  • Disturbance Ecology Consortium. 2020. Towards a unifying framework for disturbance ecology through crowdsourced science. EcoEvoRxiv, in review,
  • 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,
  • Day, J.A.#, Diener, C.#, Otwell, A.E.#, Tams, K.E., Bebout, B., Detweiler, A., Lee, M.D., Scott, M.T., Ta, W., Ha, M., Carreon, S.A., Tong, K., Ali, A.A., Gibbons, S.M.*, and Baliga, N.S.* 2019. Negative plant-microbiome feedback limits productivity in aquaponics. bioRxiv, in review,
  • 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,