Google Scholar

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


  • 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,
  • 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,
  • 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.
  • Graham, E.B., Averill, C., Bond-Lamberty, B., Knelman, J.E., Krause, S., Peralta, A.L., Shade, A., Smith, A.P., Cheng, S.J., Fanin, N., Freund, C., Garcia, P.E., Gibbons, S.M., Van Goethem, M.W., Guebila, M.B., Kemppinen, J., Nowicki, R.J., Pausas, J.G., Reed, S.P., Rocca, J., Sengupta, A., Sihi, D., Simonin, M., Słowiński, M., Spawn, S.A., Sutherland, I., Tonkin, J.D., Wisnoski, N.I., Zipper, S.C. and Contributor Consortium. 2021. Toward a Generalizable Framework of Disturbance Ecology Through Crowdsourced Science. Frontiers in Ecology and Evolution 9:588940. doi: 10.3389/fevo.2021.588940.
  • 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,