Publications

Google Scholar

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

Preprints

• Diener, C.* and Gibbons, S.M.* 2024. Metagenomic estimation of dietary intake from human stool. bioRxiv, https://www.biorxiv.org/content/10.1101/2024.02.02.578701v1
• Carr, A., Baliga, N.S., Diener, C.*, Gibbons, S.M.* 2024. Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut. bioRxiv, https://www.biorxiv.org/content/10.1101/2023.04.28.538771v3
• Jiang, B., Quinn-Bohmann, N., Diener, C., Nathan, V.B., Han-Hallett, Y., Reddivari, L., Gibbons, S.M.*, Baloni, P.* 2024. Understanding disease-associated metabolic changes in human colon epithelial cells using iColonEpithelium metabolic reconstruction. bioRxiv, https://www.biorxiv.org/content/10.1101/2024.10.22.619644v1
• Qian, Y., Menon, S.D., Quinn-Bohmann, N., Gibbons, S.M., Venturelli, O.S.* 2025. A data-driven modeling framework for mapping genotypes to synthetic microbial community functions. bioRxiv, https://www.biorxiv.org/content/10.1101/2025.01.04.631316v1
• Tang, G., Carr, A.V., Perez, C., Ramos S., K., Levy, L., Lampe, J., Diener, C., Gibbons, S.M.* 2025. Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization. bioRxiv, https://www.biorxiv.org/content/10.1101/2025.01.07.631807v1

2024

• Byrn, A., Diener, C., Brown, B.P., Maust, B.S., Feng, C., Alinde, B.L., Gibbons, S.M., Koch, M., Gray, C.M., Jaspan, H.B., Nyangahu, D.D.* 2024. Neonates exposed to HIV but uninfected exhibit an altered gut microbiome and inflammation associated with impaired breast milk antibody function. Microbiome, https://link.springer.com/article/10.1186/s40168-024-01973-z
• Valenzuela, J.J., Christinal Immanuel, S.R., Wilson, J., Turkarslan, S., Ruiz, M., Gibbons, S.M., Hunt, K.A., Stopnisek, N., Auer, M., Zemla, M., Stahl, D.A., Baliga, N.S.* 2024. Origin of biogeographically distinct ecotypes during laboratory evolution. Nature Communications, https://doi.org/10.1038/s41467-024-51759-y
  • Behind the Paper Blog
• Sulaiman, J.E., Thompson, J., Qian, Y., Vivas, E.I., Diener, C., Gibbons, S.M., Safdar, N., Venturelli, O.S.*. 2024. Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes. Nature Communications, https://doi.org/10.1038/s41467-024-51062-w
  • Behind the Paper Blog
• Johnson-Martinez, J.P., Diener, C., Levine, A.E., Wilmanski, T., Suskind, D.L., Ralevski, A., Hadlock, J., Magis, A.T., Hood, L., Rappaport, N., Gibbons, S.M.* 2024. Aberrant bowel movement frequencies coincide with increased microbe-derived blood metabolites associated with reduced organ function. Cell Reports Medicine, https://doi.org/10.1016/j.xcrm.2024.101646
  • Coverage: ISB News, CNN, The Today Show, CBC Radio, Newsweek, BBC, NBC News, and more…
• Quinn-Bohmann, N., Wilmanski, T., Ramos S., K., Levy, L., Lampe, J., Gurry, T., Rappaport, N., Ostrem, E.M., Venturelli, O.S., Diener, C.*, Gibbons, S.M.* 2024. Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut. Nature Microbiology, https://doi.org/10.1038/s41564-024-01728-4
  • Readcube link: https://rdcu.be/dLIR3
  • Coverage: Nature Microbiology Editorial, ISB News
• Ramos S., K., Carr, A., Diener, C., Locey, K.J., Gibbons, S.M.* 2024. Island biogeography theory provides a plausible explanation for why larger vertebrates and taller humans have more diverse gut microbiomes. ISME Journal, https://doi.org/10.1093/ismejo/wrae114
  • Coverage: New Scientist
• 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, https://doi.org/10.1186/s12915-024-01887-0

2023

• Marcelino, V.R.*, Welsh, C., Diener, C., Gulliver, E.L., Rutten, E.L., Young, R.B., Giles, E.M., Gibbons, S.M., Greening, C., Forester, S.C.* 2023. Disease-specific loss of microbial cross-feeding interactions in the human gut. Nature Communications, https://www.nature.com/articles/s41467-023-42112-w
• Happel, A.*, Rametse, L., Perumaul, B., Diener, C., Gibbons, S.M., Nyangahu, D.D., Donald, K.A., Gray, C., Jaspan, H.B. 2023. Bifidobacterium infantis supplementation versus placebo in early life to improve immunity in infants exposed to HIV: a protocol for a randomized trial. BMC Complementary Medicine and Therapies, https://doi.org/10.1186/s12906-023-04208-0
• 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
  • Nature Bioengineerig Community Blog Post
• Wilmanski, T.*, Gibbons, S.M.* 2023. A changing gut virome ecological landscape with longevity. Trends in Microbiology, https://www.cell.com/trends/microbiology/fulltext/S0966-842X(23)00225-1 
• Diener, C.*, Gibbons, S.M.* 2023. Coarse graining the human gut microbiome. Cell Host & Microbe, https://doi.org/10.1016/j.chom.2023.06.001
• Diener, C.*, Gibbons, S.M.* 2023. More is different: metabolic modeling of diverse microbial communities. mSystems, https://doi.org/10.1128/msystems.01270-22
• Watanabe, K., Wilmanski, T., Diener, C., Earls, J.C., Zimmer, A., Lincoln, B., Hadlock, J.J., Lovejoy, J.C., Gibbons, S.M., Magis, A.T., Hood, L., Price, N.D., Rappaport, N.* 2023. Multiomic signatures of body mass index identify heterogeneous health phenotypes and responses to a lifestyle intervention. Nature Medicine, https://www.nature.com/articles/s41591-023-02248-0
  • Coverage: ISB News

2022

• 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, https://www.nature.com/articles/s42255-022-00670-1
  • ReadCube link: https://rdcu.be/cZpgI
  • Coverage: ScienceDaily, ISB News, PNAS Journal Club
• Wilmanski, T., Gibbons, S.M.*, Price, N.D.* 2022. Healthy aging and the human gut microbiome: why we cannot just turn back the clock. Nature Aging, https://doi.org/10.1038/s43587-022-00294-w
  • ReadCube Link: rdcu.be/cWrT0
• Gibbons, S.M.*#, Gurry, T.#, Lampe, J.W.#, Chakrabarti, A., Dam, V., Everard, A., Goas, A., Gabriele, G., Kleerebezem, M., Lane, J., Maukonen, J., Penna, A.L.B., Pot, B., Valdes, A.M., Walton, G., Weiss, A., Zanzer, Y.C., Venlet, N.V.*, Miani, M.* 2022. Perspective: leveraging the gut microbiota to predict personalized responses to dietary, prebiotic, and probiotic interventions. Advances in Nutrition, https://doi.org/10.1093/advances/nmac075
• 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, https://doi.org/10.1016/j.medj.2022.04.007
  • Coverage: ISB News, Science Daily, and Medical News Today

2021

• 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, https://doi.org/10.1128/mSystems.00964-21
  • Coverage: ISB News, Medical News Today, Geekwire, ScienceDaily, The Washington Post
• Kordahi, M.C., Stanaway, I.B., Avril, M., Chac, D., Blanc, M., Ross, B., Diener, C., Jain, S., McCleary, P., Parker, A., Friedman, V., Huang, J., Burke, W., Gibbons, S.M., Willis, A.D., Darveau, R.P., Grady, W.M., Ko, C.W., DePaolo, R.W.* 2021. Genomic and functional characterization of a mucosal symbiont involved in early-stage colorectal cancer. Cell Host & Microbe, https://doi.org/10.1016/j.chom.2021.08.013
  • Coverage: UW Newsroom
• Wilmanski, T., Rappaport, N., Diener, C., Gibbons, S.M.*, Price, N.D.* 2021. From taxonomy to metabolic output: what factors define gut microbiome health? Gut Microbes, 13:1, 1-20, DOI: 10.1080/19490976.2021.1907270
• 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
  • Coverage: The Scientist and MIT News
• 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
  • Behind the Paper blog post
• 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, https://doi.org/10.1038/s42255-021-00348-0
  • ReadCube link: https://rdcu.be/cfslJ
  • Hear lead author Dr. Tomasz Wilmanski discuss these results on the Closer to the Phenotype podcast
  • Coverage: New York Times, ISB News, and Science Daily
• 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. https://doi.org/10.1371/journal.pone.0247534
• Zimmer, A., Korem, Y., Rappaport, N., Wilmanski, T., Baloni, P., Jade, K., Robinson, M., Magis, A.T., Lovejoy, J., Gibbons, S.M., Hood, L.*, Price, N.D.* 2021. The geometry of clinical labs and wellness states from deeply phenotypes humans. Nature Communications, 12:3578 https://doi.org/10.1038/s41467-021-23849-8
• 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. https://doi.org/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 http://msystems.asm.org/content/6/1/e01194-20.abstract
• 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.
• 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

2020

• 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, https://doi.org/10.1038/s41467-020-18871-1
  • Coverage: ISB News
• Gibbons., S.M.* 2020. Keystone taxa indispensable for microbiome recovery. Nature Microbiology, 5, 1067–1068. https://doi.org/10.1038/s41564-020-0783-0
  • ReadCube link rdcu.be/b6qCm
• 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
  • Coverage: ISB News
• Diener, C., Gibbons, S.M.*, Resendis-Antonio, O.* 2020. MICOM: metagenome-scale modeling to infer metabolic interactions in the gut microbiota. mSystems, https://journals.asm.org/doi/10.1128/mSystems.00606-19
  • Coverage: ISB News
  • MICOM website

2019

• Gibbons, S.M.* 2019. Defining microbiome health through a host lens. mSystems. https://doi.org/10.1128/mSystems.00155-19
• 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. NatureBiotechnology, https://doi.org/10.1038/s41587-019-0233-9
  • Coverage: GeekWire, The Record on KUOW, and ISB News
  • Nature Bioengineering Community blog post, Metabolon blog post
•  
• 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
  • Coverage: ScienceDaily and MIT News
• 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, https://doi.org/10.1038/s41587-019-0209-9
• 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, https://doi.org/10.1038/s41396-019-0459-z
  • ReadCube Link: rdcu.be/bH0Ue
  • Blog Post
• 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
  • Coverage: Science Daily
• 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

2018

• 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. https://doi.org/10.1038/s41598-018-30783-1
  • Coverage: MIT News
• 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. https://doi.org/10.1111/1462-2920.14378
• 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., Duvallet, C., Alm, E.J.* 2018. Correcting for batch effects in case-control microbiome studies. PloS Computational Biology, https://doi.org/10.1371/journal.pcbi.1006102
  • blog post on fuzzy zeros
• 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

2017

• 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
  • Coverage: Science Friday, Wired, and Nature News and Views
• 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
  • Claire Duvallet won the Junior Parasite Award based on this work
  • blog post
• 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, http://dx.doi.org/10.1371/journal.pcbi.1005364
  • blog post

2016

• 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

2015

• 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
  • Coverage: The Scientist, The Huffington Post, and the Science Life Blog.
• 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
  • Coverage: Time, the New York Times, National Public Radio, the Science Life Blog, and featured in Ed Yong’s book “I Contain Multitudes”
• 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.
  • Coverage: Los Angeles Times, National Geographic, and The Guardian.
• 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

2014

• 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
  • Coverage: The Washington Post, Slate, The Scientist, New Scientist, Nature World News, Wired, National Public Radio, Discover Magazine, and National Geographic
• 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

2013

• 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
  • Coverage: National Geographic and the Science Life Blog
• 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

2012

• 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

2011

• 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

2009

• 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