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Examples of publications related to the gut microbiota from 1996 to present

(for a full list via PubMed, click here)

Bry, L., Falk, P.G., Midtvedt, T., and Gordon, J.I. A model of host-microbial interactions in an open mammalian ecosystem. Science 273: 1380-1383 (1996).

Hooper, L.V., Xu, J., Falk, P.G., Midtvedt, T., and Gordon, J.I. A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. Proc. Natl. Acad. Sci. USA, 96: 9833-9838 (1999).

Hooper, L.V., Wong, M.H., Thelin, A., Hansson, L., Falk, P.G, and Gordon, J.I. Molecular analysis of commensal host-microbial relationships in the intestine. Science 291: 881-884 (2001).

Hooper, L.V. and Gordon, J.I. Commensal host-bacterial relationships in the gut. Science 292:1115-1118 (2001).

Stappenbeck, T.S., Hooper, L.V., Gordon, J.I. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc. Natl. Acad. Sci. USA 99:15451-15455 (2002).

Hooper, L.V., Stappenbeck, T.S., Hong, C.V., Gordon, J.I. Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nature Immunol. 4: 269-273 (2003).

Xu, J., Bjursell, M.K., Himrod, J., Deng, S., Carmichael, L.K., Chiang, H.C., Hooper, L.V., and Gordon, J.I. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299: 2074-2076 (2003).

Xu, J., and Gordon, J.I. Honor thy symbionts. Proc. Natl. Acad. Sci. USA 100: 10452-10459 (2003).

Rawls, J.F., Samuel, B.S., and Gordon, J.I. Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc. Natl. Acad. Sci. USA 101: 4596-4601 (2004).

Bäckhed, F., Ding, H., Wang, T., Hooper, L.V., Koh, G.Y., Nagy, A., Semenkovich, C.F. and Gordon, J.I. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl. Acad. Sci. USA 101: 15718-15723 (2004).

Sonnenburg, J.L., Xu, J., Leip, D.D., Chen, C.H., Westover, B.P., Weatherford, J., Buhler, J.D., and Gordon, J.I. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307: 1955-1959 (2005).

Ley, R.E., Bäckhed, F., Turnbaugh, P., Lozupone, C.A., Knight, R.D., and Gordon, J.I. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA 102: 11070-11075 (2005).

Ley, R.E., Peterson, D.A., and Gordon, J.I Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124: 837-848 (2006).

Sonnenburg, E.D., Sonnenburg, J.L., Manchester, J.K., Hansen, E.E., Chiang, H.C., and Gordon, J.I. A hybrid two-component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism. Proc. Natl. Acad. Sci. USA 103: 8834-8839 (2006).

Rawls, J.F., Mahowald, M.A., Ley, R.E., and Gordon, J.I. Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127: 423-433 (2006).

Turnbaugh, P.J., Ley, R.E., Mahowald, M.A., Magrini, V., Mardis, E.R. and Gordon, J.I. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027–1031 (2006).

Ley, R.E., Turnbaugh, P.J., Klein, S., and Gordon, J.I. Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022-1023 (2006).

Bäckhed, F., Manchester, J.K., Semenkovich, C.F., and Gordon, J.I. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc. Natl. Acad. Sci. USA 104: 979–984 (2007).

Xu, J., Mahowald, M.A., Ley, R.E., Lozupone, C.A., Hamady, M., Martens, E.C., Henrissat, B., Coutinho, P.M., Minx, P., Latreille, P., Cordum, H., Van Brunt, A., Kim, K., Fulton, R.S., Fulton, L.A., Clifton, S.W., Wilson, R.K., Knight, R.D., and Gordon, J.I. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol. 5: e156 (2007).  PMC1892571.

Peterson, D.A., McNulty, N.P., Guruge, J.L., and Gordon, J.I. IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host and Microbe 2: 328-339 (2007).

Turnbaugh, P.J., Bäckhed, F., Fulton, L. and Gordon, J.I. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome Cell Host and Microbe 3: 213-223 (2008).

Ley, R.E., Hamady, M., Lozupone, C., Turnbaugh, P.J., Ramey, R.R., Bircher, J.S., Schlegel, M.L., Tucker, T.A., Schrenzel, M.D., Knight, R., and Gordon, J.I. Evolution of mammals and their gut microbes. Science 320:1647-1651 (2008). PMC26490005.

Martens, E.C., Chiang, H.C., and Gordon, J.I. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host and Microbe 4: 447-457 (2008). PMC2605320.

Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., Sogin, M.L., Jones, W.J., Roe, B.A., Affourtit, J.P., Egholm, M., Henrissat, B., Heath, A.C. Knight, R. and Gordon, J.I. A core gut microbiome in obese and lean twins. Nature 457: 480-484 (2009). PMC2677729.

Mahowald, M.A., Rey, F.E., Seedorf, H., Turnbaugh, P.J., Fulton, R.S., Wollam, A., Shah, N., Wang, C., Magrini, V., Wilson, R.K., Cantarel, B.L. Coutinho, P.M., Henrissat, B., Crock, L.W., Russell, A., Verberkmoes, N.C., Hettich, R.L., and Gordon, J,I., Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc. Natl. Acad. Sci. USA 106: 5859-5864 (2009). PMC2660063.

Martens, E.C., Roth, R., Heuser, J., and Gordon, J.I. Coordinate regulation of glycan degradation and capsule synthesis by a prominent human gut symbiont. J. Biol. Chem. 248: 18445-57 (2009). PMC2709373.

Crawford, P.A., Crowley, J.R., Sambandam, N., Muegge, B., Costello, E., Hamady, M., Knight, R., and Gordon, J.I. Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc. Natl. Acad. Sci. USA 106:11276-81(2009) PMC2700149.

Goodman, A.L., McNulty, N.P., Zhao, Y., Leip, D., Mitra, R.D., Lozupone, C.A., Knight, R., and Gordon, J.I. Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host and Microbe 6:279-289 (2009). PMC2895552.

Turnbaugh, P.J., Ridaura, V.K., Faith, J.J., Rey, F.E., Knight, R. and Gordon, J.I. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Science Trans. Med. 1: 6ra14 (2009). PMC2894525.

Rey, F., Faith, J., Bain, J., Muehlbauer, M., Stevens, R., Newgard, C., and Gordon, J.I. Dissecting the in vivo metabolic potential of two human gut acetogens. J. Biol. Chem. 285: 22082-22090 (2010). PMC2903421.

Reyes, A., Haynes, M., Hanson, N., Angly, F., Heath, A., Rohwer, F., and Gordon, J.I. Viruses in the fecal microbiota of monozygotic twins and their mothers.  Nature 466: 334-338 (2010). PMC2919852.

Hansen, E., Lozupone, C.A., Rey, F.E., Wu, M., Guruge, J.L., Narra, A., Goodfellow, J., Zaneveld, J.R., McDonald, D.T., Goodrich, J.A., Heath, A.C., Knight, R., and Gordon, J.I. Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii: studied in twins. Proc. Natl. Acad. Sci. USA 108: 4599-4606 (2011). PMC3063581.

Goodman, A.L., Kallstrom, G., Faith, J.J., Reyes, A., Moore, A., Dantas, G., and Gordon, J.I. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl. Acad. Sci. USA, 108: 6252-6257 (2011). PMC3076821.

Kau, A.L., Ahern, P.P., Griffin, N.W., Goodman, A.L., and Gordon, J.I. Human nutrition, the gut microbiome and the immune system. Nature 474: 327-336 (2011). PMC3298082.

Muegge, B., Kuczynski, J., Knights, D., Clemente, J.C., Gonzalez, A., Fontana, L., Henrissat, B., Knight, R. and Gordon, J.I. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332: 970-974 (2011). PMC3303602.

Faith, J.J., McNulty, N.P., Rey, F.E., and Gordon, J.I. Predicting a human gut microbiota’s response to diet in gnotobiotic mice. Science 333: 101-104 (2011). PMC3303606.

McNulty, N, Yatsunenko, T, Hsiao, A., Faith, J., Muegge, B., Goodman, A., Henrissat, B., Oozeer, R., Cools-Portier, S., Gobert, G., Chervaux, C., Knights, D., Lozupone, C., Knight, R., Duncan, A.E., Bain, J.R., Muehlbauer, M.J., Newgard, C.B., Heath, A.C., and Gordon, J.I. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Science Translational Medicine 3: 106ra106 (2011). PMC3303609.

Martens, E.C., Lowe, E., Abbott, W., Chiang, H., Pudlo, N., Wu, M., McNulty, N., Abbott, W., Henrissat, B., Gilbert, H.J., Bolam, D.N., and Gordon, J.I. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biology 9: e10001221 (2011). PMC3243724.

Benezra, A., DeStefano, J., and Gordon, J.I. Anthropology of microbes, Proc. Natl. Acad. Sci. USA 109: 6378-6381(2012). PMC3340042.

Yatsunenko, T., Rey, F.E., Manary, M.J., Trehan, I., Dominguez-Bello, M.G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R.N., Anokhin, A.P., Heath, A.C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J.G., Lozupone, C.A., Lauber, C., Clemente, J.C., Knights, D., Knight, R., and Gordon, J.I. Human gut microbiome viewed across age and geography.  Nature 486: 222-227 (2012). PMC337638.

Gordon, J.I., Honor thy gut symbionts redux. Science 336: 1251-1253 (2012)..

Smith, M.I., Yatsunenko, T., Manary, M.J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A., Rich, S.S., Concannon, P., Mychaleckyj, J.C., Liu, J., Houpt, E., Li, J.V., Holmes, E., Nicholson, J., Knights, D., Ursell, L.K., Knight, R., and Gordon, J.I. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor.  Science 339: 548-554 (2013). PMC3667500.

Faith, J.J., Guruge, J.L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A.L., Clemente, J.C., Knight, R., Heath, A.C., Leibel, R.L., Rosenbaum, M., and Gordon, J.I. The long-term stability of the human gut microbiota. Science 341: 1237439 (2013). PMC3751589.

Rey, F.E., Gonzalez, M., Cheng, J., Wu, M., Ahern, P.P., and Gordon, J.I. The metabolic niche of a prominent sulfate-reducing human gut bacterium. Proc. Natl. Acad. Sci. 110: 13582-13587 (2013). PMC3746858.

McNulty, N.P., Wu, M., Erickson, A.R., Martens, E.C., Pudlo, N.A., Muegge, B., Henrissat, B., Hettich, R.L., and Gordon, J.I. Effects of diet on resource utilization by a defined model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome, PLoS Biology 11: e1001637 (2013). PMC3747994.

Ridaura, V.K., Faith, J.J., Rey, F.E., Cheng, J., Duncan, A.E., Kau, A.L., Lombard, V., Henrissat, B., Bain, J.R., Muehlbauer, M.J., Ilkayeva, O., Semenkovich, C.F., Funai, K., Lyle, B.J., Martini, M.C. Ursell, L.K., Clemente, J.C., Van Treuren, W., Walters, W.A., Knight, R.,  Newgard, C.B., Heath, A.C., and Gordon, J.I. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341: 1241214 (2013). PMC3829625.

Reyes, A., Wu, M., McNulty, N.P., Rohwer, F., and Gordon, J.I. Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut. Proc. Natl. Acad. Sci. USA 110: 20236-20241 (2013). PMC3864308.

Faith, J.J., Ahern, P.P., Ridaura, V.K., Cheng, J., and Gordon, J.I. Identifying gut microbiome-host phenotype relationships using combinatorial communities in gnotobiotic mice, Science Translational Medicine 6: 220ra11 (2014). PMC4118768.

Subramanian, S., Huq, S., Yatsunenko, T., Haque, R., Mahfuz, M., Alam, M.A., Benezra, A., DeStefano, J., Meier, M.F., Muegge, B.D., Barratt, M.J., Zhang, Q., Province, M.A., Petri, W.A., Ahmed, T., and Gordon, J.I. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 509: 417-421 (2014).

Hsiao, A., Ahmed, A.M., Subramanian, S., Griffin, N., Ahmed, T., Haque, R., and Gordon, J.I.  Members of the human gut microbiome involved in recovery from Vibrio cholerae infection. Nature, 515: 423-426 (2014).

Seedorf, H. Griffin, N.W., Ridaura, V.K., Reyes, A., Cheng, J., Rey, F.E., Simon, G.M., Scheffrahn, R.H., Wobken, D., Spormann, A.M., Ursell, L., Pirrung, M., Robbins-Pianka, A., Van Treuren, W.V., Cantarel, B.L., Lombard, V., Henrissat, B., Knight, R. and Gordon, J.I. Bacteria from diverse habitats colonize and compete in the mouse gut. Cell, 159: 253-266 (2014) PMCID: PMC4194163.

Kau, A.L., Planer, J.D., Liu, J., Rao, S., Yatsunenko, T., Trehan, I., Manary, M.J., Liu, T-C., Stappenbeck, T.S., Maleta, K.M., Ashorn, P., Dewey, K.G., Houpt, E.R., Hsieh, C-S., and Gordon, J.I. Functional characterization of IgA-targeted bacteria taxa from undernourished Malawian children that produce diet-dependent enteropathy. Science Transl. Med. 7: 276ra24  (2015).

Subramanian, S., Blanton, L., Frese, S.A., Charbonneau, M., Mills, D.A., and Gordon, J.I. Cultivating healthy growth and nutrition through the gut microbiota. Cell 161: 36-48 (2015).

Reyes, A., Blanton, L.V., Cao, S., Zhao, G., Manary, M.J., Trehan, I., Smith, M.I., Wang, D., Virgin, H.W., Rohwer, R., and Gordon, J.I.  Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proc. Natl. Acad. Sci. USA, 112: 11941-11946 (2015).

Dey, N., Wagner, V.E., Blanton, L.V., Cheng, J., Fontana, L., Haque, R., Ahmed, T., and Gordon, J.I. Regulators of gut motility revealed by a gnotobiotic model of diet-microbiome interactions related to travel. Cell, 163: 95-107 (2015).

Wu, M., McNulty, N.P., Rodionov, D.A., Khoroshkin, M.S., Griffin, N.W., Cheng, J., Latreille, P., Kerstetter, R.A., Terrapon, N., Henrissat, B., Osterman, A.L., and Gordon, J.I.  Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides, Science, 350: aac5992 (2015).

Charbonneau, M.R., O’Donnell, D., Blanton, L.V., Totten, S.M., Davis, J.C.C., Barratt, M. J., Cheng, J., Guruge, J., Talcott, M., Bain, J., Muehlbauer, M.J., Ilkayeva, O., Wu, C., Struckmeyer, T., Barile, D., Mangani, C., Jorgensen, J., Fan, Y-M., Maleta, K., Dewey, K.G., Ashorn, P., Newgard, C.B., Lebrilla, C., Mills, D.A., and Gordon, J.I. Growth promotion by sialylated milk oligosaccharides in gnotobiotic models of infant undernutrition. Cell, 164, 859-871 (2016).

Blanton, L.V., Charbonneau, M.R., Salih, T., Barratt, M.J., Venkatesh, S., Ilkaveya, O., Subramanian, S., Manary, M.J., Trehan, I., Jorgensen, J.M., Fan, Y., Henrissat, B., Leyn, S.A., Rodionov, D.A., Osterman, A.L., Maleta, K.M., Newgard, C.B., Ashorn, P., Dewey, K.G., and Gordon, J.I. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children, Science, 351, aad3311 (2016).

Planer, J.D., Peng, Y., Kau, A.L., Blanton, L.V., Ndao, I.M., Tarr, P.I., Warner, B.B., and Gordon, J.I. Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice. Nature, in press doi:10.1038/nature17940 (2016).