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Supplemental Data

Wagner VE, Dey N, Guruge J, Hsiao A, Ahern PP, Semenkovich NP, Blanton LV, Cheng J, Griffin N, Stappenbeck TS, Ilkayeva O, Newgard CB, Petri W, Haque R, Ahmed T, Gordon JI. Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition. Sci Transl Med. 2016 Nov 23;8(366):366ra164. PMID: 27881825
Abstract Reprint Full Text

Kau AL, Planer JD, Liu J, Rao S, Yatsunenko T, Trehan I, Manary MJ6, Liu TC, Stappenbeck TS, Maleta KM, Ashorn P, Dewey KG, Houpt ER, Hsieh CS, Gordon JI. Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy. Sci Transl Med. 2015 Feb 25;7(276):276ra24. doi: 10.1126/scitranslmed.aaa4877.
Abstract  •  Reprint  •  Full Text

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., VanArendonk, L. G., Zhang, Q., Province, M. A., Petri, W. A. Jr, Ahmed, T., Gordon, J. I. Persistent Gut Microbiota Immaturity in Malnourished Bangladeshi Children. Nature (2014) doi: 10.1038/nature13421. Additional Information

V.K. Ridaura et. al. Science (2013). Ridaura_RDPtrained_dataset for assigning taxonomy of 16S rRNA reads: Ridaura_RDPtrained_dataset.gz

Smith M.I., Yatsunenko T., Manary M.J., Trehan I., Mkakosya R., Cheng J., Kau A.L., 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., Gordon J.I. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science. 2013 Feb 1;339(6119):548-54.
Additional Information (Zip file 861KB) KEGG KO table (Zip file 500KB)

Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. Additional Information

Nature. 2012 May 9;486(7402):222-7. doi: 10.1038/nature11053

McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL, Henrissat B, Oozeer R, Cools-Portier S, Gobert G, Chervaux C, Knights D,Lozupone CA, Knight R, Duncan AE, Bain JR, Muehlbauer MJ, Newgard CB, Heath AC, Gordon JI. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med (2011). Additional Information

Demos for INSEQ_analysis pipeline (Zip file 891MB)

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  2011. Supplemental Information

Hansen, Elizabeth "Gene annotations for Methanobrevibacter smtihii strains isolated from human fecal samples"

Faith, J., Rey, R., Gordon, J.I. Reyniers and Sacksteder, 1957 (PDF)

Turnbaugh, P.J., Quince, C., Faith, J.J., McHardy, A.C., Yatsunenko, T., Niazi, F., Affourtit, J., Egholm, M., Henrissat, B., Knight, R., and Gordon, J.I. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. PNAS (2010). Supplementary Information

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. Sci. Transl. Med 6ra14 (2009). Supplementary Information

Marios Giannakis, Helene Kling Bäckhed, Swaine L. Chen, Jeremiah J. Faith, Meng Wu, Janaki L. Guruge, Lars Engstrand, and Jeffrey I. Gordon. The Response of Gastric Epithelial Progenitors to Helicobacter pylori Isolates Obtained from Swedish Patients with Chronic Atrophic Gastritis. J Biol Chem. [DOI:10.1074/jbc.M109.052738](1 September 2009). Supplemental Information

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 [DOI: 10.1038/nature07540] (30 November 2008). Supplemental Information

Ley, R. E., M. Hamady, C. Lozupone, P. J. Turnbaugh, R. R. Ramey, J. S. Bircher, M. L. Schlegel, T. A. Tucker, M. D. Schrenzel, R. Knight, and J. I. Gordon. Evolution of Mammals and Their Gut Microbes. Science Express [DOI: 10.1126/science.1155725](22 May 2008) Supplemental Information

Ley, R.E., Turnbaugh, P.J., Klein, S., and Gordon, J.I. Human gut microbes linked to obesity. Nature, 444:1022–1023 (2006). Supplemental Information (ZIP File)

Ley, R. E., Backhed, 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). Supplemental Information (ZIP File)

Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, Fulton R, Latreille P, Kim K, Wilson RK, Gordon JI. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci USA, 2007 Jun 19;104(25):10643-8. Epub 2007 Jun 11. Supplemental Information

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

Bäckhed, F., Ley, R.E., Sonnenburg, J.L., Peterson, D.A., and Gordon, J.I. (2005) Host-bacterial mutualism in the human intestine, Science 307:1915-1920. Supplemental Information

Oh, J.D. Karam, S. and Gordon, J.I. (2005) Intracellular Helicobacter pylori in gastric epithelial progenitors, Proc. Natl. Acad. Sci. USA 102: 5186-5191 (2005). Supplemental Information

Syder, A.J.*, Karam, S.M.*, Mills, J.C., Ippolito, J.E., Ansari, H.R., Farook,V., and Gordon, J.I. (2004) A transgenic mouse model of metastatic carcinoma involving trans-differentiation of a gastric epithelial lineage progenitor to a neuroendocrine phenotype. Proc. Natl. Acad. Sci. USA, 101: 4471-4476.  Supplemental Information  (* Both authors contributed equally)

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

Xu, J., Bjursell, M.K., Himrod, J., Deng, S., Carmichael, L.K., Chiang, H.C., Hooper, L.V., and Gordon, J.I. (2003) A Genomic View of the Human-Bacteroides thetaiotaomicron Symbiosis, Science, 299: 2074-2076. Supplemental information

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

Mills, J.C. and Gordon, J.I. (2001) A new approach for filtering noise from high-density oligonucleotide microarray datasets. Nucleic Acids Research 29(13). Supplemental information