Faith Laboratory in the Icahn School of Medicine at Mount Sinai; Reverse engineering the interactions between our diets, our gut microbes and microbiome, and our health


h-index and citation counts


Traditional journals

  1. E.J. Contijoch, G.J. Britton, C. Yang, I. Mogno, Z. Li, R. Ng, S.R. Llewellyn, S. Hira, C. Johnson, K.M. Rabinowitz, R. Barkan, I. Dotan, R.P. Hirten, S.C. Fu, Y. Luo, N. Yang, T. Luong, P.R. Labrias, S. Lira, I. Peter, A. Grinspan, J.C. Clemente, R. Kosoy, S. Kim-Schulze, X. Qin, A. Castillo, A. Hurley, A. Atreja, J. Rogers, F. Fasihuddin, M. Saliaj, A. Nolan, P. Reyes-Mercedes, C. Rodriguez, S. Aly, K. Santa-Cruz, L.A. Peters, M. Suárez-Fariñas, R. Huang, K. Hao, J. Zhu, B. Zhang, B. Losic, H. Irizar, W.M. Song, A. Di Narzo, W. Wang, B.L. Cohen, C. DiMaio, D. Greenwald, S. Itzkowitz, A.L. Lucas, J. Marion, E. Maser, R. Ungaro, S. Nayagmon, J. Novak, B. Shah, T. Ullman, P. Rubin, J. George, P. Legnina, S.E. Telesco, J.R. Friedman, C. Brodmerkel, S. Plevy, J. Cho, J.F. Colombel, E. Schadt, C. Argmann, M. Dubinsky, A. Kasarskis, B. Sands, J.J. Faith. Gut microbiota density influences host physiology and is shaped by host and microbial factors. eLife 2019.

  2. G.J. Britton, E.J. Contijoch, I. Mogno, O.H. Vennaro, S.R. Llewellyn, R. Ng, Z. Li, A. Mortha, M. Merad, A. Das, D. Gevers, D.P.B. McGovern, N. Singh, J. Braun, J.P. Jacobs, J.C. Clemente, A. Grinspan, B.E. Sands, J.F. Colombel, M.C. Dubinsky, J.J. Faith. Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt(+) Regulatory T Cells and Exacerbate Colitis in Mice. Immunity. 2019 Jan 15;50(1):212-224.e4. doi: 10.1016/j.immuni.2018.12.015.

  3. S. Paramsothy, S. Nielsen, M.A. Kamm, N.P. Deshpande, J.J. Faith, J.C. Clemente, R. Paramsothy, A.J. Walsh, J. van den Bogaerde, D. Samuel, R.W.L. Leong, S. Connor, W. Ng, E. Lin, T.J. Borody, M.R. Wilkins, J.F. Colombel, H.M. Mitchell, N.O. Kaakoush. Specific Bacteria and Metabolites Associated with Response to Fecal Microbiota Transplantation in Patients with Ulcerative Colitis. Gastroenterology. 2018 Dec 6. pii: S0016-5085(18)35387-3. doi: 10.1053/j.gastro.2018.12.001.

  4. L. Chen, Z. He, A.C. Iuga, S.N. Martins Filho, J.J. Faith, J.C. Clemente, M. Deshpande, A. Jayaprakash, J.F. Colombel, J.J. Lafaille, R. Sachidanandam, G.C. Furtado, S.A. Lira. Diet Modifies Colonic Microbiota and CD4(+) T Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-cell Expression of Interleukin 23. Gastroenterology. 2018 Jun 14.

  5. J. Beaulaurier, S. Zhu, G. Deikus, I. Mogno, X.S. Zhang, A. Davis-Richardson, R. Canepa, E.W. Triplett, J.J. Faith, R. Sebra, E.E. Schadt, G. Fang. Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nat Biotechnol. 2017 Dec 11. doi: 10.1038/nbt.4037.

  6. S.R. Llewellyn, G.J. Britton, E.J. Contijoch, O.H. Vennaro, A. Mortha, J.F. Colombel, A. Grinspan, J.C. Clemente, M. Merad, J.J. Faith. Interactions between diet and the intestinal microbiota alter intestinal permeability and colitis severity in mice. Gastroenterology. 2017 Nov 23. pii: S0016-5085(17)36388-6. doi: 10.1053/j.gastro.2017.11.030.

  7. L.A. Peters, J. Perrigoue, A. Mortha, A. Iuga, W.M. Song, E.M. Neiman, S.R. Llewellyn, A. Di Narzo, B.A. Kidd, S.E. Telesco, Y. Zhao, A. Stojmirovic, J. Sendecki, K. Shameer, R. Miotto, B. Losic, H. Shah, E. Lee, M. Wang, J.J. Faith, A. Kasarskis, C. Brodmerkel, M. Curran, A. Das, J.R. Friedman, Y. Fukui, M.B. Humphrey, B.M. Iritani, N. Sibinga, T.K. Tarrant, C. Argmann, K. Hao, P. Roussos, J. Zhu, B. Zhang, R. Dobrin, L.F. Mayer, E.E. Schadt. A functional genomics predictive network model identifies regulators of inflammatory bowel disease. Nat Genet. 2017 Oct;49(10):1437-1449. doi: 10.1038/ng.3947.

  8. A. Chudnovskiy, A. Mortha, V. Kana, A. Kennard, J.D. Ramirez, A. Rahman, R. Remark, I. Mogno, R. Ng, S. Gnjatic, E.D. Amir, A. Solovyov, B. Greenbaum, J. Clemente, J.J. Faith, Y. Belkaid, M.E. Grigg, M. Merad. Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome. Cell. 2016 Oct 6;167(2):444-456.e14. doi: 10.1016/j.cell.2016.08.076.

  9. D. Ruane, A. Chorny, H. Lee, J.J. Faith, G. Pandey, M. Shan, N. Simchoni, A. Rahman, A. Garg, E.G. Weinstein, M. Oropallo, M. Gaylord, R. Ungaro, C. Cunningham-Rundles, K. Alexandropoulos, D. Mucida, M. Merad, A. Cerutti, S. Mehandru. Microbiota regulate the ability of lung dendritic cells to induce IgA class-switch recombination and generate protective gastrointestinal immune responses. J Exp Med. 2016 Jan 11;213(1):53-73.

  10. D. Zhang, G. Chen, D. Manwani, A. Mortha, C. Xu, J.J. Faith, R.D. Burk, Y. Kunisaki, J.E. Jang, C. Scheiermann, M. Merad, P.S. Frenette. Neutrophil ageing is regulated by the microbiome. Nature. 2015 Sep 24;525(7570):528-32.

  11. J.J. Faith*, P.A. Ahern*, V.K. Ridaura, J. Cheng, and J.I. Gordon. Identifying Gut Microbe-Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice. Sci Transl Med. 2014 Jan 22.

  12. V.K. Ridaura, J.J. Faith, F.E. Rey, J. Cheng, A.E. Duncan, A.L. Kau, N.W. Griffin, V. Lombard, B. Henrissat, J.R. Bain, M.J. Mehlbauer, O. Ilkayeva, C.F. Semenkovich, K. Funai, D.K. Hayashi, M.C. Martini, L.K. Ursell J.C. Clemente, W.V. Treuren, W.A. Walters, R. Knight, C.B. Newgard, A.C. Heath, J.I. Gordon. Cultured gut bacterial consortia from twins discordant for obesity modulate adiposity and metabolic phenotypes in gnotobiotic mice. Science. 2013 Sept 6.

  13. J.J. Faith, J.L. Guruge, M. Charbonneau, S. Subramanian, H.S. Seedorf, A.L. Goodman, J.C. Clemente, R. Knight, A.C. Heath, R.L. Leibel, M. Rosenbaum, J.I. Gordon. The long-term stability of the human gut microbiota. Science. 2013 Jul 5.

  14. N.A. Bokulich, S. Subramanian, J.J. Faith, D. Gevers, J.I. Gordon, R. Knight, D.A. Mills, J.G. Caporaso. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 2012 Dec 2. doi: 10.1038/nmeth.2276.

  15. C. Lozupone, K. Faust, J. Raes, J.J. Faith, D.N. Frank, J. Zaneveld, J.I. Gordon, R. Knight. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res. 2012 Jun 4.

  16. N.P. McNulty, T. Yatsunenko, A. Hsiao, J.J. Faith, B.D. Muegge, A.L. Goodman, B. Henrissat, R. Oozeer, S. Cools-Portier, G. Gobert, C. Chervaux, D. Knights, C.A. Lozupone, R. Knight, A.E. Duncan, J.R. Bain, M.J. Muehlbauer, C.B. Newgard, A.C. Heath, J.I. Gordon. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med. 2011 Oct 26;3(106):106ra106.

  17. J.J. Faith, N.P. McNulty, F.E. Rey, and J.I. Gordon. Predicting a Human Gut Microbiota’s Response to Diet in Gnotobiotic Mice. Science. 2011 Jul 1;333(6038):101-4. Epub 2011 May 19.

  18. A.L. Goodman, G.K. Kallstrom, J.J. Faith, A. Reyes, A. Moore, G. Dantas, and J.I. Gordon. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6252-7. Epub 2011 Mar 21.

  19. F.E. Rey*, J.J. Faith*, J. Bain, M.J. Muehlbauer, R.D. Stevens, C.B. Newgard, and J.I. Gordon. Dissecting the in vivo metabolic potential of two human gut acetogens. J Biol Chem. 2010 Jul 16;285(29):22082-90. Epub 2010 May 5.

  20. P.J. Turnbaugh, C. Quince, J.J. Faith, A.C. McHardy, T. Yatsunenko, F. Niazi, J. Affourtit, M. Egholm, B. Henrissat, R. Knight, and J.I. Gordon. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7503-8. Epub 2010 Apr 2.

  21. P.J. Turnbaugh, V.K. Ridaura, J.J. Faith, F.E. Rey, R. Knight, and J.I. Gordon. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009 Nov 11;1(6):6ra14.

  22. M. Giannakis*, H.K. Backhed*, S.L. Chen*, J.J. Faith*, M. Wu, J.L. Guruge, L. Engstrand, and J.I. Gordon. The response of gastric epithelial progenitors to Helicobacter pylori isolates obtained from Swedish patients with chronic atrophic gastritis. J Biol Chem. 2009 Oct 30;284(44):30383-94. Epub 2009 Sep 1.

  23. J.J. Faith, M.E. Driscoll, V.A. Fusaro, E.J. Cosgrove, B. Hayete, F.S. Juhn, S.J. Schneider, and T.S. Gardner. Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res. 2008 Jan;36(Database issue):D866-70. Epub 2007 Oct 11.

  24. J.J. Faith, A.J. Olson, T.S. Gardner, and R. Sachidanandam. Lightweight Genome Viewer: portable software for browsing genomics data in its chromosomal context. BMC Bioinformatics. 2007 Sep 18;8:344.

  25. J.J. Faith*, B. Hayete*, J.T. Thaden, I. Mogno, J. Wierzbowski, G. Cottarel, S. Kasif, J.J. Collins, and T.S. Gardner. Large-scale computational mapping and experimental validation of Escherichia coli transcriptional regulatory interactions from a compendium of expression profiles. PLoS Biology. 2007 Jan;5(1):e8.

  26. L.A. Nahum, M.T. Reynolds, Z.O. Wang, J.J. Faith, R. Jonna, Z.J. Jiang, T.J. Meyer, and D.D. Pollock. EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity. BMC Bioinformatics. 2006 Sep 6;7 Suppl 2:S7.

  27. S.Z. Raina, J.J. Faith, H. Seligmann, T. Disotell, C-B. Stewart, and D.D. Pollock. Evolution of base substitution gradients in primate mitochondrial genomes. Genome Res. 2005 May;15(5):665-73.

  28. J.J. Faith and D.D. Pollock. Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics. Oct;165(2):735-45.

  29. M.S. Philips, R. Lawrence, R. Sachidanandam, A.P. Morris, D.J. Balding, M.A. Donaldson, J.F. Studebaker, W.M. Ankener, S.V. Alfisi, F.S. Kuo, A.L. Camisa, V. Pazorov, K.E. Scott, B.J. Carey, J.J. Faith, G. Katari, H.A Bhatti, J.M. Cyr, V. Derohannessian, C. Elosua, A.M. Forman, N.M. Grecco, C.R. Hock, J.M. Kuebler, J.A. Lathrop, M.A. Mockler, E.P. Nachtman, S.L. Restine, S.A. Varde, M.J. Hozza, C.A. Gelfand, J. Broxholme, G.R. Abecasis, M.T Boyce-Jacino, and L.R. Cardon. Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nature Genetics. 2003 Mar;33(3):382-7. Epub 2003 Feb 18.

Reviews and Commentaries

  1. J.J. Faith+, J.F. Colombel+, and J.I. Gordon+. Identifying strains that contribute to complex diseases through the study of microbial inheritance. Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):633-40.

  2. P.P. Ahern*, J.J. Faith*, and J.I. Gordon. Mining the human gut microbiota for effector strains that shape the immune system. Immunity. 2014 Jun 19;40(6):815-23.

  3. J.J. Faith*, F.E. Rey*, D. O’Donnell, M. Karlsson, N.P. McNulty, G. Kallstrom, A.L. Goodman, and J.I. Gordon. Creating and characterizing communities of human gut microbes in gnotobiotic mice. ISME Journal. 2010. Sep;4(9):1094-8. Epub 2010 Jul 22.

  4. T.S. Gardner and J.J. Faith. Reverse-engineering transcription control networks. Physics of Life Reviews. 2010 Apr 22;2(1):65-88.

* = co-first author
+ = co-corresponding author