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


  1. A. Chen-Liaw, V. Aggarwala, I. Mogno, C. Haifer, Z. Li, J. Eggers, D. Helmus, A. Hart, J. Wehkamp, E Lamousé-Smith, R.L. Kerby, F.E. Rey, J.F. Colombel, M.A. Kamm, T.J. Borody, A. Grinspan, S. Paramsothy, N.O. Kaakoush, M.C. Dubinsky, J.J. Faith. Gut microbiota bacterial strain richness is species specific and limits therapeutic engraftment. bioRxiv 2022

  2. J.J. Faith, A. Chen-Liaw, V. Aggarwala, N.O. Kaakoush, T.J. Borody, H. Mitchell, M.A. Kamm, S. Paramsothy, E.S. Snitkin, I. Mogno. Strain population structure varies widely across bacterial species and predicts strain colonization in unrelated individuals. bioRxiv 2020.10.17.343640; doi:

Select traditional journal publications

  1. M.P. Spindler, I. Mogno, P. Suri, G.J. Britton+, J.J. Faith+. Species-specific CD4+ T cells enable prediction of mucosal immune phenotypes from microbiota composition. Proc Natl Acad Sci U S A. 2023 Mar 21;120(12):e2215914120. doi: 10.1073/pnas.2215914120.

  2. M.P. Spindler, S.S. Siu, I. Mogno, Z. Li, C. Yang, S. Mehandru, G.J. Britton+, J.J. Faith+. Human gut microbiota stimulate defined innate immune responses that vary from phylum to strain. Cell Host Microbe. 2022 Oct 12;30(10):1481-1498.e5. doi: 10.1016/j.chom.2022.08.009.

  3. C. Yang, A. Chen-Liaw, M.P. Spindler, D. Tortorella, T.M. Moran, A. Cerutti, J.J. Faith. Immunoglobulin A Antibody Composition Is Sculpted to Bind the Self Gut Microbiome. Science Immunology. 2022 Jul 15;7(73):eabg3208. doi: 10.1126/sciimmunol.abg3208.

  4. V. Aggarwala, I. Mogno, Z. Li, C. Yang, G.J. Britton, A. Chen-Liaw, J. Mitcham, G. Bongers, D. Gevers, J.C. Clemente, J.F. Colombel, A. Grinspan, J.J. Faith. Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes. Nat Microbiol. 2021 Oct;6(10):1309-1318. doi: 10.1038/s41564-021-00966-0.

  5. G.J. Britton*, A. Chen-Liaw*, F. Cossarini*, A.E. Livanos*, M.P. Spindler*, T. Plitt, J. Eggers, I. Mogno, A. Gonzalez-Reiche, S. Siu, M. Tankelevich, L. Grinspan, R.E. Dixon, D. Jha, G. Martinez-Delgado, F. Amanat, D.A. Hoagland, B. tenOever, M.C. Dubinsky, M. Merad, H. van Bakel, F. Krammer, G. Bongers, S. Mehandru, J.J. Faith. Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19. Sci Rep. 2021 Jun 25;11(1):13308. doi: 10.1038/s41598-021-92740-9.

  6. G.J. Britton, E.J. Contijoch, M.P. Spindler, V. Aggarwala, B. Dogan, G. Bongers, L. San Mateo, A. Baltus, A. Das, D. Gevers, T.J. Borody, N.O. Kaakoush, M.A. Kamm, H. Mitchell, S. Paramsothy, J.C. Clemente, J.F. Colombel, K.W. Simpson, M.C. Dubinsky, A. Grinspan, J.J. Faith. Defined microbiota transplant restores Th17/RORγt+ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas. Proc Natl Acad Sci U S A. 2020 Sep 1;117(35):21536-21545. doi: 10.1073/pnas.1922189117.

  7. C. Yang, I. Mogno, E.J. Contijoch, J.N. Borgerding, V. Aggarwala, Z. Li, S. Siu, E.K. Grasset, D.S. Helmus, M.C. Dubinsky, S. Mehandru, A. Cerutti, J.J. Faith. Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation. Cell Host Microbe. 2020 Mar 11;27(3):467-475.e6. doi: 10.1016/j.chom.2020.01.016.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. J.J. Faith and D.D. Pollock. Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics. 2003 Oct;165(2):735-45.

Reviews and Commentaries

  1. T. Plitt and J.J. Faith. The unexplored microbes in health and disease. Semin Immunol. 2023 Feb 27;66:101735. doi: 10.1016/j.smim.2023.101735.

  2. G.J. Britton and J.J. Faith. Causative Microbes in Host-Microbiome Interactions. Annu Rev Microbiol. 2021 Oct 8;75:223-242.

  3. 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.

  4. 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.

  5. 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.

  6. 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