Publications

Present - 2020

  • Kuziel GA, Lozano GL, Simian C, Li L, Manion J, Stephen-Victor E, Chatila T, Dong M, Weng JK, Rakoff-Nahoum S. Functional diversification of dietary plant small molecules by the gut microbiome. Cell. 2025. Advance online publication. PMID: [Not available yet]. https://doi.org/10.1016/j.cell.2025.01.045

  • Stephen-Victor E, Kuziel GA, Martinez-Blanco M, Jugder BE, Benamar M, Wang Z, Chen Q, Lozano GL, Abdel-Gadir A, Cui Y, Fong J, Saint-Denis E, Chang I, Nadeau KC, Phipatanakul W, Zhang A, Farraj FA, Holder-Niles F, Zeve D, Breault DT, Schmitz-Abe K, Rachid R, Crestani E, Rakoff-Nahoum S, Chatila TA. RELMβ sets the threshold for microbiome-dependent oral tolerance. Nature. 2025;638(8051):760–8. PMID: [Not available yet]. https://doi.org/10.1038/s41586-024-08440-7

  • Kuziel GA, Rakoff-Nahoum S. The gut microbiome. Curr Biol. 2022;32(6):R257–64. PMID: 35349808. https://doi.org/10.1016/j.cub.2022.02.023

  • Park S, Rao C, Coyte KZ, Kuziel GA, Zhang Y, Huang W, Franzosa EA, Weng JK, Huttenhower C, Rakoff-Nahoum S. Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite. Cell. 2022;185(3):513–29. PMID: 35120663. https://doi.org/10.1016/j.cell.2022.01.002

  • Rao C, Coyte K, Bainter W, Geha R, Martin C, Rakoff-Nahoum S. Multi-kingdom ecological drivers of microbiota assembly in preterm infants. Nature. 2021;591(7851):633–8. PMID: 33627867. https://doi.org/10.1038/s41586-021-03241-8

  • Coyte KZ, Rao C, Rakoff-Nahoum S, Foster KR. Ecological rules for the assembly of microbiome communities. PLOS Biol. 2021;19(2):e3001116. PMID: 33606675. https://doi.org/10.1371/journal.pbio.3001116

2019 - 2010

  • Coyte K, Rakoff-Nahoum S. Understanding competition and cooperation within the mammalian gut microbiome. Curr Biol. 2019 Jun 3;29(11):R538-R544. PMID: 31163167. https://doi.org/10.1016/j.cub.2019.04.017

  • Mead BE, Ordovas-Montanes J, Braun AP, Levy LE, Bhargava P, Szucs MJ, Ammendolia DA, MacMullan MA, Yin X, Hughes TK, Wadsworth MH 2nd, Ahmad R, Rakoff-Nahoum S, Carr SA, Langer R, Collins JJ, Shalek AK, Karp JM. Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. BMC Biol. 2018 Jun 5;16(1):62. PMID: 29871632. https://doi.org/10.1186/s12915-018-0527-2

  • Foster, KR, Schluter J., Coyte KZ. and Rakoff-Nahoum, S. The evolution of the host microbiome as an ecosystem on a leash. Nature. 2017 Aug 2;548(7665):43-51. PMID: 28770836. https://doi.org/10.1038/nature23292

  • Sasabe S, Miyoshi Y, Rakoff-Nahoum S, Zhang T, Mita M, Davis BM, Hamase K, Waldor MK. Interplay between microbial D-amino acids and host D-amino acid oxidase modifies murine mucosal defence and gut microbiota. Nat Microbiol. 2016 July 25;1:16125. PMID: 27670111. https://doi.org/10.1038/nmicrobiol.2016.125

  • Rakoff-Nahoum S, Foster KR, Comstock LE. The evolution of cooperation within the gut microbiota. Nature. 2016 Apr 25;533:255-259. PMID: 27111508. https://doi.org/10.1038/nature17626

  • Rakoff-Nahoum S. Another Reason to Thank Mom: Gestational Effects of Microbiota Metabolites. Cell Host Microbe. 2016 Apr 13;19(4):425-7. PMID: 27078061. https://doi.org/10.1016/j.chom.2016.03.012

  • McLoughlin K, Schluter K, Rakoff-Nahoum S, Smith A, Foster KR. 2016. Host selection of microbiota via differential adhesion. Cell Host Microbe. 2016 Apr 13;19(4):550-9. PMID: 27053168. https://doi.org/10.1016/j.chom.2016.02.021

  • Ordovas-Montanes J, Rakoff-Nahoum S, Huang S, Riol-Blanco L, Barreiro O, von Andrian UH. The Regulation of Immunological Processes by Peripheral Neurons in Homeostasis and Disease. Trends Immunol. 2015 Oct;36(10):578-604. Review. PMID: 26431937. https://doi.org/10.1016/j.it.2015.08.007

  • Rakoff-Nahoum S, Kong Y, Kleinstein SH, Subramanian S, Ahern PP, Gordon JI, Medzhitov R. Analysis of gene-environment interactions in postnatal development of the mammalian intestine. Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):1929-36. PMID: 25691701. https://doi.org/10.1073/pnas.1424886112

  • Rakoff-Nahoum S, Comstock LE. Immunology: Starve a fever, feed the microbiota. Nature. 2014 Oct 30;514(7524):576-7. Epub 2014 Oct 1. PMID: 25274298. https://doi.org/10.1038/nature13756

  • Rakoff-Nahoum S, Coyne MJ, Comstock LE. An ecological network of polysaccharide utilization among human intestinal symbionts. Curr Biol. 2014 Jan 6;24(1):40-9. PMID: 24332541. https://doi.org/10.1016/j.cub.2013.10.077

  • Rakoff-Nahoum S, Bousvaros A. Innate and adaptive immune connections in inflammatory bowel diseases. Curr Opin Gastroenterol. 2010 Nov;26(6):572-7. Review. PMID: 20871398. https://doi.org/10.1097/MOG.0b013e32833f126d

2009 - 2000

  • Rakoff-Nahoum S, Medzhitov R. Toll-like receptors and cancer. Nat Rev Cancer. 2009 Jan;9(1):57-63. Review. PMID: 19052556. https://doi.org/10.1038/nrc2541

  • Rakoff-Nahoum S, Medzhitov R. Innate immune recognition of the indigenous microbial flora. Mucosal Immunol. 2008 Nov;1 Suppl 1:S10-4. Review. PMID: 19079220. https://doi.org/10.1038/mi.2008.49

  • Rakoff-Nahoum S, Medzhitov R. Role of toll-like receptors in tissue repair and tumorigenesis. Biochemistry (Mosc). 2008 May;73(5):555-61. Review. PMID: 18605980. https://doi.org/10.1134/s0006297908050088

  • Rakoff-Nahoum S, Medzhitov R. Regulation of spontaneous intestinal tumorigenesis through the adaptor protein MyD88. Science. 2007 Jul 6;317(5834):124-7. PMID: 17615359. https://doi.org/10.1126/science.1140488

  • Garrison KE, Jones RB, Meiklejohn DA, Anwar N, Ndhlovu LC, Chapman JM, Erickson AL, Agrawal A, Spotts G, Hecht FM, Rakoff-Nahoum S, Lenz J, Ostrowski MA, Nixon DF. T cell responses to human endogenous retroviruses in HIV-1 infection. PLoS Pathog. 2007 Nov;3(11):e165. PMID: 17997601. https://doi.org/10.1371/journal.ppat.0030165

  • Rakoff-Nahoum S, Medzhitov R. Prostaglandin-secreting cells: a portable first aid kit for tissue repair. J Clin Invest. 2007 Jan;117(1):83-6. PMID: 17200710. https://doi.org/10.1172/JCI30865

  • Rakoff-Nahoum S, Hao L, Medzhitov R. Role of toll-like receptors in spontaneous commensal-dependent colitis. Immunity. 2006 Aug;25(2):319-29. PMID: 16879997. https://doi.org/10.1016/j.immuni.2006.06.010

  • Rakoff-Nahoum S. Why cancer and inflammation? Yale J Biol Med. 2006 Dec;79(3-4):123-30. Review. PMID: 17940622.

  • Rakoff-Nahoum S, Kuebler PJ, Heymann JJ, E Sheehy M, Ortiz GM, S Ogg G, Barbour JD, Lenz J, Steinfeld AD, Nixon DF. Detection of T lymphocytes specific for human endogenous retrovirus K (HERV-K) in patients with seminoma. AIDS Res Hum Retroviruses. 2006 Jan;22(1):52-6. PMID: 16438646. https://doi.org/10.1089/aid.2006.22.52

  • Rakoff-Nahoum S, Medzhitov R. Role of the innate immune system and host-commensal mutualism. Curr Top Microbiol Immunol. 2006;308:1-18. Review. PMID: 16922084. https://doi.org/10.1007/3-540-30657-9_1

  • Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell. 2004 Jul 23;118(2):229-41. PMID: 15260992. https://doi.org/10.1016/j.cell.2004.07.002