Lab: SRN Lab

The goal of the Rakoff-Nahoum lab is a comprehensive understanding of the host-associated microbiota at various levels of biological organization: from genes to molecules to organisms to ecosystems, and importantly, the determination of cause and effect. To achieve this, we couple empirical approaches with ecological and evolutionary frameworks. We use the tools of classic bacterial genetics of gut anaerobes including the cultivation, random and directed mutagenesis of individual members of the mammalian microbiota (Bacteroides, Firmicutes, Actinobacteria), in vitro and in vivo experimental and gnotobiotic systems to study the adaptation of gut bacteria to the environment, computational approaches to microbiome ecology, and high throughput in vitro pipelines for the cultivation, genetic, chemical and phenotypic analysis of the effects of members of the microbiota on each other and the host, with focus on innate and adaptive immunity.

Current focuses in the Rakoff-Nahoum lab center in six non-mutually exclusive dimensions: 1) genetic and molecular mechanisms of cooperation and competition among the gut and female reproductive tract microbiome, 2) the role of microbial metabolites in gut microbial ecology, 3) the glycobiology of host-microbiome interactions, 4) microbiome ecology in human populations, focusing on pediatric health and disease, 5) metabolism of dietary and microbial bioactive molecules by the microbiome and impact on host innate and adaptive immunity, 6) the role of gut and FRT community function in inflammation.


Dr. Rakoff-Nahoum received B.A.’s in Biology and Religious Studies at Brown University, and both an M.D. and Ph.D in Immunobiology from Yale University, performing graduate work with Ruslan Medzhitov, studying pattern recognition of the microbiota. During clinical training in Pediatrics in the Boston Combined Residency Program and in Pediatric Infectious Diseases at Boston Children’s Hospital, he performed postdoctoral work with Laurie Comstock, studying social evolution in gut microbial communities. Dr. Rakoff-Nahoum’s lab is supported by an NIH Director’s New Innovator Award,the Pew Scholars Program in Biomedical Sciences, a Basil O’Connor Award from the March of Dimes, and a Career Award for Medical Scientists from the Burroughs Wellcome Foundation. Dr. Rakoff-Nahoum’s clinical focus is in the immunocompromised infectious diseases pediatric population.


Publications powered by Harvard Catalyst Profiles

  1. Ecological rules for the assembly of microbiome communities. PLoS Biol. 2021 Feb 19; 19(2):e3001116. View abstract
  2. Combined immunodeficiency due to a mutation in the ?1 subunit of the coat protein I complex. J Clin Invest. 2021 Feb 01; 131(3). View abstract
  3. Stress ulcer prophylaxis versus placebo-a blinded randomized control trial to evaluate the safety of two strategies in critically ill infants with congenital heart disease (SUPPRESS-CHD). Trials. 2020 Jun 29; 21(1):590. View abstract
  4. Distribution and storage of inflammatory memory in barrier tissues. Nat Rev Immunol. 2020 05; 20(5):308-320. View abstract
  5. Understanding Competition and Cooperation within the Mammalian Gut Microbiome. Curr Biol. 2019 06 03; 29(11):R538-R544. View abstract
  6. Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. BMC Biol. 2018 06 05; 16(1):62. View abstract
  7. The evolution of the host microbiome as an ecosystem on a leash. Nature. 2017 08 02; 548(7665):43-51. View abstract
  8. Interplay between microbial d-amino acids and host d-amino acid oxidase modifies murine mucosal defence and gut microbiota. Nat Microbiol. 2016 07 25; 1(10):16125. View abstract
  9. The evolution of cooperation within the gut microbiota. Nature. 2016 05 12; 533(7602):255-9. View abstract
  10. Another Reason to Thank Mom: Gestational Effects of Microbiota Metabolites. . 2016 Apr 13; 19(4):425-7. View abstract
  11. Host Selection of Microbiota via Differential Adhesion. . 2016 Apr 13; 19(4):550-9. View abstract
  12. The Regulation of Immunological Processes by Peripheral Neurons in Homeostasis and Disease. Trends Immunol. 2015 Oct; 36(10):578-604. View abstract
  13. 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. View abstract
  14. Immunology: Starve a fever, feed the microbiota. Nature. 2014 Oct 30; 514(7524):576-7. View abstract
  15. An ecological network of polysaccharide utilization among human intestinal symbionts. Curr Biol. 2014 Jan 06; 24(1):40-49. View abstract
  16. Innate and adaptive immune connections in inflammatory bowel diseases. Curr Opin Gastroenterol. 2010 Nov; 26(6):572-7. View abstract
  17. Toll-like receptors and cancer. Nat Rev Cancer. 2009 Jan; 9(1):57-63. View abstract
  18. Innate immune recognition of the indigenous microbial flora. Mucosal Immunol. 2008 Nov; 1 Suppl 1:S10-4. View abstract
  19. Role of toll-like receptors in tissue repair and tumorigenesis. Biochemistry (Mosc). 2008 May; 73(5):555-61. View abstract
  20. T cell responses to human endogenous retroviruses in HIV-1 infection. PLoS Pathog. 2007 Nov; 3(11):e165. View abstract
  21. Regulation of spontaneous intestinal tumorigenesis through the adaptor protein MyD88. Science. 2007 Jul 06; 317(5834):124-7. View abstract
  22. Prostaglandin-secreting cells: a portable first aid kit for tissue repair. J Clin Invest. 2007 Jan; 117(1):83-6. View abstract
  23. Why cancer and inflammation? Yale J Biol Med. 2006 Dec; 79(3-4):123-30. View abstract
  24. Retraction: Regulation of class II expression in monocytic cells after HIV-1 infection. J Immunol. 2006 Nov 01; 177(9):6561. View abstract
  25. Role of toll-like receptors in spontaneous commensal-dependent colitis. Immunity. 2006 Aug; 25(2):319-29. View abstract
  26. Role of the innate immune system and host-commensal mutualism. Curr Top Microbiol Immunol. 2006; 308:1-18. View abstract
  27. 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. View abstract
  28. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell. 2004 Jul 23; 118(2):229-41. View abstract
  29. Regulation of class II expression in monocytic cells after HIV-1 infection. J Immunol. 2001 Aug 15; 167(4):2331-42. View abstract