Seth Rakoff-Nahoum
Seth Rakoff-Nahoum
Associate Professor of Pediatrics

Boston Children's Hospital
300 Longwood Ave.
Boston MA 02115
Tel: 617-525-2663

Lab Size: Between 5-10


Despite the growing recognition of the importance of the microbiota to humans, there are fundamental aspects of the microbiota and its relation to the host that are largely unexplored.  These range from knowledge of the basic biology of individual strains and species, to higher level understanding of the mechanistic and ecological interactions between members of the microbiota, the environment and the host.

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 systems to study the adaptation of gut bacteria to the environment (such as using TnSeq), mouse gnotobiotics, 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.

Current focus in the Rakoff-Nahoum lab center in four 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 and host interactions, 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.


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.

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.

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.

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.

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