BBS Faculty Member - Seth Rakoff-Nahoum

Seth Rakoff-Nahoum

Assistant Professor

Boston Children's Hospital
Department of Medicine, Enders
300 Longwood Avenue
Boston, MA 02115
Tel: 617-919-2999
Fax: 617-730-0254
Visit my lab page here.

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 and phenotypic analysis of the effects of members of the microbiota on each other and the host.

Current focusses 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 and 4) microbiome ecology in human populations, focusing on pediatric health and disease.

Last Update: 8/12/2019


For a complete listing of publications click here.



Coyte KZ, Rakoff-Nahoum S. Understanding Competition and Cooperation
within the Mammalian Gut Microbiome. Curr Biol. 2019 Jun 3;29(11):R538-R544. doi:
10.1016/j.cub.2019.04.017. Review. PubMed 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. doi: 10.1186/s12915-018-0527-2. PubMed
PMID: 29871632; PubMed Central PMCID: PMC5989470.

Foster KR, Schluter J, Coyte KZ, Rakoff-Nahoum S. The evolution of the host
microbiome as an ecosystem on a leash. Nature. 2017 Aug 2;548(7665):43-51. doi:
10.1038/nature23292. PubMed PMID: 28770836; PubMed Central PMCID: PMC5749636.

Sasabe J, 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
Jul 25;1(10):16125. doi: 10.1038/nmicrobiol.2016.125. PubMed PMID: 27670111;
PubMed Central PMCID: PMC5074547.

Rakoff-Nahoum S, Foster KR, Comstock LE. The evolution of cooperation within
the gut microbiota. Nature. 2016 May 12;533(7602):255-9. doi:
10.1038/nature17626. Epub 2016 Apr 25. PubMed PMID: 27111508; PubMed Central
PMCID: PMC4978124.

© 2016 President and Fellows
of Harvard College