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.


  The gut microbiome.

Kuziel GA, Rakoff-Nahoum S.Curr Biol. 2022 Mar 28;32(6):R257-R264. doi: 10.1016/j.cub.2022.02.023.PMID: 35349808


  Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite.

Park SY, Rao C, Coyte KZ, Kuziel GA, Zhang Y, Huang W, Franzosa EA, Weng JK, Huttenhower C, Rakoff-Nahoum S.Cell. 2022 Feb 3;185(3):513-529.e21. doi: 10.1016/j.cell.2022.01.002.PMID: 35120663


  Multi-kingdom ecological drivers of microbiota assembly in preterm infants.

Rao C, Coyte KZ, Bainter W, Geha RS, Martin CR, Rakoff-Nahoum S.Nature. 2021 Mar;591(7851):633-638. doi: 10.1038/s41586-021-03241-8. Epub 2021 Feb 24.PMID: 33627867 Free PMC article.


  Ecological rules for the assembly of microbiome communities.

Coyte KZ, Rao C, Rakoff-Nahoum S, Foster KR.PLoS Biol. 2021 Feb 19;19(2):e3001116. doi: 10.1371/journal.pbio.3001116. eCollection 2021 Feb.PMID: 33606675 Free PMC article.