Seth Rakoff-Nahoum

Research Description

Mechanistic Evolutionary Ecology of Host-associated Microbiomes
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 focusses 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.