Gut-Diet Relationship

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Our intestines are populated by an almost unimaginably large number of microbial cells, most of which are bacteria. This species assemblage operates as a microbial metabolic organ, performing myriad tasks that contribute to our well-being, including processing components of our diet. The way this incredible machine assembles itself and operates remains mysterious. One approach to understanding its properties is to create artificial communities composed of a limited number of sequenced human gut bacterial species and to install them in the guts of germ-free mice that are then fed different diets.

In this report, this approach is adopted. It is described that the genome sequence of a new gut bacterial isolate, Bacteroides cellulosilyticus WH2, which is equipped with an unprecedented number of carbohydrate active enzymes. Deploying four different “omics” technologies, the response to diet is characterized, the relative stability, and the temporal dynamics of a 12-species artificial bacterial assemblage (including B. cellulosilyticus WH2) implanted in germ-free mouse guts. They also combine high-throughput substrate utilization screens and RNA-Seq to generate reference data analogous to a “Rosetta stone” in order to decipher what types of carbohydrates B. cellulosilyticus encounters and uses within the gut, and how it interacts with other organisms that have similar and/or distinct “professions.”

This work sets the stage for future ecological and metabolic studies of more complex assemblages that more fully emulate the properties of our native gut communities

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