Kovatcheva-Datchary, P. et al. Cell Rep. 26, 3772–3783 (2019).

The gut microbiota plays a critical role in human metabolism through, for example, the production of short-chain fatty acids. Yet it is still a challenge to decipher microbe–diet–host interplay owing to the lack of fully characterized microorganisms and the lack of understanding regarding bacterial interactions with complex food networks. To ease the complexity, Kovatcheva-Datchary et al. developed a mouse model that is colonized with a simplified intestinal microbiota (SIM) containing ten known bacterial strains from the human gut microbiome. They fed the SIM mice different diets including high fiber, high fat/high sucrose, or zero fat/high sucrose. They observed a reduced abundance of fiber-degrading bacteria when dietary fiber was limited. Using RNA sequencing, they were able to annotate the altered genes associated with metabolism that are induced by a change in diet. In addition, the simplified mouse model allows researchers to assess how dietary interventions affect circulating metabolites through metabolomic analysis of the plasma.