The microbiome’s fiber degradation profile and its relationship with the host diet

Abstract

Background: The relationship between the gut microbiome and diet has been the focus of numerous recent studies. Such studies aim to characterize the impact of diet on the composition of the microbiome, as well as the microbiome’s ability to utilize various compounds in the diet and produce metabolites that may be beneficial for the host. Consumption of dietary fibers (DFs)—polysaccharides that cannot be broken down by the host’s endogenous enzymes and are degraded primarily by members of the microbiome—is known to have a profound effect on the microbiome. Yet, a comprehensive characterization of microbiome compositional and functional shifts in response to the consumption of specific DFs is still lacking. Results: Here, we introduce a computational framework, coupling metagenomic sequencing with careful annotation of polysaccharide degrading enzymes and DF structures, for inferring the metabolic ability of a given microbiome sample to utilize a broad catalog of DFs. We demonstrate that the inferred fiber degradation profile (IFDP) generated by our framework accurately reflects the dietary habits of various hosts across four independent datasets. We further demonstrate that IFDPs are more tightly linked to the host diet than commonly used taxonomic and functional microbiome-based profiles. Finally, applying our framework to a set of ~700 metagenomes that represents large human population cohorts from 9 different countries, we highlight intriguing global patterns linking DF consumption habits with microbiome capacities. Conclusions: Combined, our findings serve as a proof-of-concept for the use of DF-specific analysis for providing important complementary information for better understanding the relationship between dietary habits and the gut microbiome.