Diet-linked dynamics of metagenomes and metatranscriptomes

The microbiome is crucial for host processes such as metabolism and is modulated by host diet. The specific interactions between microbial enzymes and dietary compounds are not yet known. To understand these mechanisms, we assess the relationship between dietary compounds and metabolic pathways that are carried and transcribed by individual species. Here, we report on the gut microbiome of 307 participants from the Health Professionals Follow-Up Study, a prospective cohort designed to relate nutrition to health outcomes. The gut metagenome of each participant was surveyed at four timepoints with short (1-3 days) and long (6 month) time intervals. Metatranscriptomes were also generated for 96 participants. These data were complemented with seven-day dietary recalls and long-term dietary histories from food frequency questionnaires. Taxonomic profiling and metabolic reconstruction were performed using MetaPhlAn2 and HUMAaN2, respectively. We integrated the profiled taxonomy and metabolic pathways with dietary compounds using a multivariate linear model
(MaAsLin2). We revealed a "core" set of pathways encoded by many species, and a variably transcribed set that consists of specialized pathways. Dietary fiber was associated with metagenomic pathways such as nucleotide and amino acid biosynthesis, in addition to the carbohydrate fermenter, Collinsella aerofacians. A Gaussian process model is applied to assess the longitudinal relationship between microbiome features and dietary variables. Our findings could help us understand the direct mechanism by which bioavailability impacts microbial metabolism.