Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome

Untargeted plasma metabolites in Dutch cohorts

In this study, we examined plasma metabolomes in 1,679 fasting plasma samples from 1,368 individuals from two LLD⁵ sub-cohorts (LLD₁ and LLD₂) and the GoNL⁶ cohort (Extended Data Fig. 1 and Supplementary Table 1). The LLD₁ cohort was the discovery cohort, with information about genetics, diet and the gut microbiome available for 1,054 participants. Moreover, 311 LLD₁ subjects were followed up 4 years later (LLD₁ follow-up). We also included two independent replication cohorts: 237 LLD₂ participants for whom we had genetic and dietary data and 77 GoNL participants for whom only genetic data were available (Extended Data Fig. 1 and Supplementary Table 1). Untargeted metabolomics profiling was done using flow-injection time-of-flight mass spectrometry (FI-MS)^10,11, which yielded plasma levels of 1,183 metabolites (Supplementary Table 2). These metabolites covered a wide range of lipids, organic acids, phenylpropanoids, benzenoids and other metabolites (Extended Data Fig. 2a). As we observed weak (absolute r_Spearman < 0.2) correlations among the 1,183 metabolites (Extended Data Fig. 2b), data reduction was not required and, consequently, all metabolites were subjected to subsequent analyses. We validated the identification and quantification of some metabolites (for example, bile acids, creatinine, lactate, phenylalanine and isoleucine) by comparing their abundance levels from FI-MS with those previously determined by liquid…