Integrating dietary data into microbiome studies: a step forward for Nutri-metaomics. Human gut metagenome

Diet is recognised as the main driver of changes in gut microbiota. However, linking habitual dietary intake to microbiome composition and activity remains a challenge, leading to most microbiome studies with little or no dietary information. To fill this knowledge gap, we conducted two consecutive studies (n=84: a first pilot study (n=40) to build a web-based semi-quantitative simplified FFQ (sFFQ) based on three 24-hour dietary recalls; a second study (n=44) served to validate the newly developed sFFQ using 3DRs as reference method and to relate gut microbiome profiling (16S rRNA gene) with the extracted dietary and lifestyle data. Relative validation analysis provided acceptable classification and agreement for 13 out of 24 (54%) food groups and 20 out of 29 nutrients (69%) based on intraclass correlation coefficient, cross-classification, Spearman's correlation, Wilcoxon test, and Bland-Altman. Microbiome analysis showed that higher diversity was positively associated with age, vaginal birth, and intake of fruit. In contrast, diversity was negatively associated with BMI, processed meats, ready-to-eat meals, sodium and saturated fat. Our analysis also revealed a correlation between food groups or nutrients and microbial composition. Overall, here we provide the first dietary assessment tool to be validated and correlated with microbiome data for population studies.