Functional metagenomic profiling of the intestinal microbiome in subjects consuming omnivore, ovo-lacto-vegetarian and vegan diets
Ilario Ferrocino, Francesca De Filippis, Angela McCann, Raffaella Di Cagno, Silvia Turroni, Erasmo Neviani, Maria De Angelis, Danilo Ercolini, Paul O’Toole, Luca Cocolin
Several studies have reported how lifestyle factors such as diet, age or geographic location influence the composition or function of gut microbiota. In particular, habitual diet appears to be an important factor. Three main dietary habits are apparent worldwide: omnivore (O), ovo-lacto-vegetarian (VG) and vegan (V). In order to study the effect of dietary habits on the gut metagenome we applied shotgun sequencing to total fecal bacterial DNA in a selection of 27 volunteers (8 O, 9 VG, 10 V) belonging to a well‐characterized Italian cohort. Functional characterization of the shotgun sequence reads in the KEGG database was performed, in order to identify the relative abundance of specific metabolic pathways characteristic for each dietary group. The pathway enrichment analysis of the metagenomes showed an increased abundance of genes involved in the riboflavin metabolism pathway (ko00740) in VG compared to O and one carbon pool by folate pathway (ko00670) compared to V. Moreover, V showed an increased abundance in genes involved in fatty acid biosynthesis (ko00071), amino sugar and nucleotide sugar metabolism (ko00520), butanoate (ko00650) and propanoate (ko00640) metabolism compared to O. Sequences were also assembled and the resulting contigs were then searched for key microbial genes in butyrate, acetate and propanoate production, revealing significantly higher gene counts for butyrate, acetate and propanoate producing enzymes in V compared to VG and O. Taxonomic composition was assessed by using the MetaPhlAn2 and a PCoA based on Euclidean distances was carried out. No clear separation of subjects based on diet was found, suggesting that diet can potentially drive the enrichment in key microbial genes in the gut, regardless the taxonomic composition. The use of metagenomics approaches promises to accelerate progress in understanding the interactions between diet habits and the human gut microbiota and to identify metabolic markers specific to the type of diet.
