Fig. 1.

General overview of the metagenomic approaches available for gut microbiota characterization. Starting from DNA extraction of the intestinal microbial community, the subsequent high‐throughput sequencing provides taxonomic insight into the gut microbiota down to the genus and species levels for 16S rRNA gene and ITS microbial profiling respectively. In addition to the taxonomic composition, whole shotgun metagenomics allows the reconstruction of the microbial genomes and prediction of the bacterial functional features.