Abstract
Gut microbiota is considered as a human organ with its own specific functions and complexity. Development of novel techniques such as shut gun sequencing, metagenomics, and next-generation sequencing (NGS) has enabled bypassing the traditional culturedependent bias and has significantly expanded our understanding of the composition, diversity, and roles of the gut microbiota in human health and diseases. Although amplicon sequencing characterizes the taxonomic composition of the gut microbiome, it is impossible to cover the direct evidence of the microbial biological functions related to the gut microbial community. Hence, the critical next step for gut microbiome studies is shifting from gene/ genome-centric analysis to mechanism-centric techniques by integrating omics data with experimental results. Realizing gut microbial diversity and their bioactive metabolites function will provide insight into the clinical application of gut microbiota in diagnoses and treatments of several diseases. In this review, we focused on explaining the conventional and advanced microbiome analysis techniques regarding gut microbiota investigation with considering the advantages and disadvantages of the platforms.