Is metagenomics resolving identification of functions in microbial communities?

We are coming up on the tenth anniversary of the broad use of the method involving whole metagenome shotgun sequencing, referred to as metagenomics. The application of this approach has definitely revolutionized microbiology and the related fields, including the realization of the importance of the human microbiome. As such, metagenomics has already provided a novel outlook on the complexity and dynamics of microbial communities that are an important part of the biosphere of the planet. Accumulation of massive amounts of sequence data also caused a surge in the development of bioinformatics tools specially designed to provide pipelines for data analysis and visualization. However, a critical outlook into the field is required to appreciate what could be and what has currently been gained from the massive sequence databases that are being generated with ever-increasing speed. We are coming up on the tenth anniversary of metagenomics, the method involving whole shotgun sequencing of community DNA. It is marked by dramatic changes in the rate of sequence data accumulation, presenting new challenges in the massive data analysis. I here present a critical outlook at the current state of metagenomics, with special focus on the potential of metagenomics for gaining insights into the function of complex microbial communities.