Exploration of the human microbiome can now be conducted by massive DNA sequencing. An approach we name quantitative metagenomics provides a detailed view of the structure of microbial communities. Typically some 50 million short DNA sequences are generated for each individual; they are used to monitor presence and abundance of 3.3 to 10 million microbial genes found in the gut communities. Gene profiles are thus generated for each sample. The profiles are correlated with the metadata related to human health status and/or lifestyle by appropriate statistical approaches. The analytical space can be greatly simplified and the signal de-noised by clustering genes that are carried by the same genetic elements via abundance co-variance; about a half of the microbial genes can be assigned to some 8000 clusters representing bacterial species, phages, plasmids, CRISPR elements etc. Using these approaches we have found that one of four people has low gut microbial richness and harbors a less healthy microbiome. The loss of richness is correlated with a higher risk to develop metabolic syndrome associated pathologies such as type 2 diabetes, hepatic and cardio-vascular complications. The loss can be detected accurately and corrected, at least in part, by a nutritional intervention, in parallel with amelioration of metabolic parameters. We thus seem to be in a position to detect the risk and act to alleviate it and possibly delay advent of common chronic diseases.