Growing evidence indicates that the composition of the gut microbiome is altered in complex diseases. Qin et al. carried out a metagenome-wide association study of the gut microbiome from 345 Chinese individuals with type 2 diabetes (T2D) and identified approximately 60,000 microbial markers for the disease. They also developed a new concept for classifying metagenomic data: the metagenomic linkage group, which provides a species-level description of the data without the need for traditional taxonomy. Data analysis indicated that patients with T2D have only moderate intestinal dysbiosis but that butyrate-producing bacteria (which are potentially beneficial) are less abundant and opportunistic pathogens are more abundant in these individuals than in healthy controls. Although a causal link between the observed microbiome changes and T2D has not been shown, the gut microbiome could be used to monitor the risk of T2D development.