Genomics: Resident risks

Abstract

An innovative method for probing the genomes of the vast community of microorganisms that inhabit the human gut provides an alternative approach to identifying risk factors for type 2 diabetes.

Figure 1. Mining the metagenome

Qin et al. studied the metagenome of the human gut — the combined genomes of the trillions of its resident microorganisms — in the search for microbial species and gene functions that are associated with type 2 diabetes. First, they identified microbial gene markers and determined the abundance of these markers in stool samples from a group of patients with type 2 diabetes and from a control group of people without the disease. The authors then clustered these markers according to their relative abundance, and assigned markers that had similar abundance profiles within either the patient or the control group to a metagenomic linkage group (MLG). In this example, MLG1 is over-represented in the patient group, MLG2 is similarly represented in patient and control groups and MLG3 is over-represented in the control group. The use of MLGs reduced the number of associations for subsequent analysis, minimized redundancy and allowed rare gene markers to be taken into account.