Second-generation sequencing technologies are fueling a vast increase in the number and scope of metagenome projects. There is a great need for the development of new methods for visualizing the relationships between multiple metagenomic data sets. To address this, a novel approach is presented that combines the use of taxonomic analysis, ecological indices and non-hierarchical clustering to provide a network representation of the relationships between different metagenome data sets. The approach is illustrated using several published data sets of different types, including metagenomes, metatranscriptomes and 16S ribosomal profiles. Application of the approach to the same data summarized at different taxonomical levels gives rise to remarkably similar networks, indicating that the analysis is very robust. Importantly, the networks provide the both visual definition and metric quantification for the non-rooted relationship between samples, combining the desirable characteristics of other tools into one.