Although chromosome organization in microorganisms has been investigated in single species, similar analyses of whole genomes in complex environmental microbial communities have been limited. Marbouty et al. developed a metagenomic chromosome conformation capture approach (termed meta3C) for the characterization of the average organization of individual genomes in mixed microbial communities. This approach, which is based on measuring the frequency with which two chromosomal segments come in contact, was tested on an artificial mixture of bacterial species and an environmental sample of unknown composition; the authors identified genomic regions that could be matched to a specific species and revealed the three-dimensional structure of the genomes in the mixed populations. Thus, meta3C has the potential to be used for the analysis of chromosome organization in environmental microbial communities.