Abstract
Genomic analyses of microbial populations in their natural environment remain limited by the difficulty to assemble full genomes of individual species. Consequently, the chromosome organization of microorganisms has been investigated in a few model species, but the extent to which the features described can be generalized to other taxa remains unknown. Using controlled mixes of bacterial and yeast species, we developed meta3C, a metagenomic chromosome conformation capture approach that allows characterizing individual genomes and their average organization within a mix of organisms. Not only can meta3C be applied to species already sequenced, but a single meta3C library can be used for assembling, scaffolding and characterizing the tridimensional organization of unknown genomes. By applying meta3C to a semi-complex environmental sample, we confirmed its promising potential. Overall, this first meta3C study highlights the remarkable diversity of microorganisms chromosome organization, while providing an elegant and integrated approach to metagenomic analysis.
Highlights
Microbial species have for a long time been studied individually, leading to the development of applications in fields as diverse as agronomy, environment, or medicine
As in a typical 3C experiment squares appeared on the diagonal of the matrix, revealing individual chromosomes: the circular chromosomes of both E. coli and B. subtilis were recovered as separate entities, whereas the two chromosomes of V. cholerae yielded two squares exhibiting higher contact frequencies with each other than with the chromosomes of the other species—as expected since these chromosomes share the same cellular compartment (Figure 1B)
We recovered three populations of bins that corresponded to the three bacterial genomes, with the two chromosomes of V. cholerae being visualized in close vicinity to each other
Summary
Microbial species have for a long time been studied individually, leading to the development of applications in fields as diverse as agronomy, environment, or medicine. A number of techniques have been developed to improve the resolution and accuracy of individual genome assembly in mixed populations, for instance by separating the species prior to sequencing (Fitzsimons et al, 2013) or by refining the clustering and scaffolding procedures used to process sequence data (Albertsen et al, 2013). These approaches remain generally limited by the use of complex technologies and/or by the need to construct multiple libraries. The frequency with which two chromosomal segments come in contact, as measured
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