Side-by-side comparison of chromosome folding and prophage activation in the OMM12 consortium in vitro and in vivo

The gut microbiota is a complex microbial community that is associated with human health and disease. It is mainly composed of bacteria and their viruses, bacteriophages. However, mainly due to technical limitations, the interactions between these two key components are still largely unknown. In particular, the impact of the gut environment on bacteria and their associated prophages is yet to be deciphered. Here, we performed Hi-C on the 12 bacterial strains of the gnotobiotic mouse line OMM12. Besides providing high-resolution contact maps of the chromosome 3D organization of the different species in vitro and in vivo, revealing a large diversity of architectures and an overall stability of the system, the DNA contacts also pointed at prophages 3D signatures. We predicted 16 functional prophages based on their 3D signatures, identified circularization signal and observed different patterns depending on the studied condition. The concomitant analysis of the virome showed that 11 of these prophages were indeed found in the viral fraction in vivo and/or in vitro while two others were only detected using virome sequencing. The present study highlights the value of the Hi-C approach to predict functional prophages and for the study of phage-bacteria interaction dynamics. It also provides a solid and large set of data for OMM12 model users and future studies.