Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria

Microbiome

Research

Laurent Debarbieux¹  Quentin Lamy-Besnier²  Devon E. Conti³  Marie Titecat⁴  Marc Monot⁵  Julian R. Garneau⁵  Romain Koszul⁶  Martial Marbouty⁶  Amaury Bignaud⁷  Alexandra Von Strempel⁸  Bärbel Stecher⁹ 

[1] Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 25-28 Rue du Dr Roux, 75015, Paris, France;Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 25-28 Rue du Dr Roux, 75015, Paris, France;Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France;Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 25-28 Rue du Dr Roux, 75015, Paris, France;Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France;Sorbonne Université, Collège Doctoral, Paris, France;Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 25-28 Rue du Dr Roux, 75015, Paris, France;Université de Lille, INSERM, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, 59000, Lille, France;Institut Pasteur, Université Paris Cité, Plate-Forme Technologique Biomics, 75015, Paris, France;Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France;Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France;Sorbonne Université, Collège Doctoral, Paris, France;Max Von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany;Max Von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany;German Center for Infection Research (DZIF), Partner Site LMU Munich, Munich, Germany;

关键词: Phages;    Gut;    HiC;    Virome;    OMM12;    3D signatures;   

DOI  :  10.1186/s40168-023-01541-x

 received in 2022-12-05, accepted in 2023-04-04,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundBacteria and their viruses, bacteriophages, are the most abundant entities of the gut microbiota, a complex community of microorganisms associated with human health and disease. In this ecosystem, 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.ResultsTo gain insight into the activity of lysogenic bacteriophages within the context of their host genomes, we performed proximity ligation-based sequencing (Hi-C) in both in vitro and in vivo conditions on the 12 bacterial strains of the OMM12 synthetic bacterial community stably associated within mice gut (gnotobiotic mouse line OMM12). High-resolution contact maps of the chromosome 3D organization of the bacterial genomes revealed a wide diversity of architectures, differences between environments, and an overall stability over time in the gut of mice. The DNA contacts pointed at 3D signatures of prophages leading to 16 of them being predicted as functional. We also identified circularization signals and observed different 3D patterns between in vitro and in vivo conditions. Concurrent virome analysis showed that 11 of these prophages produced viral particles and that OMM12 mice do not carry other intestinal viruses.ConclusionsThe precise identification by Hi-C of functional and active prophages within bacterial communities will unlock the study of interactions between bacteriophages and bacteria across conditions (healthy vs disease).5K7HmgUAJkeE_nXCFwpwyqVideo Abstract

【 授权许可】

CC BY   
© The Author(s) 2023

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