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Lysogeny is prevalent and widely distributed in the murine gut microbiota

The ISME Journalvolume 12pages11271141 (2018) | Download Citation

Abstract

Bacteriophages are central members and potential modulators of the gut microbiome; however, the ecological and evolutionary relationships of gut bacteria and phages are poorly understood. Here we investigated the abundance and diversity of lysogenic bacteria (lysogens) in the bacterial community of C57BL/6J mice by detecting integrated prophages in genomes reconstructed from the metagenome of commensal bacteria. For the activities of lysogens and prophages, we compared the prophage genomes with the metagenome of free phages. The majority of commensal bacteria in different taxa were identified as lysogens. More lysogens were found among Firmicutes and Proteobacteria, than among Bacteroidetes and Actinobacteria. The prophage genomes shared high sequence similarity with the metagenome of free phages, indicating that most lysogens appeared to be active, and that prophages are spontaneously induced as active phages; dietary interventions changed the composition of the induced prophages. By contrast, CRISPR-Cas systems were present in few commensal bacteria, and were rarely active against gut phages. The structure of the bacteria-phage infection networks was “nested-modular”, with modularity emerging across taxonomic scales, indicating that temperate phage features have developed over a long phylogenetic timescale. We concluded that phage generalists contribute to the prevalence of lysogeny in the gut ecosystem.

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Acknowledgements

This work was supported by grants from the Basic Science Research Program (2015R1D1A4A01019807) funded by the Ministry of Education, the Mid-Career Researcher Program (2016R1E1A1A02921587) funded by the Ministry of Science, ICT & Future Planning through the National Research Foundation of Korea, and the Agricultural Microbiome R&D Program (grant number: 914006-4) funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA) through Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry (IPET). We thank Dr. Donovan H. Parks, Dr. Simon Roux, Dr. Ben Bolduc and Dr. Ho Bin Jang for technical advice in computational analyses.

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  1. Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea

    • Min-Soo Kim
    •  & Jin-Woo Bae

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Correspondence to Jin-Woo Bae.

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