Lysogeny is prevalent and widely distributed in the murine gut microbiota

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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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  1. 1.

    Mirzaei MK, Maurice CF. Ménage à trois in the human gut: interactions between host, bacteria and phages. Nat Rev Microbiol. 2017;15:397–408.

  2. 2.

    Borrel G, McCann A, Deane J, Neto MC, Lynch DB, Brugere JF, et al. Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome. ISME J. 2017;11:2059–74.

  3. 3.

    Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature. 2013;500:232–6.

  4. 4.

    Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 2011;21:1616–25.

  5. 5.

    Kim MS, Park EJ, Roh SW, Bae JW. Diversity and abundance of single-stranded DNA viruses in human feces. Appl Environ Microbiol. 2011;77:8062–70.

  6. 6.

    Lim ES, Zhou Y, Zhao G, Bauer IK, Droit L, Ndao IM, et al. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med. 2015;21:1228–34.

  7. 7.

    Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature. 2010;466:334–8.

  8. 8.

    Kim MS, Bae JW. Spatial disturbances in altered mucosal and luminal gut viromes of diet-induced obese mice. Environ Microbiol. 2016;18:1498–510.

  9. 9.

    Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 2015;160:447–60.

  10. 10.

    Yang JY, Kim MS, Kim E, Cheon JH, Lee YS, Kim Y, et al. Enteric viruses ameliorate gut inflammation via Toll-like receptor 3 and Toll-like receptor 7-mediated interferon-β production. Immunity. 2016;44:889–900.

  11. 11.

    Zhao G, Vatanen T, Droit L, Park A, Kostic AD, Poon TW, et al. Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children. Proc Natl Acad Sci USA. 2017;114:E6166–E6175.

  12. 12.

    Weinbauer MG. Ecology of prokaryotic viruses. FEMS Microbiol Rev. 2004;28:127–81.

  13. 13.

    Howard-Varona C, Hargreaves KR, Abedon ST, Sullivan MB. Lysogeny in nature: mechanisms, impact and ecology of temperate phages. ISME J. 2017;11:1511–20.

  14. 14.

    Jiang SC, Paul JH. Seasonal and diel abundance of viruses and occurrence of lysogeny/bacteriocinogeny in the marine-environment. Mar Ecol Progress Ser. 1994;104:163–72.

  15. 15.

    Jiang SC, Paul JH. Occurrence of lysogenic bacteria in marine microbial communities as determined by prophage induction. Mar Ecol Progress Ser. 1996;142:27–38.

  16. 16.

    Knowles B, Bailey B, Boling L, Breitbart M, Cobian-Guemes A, Del Campo J, et al. Variability and host density independence in inductions-based estimates of environmental lysogeny. Nat Microbiol. 2017;2:17064.

  17. 17.

    Paul JH, Weinbauer M. Detection of lysogeny in marine environments. Man Aquat Viral Ecol. 2010;4:30–33.

  18. 18.

    Sangwan N, Xia F, Gilbert JA. Recovering complete and draft population genomes from metagenome datasets. Microbiome. 2016;4:8.

  19. 19.

    Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol. 2014;32:822–8.

  20. 20.

    Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 2013;23:111–20.

  21. 21.

    Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013;31:533–8.

  22. 22.

    Ormerod KL, Wood DL, Lachner N, Gellatly SL, Daly JN, Parsons JD, et al. Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome. 2016;4:36.

  23. 23.

    Carmody RN, Gerber GK, Luevano JM Jr., Gatti DM, Somes L, Svenson KL, et al. Diet dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe. 2015;17:72–84.

  24. 24.

    Howe A, Ringus DL, Williams RJ, Choo ZN, Greenwald SM, Owens SM, et al. Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice. ISME J. 2016;10:1217–27.

  25. 25.

    Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. Laboratory procedures to generate viral metagenomes. Nat Protoc. 2009;4:470–83.

  26. 26.

    Zoetendal EG, Heilig HG, Klaassens ES, Booijink CC, Kleerebezem M, Smidt H, et al. Isolation of DNA from bacterial samples of the human gastrointestinal tract. Nat Protoc. 2006;1:870–3.

  27. 27.

    Reyes A, Blanton LV, Cao S, Zhao G, Manary M, Trehan I, et al. Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proc Natl Acad Sci USA. 2015;112:11941–6.

  28. 28.

    Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28:1420–8.

  29. 29.

    Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. Peer J. 2015;3:e1165.

  30. 30.

    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.

  31. 31.

    Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. Peer J. 2015;3:e985.

  32. 32.

    Roux S, Hallam SJ, Woyke T, Sullivan MB. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife. 2015;4:e08490.

  33. 33.

    Hurwitz BL, Sullivan MB. The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS ONE. 2013;8:e57355.

  34. 34.

    Bolduc B, Jang HB, Doulcier G, You ZQ, Roux S, Sullivan MB. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. Peer J. 2017;5:e3243.

  35. 35.

    Edgar RC. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics. 2007;8:18.

  36. 36.

    Biswas A, Gagnon JN, Brouns SJ, Fineran PC, Brown CM. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol. 2013;10:817–27.

  37. 37.

    Edwards RA, McNair K, Faust K, Raes J, Dutilh BE. Computational approaches to predict bacteriophage-host relationships. FEMS Microbiol Rev. 2016;40:258–72.

  38. 38.

    Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 2004;32:11–16.

  39. 39.

    Almeida-Neto M, Guimaraes P, Guimaraes PR, Loyola RD, Ulrich W. A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement. Oikos. 2008;117:1227–39.

  40. 40.

    Beckett SJ, Boulton CA, Williams HT. FALCON: a software package for analysis of nestedness in bipartite networks. F1000 Res. 2014;3:185.

  41. 41.

    Barber MJ. Modularity and community detection in bipartite networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2007;76:066102.

  42. 42.

    Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, et al. A catalog of the mouse gut metagenome. Nat Biotechnol. 2015;33:1103–8.

  43. 43.

    Wannemuehler MJ, Overstreet AM, Ward DV, Phillips GJ. Draft genome sequences of the altered schaedler flora, a defined bacterial community from gnotobiotic mice. Genome Announc. 2014;2:e00287–14.

  44. 44.

    Duck LW, Walter MR, Novak J, Kelly D, Tomasi M, Cong Y, et al. Isolation of flagellated bacteria implicated in Crohn’s disease. Inflamm Bowel Dis. 2007;13:1191–201.

  45. 45.

    Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res. 2003;13:145–58.

  46. 46.

    Touchon M, Bernheim A, Rocha EP. Genetic and life-history traits associated with the distribution of prophages in bacteria. ISME J. 2016;10:2744–54.

  47. 47.

    De Paepe M, Tournier L, Moncaut E, Son O, Langella P, Petit MA. Carriage of λ latent virus is costly for its bacterial host due to frequent reactivation in monoxenic mouse intestine. PLoS Genet. 2016;12:e1005861.

  48. 48.

    Lugli GA, Milani C, Turroni F, Tremblay D, Ferrario C, Mancabelli L, et al. Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota. Environ Microbiol. 2016;18:2196–213.

  49. 49.

    Kim KH, Bae JW. Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl Environ Microbiol. 2011;77:7663–8.

  50. 50.

    Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenk SM, Goldsmith DB, et al. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. Peer J. 2016;4:e2777.

  51. 51.

    Minot S, Bryson A, Chehoud C, Wu GD, Lewis JD, Bushman FD. Rapid evolution of the human gut virome. Proc Natl Acad Sci USA. 2013;110:12450–5.

  52. 52.

    Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, et al. Classification and quantification of bacteriophage taxa in human gut metagenomes. ISME J. 2014;8:1391–402.

  53. 53.

    Nanda AM, Thormann K, Frunzke J. Impact of spontaneous prophage induction on the fitness of bacterial populations and host-microbe interactions. J Bacteriol. 2015;197:410–9.

  54. 54.

    Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010;327:167–70.

  55. 55.

    Weitz JS, Poisot T, Meyer JR, Flores CO, Valverde S, Sullivan MB, et al. Phage-bacteria infection networks. Trends Microbiol. 2013;21:82–91.

  56. 56.

    Bailly-Bechet M, Vergassola M, Rocha E. Causes for the intriguing presence of tRNAs in phages. Genome Res. 2007;17:1486–95.

  57. 57.

    Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, et al. Uncovering Earth’s virome. Nature. 2016;536:425–30.

  58. 58.

    Popa O, Landan G, Dagan T. Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction. ISME J. 2017;11:543–54.

  59. 59.

    Flores CO, Valverde S, Weitz JS. Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages. ISME J. 2013;7:520–32.

  60. 60.

    Reyes A, Wu M, McNulty NP, Rohwer FL, Gordon JI. Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut. Proc Natl Acad Sci USA. 2013;110:20236–41.

  61. 61.

    Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 2014;5:4498.

  62. 62.

    Manrique P, Bolduc B, Walk ST, van der Oost J, de Vos WM, Young MJ. Healthy human gut phageome. Proc Natl Acad Sci USA. 2016;113:10400–5.

  63. 63.

    Feiner R, Argov T, Rabinovich L, Sigal N, Borovok I, Herskovits AA. A new perspective on lysogeny: prophages as active regulatory switches of bacteria. Nat Rev Microbiol. 2015;13:641–50.

  64. 64.

    Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, et al. Prophages mediate defense against phage infection through diverse mechanisms. ISME J. 2016;10:2854–66.

  65. 65.

    Obeng N, Pratama AA, Elsas JD. The significance of mutualistic phages for bacterial ecology and evolution. Trends Microbiol. 2016;24:440–9.

  66. 66.

    Duerkop BA, Clements CV, Rollins D, Rodrigues JL, Hooper LV. A composite bacteriophage alters colonization by an intestinal commensal bacterium. Proc Natl Acad Sci USA. 2012;109:17621–6.

  67. 67.

    Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, et al. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci USA. 2013;110:10771–6.

  68. 68.

    Silveira CB, Rohwer FL. Piggyback-the-Winner in host-associated microbial communities. NPJ Biofilms Micro. 2016;2:16010.

  69. 69.

    Zuo T, Wong SH, Lam K, Lui R, Cheung K, Tang W et al. Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome. Gut. 2017.

  70. 70.

    Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB, et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci USA. 2013;110:9066–71.

  71. 71.

    Johansson ME, Gustafsson JK, Holmen-Larsson J, Jabbar KS, Xia L, Xu H, et al. Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis. Gut. 2014;63:281–91.

  72. 72.

    McGuckin MA, Linden SK, Sutton P, Florin TH. Mucin dynamics and enteric pathogens. Nat Rev Microbiol. 2011;9:265–78.

  73. 73.

    Knowles B, Silveira CB, Bailey BA, Barott K, Cantu VA, Cobian-Guemes AG, et al. Lytic to temperate switching of viral communities. Nature. 2016;531:466–70.

  74. 74.

    Maurice CF, Haiser HJ, Turnbaugh PJ. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell. 2013;152:39–50.

  75. 75.

    Brown CT, Olm MR, Thomas BC, Banfield JF. Measurement of bacterial replication rates in microbial communities. Nat Biotechnol. 2016;34:1256–63.

  76. 76.

    Shin NR, Whon TW, Bae JW. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 2015;33:496–503.

  77. 77.

    Krupovic M, Forterre P. Single-stranded DNA viruses employ a variety of mechanisms for integration into host genomes. Ann N Y Acad Sci. 2015;1341:41–53.

  78. 78.

    Thingstad TF. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol Oceanogr. 2000;45:1320–8.

  79. 79.

    Paul JH. Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J. 2008;2:579–89.

  80. 80.

    Weitz JS, Beckett SJ, Brum JR, Cael BB, Dushoff J. Lysis, lysogeny and virus-microbe ratios. Nature. 2017;549:E1–E3.

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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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