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Volumn 10, Issue , 2019, Pages

Gut Bacteriophage: Current Understanding and Challenges

Author keywords

bacteriophage; microbiome; microbiota; phage host interactions; virome

Indexed keywords

BACTERIOPHAGE; COMPUTER MODEL; GASTROINTESTINAL TRACT; HOST INTERACTION; HUMAN; INFANCY; MICROBIOME; NONHUMAN; REVIEW;

EID: 85076910640     PISSN: None     EISSN: 16642392     Source Type: Journal    
DOI: 10.3389/fendo.2019.00784     Document Type: Review
Times cited : (138)

References (174)
  • 1
    • 84988864262 scopus 로고    scopus 로고
    • Revised estimates for the number of human and bacteria cells in the body
    • 27541692
    • Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. (2016) 14:e1002533. 10.1371/journal.pbio.100253327541692
    • (2016) PLoS Biol , vol.14 , pp. e1002533
    • Sender, R.1    Fuchs, S.2    Milo, R.3
  • 2
    • 68249110221 scopus 로고    scopus 로고
    • The role of pH in determining the species composition of the human colonic microbiota
    • 19397676
    • Duncan SH, Louis P, Thomson JM, Flint HJ. The role of pH in determining the species composition of the human colonic microbiota. Environ Microbiol. (2009) 11:2112–22. 10.1111/j.1462-2920.2009.01931.x19397676
    • (2009) Environ Microbiol , vol.11 , pp. 2112-2122
    • Duncan, S.H.1    Louis, P.2    Thomson, J.M.3    Flint, H.J.4
  • 3
    • 84873299448 scopus 로고    scopus 로고
    • Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota
    • 23127782
    • Espey MG. Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota. Free Rad Biol Med. (2013) 55:130–40. 10.1016/j.freeradbiomed.2012.10.55423127782
    • (2013) Free Rad Biol Med , vol.55 , pp. 130-140
    • Espey, M.G.1
  • 5
    • 84952942226 scopus 로고    scopus 로고
    • Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates
    • 26069274
    • Vandeputte D, Falony G, Vieira-Silva S, Tito RY, Joossens M, Raes J. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut. (2016) 65:57–62. 10.1136/gutjnl-2015-30961826069274
    • (2016) Gut , vol.65 , pp. 57-62
    • Vandeputte, D.1    Falony, G.2    Vieira-Silva, S.3    Tito, R.Y.4    Joossens, M.5    Raes, J.6
  • 6
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • 20203603
    • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. (2010) 464:59. 10.1038/nature0882120203603
    • (2010) Nature , vol.464 , pp. 59
    • Qin, J.1    Li, R.2    Raes, J.3    Arumugam, M.4    Burgdorf, K.S.5    Manichanh, C.6
  • 8
    • 15544376418 scopus 로고    scopus 로고
    • Glycan foraging in vivo by an intestine-adapted bacterial symbiont
    • 15790854
    • Sonnenburg JL, Xu J, Leip DD, Chen C-H, Westover BP, Weatherford J, et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science. (2005) 307:1955–9. 10.1126/science.110905115790854
    • (2005) Science , vol.307 , pp. 1955-1959
    • Sonnenburg, J.L.1    Xu, J.2    Leip, D.D.3    Chen, C.-H.4    Westover, B.P.5    Weatherford, J.6
  • 9
    • 55949124035 scopus 로고    scopus 로고
    • Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients
    • 18936492
    • Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG, Gratadoux J-J, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci USA. (2008) 105:16731–6. 10.1073/pnas.080481210518936492
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 16731-16736
    • Sokol, H.1    Pigneur, B.2    Watterlot, L.3    Lakhdari, O.4    Bermúdez-Humarán, L.G.5    Gratadoux, J.-J.6
  • 10
    • 84897138296 scopus 로고    scopus 로고
    • Role of the microbiota in immunity and inflammation
    • 24679531
    • Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. (2014) 157:121–41. 10.1016/j.cell.2014.03.01124679531
    • (2014) Cell , vol.157 , pp. 121-141
    • Belkaid, Y.1    Hand, T.W.2
  • 11
    • 84924455205 scopus 로고    scopus 로고
    • Irritable bowel syndrome: a clinical review
    • 25734736
    • Chey WD, Kurlander J, Eswaran S. Irritable bowel syndrome: a clinical review. JAMA. (2015) 313:949–58. 10.1001/jama.2015.095425734736
    • (2015) JAMA , vol.313 , pp. 949-958
    • Chey, W.D.1    Kurlander, J.2    Eswaran, S.3
  • 12
    • 84994792268 scopus 로고    scopus 로고
    • The central nervous system and the gut microbiome
    • 27814521
    • Sharon G, Sampson TR, Geschwind DH, Mazmanian SK. The central nervous system and the gut microbiome. Cell. (2016) 167:915–32. 10.1016/j.cell.2016.10.02727814521
    • (2016) Cell , vol.167 , pp. 915-932
    • Sharon, G.1    Sampson, T.R.2    Geschwind, D.H.3    Mazmanian, S.K.4
  • 14
    • 85023608430 scopus 로고    scopus 로고
    • Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention
    • 28628112
    • Liu R, Hong J, Xu X, Feng Q, Zhang D, Gu Y, et al. Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention. Nat Med. (2017) 23:859. 10.1038/nm.435828628112
    • (2017) Nat Med , vol.23 , pp. 859
    • Liu, R.1    Hong, J.2    Xu, X.3    Feng, Q.4    Zhang, D.5    Gu, Y.6
  • 15
    • 85063786613 scopus 로고    scopus 로고
    • Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
    • 30936547
    • Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat Med. (2019) 25:679. 10.1038/s41591-019-0406-630936547
    • (2019) Nat Med , vol.25 , pp. 679
    • Wirbel, J.1    Pyl, P.T.2    Kartal, E.3    Zych, K.4    Kashani, A.5    Milanese, A.6
  • 16
    • 34548792911 scopus 로고    scopus 로고
    • Marine viruses—major players in the global ecosystem
    • 17853907
    • Suttle CA. Marine viruses—major players in the global ecosystem. Nat Rev Microbiol. (2007) 5:801. 10.1038/nrmicro175017853907
    • (2007) Nat Rev Microbiol , vol.5 , pp. 801
    • Suttle, C.A.1
  • 17
    • 83655191021 scopus 로고    scopus 로고
    • Marine viruses: truth or dare
    • Breitbart M. Marine viruses: truth or dare. Ann Rev Mar Sci. (2011) 4:425–48. 10.1146/annurev-marine-120709-142805
    • (2011) Ann Rev Mar Sci , vol.4 , pp. 425-448
    • Breitbart, M.1
  • 19
    • 84874530236 scopus 로고    scopus 로고
    • The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology
    • 23468974
    • 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. 10.1371/journal.pone.005735523468974
    • (2013) PLoS ONE , vol.8 , pp. e57355
    • Hurwitz, B.L.1    Sullivan, M.B.2
  • 20
    • 84921568760 scopus 로고    scopus 로고
    • Depth-stratified functional and taxonomic niche specialization in the ‘core'and ‘flexible'Pacific Ocean Virome
    • 25093636
    • Hurwitz BL, Brum JR, Sullivan MB. Depth-stratified functional and taxonomic niche specialization in the ‘core'and ‘flexible'Pacific Ocean Virome. ISME J. (2015) 9:472. 10.1038/ismej.2014.14325093636
    • (2015) ISME J , vol.9 , pp. 472
    • Hurwitz, B.L.1    Brum, J.R.2    Sullivan, M.B.3
  • 22
    • 33747369803 scopus 로고    scopus 로고
    • Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts
    • 16802857
    • Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol. (2006) 4:e234. 10.1371/journal.pbio.004023416802857
    • (2006) PLoS Biol , vol.4 , pp. e234
    • Sullivan, M.B.1    Lindell, D.2    Lee, J.A.3    Thompson, L.R.4    Bielawski, J.P.5    Chisholm, S.W.6
  • 23
    • 84864102582 scopus 로고    scopus 로고
    • Shiga toxin-producing Escherichia coli O104: H4: a new challenge for microbiology
    • 22504816
    • Muniesa M, Hammerl JA, Hertwig S, Appel B, Brüssow H. Shiga toxin-producing Escherichia coli O104: H4: a new challenge for microbiology. Appl Environ Microbiol. (2012) 78:4065–73. 10.1128/AEM.00217-1222504816
    • (2012) Appl Environ Microbiol , vol.78 , pp. 4065-4073
    • Muniesa, M.1    Hammerl, J.A.2    Hertwig, S.3    Appel, B.4    Brüssow, H.5
  • 25
    • 84922245262 scopus 로고    scopus 로고
    • Disease-specific alterations in the enteric virome in inflammatory bowel disease
    • 25619688
    • 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. 10.1016/j.cell.2015.01.00225619688
    • (2015) Cell , vol.160 , pp. 447-460
    • Norman, J.M.1    Handley, S.A.2    Baldridge, M.T.3    Droit, L.4    Liu, C.Y.5    Keller, B.C.6
  • 27
    • 85062658723 scopus 로고    scopus 로고
    • Gut mucosal virome alterations in ulcerative colitis
    • 30842211
    • Zuo T, Lu XJ, Zhang Y, Cheung CP, Lam S, Zhang F, et al. Gut mucosal virome alterations in ulcerative colitis. Gut. (2019) 68:1–11. 10.1136/gutjnl-2018-31813130842211
    • (2019) Gut , vol.68 , pp. 1-11
    • Zuo, T.1    Lu, X.J.2    Zhang, Y.3    Cheung, C.P.4    Lam, S.5    Zhang, F.6
  • 28
    • 84918533502 scopus 로고    scopus 로고
    • Characterization of virus-like particles associated with the human faecal and caecal Characterization of virus-like particles associated with the human faecal and caecal microbiota
    • 25463385
    • Hoyles L, Mccartney AL, Neve H, Gibson GR, Sanderson JD, Heller KJ, et al. Characterization of virus-like particles associated with the human faecal and caecal Characterization of virus-like particles associated with the human faecal and caecal microbiota. Res Microbiol. (2014) 165:803–12. 10.1016/j.resmic.2014.10.00625463385
    • (2014) Res Microbiol , vol.165 , pp. 803-812
    • Hoyles, L.1    Mccartney, A.L.2    Neve, H.3    Gibson, G.R.4    Sanderson, J.D.5    Heller, K.J.6
  • 29
    • 85052907786 scopus 로고    scopus 로고
    • Reproducible protocols for metagenomic analysis of human faecal phageomes
    • 29631623
    • Shkoporov AN, Ryan FJ, Draper LA, Forde A, Stockdale SR, Daly KM, et al. Reproducible protocols for metagenomic analysis of human faecal phageomes. Microbiome. (2018) 6:68. 10.1186/s40168-018-0446-z29631623
    • (2018) Microbiome , vol.6 , pp. 68
    • Shkoporov, A.N.1    Ryan, F.J.2    Draper, L.A.3    Forde, A.4    Stockdale, S.R.5    Daly, K.M.6
  • 30
    • 0141891348 scopus 로고    scopus 로고
    • Metagenomic analyses of an uncultured viral community from human feces
    • 14526037
    • Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, Salamon P, et al. Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol. (2003) 185:6220–3. 10.1128/JB.185.20.6220-6223.200314526037
    • (2003) J Bacteriol , vol.185 , pp. 6220-6223
    • Breitbart, M.1    Hewson, I.2    Felts, B.3    Mahaffy, J.M.4    Nulton, J.5    Salamon, P.6
  • 31
    • 85030318437 scopus 로고    scopus 로고
    • Viral communities of the human gut: metagenomic analysis of composition and dynamics
    • 29026445
    • Aggarwala V, Liang G, Bushman FD. Viral communities of the human gut: metagenomic analysis of composition and dynamics. Mobile DNA. (2017) 8:12. 10.1186/s13100-017-0095-y29026445
    • (2017) Mobile DNA , vol.8 , pp. 12
    • Aggarwala, V.1    Liang, G.2    Bushman, F.D.3
  • 32
    • 50749121524 scopus 로고
    • An investigation on the nature of ultra-microscopic viruses
    • Twort FW. An investigation on the nature of ultra-microscopic viruses. Lancet. (1915) 186:1241–3. 10.1016/S0140-6736(01)20383-3
    • (1915) Lancet , vol.186 , pp. 1241-1243
    • Twort, F.W.1
  • 33
    • 85061046008 scopus 로고    scopus 로고
    • A human gut bacterial genome and culture collection for improved metagenomic analyses
    • 30718869
    • Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, et al. A human gut bacterial genome and culture collection for improved metagenomic analyses. Nat Biotechnol. (2019) 37:186. 10.1038/s41587-018-0009-730718869
    • (2019) Nat Biotechnol , vol.37 , pp. 186
    • Forster, S.C.1    Kumar, N.2    Anonye, B.O.3    Almeida, A.4    Viciani, E.5    Stares, M.D.6
  • 34
    • 85061025040 scopus 로고    scopus 로고
    • Virome diversity correlates with intestinal microbiome diversity in adult monozygotic twins
    • 30763537, :.e265
    • Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector TD, Bell JT, et al. Virome diversity correlates with intestinal microbiome diversity in adult monozygotic twins. Cell Host Microbe. (2019) 25:261–72.e265. 10.1016/j.chom.2019.01.01930763537
    • (2019) Cell Host Microbe , vol.25 , pp. 261-272
    • Moreno-Gallego, J.L.1    Chou, S.P.2    Di Rienzi, S.C.3    Goodrich, J.K.4    Spector, T.D.5    Bell, J.T.6
  • 35
    • 85076001100 scopus 로고    scopus 로고
    • Whole-virome analysis sheds light on viral dark matter in inflammatory bowel disease
    • 31757768, [Epub ahead of print]
    • Clooney AG, Sutton TDS, Shkoporov AN, Holohan RK, Daly KM, O'Regan O, et al. Whole-virome analysis sheds light on viral dark matter in inflammatory bowel disease. Cell Host Microbe. (2019). 10.1016/j.chom.2019.10.00931757768. [Epub ahead of print].
    • (2019) Cell Host Microbe
    • Clooney, A.G.1    Sutton, T.D.S.2    Shkoporov, A.N.3    Holohan, R.K.4    Daly, K.M.5    O'Regan, O.6
  • 36
    • 85006073389 scopus 로고    scopus 로고
    • Towards quantitative viromics for both double-stranded and single-stranded DNA viruses
    • 28003936
    • Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB, et al. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ. (2016) 4:e2777. 10.7717/peerj.277728003936
    • (2016) PeerJ , vol.4 , pp. e2777
    • Roux, S.1    Solonenko, N.E.2    Dang, V.T.3    Poulos, B.T.4    Schwenck, S.M.5    Goldsmith, D.B.6
  • 38
    • 85060649058 scopus 로고    scopus 로고
    • Choice of assembly software has a critical impact on virome characterisation
    • 30691529
    • Sutton TD, Clooney AG, Ryan FJ, Ross RP, Hill C. Choice of assembly software has a critical impact on virome characterisation. Microbiome. (2019) 7:12. 10.1186/s40168-019-0626-530691529
    • (2019) Microbiome , vol.7 , pp. 12
    • Sutton, T.D.1    Clooney, A.G.2    Ryan, F.J.3    Ross, R.P.4    Hill, C.5
  • 39
    • 1942486000 scopus 로고    scopus 로고
    • Ecology of prokaryotic viruses
    • 15109783
    • Weinbauer MG. Ecology of prokaryotic viruses. FEMS Microbiol Rev. (2004) 28:127–81. 10.1016/j.femsre.2003.08.00115109783
    • (2004) FEMS Microbiol Rev , vol.28 , pp. 127-181
    • Weinbauer, M.G.1
  • 40
    • 84959018637 scopus 로고    scopus 로고
    • Replication and maintenance of linear phage-plasmid N15
    • 26104561
    • Ravin NV. Replication and maintenance of linear phage-plasmid N15. Microbiol Spectr. (2015) 3:71–82. 10.1128/microbiolspec.PLAS-0032-201426104561
    • (2015) Microbiol Spectr , vol.3 , pp. 71-82
    • Ravin, N.V.1
  • 41
    • 84953231449 scopus 로고    scopus 로고
    • Viral transmission dynamics at single-cell resolution reveal transiently immune subpopulations caused by a carrier state association
    • 26720743
    • Cenens W, Makumi A, Govers SK, Lavigne R, Aertsen A. Viral transmission dynamics at single-cell resolution reveal transiently immune subpopulations caused by a carrier state association. PLoS Genet. (2016) 11:e1005770. 10.1371/journal.pgen.100577026720743
    • (2016) PLoS Genet , vol.11 , pp. e1005770
    • Cenens, W.1    Makumi, A.2    Govers, S.K.3    Lavigne, R.4    Aertsen, A.5
  • 42
    • 84994500716 scopus 로고    scopus 로고
    • Simulation of the M13 life cycle I: assembly of a genetically-structured deterministic chemical kinetic simulation
    • 27644585
    • Smeal SW, Schmitt MA, Pereira RR, Prasad A, Fisk JD. Simulation of the M13 life cycle I: assembly of a genetically-structured deterministic chemical kinetic simulation. Virology. (2017) 500:259–74. 10.1016/j.virol.2016.08.01727644585
    • (2017) Virology , vol.500 , pp. 259-274
    • Smeal, S.W.1    Schmitt, M.A.2    Pereira, R.R.3    Prasad, A.4    Fisk, J.D.5
  • 43
    • 77951104433 scopus 로고    scopus 로고
    • Bacteriophage resistance mechanisms
    • 20348932
    • Labrie SJ, Samson JE, Moineau S. Bacteriophage resistance mechanisms. Nat Rev Microbiol. (2010) 8:317. 10.1038/nrmicro231520348932
    • (2010) Nat Rev Microbiol , vol.8 , pp. 317
    • Labrie, S.J.1    Samson, J.E.2    Moineau, S.3
  • 44
    • 85060853186 scopus 로고    scopus 로고
    • (Ph) ighting phages: how bacteria resist their parasites
    • 30763533
    • Rostøl JT, Marraffini L. (Ph) ighting phages: how bacteria resist their parasites. Cell Host Microbe. (2019) 25:184–94. 10.1016/j.chom.2019.01.00930763533
    • (2019) Cell Host Microbe , vol.25 , pp. 184-194
    • Rostøl, J.T.1    Marraffini, L.2
  • 45
    • 0021092925 scopus 로고
    • Genetic study of a membrane protein: DNA sequence alterations due to 17 lamB point mutations affecting adsorption of phage lambda
    • 11894913
    • Clement J-M, Lepouce E, Marchal C, Hofnung M. Genetic study of a membrane protein: DNA sequence alterations due to 17 lamB point mutations affecting adsorption of phage lambda. EMBO J. (1983) 2:77–80. 10.1002/j.1460-2075.1983.tb01384.x11894913
    • (1983) EMBO J , vol.2 , pp. 77-80
    • Clement, J.-M.1    Lepouce, E.2    Marchal, C.3    Hofnung, M.4
  • 46
    • 84905668783 scopus 로고    scopus 로고
    • A phage protein that inhibits the bacterial ATPase required for type IV pilus assembly
    • 25049409
    • Chung IY, Jang HJ, Bae HW, Cho YH. A phage protein that inhibits the bacterial ATPase required for type IV pilus assembly. Proc Natl Acad Sci USA. (2014) 111:11503–8. 10.1073/pnas.140353711125049409
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. 11503-11508
    • Chung, I.Y.1    Jang, H.J.2    Bae, H.W.3    Cho, Y.H.4
  • 47
    • 85018444734 scopus 로고    scopus 로고
    • Survey on the phage resistance mechanisms displayed by a dairy Lactobacillus helveticus strain
    • 28576359
    • Zago M, Orrù L, Rossetti L, Lamontanara A, Fornasari ME, Bonvini B, et al. Survey on the phage resistance mechanisms displayed by a dairy Lactobacillus helveticus strain. Food Microbiol. (2017) 66:110–6. 10.1016/j.fm.2017.04.01428576359
    • (2017) Food Microbiol , vol.66 , pp. 110-116
    • Zago, M.1    Orrù, L.2    Rossetti, L.3    Lamontanara, A.4    Fornasari, M.E.5    Bonvini, B.6
  • 48
    • 23744448545 scopus 로고    scopus 로고
    • Escherichia coli K1's capsule is a barrier to bacteriophage T7
    • 16085886
    • Scholl D, Adhya S, Merril C. Escherichia coli K1's capsule is a barrier to bacteriophage T7. Appl Environ Microbiol. (2005) 71:4872–4. 10.1128/AEM.71.8.4872-4874.200516085886
    • (2005) Appl Environ Microbiol , vol.71 , pp. 4872-4874
    • Scholl, D.1    Adhya, S.2    Merril, C.3
  • 49
    • 84941877295 scopus 로고    scopus 로고
    • Outer-membrane vesicles from Gram-negative bacteria: biogenesis and functions
    • 26373371
    • Schwechheimer C, Kuehn MJ. Outer-membrane vesicles from Gram-negative bacteria: biogenesis and functions. Nat Rev. Microbiol. (2015) 13:605. 10.1038/nrmicro352526373371
    • (2015) Nat Rev. Microbiol , vol.13 , pp. 605
    • Schwechheimer, C.1    Kuehn, M.J.2
  • 50
    • 84928402372 scopus 로고    scopus 로고
    • The phage tail tape measure protein, an inner membrane protein and a periplasmic chaperone play connected roles in the genome injection process of E. coli phage HK97
    • 25532427
    • Cumby N, Reimer K, Mengin-Lecreulx D, Davidson AR, Maxwell KL. The phage tail tape measure protein, an inner membrane protein and a periplasmic chaperone play connected roles in the genome injection process of E. coli phage HK97. Mol Microbiol. (2015) 96:437–47. 10.1111/mmi.1291825532427
    • (2015) Mol Microbiol , vol.96 , pp. 437-447
    • Cumby, N.1    Reimer, K.2    Mengin-Lecreulx, D.3    Davidson, A.R.4    Maxwell, K.L.5
  • 51
    • 22544464152 scopus 로고    scopus 로고
    • The biology of restriction and anti-restriction
    • 15979932
    • Tock MR, Dryden DT. The biology of restriction and anti-restriction. Curr Opin Microbiol. (2005) 8:466–72. 10.1016/j.mib.2005.06.00315979932
    • (2005) Curr Opin Microbiol , vol.8 , pp. 466-472
    • Tock, M.R.1    Dryden, D.T.2
  • 53
    • 84867049470 scopus 로고    scopus 로고
    • Staphylococcal pathogenicity island interference with helper phage reproduction is a paradigm of molecular parasitism
    • 22991467
    • Ram G, Chen J, Kumar K, Ross HF, Ubeda C, Damle PK, et al. Staphylococcal pathogenicity island interference with helper phage reproduction is a paradigm of molecular parasitism. Proc Natl Acad Sci USA. (2012) 109:16300–5. 10.1073/pnas.120461510922991467
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 16300-16305
    • Ram, G.1    Chen, J.2    Kumar, K.3    Ross, H.F.4    Ubeda, C.5    Damle, P.K.6
  • 54
    • 84897845950 scopus 로고    scopus 로고
    • A widespread bacteriophage abortive infection system functions through a Type IV toxin–antitoxin mechanism
    • 24465005
    • Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC. A widespread bacteriophage abortive infection system functions through a Type IV toxin–antitoxin mechanism. Nucleic Acids Res. (2014) 42:4590–605. 10.1093/nar/gkt141924465005
    • (2014) Nucleic Acids Res , vol.42 , pp. 4590-4605
    • Dy, R.L.1    Przybilski, R.2    Semeijn, K.3    Salmond, G.P.4    Fineran, P.C.5
  • 55
    • 84991389384 scopus 로고    scopus 로고
    • Evolutionary ecology of prokaryotic immune mechanisms
    • 27412881
    • Van Houte S, Buckling A, Westra ER. Evolutionary ecology of prokaryotic immune mechanisms. Microbiol Mol Biol Rev. (2016) 80:745–63. 10.1128/MMBR.00011-1627412881
    • (2016) Microbiol Mol Biol Rev , vol.80 , pp. 745-763
    • Van Houte, S.1    Buckling, A.2    Westra, E.R.3
  • 56
    • 0029019569 scopus 로고
    • The superinfection exclusion gene (sieA) of bacteriophage P22: identification and overexpression of the gene and localization of the gene product
    • 7768804
    • Hofer B, Ruge M, Dreiseikelmann B. The superinfection exclusion gene (sieA) of bacteriophage P22: identification and overexpression of the gene and localization of the gene product. J Bacteriol. (1995) 177:3080–6. 10.1128/jb.177.11.3080-3086.19957768804
    • (1995) J Bacteriol , vol.177 , pp. 3080-3086
    • Hofer, B.1    Ruge, M.2    Dreiseikelmann, B.3
  • 57
    • 84884286187 scopus 로고    scopus 로고
    • Revenge of the phages: defeating bacterial defences
    • 23979432
    • Samson JE, Magadán AH, Sabri M, Moineau S. Revenge of the phages: defeating bacterial defences. Nat Rev Microbiol. (2013) 11:675. 10.1038/nrmicro309623979432
    • (2013) Nat Rev Microbiol , vol.11 , pp. 675
    • Samson, J.E.1    Magadán, A.H.2    Sabri, M.3    Moineau, S.4
  • 58
    • 34447620875 scopus 로고    scopus 로고
    • The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities
    • 17585937
    • Leiman PG, Battisti AJ, Bowman VD, Stummeyer K, Mühlenhoff M, Gerardy-Schahn R, et al. The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities. J Mol Biol. (2007) 371:836–49. 10.1016/j.jmb.2007.05.08317585937
    • (2007) J Mol Biol , vol.371 , pp. 836-849
    • Leiman, P.G.1    Battisti, A.J.2    Bowman, V.D.3    Stummeyer, K.4    Mühlenhoff, M.5    Gerardy-Schahn, R.6
  • 59
    • 84870625727 scopus 로고    scopus 로고
    • Interaction of bacteriophage l with its E. coli receptor, LamB
    • 23202520
    • Chatterjee S, Rothenberg E. Interaction of bacteriophage l with its E. coli receptor, LamB. Viruses. (2012) 4:3162–78. 10.3390/v411316223202520
    • (2012) Viruses , vol.4 , pp. 3162-3178
    • Chatterjee, S.1    Rothenberg, E.2
  • 61
    • 85073764060 scopus 로고    scopus 로고
    • Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
    • 31086738
    • Warwick-Dugdale J, Solonenko N, Moore K, Chittick L, Gregory AC, Allen MJ, et al. Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands. PeerJ. (2019) 7:e6800. 10.7717/peerj.680031086738
    • (2019) PeerJ , vol.7 , pp. e6800
    • Warwick-Dugdale, J.1    Solonenko, N.2    Moore, K.3    Chittick, L.4    Gregory, A.C.5    Allen, M.J.6
  • 62
    • 84872607723 scopus 로고    scopus 로고
    • Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system
    • 23242138
    • Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature. (2013) 493:429. 10.1038/nature1172323242138
    • (2013) Nature , vol.493 , pp. 429
    • Bondy-Denomy, J.1    Pawluk, A.2    Maxwell, K.L.3    Davidson, A.R.4
  • 63
    • 33846591325 scopus 로고    scopus 로고
    • A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs
    • 17188297
    • Bair CL, Black LW. A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs. J Mol Biol. (2007) 366:768–78. 10.1016/j.jmb.2006.11.05117188297
    • (2007) J Mol Biol , vol.366 , pp. 768-778
    • Bair, C.L.1    Black, L.W.2
  • 64
    • 84874388110 scopus 로고    scopus 로고
    • A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity
    • 23446421
    • Seed KD, Lazinski DW, Calderwood SB, Camilli A. A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature. (2013) 494:489. 10.1038/nature1192723446421
    • (2013) Nature , vol.494 , pp. 489
    • Seed, K.D.1    Lazinski, D.W.2    Calderwood, S.B.3    Camilli, A.4
  • 65
    • 85015931686 scopus 로고    scopus 로고
    • Bacteria–bacteriophage coevolution in the human gut: implications for microbial diversity and functionality
    • 28342597
    • Scanlan PD. Bacteria–bacteriophage coevolution in the human gut: implications for microbial diversity and functionality. Trends Microbiol. (2017) 25:614–23. 10.1016/j.tim.2017.02.01228342597
    • (2017) Trends Microbiol , vol.25 , pp. 614-623
    • Scanlan, P.D.1
  • 66
    • 84939135810 scopus 로고    scopus 로고
    • Inter-individual differences in the gene content of human gut bacterial species
    • 25896518
    • Zhu A, Sunagawa S, Mende DR, Bork P. Inter-individual differences in the gene content of human gut bacterial species. Genome Biol. (2015) 16:82. 10.1186/s13059-015-0646-925896518
    • (2015) Genome Biol , vol.16 , pp. 82
    • Zhu, A.1    Sunagawa, S.2    Mende, D.R.3    Bork, P.4
  • 67
    • 54049140617 scopus 로고    scopus 로고
    • Host–parasite coevolution and patterns of adaptation across time and space
    • 18717749
    • Gandon S, Buckling A, Decaestecker E, Day T. Host–parasite coevolution and patterns of adaptation across time and space. J Evol Biol. (2008) 21:1861–6. 10.1111/j.1420-9101.2008.01598.x18717749
    • (2008) J Evol Biol , vol.21 , pp. 1861-1866
    • Gandon, S.1    Buckling, A.2    Decaestecker, E.3    Day, T.4
  • 68
    • 84931749101 scopus 로고    scopus 로고
    • Host-parasite coevolutionary arms races give way to fluctuating selection
    • 21521436
    • Hall AR, Scanlan PD, Morgan AD, Buckling A. Host-parasite coevolutionary arms races give way to fluctuating selection. Ecol Lett. (2011) 14:635–42. 10.1111/j.1461-0248.2011.01624.x21521436
    • (2011) Ecol Lett , vol.14 , pp. 635-642
    • Hall, A.R.1    Scanlan, P.D.2    Morgan, A.D.3    Buckling, A.4
  • 69
    • 85060602468 scopus 로고    scopus 로고
    • “I will survive”: a tale of bacteriophage-bacteria coevolution in the gut
    • De Sordi L, Lourenço M, Debarbieux L. “I will survive”: a tale of bacteriophage-bacteria coevolution in the gut. Gut Microbes. (2019) 10:92–9. 10.1080/19490976.2018.1474322
    • (2019) Gut Microbes , vol.10 , pp. 92-99
    • De Sordi, L.1    Lourenço, M.2    Debarbieux, L.3
  • 70
    • 85019133486 scopus 로고    scopus 로고
    • metaSPAdes: a new versatile metagenomic assembler
    • 28298430
    • Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. (2017) 27:824–34. 10.1101/gr.213959.11628298430
    • (2017) Genome Res , vol.27 , pp. 824-834
    • Nurk, S.1    Meleshko, D.2    Korobeynikov, A.3    Pevzner, P.A.4
  • 71
    • 85072691300 scopus 로고    scopus 로고
    • Multiple phase-variable mechanisms, including capsular polysaccharides, modify bacteriophage susceptibility in Bacteroides thetaiotaomicron
    • Porter NT, Hryckowian AJ, Merrill BD, Gardner JO, Singh S, Sonnenburg JL, et al. Multiple phase-variable mechanisms, including capsular polysaccharides, modify bacteriophage susceptibility in Bacteroides thetaiotaomicron. BioRxiv [Preprint]. (2019). 10.1101/521070
    • (2019) BioRxiv [Preprint]
    • Porter, N.T.1    Hryckowian, A.J.2    Merrill, B.D.3    Gardner, J.O.4    Singh, S.5    Sonnenburg, J.L.6
  • 72
    • 85069527298 scopus 로고    scopus 로고
    • Phage-resistant phase-variant sub-populations mediate herd immunity against bacteriophage invasion of bacterial meta-populations
    • 31333609
    • Turkington CJR, Morozov A, Clokie MRJ, Bayliss CD. Phage-resistant phase-variant sub-populations mediate herd immunity against bacteriophage invasion of bacterial meta-populations. Front Microbiol. 10. 10.3389/fmicb.2019.0147331333609
    • Front Microbiol , pp. 10
    • Turkington, C.J.R.1    Morozov, A.2    Clokie, M.R.J.3    Bayliss, C.D.4
  • 73
    • 36549004621 scopus 로고    scopus 로고
    • Gene expression of commensal Lactobacillus johnsonii strain NCC533 during in vitro growth and in the murine gut
    • 17827285
    • Denou E, Berger B, Barretto C, Panoff J-M, Arigoni F, Brüssow H. Gene expression of commensal Lactobacillus johnsonii strain NCC533 during in vitro growth and in the murine gut. J Bacteriol. (2007) 189:8109–19. 10.1128/JB.00991-0717827285
    • (2007) J Bacteriol , vol.189 , pp. 8109-8119
    • Denou, E.1    Berger, B.2    Barretto, C.3    Panoff, J.-M.4    Arigoni, F.5    Brüssow, H.6
  • 74
    • 84869214358 scopus 로고    scopus 로고
    • Virulent bacteriophages can target O104: H4 enteroaggregative Escherichia coli in the mouse intestine
    • 23006754
    • Maura D, Galtier M, Le Bouguénec C, Debarbieux L. Virulent bacteriophages can target O104: H4 enteroaggregative Escherichia coli in the mouse intestine. Antimicrob Agents Chemother. (2012) 56:6235–42. 10.1128/AAC.00602-1223006754
    • (2012) Antimicrob Agents Chemother , vol.56 , pp. 6235-6242
    • Maura, D.1    Galtier, M.2    Le, B.C.3    Debarbieux, L.4
  • 75
    • 85028673472 scopus 로고    scopus 로고
    • Bacteriophages targeting adherent invasive Escherichia coli strains as a promising new treatment for Crohn's disease
    • 28130329
    • Galtier M, Sordi LD, Sivignon A, De Vallée A, Maura D, Neut C, et al. Bacteriophages targeting adherent invasive Escherichia coli strains as a promising new treatment for Crohn's disease. J Crohn Colitis. (2017) 11:840–7. 10.1093/ecco-jcc/jjw22428130329
    • (2017) J Crohn Colitis , vol.11 , pp. 840-847
    • Galtier, M.1    Sordi, L.D.2    Sivignon, A.3    De, V.A.4    Maura, D.5    Neut, C.6
  • 76
    • 85018297391 scopus 로고    scopus 로고
    • Ménage à trois in the human gut: interactions between host, bacteria and phages
    • 28461690
    • Mirzaei MK, Maurice CF. Ménage à trois in the human gut: interactions between host, bacteria and phages. Nat Rev Microbiol. (2017) 15:397. 10.1038/nrmicro.2017.3028461690
    • (2017) Nat Rev Microbiol , vol.15 , pp. 397
    • Mirzaei, M.K.1    Maurice, C.F.2
  • 77
    • 0033826796 scopus 로고    scopus 로고
    • Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems
    • 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. 10.4319/lo.2000.45.6.1320
    • (2000) Limnol Oceanogr , vol.45 , pp. 1320-1328
    • Thingstad, T.F.1
  • 78
    • 84875092761 scopus 로고    scopus 로고
    • Virus-host swinging party in the oceans: incorporating biological complexity into paradigms of antagonistic coexistence
    • 22934242
    • Avrani S, Schwartz DA, Lindell D. Virus-host swinging party in the oceans: incorporating biological complexity into paradigms of antagonistic coexistence. Mobile Genet Elem. (2012) 2:88–95. 10.4161/mge.2003122934242
    • (2012) Mobile Genet Elem , vol.2 , pp. 88-95
    • Avrani, S.1    Schwartz, D.A.2    Lindell, D.3
  • 79
    • 85060870452 scopus 로고    scopus 로고
    • Bacteriophages of the human gut: the “known unknown” of the microbiome
    • 30763534
    • Shkoporov AN, Hill C. Bacteriophages of the human gut: the “known unknown” of the microbiome. Cell Host Microbe. (2019) 25:195–209. 10.1016/j.chom.2019.01.01730763534
    • (2019) Cell Host Microbe , vol.25 , pp. 195-209
    • Shkoporov, A.N.1    Hill, C.2
  • 81
    • 84943657766 scopus 로고    scopus 로고
    • Early life dynamics of the human gut virome and bacterial microbiome in infants
    • 26366711
    • 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. 10.1038/nm.395026366711
    • (2015) Nat Med , vol.21 , pp. 1228
    • Lim, E.S.1    Zhou, Y.2    Zhao, G.3    Bauer, I.K.4    Droit, L.5    Ndao, I.M.6
  • 82
    • 77954627922 scopus 로고    scopus 로고
    • Viruses in the faecal microbiota of monozygotic twins and their mothers
    • 20631792
    • 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. 10.1038/nature0919920631792
    • (2010) Nature , vol.466 , pp. 334
    • Reyes, A.1    Haynes, M.2    Hanson, N.3    Angly, F.E.4    Heath, A.C.5    Rohwer, F.6
  • 83
    • 85059602498 scopus 로고    scopus 로고
    • A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision
    • 30554875, :.e213
    • Silpe JE, Bassler BL. A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Cell. (2019) 176:268–80.e213. 10.1016/j.cell.2018.10.05930554875
    • (2019) Cell , vol.176 , pp. 268-280
    • Silpe, J.E.1    Bassler, B.L.2
  • 85
    • 85021813111 scopus 로고    scopus 로고
    • Piggyback-the-Winner in host-associated microbial communities
    • 28721247
    • Silveira CB, Rohwer FL. Piggyback-the-Winner in host-associated microbial communities. NPJ Biofilms Microbio. (2016) 2:16010. 10.1038/npjbiofilms.2016.1028721247
    • (2016) NPJ Biofilms Microbio , vol.2 , pp. 16010
    • Silveira, C.B.1    Rohwer, F.L.2
  • 86
    • 84879515171 scopus 로고    scopus 로고
    • Bacteriophage adhering to mucus provide a non–host-derived immunity
    • 23690590
    • 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. 10.1073/pnas.130592311023690590
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. 10771-10776
    • Barr, J.J.1    Auro, R.2    Furlan, M.3    Whiteson, K.L.4    Erb, M.L.5    Pogliano, J.6
  • 87
    • 84946594594 scopus 로고    scopus 로고
    • Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters
    • 26483471
    • Barr JJ, Auro R, Sam-Soon N, Kassegne S, Peters G, Bonilla N, et al. Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters. Proc Natl Acad Sci USA. (2015) 112:13675–80. 10.1073/pnas.150835511226483471
    • (2015) Proc Natl Acad Sci USA , vol.112 , pp. 13675-13680
    • Barr, J.J.1    Auro, R.2    Sam-Soon, N.3    Kassegne, S.4    Peters, G.5    Bonilla, N.6
  • 88
    • 85056762814 scopus 로고    scopus 로고
    • Virome biogeography in the lower gastrointestinal tract of rhesus macaques with chronic diarrhea
    • 30468938
    • Zhao G, Droit L, Gilbert MH, Schiro FR, Didier PJ, Si X, et al. Virome biogeography in the lower gastrointestinal tract of rhesus macaques with chronic diarrhea. Virology. (2019) 527:77–88. 10.1016/j.virol.2018.10.00130468938
    • (2019) Virology , vol.527 , pp. 77-88
    • Zhao, G.1    Droit, L.2    Gilbert, M.H.3    Schiro, F.R.4    Didier, P.J.5    Si, X.6
  • 89
    • 84903378191 scopus 로고    scopus 로고
    • Classification and quantification of bacteriophage taxa in human gut metagenomes
    • 24621522
    • 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. 10.1038/ismej.2014.3024621522
    • (2014) ISME J , vol.8 , pp. 1391
    • Waller, A.S.1    Yamada, T.2    Kristensen, D.M.3    Kultima, J.R.4    Sunagawa, S.5    Koonin, E.V.6
  • 90
    • 85042880915 scopus 로고    scopus 로고
    • A human gut phage catalog correlates the gut phageome with type 2 diabetes
    • 29391057
    • Ma Y, You X, Mai G, Tokuyasu T, Liu C. A human gut phage catalog correlates the gut phageome with type 2 diabetes. Microbiome. (2018) 6:24. 10.1186/s40168-018-0410-y29391057
    • (2018) Microbiome , vol.6 , pp. 24
    • Ma, Y.1    You, X.2    Mai, G.3    Tokuyasu, T.4    Liu, C.5
  • 91
    • 85046684250 scopus 로고    scopus 로고
    • Viromes of one year old infants reveal the impact of birth mode on microbiome diversity
    • 29761040
    • Mccann A, Ryan FJ, Stockdale SR, Dalmasso M, Blake T, Ryan CA, et al. Viromes of one year old infants reveal the impact of birth mode on microbiome diversity. PeerJ. (2018) 6:e4694. 10.7717/peerj.469429761040
    • (2018) PeerJ , vol.6 , pp. e4694
    • Mccann, A.1    Ryan, F.J.2    Stockdale, S.R.3    Dalmasso, M.4    Blake, T.5    Ryan, C.A.6
  • 92
    • 83155190998 scopus 로고    scopus 로고
    • Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses
    • 21926223
    • 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. 10.1128/AEM.00289-1121926223
    • (2011) Appl Environ Microbiol , vol.77 , pp. 7663-7668
    • Kim, K.H.1    Bae, J.W.2
  • 94
    • 84884563236 scopus 로고    scopus 로고
    • Bacteriophages in gut samples from pediatric Crohn's disease patients: metagenomic analysis using 454 pyrosequencing
    • 23749273
    • Wagner J, Maksimovic J, Farries G, Sim WH, Bishop RF, Cameron DJ, et al. Bacteriophages in gut samples from pediatric Crohn's disease patients: metagenomic analysis using 454 pyrosequencing. Inflam Bowel Dis. (2013) 19:1598–608. 10.1097/MIB.0b013e318292477c23749273
    • (2013) Inflam Bowel Dis , vol.19 , pp. 1598-1608
    • Wagner, J.1    Maksimovic, J.2    Farries, G.3    Sim, W.H.4    Bishop, R.F.5    Cameron, D.J.6
  • 95
    • 39649093188 scopus 로고    scopus 로고
    • Dysbiosis in inflammatory bowel disease: a role for bacteriophages?
    • 18268057
    • Lepage P, Colombet J, Marteau P, Sime-Ngando T, Doré J, Leclerc M. Dysbiosis in inflammatory bowel disease: a role for bacteriophages? Gut. (2008) 57:424–5. 10.1136/gut.2007.13466818268057
    • (2008) Gut , vol.57 , pp. 424-425
    • Lepage, P.1    Colombet, J.2    Marteau, P.3    Sime-Ngando, T.4    Doré, J.5    Leclerc, M.6
  • 96
    • 84942883364 scopus 로고    scopus 로고
    • Gut DNA viromes of Malawian twins discordant for severe acute malnutrition
    • 26351661
    • 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. 10.1073/pnas.151428511226351661
    • (2015) Proc Natl Acad Sci USA , vol.112 , pp. 11941-11946
    • Reyes, A.1    Blanton, L.V.2    Cao, S.3    Zhao, G.4    Manary, M.5    Trehan, I.6
  • 97
    • 85059228576 scopus 로고    scopus 로고
    • Enteric virome and bacterial microbiota in children with ulcerative colitis and Crohn disease
    • 30169455
    • Fernandes MA, Verstraete SG, Phan TG, Deng X, Stekol E, Lamere B, et al. Enteric virome and bacterial microbiota in children with ulcerative colitis and Crohn disease. J Pediatr Gastroenterol Nutr. (2019) 68:30–6. 10.1097/MPG.000000000000214030169455
    • (2019) J Pediatr Gastroenterol Nutr , vol.68 , pp. 30-36
    • Fernandes, M.A.1    Verstraete, S.G.2    Phan, T.G.3    Deng, X.4    Stekol, E.5    Lamere, B.6
  • 98
    • 84930008169 scopus 로고    scopus 로고
    • A structured annotation frame for the transposable phages: a new proposed family “Saltoviridae” within the Caudovirales
    • 25500185
    • Hulo C, Masson P, Le Mercier P, Toussaint A. A structured annotation frame for the transposable phages: a new proposed family “Saltoviridae” within the Caudovirales. Virology. (2015) 477:155–63. 10.1016/j.virol.2014.10.00925500185
    • (2015) Virology , vol.477 , pp. 155-163
    • Hulo, C.1    Masson, P.2    Le Mercier, P.3    Toussaint, A.4
  • 99
    • 85018974675 scopus 로고    scopus 로고
    • vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria
    • 28480138
    • Bolduc B, Jang HB, Doulcier G, You Z-Q, Roux S, Sullivan MB. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ. (2017) 5:e3243. 10.7717/peerj.324328480138
    • (2017) PeerJ , vol.5 , pp. e3243
    • Bolduc, B.1    Jang, H.B.2    Doulcier, G.3    You, Z.-Q.4    Roux, S.5    Sullivan, M.B.6
  • 101
    • 84986587931 scopus 로고    scopus 로고
    • The double-stranded DNA virosphere as a modular hierarchical network of gene sharing
    • 27486193
    • Iranzo J, Krupovic M, Koonin EV. The double-stranded DNA virosphere as a modular hierarchical network of gene sharing. mBio. (2016) 7:e00978–16. 10.1128/mBio.00978-1627486193
    • (2016) mBio , vol.7 , pp. e00978-e916
    • Iranzo, J.1    Krupovic, M.2    Koonin, E.V.3
  • 102
    • 85065314281 scopus 로고    scopus 로고
    • Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
    • Jang HB, Bolduc B, Zablocki O, Kuhn JH, Roux S, Adriaenssens EM, et al. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat Biotechnol. (2019) 37:632. 10.1038/s41587-019-0100-8
    • (2019) Nat Biotechnol , vol.37 , pp. 632
    • Jang, H.B.1    Bolduc, B.2    Zablocki, O.3    Kuhn, J.H.4    Roux, S.5    Adriaenssens, E.M.6
  • 103
    • 84870829895 scopus 로고    scopus 로고
    • Reference-independent comparative metagenomics using cross-assembly: crAss
    • 23074261
    • Dutilh BE, Schmieder R, Nulton J, Felts B, Salamon P, Edwards RA, et al. Reference-independent comparative metagenomics using cross-assembly: crAss. Bioinformatics. (2012) 28:3225–31. 10.1093/bioinformatics/bts61323074261
    • (2012) Bioinformatics , vol.28 , pp. 3225-3231
    • Dutilh, B.E.1    Schmieder, R.2    Nulton, J.3    Felts, B.4    Salamon, P.5    Edwards, R.A.6
  • 104
    • 84905041075 scopus 로고    scopus 로고
    • A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
    • 25058116
    • 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) 5:5498. 10.1038/ncomms549825058116
    • (2014) Nat Commun , vol.5 , pp. 5498
    • Dutilh, B.E.1    Cassman, N.2    Mcnair, K.3    Sanchez, S.E.4    Silva, G.G.5    Boling, L.6
  • 105
    • 85068899860 scopus 로고    scopus 로고
    • Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
    • 31285584
    • Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, et al. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol. (2019) 4:1727–36. 10.1038/s41564-019-0494-631285584
    • (2019) Nat Microbiol , vol.4 , pp. 1727-1736
    • Edwards, R.A.1    Vega, A.A.2    Norman, H.M.3    Ohaeri, M.4    Levi, K.5    Dinsdale, E.A.6
  • 106
    • 85056598186 scopus 로고    scopus 로고
    • ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis
    • 30429469
    • Shkoporov AN, Khokhlova EV, Fitzgerald CB, Stockdale SR, Draper LA, Ross RP, et al. ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis. Nat Commun. (2018) 9:4781. 10.1038/s41467-018-07225-730429469
    • (2018) Nat Commun , vol.9 , pp. 4781
    • Shkoporov, A.N.1    Khokhlova, E.V.2    Fitzgerald, C.B.3    Stockdale, S.R.4    Draper, L.A.5    Ross, R.P.6
  • 107
    • 85056591119 scopus 로고    scopus 로고
    • Biology and taxonomy of crass-like bacteriophages, the most abundant virus in the human gut
    • 30449316, :.e656
    • Guerin E, Shkoporov A, Stockdale SR, Clooney AG, Ryan FJ, Sutton TDS, et al. Biology and taxonomy of crass-like bacteriophages, the most abundant virus in the human gut. Cell Host Microbe. (2018) 24:653–64.e656. 10.1016/j.chom.2018.10.00230449316
    • (2018) Cell Host Microbe , vol.24 , pp. 653-664
    • Guerin, E.1    Shkoporov, A.2    Stockdale, S.R.3    Clooney, A.G.4    Ryan, F.J.5    Sutton, T.D.S.6
  • 108
    • 85033594015 scopus 로고    scopus 로고
    • Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut
    • 29133882
    • Yutin N, Makarova KS, Gussow AB, Krupovic M, Segall A, Edwards RA, et al. Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut. Nat Microbiol. (2018) 3:38. 10.1038/s41564-017-0053-y29133882
    • (2018) Nat Microbiol , vol.3 , pp. 38
    • Yutin, N.1    Makarova, K.S.2    Gussow, A.B.3    Krupovic, M.4    Segall, A.5    Edwards, R.A.6
  • 109
    • 85058316436 scopus 로고    scopus 로고
    • Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation
    • 30526683
    • Draper LA, Ryan FJ, Smith MK, Jalanka J, Mattila E, Arkkila PA, et al. Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation. Microbiome. (2018) 6:220. 10.1186/s40168-018-0598-x30526683
    • (2018) Microbiome , vol.6 , pp. 220
    • Draper, L.A.1    Ryan, F.J.2    Smith, M.K.3    Jalanka, J.4    Mattila, E.5    Arkkila, P.A.6
  • 110
    • 84901045055 scopus 로고    scopus 로고
    • Alternative bacteriophage life cycles: the carrier state of Campylobacter jejuni
    • 24671947
    • Siringan P, Connerton PL, Cummings NJ, Connerton IF. Alternative bacteriophage life cycles: the carrier state of Campylobacter jejuni. Open Biol. (2014) 4:130200. 10.1098/rsob.13020024671947
    • (2014) Open Biol , vol.4 , pp. 130200
    • Siringan, P.1    Connerton, P.L.2    Cummings, N.J.3    Connerton, I.F.4
  • 111
    • 85048013849 scopus 로고    scopus 로고
    • Phage puppet masters of the marine microbial realm
    • 29867096
    • Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. (2018) 3:754–66. 10.1038/s41564-018-0166-y29867096
    • (2018) Nat Microbiol , vol.3 , pp. 754-766
    • Breitbart, M.1    Bonnain, C.2    Malki, K.3    Sawaya, N.A.4
  • 112
    • 85034641556 scopus 로고    scopus 로고
    • The gut microbiota facilitates drifts in the genetic diversity and infectivity of bacterial viruses
    • 29174401, :.e803
    • De Sordi L, Khanna V, Debarbieux L. The gut microbiota facilitates drifts in the genetic diversity and infectivity of bacterial viruses. Cell Host Microbe. (2017) 22:801–8.e803. 10.1016/j.chom.2017.10.01029174401
    • (2017) Cell Host Microbe , vol.22 , pp. 801-808
    • De Sordi, L.1    Khanna, V.2    Debarbieux, L.3
  • 113
    • 84887380143 scopus 로고    scopus 로고
    • Metabolic reprogramming by viruses in the sunlit and dark ocean
    • 24200126
    • Hurwitz BL, Hallam SJ, Sullivan MB. Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biol. (2013) 14:R123. 10.1186/gb-2013-14-11-r12324200126
    • (2013) Genome Biol , vol.14 , pp. R123
    • Hurwitz, B.L.1    Hallam, S.J.2    Sullivan, M.B.3
  • 114
    • 0030057090 scopus 로고    scopus 로고
    • Lysogenic conversion by a filamentous phage encoding cholera toxin
    • 8658163
    • Waldor MK, Mekalanos JJ. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science. (1996) 272:1910–4. 10.1126/science.272.5270.19108658163
    • (1996) Science , vol.272 , pp. 1910-1914
    • Waldor, M.K.1    Mekalanos, J.J.2
  • 115
    • 84880509968 scopus 로고    scopus 로고
    • Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome
    • 23748443
    • Modi SR, Lee HH, Spina CS, Collins JJ. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature. (2013) 499:219. 10.1038/nature1221223748443
    • (2013) Nature , vol.499 , pp. 219
    • Modi, S.R.1    Lee, H.H.2    Spina, C.S.3    Collins, J.J.4
  • 116
    • 84975275010 scopus 로고    scopus 로고
    • Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses
    • 27326545
    • Enault F, Briet A, Bouteille L, Roux S, Sullivan MB, Petit M-A. Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses. ISME J. (2017) 11:237–47. 10.1038/ismej.2016.9027326545
    • (2017) ISME J , vol.11 , pp. 237-247
    • Enault, F.1    Briet, A.2    Bouteille, L.3    Roux, S.4    Sullivan, M.B.5    Petit, M.-A.6
  • 117
    • 84897526477 scopus 로고    scopus 로고
    • Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences
    • 24335607
    • Roux S, Krupovic M, Debroas D, Forterre P, Enault F. Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences. Open Biol. (2013) 3:130160. 10.1098/rsob.13016024335607
    • (2013) Open Biol , vol.3 , pp. 130160
    • Roux, S.1    Krupovic, M.2    Debroas, D.3    Forterre, P.4    Enault, F.5
  • 118
    • 85067123220 scopus 로고    scopus 로고
    • Giant oversights in the human gut virome
    • 31186296
    • Sutton TDS, Clooney AG, Hill C. Giant oversights in the human gut virome. Gut. (2019). 10.1136/gutjnl-2019-31906731186296
    • (2019) Gut
    • Sutton, T.D.S.1    Clooney, A.G.2    Hill, C.3
  • 119
    • 4544321685 scopus 로고    scopus 로고
    • Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion
    • 15353570
    • Brüssow H, Canchaya C, Hardt W-D. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev. (2004) 68:560–602. 10.1128/MMBR.68.3.560-602.200415353570
    • (2004) Microbiol Mol Biol Rev , vol.68 , pp. 560-602
    • Brüssow, H.1    Canchaya, C.2    Hardt, W.-D.3
  • 120
    • 84962090717 scopus 로고    scopus 로고
    • The significance of mutualistic phages for bacterial ecology and evolution
    • 26826796
    • Obeng N, Pratama AA, Van Elsas JD. The significance of mutualistic phages for bacterial ecology and evolution. Trends Microbiol. (2016) 24:440–9. 10.1016/j.tim.2015.12.00926826796
    • (2016) Trends Microbiol , vol.24 , pp. 440-449
    • Obeng, N.1    Pratama, A.A.2    Van Elsas, J.D.3
  • 121
    • 0015029402 scopus 로고
    • Mechanism of conversion of the Salmonella O antigen by bacteriophage ε34
    • Wright A. Mechanism of conversion of the Salmonella O antigen by bacteriophage ε34. J Bacteriol. (1971) 105:927–36.
    • (1971) J Bacteriol , vol.105 , pp. 927-936
    • Wright, A.1
  • 122
    • 0025972009 scopus 로고
    • Molecular characterization of the O-acetyl transferase gene of converting bacteriophage SF6 that adds group antigen 6 to Shigella flexneri
    • 2014005
    • Verma N, Brandt J, Verma D, Lindberg A. Molecular characterization of the O-acetyl transferase gene of converting bacteriophage SF6 that adds group antigen 6 to Shigella flexneri. Mol Microbiol. (1991) 5:71–5. 10.1111/j.1365-2958.1991.tb01827.x2014005
    • (1991) Mol Microbiol , vol.5 , pp. 71-75
    • Verma, N.1    Brandt, J.2    Verma, D.3    Lindberg, A.4
  • 123
    • 84879665278 scopus 로고    scopus 로고
    • Horizontally acquired glycosyltransferase operons drive salmonellae lipopolysaccharide diversity
    • 23818865
    • Davies MR, Broadbent SE, Harris SR, Thomson NR, Van Der Woude MW. Horizontally acquired glycosyltransferase operons drive salmonellae lipopolysaccharide diversity. PLoS Genet. (2013) 9:e1003568. 10.1371/journal.pgen.100356823818865
    • (2013) PLoS Genet , vol.9 , pp. e1003568
    • Davies, M.R.1    Broadbent, S.E.2    Harris, S.R.3    Thomson, N.R.4    Van Der Woude, M.W.5
  • 124
    • 85015281807 scopus 로고    scopus 로고
    • Inflammation boosts bacteriophage transfer between Salmonella spp
    • 28302859
    • Diard M, Bakkeren E, Cornuault JK, Moor K, Hausmann A, Sellin ME, et al. Inflammation boosts bacteriophage transfer between Salmonella spp. Science. (2017) 355:1211–5. 10.1126/science.aaf845128302859
    • (2017) Science , vol.355 , pp. 1211-1215
    • Diard, M.1    Bakkeren, E.2    Cornuault, J.K.3    Moor, K.4    Hausmann, A.5    Sellin, M.E.6
  • 126
    • 84975079122 scopus 로고    scopus 로고
    • Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut
    • 26577924
    • Castro-Mejía JL, Muhammed MK, Kot W, Neve H, Franz CM, Hansen LH, et al. Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut. Microbiome. (2015) 3:64. 10.1186/s40168-015-0131-426577924
    • (2015) Microbiome , vol.3 , pp. 64
    • Castro-Mejía, J.L.1    Muhammed, M.K.2    Kot, W.3    Neve, H.4    Franz, C.M.5    Hansen, L.H.6
  • 127
    • 33846659065 scopus 로고    scopus 로고
    • Importance of widespread gene transfer agent genes in α-proteobacteria
    • 17184993
    • Lang AS, Beatty JT. Importance of widespread gene transfer agent genes in α-proteobacteria. Trends Microbiol. (2007) 15:54–62. 10.1016/j.tim.2006.12.00117184993
    • (2007) Trends Microbiol , vol.15 , pp. 54-62
    • Lang, A.S.1    Beatty, J.T.2
  • 128
    • 85072511956 scopus 로고    scopus 로고
    • The human gut virome is highly diverse, stable, and individual specific
    • 31600503, :.e525
    • Shkoporov AN, Clooney AG, Sutton TDS, Ryan FJ, Daly KM, Nolan JA, et al. The human gut virome is highly diverse, stable, and individual specific. Cell Host Microbe. (2019) 26:527–41.e525. 10.1016/j.chom.2019.09.00931600503
    • (2019) Cell Host Microbe , vol.26 , pp. 527-541
    • Shkoporov, A.N.1    Clooney, A.G.2    Sutton, T.D.S.3    Ryan, F.J.4    Daly, K.M.5    Nolan, J.A.6
  • 129
    • 84865013146 scopus 로고    scopus 로고
    • Conservation of gene cassettes among diverse viruses of the human gut
    • 22900013
    • Minot S, Wu GD, Lewis JD, Bushman FD. Conservation of gene cassettes among diverse viruses of the human gut. PLoS ONE. (2012) 7:e42342. 10.1371/journal.pone.004234222900013
    • (2012) PLoS ONE , vol.7 , pp. e42342
    • Minot, S.1    Wu, G.D.2    Lewis, J.D.3    Bushman, F.D.4
  • 130
    • 84961777823 scopus 로고    scopus 로고
    • Altered virome and bacterial microbiome in human immunodeficiency virus-associated acquired immunodeficiency syndrome
    • 26962942
    • Monaco CL, Gootenberg DB, Zhao G, Handley SA, Ghebremichael MS, Lim ES, et al. Altered virome and bacterial microbiome in human immunodeficiency virus-associated acquired immunodeficiency syndrome. Cell Host Microbe. (2016) 19:311–22. 10.1016/j.chom.2016.02.01126962942
    • (2016) Cell Host Microbe , vol.19 , pp. 311-322
    • Monaco, C.L.1    Gootenberg, D.B.2    Zhao, G.3    Handley, S.A.4    Ghebremichael, M.S.5    Lim, E.S.6
  • 131
    • 85025599680 scopus 로고    scopus 로고
    • Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children
    • 28696303
    • 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:E6166–75. 10.1073/pnas.170635911428696303
    • (2017) Proc Natl Acad Sci USA , vol.114 , pp. E6166-E6175
    • Zhao, G.1    Vatanen, T.2    Droit, L.3    Park, A.4    Kostic, A.D.5    Poon, T.W.6
  • 132
    • 85056802026 scopus 로고    scopus 로고
    • Diagnostic potential and interactive dynamics of the colorectal cancer virome
    • 30459201
    • Hannigan GD, Duhaime MB, Ruffin MT, Koumpouras CC, Schloss PD. Diagnostic potential and interactive dynamics of the colorectal cancer virome. mBio. (2018) 9:e02248–18. 10.1128/mBio.02248-1830459201
    • (2018) mBio , vol.9 , pp. e02248-e2218
    • Hannigan, G.D.1    Duhaime, M.B.2    Ruffin, M.T.3    Koumpouras, C.C.4    Schloss, P.D.5
  • 133
    • 84922414182 scopus 로고    scopus 로고
    • Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection
    • 25057045
    • Dinh DM, Volpe GE, Duffalo C, Bhalchandra S, Tai AK, Kane AV, et al. Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection. J Infect Dis. (2014) 211:19–27. 10.1093/infdis/jiu40925057045
    • (2014) J Infect Dis , vol.211 , pp. 19-27
    • Dinh, D.M.1    Volpe, G.E.2    Duffalo, C.3    Bhalchandra, S.4    Tai, A.K.5    Kane, A.V.6
  • 134
    • 85060769201 scopus 로고    scopus 로고
    • Expansion of bacteriophages is linked to aggravated intestinal inflammation and colitis
    • 30763538, :.e288
    • Gogokhia L, Buhrke K, Bell R, Hoffman B, Brown DG, Hanke-Gogokhia C, et al. Expansion of bacteriophages is linked to aggravated intestinal inflammation and colitis. Cell Host Microbe. (2019) 25:285–99.e288. 10.1016/j.chom.2019.01.00830763538
    • (2019) Cell Host Microbe , vol.25 , pp. 285-299
    • Gogokhia, L.1    Buhrke, K.2    Bell, R.3    Hoffman, B.4    Brown, D.G.5    Hanke-Gogokhia, C.6
  • 135
    • 85027470243 scopus 로고    scopus 로고
    • Pro- and anti-inflammatory responses of peripheral blood mononuclear cells induced by Staphylococcus aureus and Pseudomonas aeruginosa phages
    • 28808331
    • Van Belleghem JD, Clement F, Merabishvili M, Lavigne R, Vaneechoutte M. Pro- and anti-inflammatory responses of peripheral blood mononuclear cells induced by Staphylococcus aureus and Pseudomonas aeruginosa phages. Sci Rep. (2017) 7:8004. 10.1038/s41598-017-08336-928808331
    • (2017) Sci Rep , vol.7 , pp. 8004
    • Van Belleghem, J.D.1    Clement, F.2    Merabishvili, M.3    Lavigne, R.4    Vaneechoutte, M.5
  • 136
    • 0034675350 scopus 로고    scopus 로고
    • Peptide-mediated transcytosis of phage display vectors in MDCK cells
    • 11006114
    • Ivanenkov VV, Menon AG. Peptide-mediated transcytosis of phage display vectors in MDCK cells. Biochem Biophys Res Commun. (2000) 276:251–7. 10.1006/bbrc.2000.335811006114
    • (2000) Biochem Biophys Res Commun , vol.276 , pp. 251-257
    • Ivanenkov, V.V.1    Menon, A.G.2
  • 137
    • 85039910974 scopus 로고    scopus 로고
    • Bacteriophage transcytosis provides a mechanism to cross epithelial cell layers
    • 29162715
    • Nguyen S, Baker K, Padman BS, Patwa R, Dunstan RA, Weston TA, et al. Bacteriophage transcytosis provides a mechanism to cross epithelial cell layers. mBio. (2017) 8:e01874–17. 10.1128/mBio.01874-1729162715
    • (2017) mBio , vol.8 , pp. e01874-e1817
    • Nguyen, S.1    Baker, K.2    Padman, B.S.3    Patwa, R.4    Dunstan, R.A.5    Weston, T.A.6
  • 142
    • 85064138980 scopus 로고    scopus 로고
    • Bacteriophage trigger antiviral immunity and prevent clearance of bacterial infection
    • 30923196
    • Sweere JM, Van Belleghem JD, Ishak H, Bach MS, Popescu M, Sunkari V, et al. Bacteriophage trigger antiviral immunity and prevent clearance of bacterial infection. Science. (2019) 363:eaat9691. 10.1126/science.aat969130923196
    • (2019) Science , vol.363 , pp. eaat9691
    • Sweere, J.M.1    Van Belleghem, J.D.2    Ishak, H.3    Bach, M.S.4    Popescu, M.5    Sunkari, V.6
  • 143
    • 84991020825 scopus 로고    scopus 로고
    • Long-term effects on luminal and mucosal microbiota and commonly acquired taxa in faecal microbiota transplantation for recurrent Clostridium difficile infection
    • 27724956
    • Jalanka J, Mattila E, Jouhten H, Hartman J, De Vos WM, Arkkila P, et al. Long-term effects on luminal and mucosal microbiota and commonly acquired taxa in faecal microbiota transplantation for recurrent Clostridium difficile infection. BMC Med. (2016) 14:155. 10.1186/s12916-016-0698-z27724956
    • (2016) BMC Med , vol.14 , pp. 155
    • Jalanka, J.1    Mattila, E.2    Jouhten, H.3    Hartman, J.4    De Vos, W.M.5    Arkkila, P.6
  • 144
    • 84905968786 scopus 로고    scopus 로고
    • Fecal microbiota transplantation for the treatment of Clostridium difficile infection: a systematic review
    • 24440934
    • Cammarota G, Ianiro G, Gasbarrini A. Fecal microbiota transplantation for the treatment of Clostridium difficile infection: a systematic review. J Clin Gastroenterol. (2014) 48:693–702. 10.1097/MCG.000000000000004624440934
    • (2014) J Clin Gastroenterol , vol.48 , pp. 693-702
    • Cammarota, G.1    Ianiro, G.2    Gasbarrini, A.3
  • 145
    • 85014315210 scopus 로고    scopus 로고
    • Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium difficile infection
    • 27866880, :.e797
    • Ott SJ, Waetzig GH, Rehman A, Moltzau-Anderson J, Bharti R, Grasis JA, et al. Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium difficile infection. Gastroenterology. (2017) 152:799–811.e797. 10.1053/j.gastro.2016.11.01027866880
    • (2017) Gastroenterology , vol.152 , pp. 799-811
    • Ott, S.J.1    Waetzig, G.H.2    Rehman, A.3    Moltzau-Anderson, J.4    Bharti, R.5    Grasis, J.A.6
  • 146
    • 33745170946 scopus 로고    scopus 로고
    • Control of bacteriophages in industrial fermentations
    • Moineau S, Lévesque C. Control of bacteriophages in industrial fermentations. Bacteriophages. (2005) 285–96. 10.1201/9780203491751.ch10
    • (2005) Bacteriophages , pp. 285-296
    • Moineau, S.1    Lévesque, C.2
  • 148
    • 85043304296 scopus 로고    scopus 로고
    • Low eukaryotic viral richness is associated with faecal microbiota transplantation success in patients with UC
    • 29066574
    • Conceição-Neto N, Deboutte W, Dierckx T, Machiels K, Wang J, Yinda KC, et al. Low eukaryotic viral richness is associated with faecal microbiota transplantation success in patients with UC. Gut. (2018) 67:1558–9. 10.1136/gutjnl-2017-31528129066574
    • (2018) Gut , vol.67 , pp. 1558-1559
    • Conceição-Neto, N.1    Deboutte, W.2    Dierckx, T.3    Machiels, K.4    Wang, J.5    Yinda, K.C.6
  • 149
    • 84983655989 scopus 로고    scopus 로고
    • Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn's disease
    • 27542133
    • Vaughn BP, Vatanen T, Allegretti JR, Bai A, Xavier RJ, Korzenik J, et al. Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn's disease. Inflam Bowel Dis. (2016) 22:2182–90. 10.1097/MIB.000000000000089327542133
    • (2016) Inflam Bowel Dis , vol.22 , pp. 2182-2190
    • Vaughn, B.P.1    Vatanen, T.2    Allegretti, J.R.3    Bai, A.4    Xavier, R.J.5    Korzenik, J.6
  • 150
    • 85031499214 scopus 로고    scopus 로고
    • Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies
    • 29050646
    • Ng SC, Shi HY, Hamidi N, Underwood FE, Tang W, Benchimol EI, et al. Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies. Lancet. (2017) 390:2769–78. 10.1016/S0140-6736(17)32448-029050646
    • (2017) Lancet , vol.390 , pp. 2769-2778
    • Ng, S.C.1    Shi, H.Y.2    Hamidi, N.3    Underwood, F.E.4    Tang, W.5    Benchimol, E.I.6
  • 151
    • 84945278237 scopus 로고    scopus 로고
    • Metagenomic analysis of Crohn's disease patients identifies changes in the virome and microbiome related to disease status and therapy, and detects potential interactions and biomarkers
    • 26313691
    • Pérez-Brocal V, García-López R, Nos P, Beltrán B, Moret I, Moya A. Metagenomic analysis of Crohn's disease patients identifies changes in the virome and microbiome related to disease status and therapy, and detects potential interactions and biomarkers. Inflamm Bowel Dis. (2015) 21:2515–32. 10.1097/MIB.000000000000054926313691
    • (2015) Inflamm Bowel Dis , vol.21 , pp. 2515-2532
    • Pérez-Brocal, V.1    García-López, R.2    Nos, P.3    Beltrán, B.4    Moret, I.5    Moya, A.6
  • 152
    • 84939935484 scopus 로고    scopus 로고
    • Bacteriophage lambda: early pioneer and still relevant
    • (,) 479–
    • Casjens SR, Hendrix RW. Bacteriophage lambda: early pioneer and still relevant. Virology. (2015) 479–480:310–30. 10.1016/j.virol.2015.02.010
    • (2015) Virology , vol.480 , pp. 310-330
    • Casjens, S.R.1    Hendrix, R.W.2
  • 153
    • 84862888459 scopus 로고    scopus 로고
    • Chapter 2–phage as a modulator of immune responses: practical implications for phage therapy
    • Łobocka M., Szybalski W., (eds), San Diego, CA, Elsevier Academic Press Inc, In:, editors., :, p
    • Górski A, Miedzybrodzki R, Borysowski J, Dabrowska K, Wierzbicki P, Ohams M, et al. Chapter 2–phage as a modulator of immune responses: practical implications for phage therapy. In: Łobocka M, Szybalski W, editors. Advances in Virus Research. San Diego, CA: Elsevier Academic Press Inc. (2012), p. 41–71.
    • (2012) Advances in Virus Research , pp. 41-71
    • Górski, A.1    Miedzybrodzki, R.2    Borysowski, J.3    Dabrowska, K.4    Wierzbicki, P.5    Ohams, M.6
  • 155
    • 85029704396 scopus 로고    scopus 로고
    • Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
    • 28948103
    • Roux S, Emerson JB, Eloe-Fadrosh EA, Sullivan MB. Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ. (2017) 5:e3817. 10.7717/peerj.381728948103
    • (2017) PeerJ , vol.5 , pp. e3817
    • Roux, S.1    Emerson, J.B.2    Eloe-Fadrosh, E.A.3    Sullivan, M.B.4
  • 156
    • 84946600312 scopus 로고    scopus 로고
    • The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome
    • 26489866
    • Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, Sanmiguel AJ, et al. The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. MBio. (2015) 6:e01578–15. 10.1128/mBio.01578-1526489866
    • (2015) MBio , vol.6 , pp. e01578-e1515
    • Hannigan, G.D.1    Meisel, J.S.2    Tyldsley, A.S.3    Zheng, Q.4    Hodkinson, B.P.5    Sanmiguel, A.J.6
  • 157
    • 78649707158 scopus 로고    scopus 로고
    • Multiple displacement amplification compromises quantitative analysis of metagenomes
    • 21116242
    • Yilmaz S, Allgaier M, Hugenholtz P. Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Methods. (2010) 7:943. 10.1038/nmeth1210-94321116242
    • (2010) Nat Methods , vol.7 , pp. 943
    • Yilmaz, S.1    Allgaier, M.2    Hugenholtz, P.3
  • 158
    • 84946776186 scopus 로고    scopus 로고
    • New perspectives on microbial community distortion after whole-genome amplification
    • 26010362
    • Probst AJ, Weinmaier T, Desantis TZ, Santo Domingo JW, Ashbolt N. New perspectives on microbial community distortion after whole-genome amplification. PLoS ONE. (2015) 10:e0124158. 10.1371/journal.pone.012415826010362
    • (2015) PLoS ONE , vol.10 , pp. e0124158
    • Probst, A.J.1    Weinmaier, T.2    Desantis, T.Z.3    Santo Domingo, J.W.4    Ashbolt, N.5
  • 160
    • 65449134335 scopus 로고    scopus 로고
    • Assembling the marine metagenome, one cell at a time
    • 19390573
    • Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, et al. Assembling the marine metagenome, one cell at a time. PLoS ONE. (2009) 4:e5299. 10.1371/journal.pone.000529919390573
    • (2009) PLoS ONE , vol.4 , pp. e5299
    • Woyke, T.1    Xie, G.2    Copeland, A.3    González, J.M.4    Han, C.5    Kiss, H.6
  • 161
    • 85012028042 scopus 로고    scopus 로고
    • Fragmentation and coverage variation in viral metagenome assemblies, and their effect in diversity calculations
    • 26442255
    • García-López R, Vázquez-Castellanos JF, Moya A. Fragmentation and coverage variation in viral metagenome assemblies, and their effect in diversity calculations. Front Bioeng Biotechnol. 3:141. 10.3389/fbioe.2015.0014126442255
    • Front Bioeng Biotechnol , vol.3 , pp. 141
    • García-López, R.1    Vázquez-Castellanos, J.F.2    Moya, A.3
  • 162
    • 85009967892 scopus 로고    scopus 로고
    • Comparing and evaluating metagenome assembly tools from a microbiologist's perspective-Not only size matters!
    • Vollmers J, Wiegand S, Kaster AK. Comparing and evaluating metagenome assembly tools from a microbiologist's perspective-Not only size matters! PLoS ONE. (2017) 12:e0169662. 10.1371/journal.pone.0169662
    • (2017) PLoS ONE , vol.12 , pp. e0169662
    • Vollmers, J.1    Wiegand, S.2    Kaster, A.K.3
  • 165
    • 85050550560 scopus 로고    scopus 로고
    • Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy
    • 30016225
    • Aiewsakun P, Adriaenssens EM, Lavigne R, Kropinski AM, Simmonds P. Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy. J Gen Virol. (2018) 99:1331–43. 10.1099/jgv.0.00111030016225
    • (2018) J Gen Virol , vol.99 , pp. 1331-1343
    • Aiewsakun, P.1    Adriaenssens, E.M.2    Lavigne, R.3    Kropinski, A.M.4    Simmonds, P.5
  • 166
    • 85069725970 scopus 로고    scopus 로고
    • Towards a genome-based virus taxonomy
    • 31337890
    • Eloe-Fadrosh EA. Towards a genome-based virus taxonomy. Nat Microbiol. (2019) 4:1249–50. 10.1038/s41564-019-0511-931337890
    • (2019) Nat Microbiol , vol.4 , pp. 1249-1250
    • Eloe-Fadrosh, E.A.1
  • 167
    • 85050566754 scopus 로고    scopus 로고
    • Virus classification–where do you draw the line?
    • 30039318
    • Simmonds P, Aiewsakun P. Virus classification–where do you draw the line? Arch Virol. (2018) 163:2037–46. 10.1007/s00705-018-3938-z30039318
    • (2018) Arch Virol , vol.163 , pp. 2037-2046
    • Simmonds, P.1    Aiewsakun, P.2
  • 168
    • 79952642773 scopus 로고    scopus 로고
    • High temperature and bacteriophages can indirectly select for bacterial pathogenicity in environmental reservoirs
    • 21423610
    • Friman VP, Hiltunen T, Jalasvuori M, Lindstedt C, Laanto E, Örmälä AM, et al. High temperature and bacteriophages can indirectly select for bacterial pathogenicity in environmental reservoirs. PLoS ONE. (2011) 6:e17651. 10.1371/journal.pone.001765121423610
    • (2011) PLoS ONE , vol.6 , pp. e17651
    • Friman, V.P.1    Hiltunen, T.2    Jalasvuori, M.3    Lindstedt, C.4    Laanto, E.5    Örmälä, A.M.6
  • 169
    • 84979899807 scopus 로고    scopus 로고
    • Experimental evolution and bacterial resistance: (co)evolutionary costs and trade-offs as opportunities in phage therapy research
    • 26459626
    • Scanlan PD, Buckling A, Hall AR. Experimental evolution and bacterial resistance: (co)evolutionary costs and trade-offs as opportunities in phage therapy research. Bacteriophage. (2015) 5:e1050153. 10.1080/21597081.2015.105015326459626
    • (2015) Bacteriophage , vol.5 , pp. e1050153
    • Scanlan, P.D.1    Buckling, A.2    Hall, A.R.3
  • 170
    • 85068482402 scopus 로고    scopus 로고
    • Hurdles for phage therapy to become a reality—an editorial comment
    • 31212885
    • Brüssow H. Hurdles for phage therapy to become a reality—an editorial comment. Viruses. (2019) 11:E557. 10.3390/v1106055731212885
    • (2019) Viruses , vol.11 , pp. E557
    • Brüssow, H.1
  • 171
    • 68349154135 scopus 로고    scopus 로고
    • A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy
    • 19673983
    • Wright A, Hawkins CH, Änggård EE, Harper DR. A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy. Clin Otolaryngol. (2009) 34:349–57. 10.1111/j.1749-4486.2009.01973.x19673983
    • (2009) Clin Otolaryngol , vol.34 , pp. 349-357
    • Wright, A.1    Hawkins, C.H.2    Änggård, E.E.3    Harper, D.R.4
  • 173
    • 85054931439 scopus 로고    scopus 로고
    • Phage therapy for a multidrug-resistant Acinetobacter baumannii craniectomy site infection
    • 29687015
    • Lavergne S, Hamilton T, Biswas B, Kumaraswamy M, Schooley RT, Wooten D. Phage therapy for a multidrug-resistant Acinetobacter baumannii craniectomy site infection. Open Forum Infect Dis. (2008) 5:ofy064. 10.1093/ofid/ofy06429687015
    • (2008) Open Forum Infect Dis , vol.5 , pp. ofy064
    • Lavergne, S.1    Hamilton, T.2    Biswas, B.3    Kumaraswamy, M.4    Schooley, R.T.5    Wooten, D.6
  • 174
    • 85075697071 scopus 로고    scopus 로고
    • Seven circles of antimicrobial hell
    • Garrett L. Seven circles of antimicrobial hell. Lancet. (2019) 393:865–7. 10.1016/S0140-6736(19)30397-6
    • (2019) Lancet , vol.393 , pp. 865-867
    • Garrett, L.1


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