F. L. Nobrega, Targeting mechanisms of tailed bacteriophages, Nat. Rev. Microbiol, vol.16, pp.760-773, 2018.

R. L. Dy, C. Richter, G. P. Salmond, and P. Fineran, Remarkable mechanisms in microbes to resist phage infections, Annu. Rev. Virol, vol.1, pp.307-331, 2014.

G. S. Ofir and R. , Contemporary phage biology: from classic models to new insights, Cell, vol.172, pp.1260-1270, 2018.

F. W. Twort, An investigation on the nature of ultra-microscopic viruses, Lancet, vol.2, pp.1241-1243, 1915.

F. Hérelle, On an invisible microbe antagonistic toward dysenteric bacilli, Compte Rendu de. l'Acad.émie des. Sci, vol.165, pp.373-375, 1917.

F. Hérelle, Studies upon Asiatic cholera, Yale J. Biol. Med, vol.1, pp.195-219, 1929.

E. G. Babalova, Zh. Mikrobiol. Epidemiol. Immunobiol, vol.45, pp.143-145, 1968.

E. Kutter, Phage therapy in clinical practice: treatment of human infections, Curr. Pharm. Biotechnol, vol.11, pp.69-86, 2010.

M. G. Weinbauer, Ecology of prokaryotic viruses, FEMS Microbiol Rev, vol.28, pp.127-181, 2004.

A. Chatterjee and B. A. Duerkop, Beyond bacteria: bacteriophage-eukaryotic host interactions reveal emerging paradigms of health and disease, Front Microbiol, vol.9, p.1394, 2018.

E. C. Keen and G. Dantas, Close encounters of three kinds: bacteriophages, commensal bacteria, and host immunity, Trends Microbiol, vol.26, pp.943-954, 2018.

L. Gogokhia, Expansion of bacteriophages is linked to aggravated intestinal inflammation and colitis, Cell Host Microbe, vol.25, pp.285-299, 2019.

V. Aggarwala, G. Liang, and F. D. Bushman, Viral communities of the human gut: metagenomic analysis of composition and dynamics, Mob. DNA, vol.8, p.12, 2017.

A. N. Shkoporov and C. Hill, Bacteriophages of the human gut: the "known unknown" of the microbiome, Cell Host Microbe, vol.25, pp.195-209, 2019.

L. De-sordi, M. Lourenco, and L. Debarbieux, The battle within: interactions of bacteriophages and bacteria in the gastrointestinal tract, Cell Host Microbe, vol.25, pp.210-218, 2019.

P. D. Scanlan, Bacteria-bacteriophage coevolution in the human hut: implications for microbial diversity and functionality, Trends Microbiol, vol.25, pp.614-623, 2017.

J. D. Van-belleghem, K. Dabrowska, M. Vaneechoutte, J. J. Barr, and P. L. Bollyky, Interactions between bacteriophage, bacteria, and the mammalian immune system, Viruses, vol.11, p.10, 2018.

S. Roux, Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes, Nat. Microbiol, vol.4, issue.11, pp.1895-1906, 2019.
URL : https://hal.archives-ouvertes.fr/pasteur-02557242

T. Zhang, RNA viral community in human feces: prevalence of plant pathogenic viruses, PLoS Biol, vol.4, p.3, 2006.

E. S. Lim, Early life dynamics of the human gut virome and bacterial microbiome in infants, Nat. Med, vol.21, pp.1228-1234, 2015.

M. W. Los, G. Wegrzyn, . Pseudolysogeny, and . Adv, Virus Res, vol.82, pp.339-348, 2012.

P. Manrique, M. Dills, and M. J. Young, The human gut phage community and its implications for health and disease, Viruses, vol.9, p.141, 2017.

A. Reyes, Viruses in the faecal microbiota of monozygotic twins and their mothers, Nature, vol.466, pp.334-338, 2010.

P. Manrique, Healthy human gut phageome, Proc. Natl Acad. Sci. USA, vol.113, pp.10400-10405, 2016.

A. C. Gregory, O. Zablocki, A. Howell, B. Bolduc, and M. Sullivan, The human gut virome database. Cold Spring Harb, 2019.

S. J. Low, M. Dzunkova, P. A. Chaumeil, D. H. Parks, and P. Hugenholtz, Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales, Nat. Microbiol, vol.4, pp.1306-1315, 2019.

J. Barylski, Analysis of spounaviruses as a case study for the overdue reclassification of tailed phages, Syst. Biol, vol.69, pp.110-123, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02362652

S. Minot, The human gut virome: inter-individual variation and dynamic response to diet, Genome Res, vol.21, pp.1616-1625, 2011.

A. N. Shkoporov, The human gut virome is highly diverse, stable, and individual specific, Cell Host Microbe, vol.26, p.525, 2019.

M. Touchon, A. Bernheim, and E. P. Rocha, Genetic and life-history traits associated with the distribution of prophages in bacteria, ISME J, vol.10, pp.2744-2754, 2016.

M. Krupovic and P. Forterre, Microviridae goes temperate: microvirus-related proviruses reside in the genomes of Bacteroidetes, PLoS ONE, vol.6, p.19893, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00593769

L. M. Bobay, E. P. Rocha, and M. Touchon, The adaptation of temperate bacteriophages to their host genomes, Mol. Biol. Evol, vol.30, pp.737-751, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01374945

J. K. Cornuault, Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes, vol.6, p.65, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01774632

G. A. Lugli, Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota, Environ. Microbiol, vol.18, pp.2196-2213, 2016.

A. S. Waller, Classification and quantification of bacteriophage taxa in human gut metagenomes, ISME J, vol.8, pp.1391-1402, 2014.

M. Kim and J. W. , Lysogeny is prevalent and widely distributed in the murine gut microbiota, ISME J, vol.12, pp.1127-1141, 2018.

J. K. Cornuault, The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02504597

J. H. Oh, Prophages in Lactobacillus reuteri are associated with fitness tradeoffs but can increase competitiveness in the gut ecosystem, Appl. Environ. Microbiol, vol.86, pp.1922-1941, 2019.

R. A. Edwards, K. Mcnair, K. Faust, J. Raes, and B. E. Dutilh, Computational approaches to predict bacteriophage-host relationships, FEMS Microbiol. Rev, vol.40, pp.258-272, 2016.

A. Stern, E. Mick, I. Tirosh, O. Sagy, and R. Sorek, CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

, Genome Res, vol.22, 1985.

D. Paez-espino, Uncovering Earth's virome, Nature, vol.536, pp.425-430, 2016.

C. Galiez, M. Siebert, F. Enault, J. Vincent, and J. Soding, WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs, Bioinformatics, vol.33, pp.3113-3114, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01982199

J. L. Moreno-gallego, Virome diversity correlates with intestinal microbiome diversity in adult monozygotic twins, Cell Host Microbe, vol.25, p.265, 2019.

E. Guerin, Biology and taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut, Cell Host Microbe, vol.24, pp.653-664, 2018.

A. N. Shkoporov, PhiCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis, Nat. Commun, vol.9, p.4781, 2018.

A. E. Devoto, Megaphages infect Prevotella and variants are widespread in gut microbiomes, Nat. Microbiol, vol.4, pp.693-700, 2019.

P. Forterre, N. Soler, M. Krupovic, E. Marguet, and H. W. Ackermann, Fake virus particles generated by fluorescence microscopy, Trends Microbiol, vol.21, pp.1-5, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00779641

B. Chackerian, Virus-like particles: flexible platforms for vaccine development, Expert Rev. Vaccines, vol.6, pp.381-390, 2007.

C. Guemes and A. G. , Viruses as winners in the game of life, Annu. Rev. Virol, vol.3, pp.197-214, 2016.

L. Hoyles, Characterization of virus-like particles associated with the human faecal and caecal microbiota, Res. Microbiol, vol.165, pp.803-812, 2014.

M. S. Kim, E. J. Park, S. W. Roh, and J. W. Bae, Diversity and abundance of singlestranded DNA viruses in human feces, Appl. Environ. Microbiol, vol.77, pp.8062-8070, 2011.

R. Sender, S. Fuchs, and R. Milo, Revised estimates for the number of human and bacteria cells in the body, PLoS Biol, vol.14, p.1002533, 2016.

H. C. Berg and E. M. Purcell, Physics of chemoreception, Biophys. J, vol.20, pp.193-219, 1977.

J. J. Barr, Bacteriophage adhering to mucus provide a non-host-derived immunity, Proc. Natl Acad. Sci. USA, vol.110, pp.10771-10776, 2013.

J. S. Fraser, Z. Yu, K. L. Maxwell, and A. R. Davidson, Ig-like domains on bacteriophages: a tale of promiscuity and deceit, J. Mol. Biol, vol.359, pp.496-507, 2006.

P. Lepage, Dysbiosis in inflammatory bowel disease: a role for bacteriophages?, Gut, vol.57, pp.424-425, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00526557

B. B. Hsu, Dynamic modulation of the gut microbiota and metabolome by bacteriophages in a mouse model, Cell Host Microbe, vol.25, p.805, 2019.

M. De-paepe, Carriage of lambda latent virus is costly for its bacterial host due to frequent reactivation in monoxenic mouse intestine, PLoS Genet, vol.12, p.1005861, 2016.

M. Weiss, In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli, Virology, vol.393, pp.16-23, 2009.

X. Zhang, Quinolone antibiotics induce Shiga toxin-encoding bacteriophages, toxin production, and death in mice, J. Infect. Dis, vol.181, pp.664-670, 2000.

A. M. Nanda, K. Thormann, and J. Frunzke, Impact of spontaneous prophage induction on the fitness of bacterial populations and host-microbe interactions, J. Bacteriol, vol.197, pp.410-419, 2015.

J. H. Oh, Dietary fructose and microbiota-derived short-chain fatty acids promote bacteriophage production in the gut symbiont Lactobacillus reuteri, Cell Host Microbe, vol.25, pp.273-284, 2019.

A. N. Samuels, M. Roggiani, J. Zhu, M. Goulian, and R. M. Kohli, The SOS response mediates sustained colonization of the mammalian gut, Infect. Immun, vol.87, pp.711-00718, 2019.

G. Jubelin, Modulation of enterohaemorrhagic Escherichia coli survival and virulence in the human gastrointestinal tract, vol.6, p.115, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02621247

S. B. Hernandez, I. Cota, A. Ducret, L. Aussel, and J. Casadesus, Adaptation and preadaptation of Salmonella enterica to bile, PLoS Genet, vol.8, p.1002459, 2012.

M. Diard, Inflammation boosts bacteriophage transfer between Salmonella spp, Science, vol.355, pp.1211-1215, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01607431

F. S. Rossmann, Phage-mediated dispersal of biofilm and distribution of bacterial virulence genes is induced by quorum sensing, PLoS Pathog, vol.11, p.1004653, 2015.

J. E. Silpe and B. L. Bassler, Phage-encoded LuxR-type receptors responsive to hostproduced bacterial quorum-sensing autoinducers, MBio, vol.10, pp.638-657, 2019.

V. L. Taylor, A. D. Fitzpatrick, Z. Islam, and K. L. Maxwell, The diverse impacts of phage morons on bacterial fitness and virulence, Adv. Virus Res, vol.103, pp.1-31, 2018.

A. Wahl, A. Battesti, and M. Ansaldi, Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host?, Mol. Microbiol, vol.111, pp.303-316, 2019.
URL : https://hal.archives-ouvertes.fr/hal-01988228

J. M. Rolain, L. Fancello, C. Desnues, and D. Raoult, Bacteriophages as vehicles of the resistome in cystic fibrosis, J. Antimicrob. Chemother, vol.66, pp.2444-2447, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02008674

L. Fancello, C. Desnues, D. Raoult, and J. M. Rolain, Bacteriophages and diffusion of genes encoding antimicrobial resistance in cystic fibrosis sputum microbiota, J. Antimicrob. Chemother, vol.66, pp.2448-2454, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02008676

D. Debroas and C. Siguret, Viruses as key reservoirs of antibiotic resistance genes in the environment, ISME J, vol.13, pp.2856-2867, 2019.

W. Calero-caceres, M. Ye, and J. L. Balcazar, Bacteriophages as environmental reservoirs of antibiotic resistance, Trends Microbiol, vol.27, pp.570-577, 2019.

S. R. Modi, H. H. Lee, C. S. Spina, and J. J. Collins, Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome, Nature, vol.499, pp.219-222, 2013.

F. Enault, Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses, ISME J, vol.11, pp.237-247, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01557484

J. Davies and D. Davies, Origins and evolution of antibiotic resistance. Microbiol, Mol. Biol. Rev, vol.74, pp.417-433, 2010.

B. A. Leigh, Cooperation among conflict: prophages protect bacteria from phagocytosis, Cell Host Microbe, vol.26, pp.450-452, 2019.

R. Feiner, A new perspective on lysogeny: prophages as active regulatory switches of bacteria, Nat. Rev. Microbiol, vol.13, pp.641-650, 2015.

L. Rabinovich, N. Sigal, I. Borovok, R. Nir-paz, and A. A. Herskovits, Prophage excision activates Listeria competence genes that promote phagosomal escape and virulence, Cell, vol.150, pp.792-802, 2012.

E. Bille, A virulence-associated filamentous bacteriophage of Neisseria meningitidis increases host-cell colonisation, PLoS Pathog, vol.13, p.1006495, 2017.

N. Obeng, A. A. Pratama, and J. D. Elsas, The significance of mutualistic phages for bacterial ecology and evolution, Trends Microbiol, vol.24, pp.440-449, 2016.

B. A. Duerkop, C. V. Clements, D. Rollins, J. L. Rodrigues, and L. V. Hooper, A composite bacteriophage alters colonization by an intestinal commensal bacterium, Proc. Natl Acad. Sci. USA, vol.109, pp.17621-17626, 2012.

N. Frazao, A. Sousa, M. Lassig, and I. Gordo, Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut, Proc. Natl Acad. Sci. USA, vol.116, pp.17906-17915, 2019.

C. Sekse, H. Solheim, A. M. Urdahl, and Y. Wasteson, Is lack of susceptible recipients in the intestinal environment the limiting factor for transduction of Shiga toxin-encoding phages?, J. Appl. Microbiol, vol.105, pp.1114-1120, 2008.

S. Zhao, Adaptive evolution within gut microbiomes of healthy people, Cell Host Microbe, vol.25, p.658, 2019.

S. Chibani-chennoufi, In vitro and in vivo bacteriolytic activities of Escherichia coli phages: implications for phage therapy, Antimicrob. Agents Chemother, vol.48, pp.2558-2569, 2004.

D. Maura and L. Debarbieux, On the interactions between virulent bacteriophages and bacteria in the gut, Bacteriophage, vol.2, pp.229-233, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01539087

L. De-sordi, V. Khanna, and L. Debarbieux, The gut microbiota facilitates drifts in the genetic diversity and infectivity of bacterial viruses, Cell Host Microbe, vol.22, p.803, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01827316

M. Gabig, The cell surface protein Ag43 facilitates phage infection of Escherichia coli in the presence of bile salts and carbohydrates, Microbiology, vol.148, pp.1533-1542, 2002.

D. Maura, M. Galtier, C. Le-bouguenec, and L. Debarbieux, Virulent bacteriophages can target O104:H4 enteroaggregative Escherichia coli in the mouse intestine, Antimicrob. Agents Chemother, vol.56, pp.6235-6242, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01538999

M. Lourenco, L. De-sordi, and L. Debarbieux, The diversity of bacterial lifestyles hampers bacteriophage tenacity, Viruses, vol.10, p.327, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01827305

H. Brussow, Bacteriophage-host interaction: from splendid isolation into a messy reality, Curr. Opin. Microbiol, vol.16, pp.500-506, 2013.

K. D. Seed, Evolutionary consequences of intra-patient phage predation on microbial populations, Elife, vol.3, p.3497, 2014.

A. Reyes, M. Wu, N. P. Mcnulty, F. L. Rohwer, and J. I. Gordon, Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut, Proc. Natl Acad. Sci. USA, vol.110, pp.20236-20241, 2013.

R. Miedzybrodzki, Clinical aspects of phage therapy, Adv. Virus Res, vol.83, pp.73-121, 2012.

S. A. Sarker and H. Brussow, From bench to bed and back again: phage therapy of childhood Escherichia coli diarrhea, Ann. N. Y. Acad. Sci, vol.1372, pp.42-52, 2016.

S. A. Sarker, Oral phage therapy of acute bacterial diarrhea with two coliphage preparations: a randomized trial in children from Bangladesh, EBio-Medicine, vol.4, pp.124-137, 2016.

S. J. Ott, Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium difficile infection, Gastroenterology, vol.152, p.797, 2017.

M. T. Jahn, A phage protein aids bacterial symbionts in eukaryote immune evasion, Cell Host Microbe, vol.26, pp.542-550, 2019.

G. V. Tetz, Bacteriophages as potential new mammalian pathogens, Sci. Rep, vol.7, p.7043, 2017.

M. Galtier, Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition, Environ. Microbiol, vol.18, pp.2237-2245, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01538960

U. Dissanayake, M. Ukhanova, Z. D. Moye, A. Sulakvelidze, and V. Mai, Bacteriophages reduce pathogenic Escherichia coli counts in mice without distorting gut microbiota, Front. Microbiol, vol.10, 1984.

H. P. Febvre, PHAGE study: effects of supplemental bacteriophage intake on inflammation and gut microbiota in healthy adults, Nutrients, vol.11, p.666, 2019.

S. A. Sarker, Oral application of Escherichia coli bacteriophage: safety tests in healthy and diarrheal children from Bangladesh, Environ. Microbiol, vol.19, pp.237-250, 2017.

B. K. Chan, Phage selection restores antibiotic sensitivity in MDR Pseudomonas aeruginosa, Sci. Rep, vol.6, p.26717, 2016.

A. Chatterjee, Bacteriophage resistance alters antibiotic-mediated intestinal expansion of Enterococci, Infect. Immun, vol.87, pp.85-104, 2019.

J. Lossouarn, Enterococcus faecalis countermeasures defeat a virulent picovirinae bacteriophage, Viruses, vol.11, p.48, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02173127

L. Rigottier-gois, The surface rhamnopolysaccharide epa of Enterococcus faecalis is a key determinant of intestinal colonization, J. Infect. Dis, vol.211, pp.62-71, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01536528

K. E. Kortright, B. K. Chan, J. L. Koff, and P. E. Turner, Phage therapy: a renewed approach to combat antibiotic-resistant bacteria, Cell Host Microbe, vol.25, pp.219-232, 2019.

A. Golomidova, E. Kulikov, A. Isaeva, A. Manykin, and A. Letarov, The diversity of coliphages and coliforms in horse feces reveals a complex pattern of ecological interactions, Appl Environ. Microbiol, vol.73, pp.5975-5981, 2007.

F. Rodriguez-valera, Explaining microbial population genomics through phage predation, Nat. Rev. Microbiol, vol.7, pp.828-836, 2009.

L. Chatelier and E. , Richness of human gut microbiome correlates with metabolic markers, Nature, vol.500, pp.541-546, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01190602

C. Torres-barcelo, The disparate effects of bacteriophages on antibiotic-resistant bacteria, Emerg. Microbes Infect, vol.7, p.168, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02629358

J. M. Norman, Disease-specific alterations in the enteric virome in inflammatory bowel disease, Cell, vol.160, pp.447-460, 2015.

J. Majewska, Oral application of T4 phage induces weak antibody production in the gut and in the blood, Viruses, vol.7, pp.4783-4799, 2015.

S. Nguyen, Bacteriophage transcytosis provides a mechanism to cross epithelial cell layers, MBio, vol.8, pp.1874-1891, 2017.

R. Barfoot, Some properties of dendritic macrophages from peripheral lymph, Immunology, vol.68, pp.233-239, 1989.

S. L. Wenger, J. H. Turner, and J. C. Petricciani, The cytogenetic, proliferative and viability effects of four bacteriophages on human lymphocytes, vol.14, pp.543-549, 1978.

R. Aronow, D. Danon, A. Shahar, and M. Aronson, Electron microscopy of in vitro endocytosis of T2 phage by cells from rabbit peritoneal exudate, J. Exp. Med, vol.120, pp.943-954, 1964.

N. A. Mabbott, D. S. Donaldson, H. Ohno, I. R. Williams, and A. Mahajan, Microfold (M) cells: important immunosurveillance posts in the intestinal epithelium, Mucosal Immunol, vol.6, pp.666-677, 2013.

J. Y. Yang, Enteric viruses ameliorate gut inflammation via Toll-like receptor 3 and Toll-like receptor 7-mediated interferon-beta production, Immunity, vol.44, pp.889-900, 2016.

J. D. Van-belleghem, F. Clement, M. Merabishvili, R. Lavigne, and M. Vaneechoutte, Pro-and anti-inflammatory responses of peripheral blood mononuclear cells induced by Staphylococcus aureus and Pseudomonas aeruginosa phages, Sci. Rep, vol.7, p.8004, 2017.

J. M. Sweere, Bacteriophage trigger antiviral immunity and prevent clearance of bacterial infection, Science, vol.363, p.9691, 2019.

H. Brussow, Hurdles for phage therapy to become a reality-an editorial comment, Viruses, vol.11, p.557, 2019.

Q. Zheng, Q. Chen, Y. Xu, C. A. Suttle, and N. Jiao, A virus infecting marine photoheterotrophic Alphaproteobacteria (Citromicrobium spp.) defines a new lineage of ssDNA viruses, Front. Microbiol, vol.9, p.1418, 2018.