Sur un microbe invisible antagoniste des bacilles dysentériques, Comptes Rendus Acad. Sci. Paris, vol.165, pp.373-375, 1917. ,
Experience of the Eliava Institute in bacteriophage therapy, Virologica Sinica, vol.69, issue.1, pp.80-81, 2015. ,
DOI : 10.1093/jac/dkt453
Use of bacteriophages in the treatment of colistin-only-sensitive Pseudomonas aeruginosa septicaemia in a patient with acute kidney injury???a case report, Critical Care, vol.363, issue.1, p.129, 2017. ,
DOI : 10.1093/femsle/fnv242
,
Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection, Antimicrob. Agents Chemother, p.61, 2017. ,
; a preliminary report of efficacy, CrossRef] [PubMed] 6. Sarker,CrossRef] [PubMed] 7. Sarker, S.A.; Brussow, H. From bench to bed and back again: Phage therapy of childhood Escherichia coli diarrhea, pp.349-357, 2009. ,
DOI : 10.3201/eid0809.020063
Isolation of Escherichia coli Bacteriophages from the Stool of Pediatric Diarrhea Patients in Bangladesh, Journal of Bacteriology, vol.186, issue.24, pp.8287-8294, 2004. ,
DOI : 10.1128/JB.186.24.8287-8294.2004
The Gut Microbiota Facilitates Drifts in the Genetic Diversity and Infectivity of Bacterial Viruses, Cell Host & Microbe, vol.22, issue.6, pp.801-808, 2017. ,
DOI : 10.1016/j.chom.2017.10.010
URL : https://hal.archives-ouvertes.fr/pasteur-01827316
Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition, Environmental Microbiology, vol.350, issue.7, pp.2237-2245, 2016. ,
DOI : 10.1126/science.aad6791
URL : https://hal.archives-ouvertes.fr/pasteur-01538960
ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.56, issue.12, pp.6235-6242 ,
DOI : 10.1128/AAC.00602-12
In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli, Virology, vol.393, issue.1, pp.16-23, 2009. ,
DOI : 10.1016/j.virol.2009.07.020
Biogeography and individuality shape function in the human skin metagenome, Nature, vol.2, issue.7520, pp.59-64, 2014. ,
DOI : 10.1080/STA-200066418
Environmental Genome Shotgun Sequencing of the Sargasso Sea, Science, vol.304, issue.5667, pp.66-74, 2004. ,
DOI : 10.1126/science.1093857
Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula, Frontiers in Microbiology, vol.49, p.647, 2014. ,
DOI : 10.1016/S0967-0637(01)00062-0
The Microbial Engines That Drive Earth's Biogeochemical Cycles, Science, vol.103, issue.32, pp.1034-1039, 2008. ,
DOI : 10.1073/pnas.0605127103
Survival of Escherichia coli in the environment: fundamental and public health aspects, The ISME Journal, vol.191, issue.2, pp.173-183, 2011. ,
DOI : 10.1128/JB.00599-08
Gene Expression of Commensal Lactobacillus johnsonii Strain NCC533 during In Vitro Growth and in the Murine Gut, Journal of Bacteriology, vol.189, issue.22, pp.8109-8119, 2007. ,
DOI : 10.1128/JB.00991-07
: Correlations between Gene Expression and Gene Variability Reflect Growth Efficiencies, Molecular Biology and Evolution, vol.67, issue.10, pp.2515-2529, 2016. ,
DOI : 10.1016/j.mrrev.2012.12.003
ABSTRACT, Infection and Immunity, vol.81, issue.10, pp.3757-3769, 2013. ,
DOI : 10.1128/IAI.00515-13
Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions, Journal of Biological Chemistry, vol.145, issue.38, pp.27806-27815, 2006. ,
DOI : 10.1038/nature03239
Transcriptome of Uropathogenic Escherichia coli during Urinary Tract Infection, Infection and Immunity, vol.72, issue.11, pp.6373-6381, 2004. ,
DOI : 10.1128/IAI.72.11.6373-6381.2004
Use of Genome-Wide Expression Profiling and Mutagenesis To Study the Intestinal Lifestyle of Campylobacter jejuni, Infection and Immunity, vol.73, issue.3, pp.1797-1810, 2005. ,
DOI : 10.1128/IAI.73.3.1797-1810.2005
Bacteriophage resistance mechanisms, Nature Reviews Microbiology, vol.153, issue.5, pp.317-327, 2010. ,
DOI : 10.1007/s00438-004-1048-y
Sorek, R. BREX is a novel phage resistance system widespread in microbial genomes, EMBO J. 2015, vol.34, pp.169-183 ,
Systematic discovery of antiphage defense systems in the microbial pangenome, Science, vol.95, issue.6379, p.359, 2018. ,
DOI : 10.1126/science.aad9822
Bacteriophage T4 Infection of Stationary Phase E. coli: Life after Log from a Phage Perspective, Frontiers in Microbiology, vol.86, issue.fnw047, 1391. ,
DOI : 10.1016/S0092-8674(00)80089-6
host: comparison of a mathematical model with the experimental data, FEMS Microbiology Letters, vol.184, issue.2, pp.156-161, 2014. ,
DOI : 10.1128/JB.184.7.1888-1894.2002
Bacteriophage T4 Development Depends on the Physiology of its Host Escherichia Coli, Microbiology, vol.143, issue.1, pp.179-185, 1997. ,
DOI : 10.1099/00221287-143-1-179
URL : http://mic.microbiologyresearch.org/deliver/fulltext/micro/143/1/mic-143-1-179.pdf?itemId=/content/journal/micro/10.1099/00221287-143-1-179&mimeType=pdf&isFastTrackArticle=
Effect of bacterial growth rate on bacteriophage population growth rate. Microbiol, 2017. ,
DOI : 10.1002/mbo3.558
URL : http://onlinelibrary.wiley.com/doi/10.1002/mbo3.558/pdf
Host-virus interactions in Escherichia coli: Effect of stationary phase on viral release from MS2-infected bacteria, J. Virol, vol.10, pp.162-165, 1972. ,
The Effect of Host-Cell Starvation on Virus-induced Lysis by MS2 Bacteriophage, Journal of General Virology, vol.31, issue.3, pp.323-330, 1976. ,
DOI : 10.1099/0022-1317-31-3-323
Phenotypic Resistance and the Dynamics of Bacterial Escape from Phage Control, PLoS ONE, vol.2, issue.4, p.94690 ,
DOI : 10.1371/journal.pone.0094690.t001
URL : https://doi.org/10.1371/journal.pone.0094690
Stochastic Receptor Expression Allows Sensitive Bacteria to Evade Phage Attack. Part I: Experiments, Biophysical Journal, vol.94, issue.11, pp.4525-4536, 2008. ,
DOI : 10.1529/biophysj.107.120212
The Population and Evolutionary Dynamics of Phage and Bacteria with CRISPR???Mediated Immunity, PLoS Genetics, vol.255, issue.2, p.1003312 ,
DOI : 10.1371/journal.pgen.1003312.s007
URL : https://doi.org/10.1371/journal.pgen.1003312
Requirement for a fluid host cell membrane in injection of coliphage T5 DNA, J. Virol, vol.49, pp.273-275, 1984. ,
On-line monitoring of changes in host cell physiology during the one-step growth cycle of Bacillus phage Bam35, Journal of Microbiological Methods, vol.69, issue.1, pp.174-179, 2007. ,
DOI : 10.1016/j.mimet.2006.12.023
infection by bacteriophage ????S1: the influence of temperature, host growth phase and media, FEMS Microbiology Letters, vol.399, issue.1, pp.13-20, 2004. ,
DOI : 10.1128/AAC.39.3.645
URL : https://academic.oup.com/femsle/article-pdf/241/1/13/19122124/241-1-13.pdf
clonal complex, Journal of Antimicrobial Chemotherapy, vol.2, issue.11, pp.3072-3080, 2016. ,
DOI : 10.1093/jac/dks261
URL : https://hal.archives-ouvertes.fr/pasteur-01539016
The role of capsule as a barrier to bacteriophage adsorption in an encapsulated Staphylococcus simulans strain, Medical Microbiology and Immunology, vol.177, issue.4, pp.229-233, 1988. ,
DOI : 10.1007/BF00211222
ABSTRACT, Applied and Environmental Microbiology, vol.79, issue.10, pp.3249-3256, 2013. ,
DOI : 10.1128/AEM.00067-13
Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions, Journal of Bacteriology, vol.197, issue.3, pp.410-419, 2015. ,
DOI : 10.1128/JB.02230-14
Bacteriophages: an underestimated role in human and animal health?, Frontiers in Cellular and Infection Microbiology, vol.181, issue.9, p.39, 2014. ,
DOI : 10.1086/315239
URL : https://hal.archives-ouvertes.fr/hal-01204359
Healthy human gut phageome, Proc. Natl. Acad. Sci. USA 2016, pp.10400-10405 ,
DOI : 10.1371/journal.pone.0035053
URL : http://www.pnas.org/content/113/37/10400.full.pdf
Biofilms: an emergent form of bacterial life, Nature Reviews Microbiology, vol.10, issue.9, pp.563-575, 2016. ,
DOI : 10.1111/j.1365-2958.2005.04938.x
Bacterial Biofilms: A Common Cause of Persistent Infections, Science, vol.284, issue.5418, pp.1318-1322, 1999. ,
DOI : 10.1126/science.284.5418.1318
Phage or foe: an insight into the impact of viral predation on microbial communities, The ISME Journal, vol.5, issue.5, pp.1171-1179, 2018. ,
DOI : 10.1371/journal.pone.0015678
Dynamic biofilm architecture confers individual and collective mechanisms of viral protection, Nature Microbiology, vol.966, issue.1, pp.26-31, 2018. ,
DOI : 10.1007/978-1-62703-245-2_4
URL : https://www.nature.com/articles/s41564-017-0050-1.pdf
Capsule-Targeting Depolymerase, Derived from Klebsiella KP36 Phage, as a Tool for the Development of Anti-Virulent Strategy, Viruses, vol.133, issue.12, p.324, 2016. ,
DOI : 10.1111/j.1432-1033.1990.tb15578.x
Bacteriophage-encoded depolymerases: their diversity and biotechnological applications, Applied Microbiology and Biotechnology, vol.28, issue.Pt 2, pp.2141-2151, 2016. ,
DOI : 10.1007/s40259-013-0081-y
Phage mobility is a core determinant of phage???bacteria coexistence in biofilms, The ISME Journal, vol.42, issue.2, pp.531-543, 2018. ,
DOI : 10.1002/bit.20544
Host adaption to the bacteriophage carrier state of Campylobacter jejuni, Research in Microbiology, vol.166, issue.6, pp.504-515, 2015. ,
DOI : 10.1016/j.resmic.2015.05.003
Alternative bacteriophage life cycles: the carrier state of Campylobacter jejuni, Open Biology, vol.9, issue.7, 2014. ,
DOI : 10.1371/journal.pgen.1003269
URL : http://rsob.royalsocietypublishing.org/content/royopenbio/4/3/130200.full.pdf
Coexistence of phage and bacteria on the boundary of self-organized refuges, Proc. Natl. Acad. Sci. USA 2012, pp.12828-12833 ,
DOI : 10.1371/journal.pbio.0040193
Spatial heterogeneity and the stability of host-parasite coexistence, Journal of Evolutionary Biology, vol.15, issue.2, pp.374-379, 2006. ,
DOI : 10.1046/j.1365-3059.2002.00683.x
Host-Parasite Coexistence: The Role of Spatial Refuges in Stabilizing Bacteria-Phage Interactions, The American Naturalist, vol.148, issue.2, pp.348-377, 1996. ,
DOI : 10.1086/285929
A growing microcolony can survive and support persistent propagation of virulent phages, Proc. Natl. Acad. Sci. USA 2018, pp.337-342 ,
DOI : 10.1073/pnas.1708954115
Phage therapy: The peculiar kinetics of self-replicating pharmaceuticals, Clinical Pharmacology & Therapeutics, vol.68, issue.3, pp.225-230, 2000. ,
DOI : 10.1067/mcp.2000.109520
Minimum bacterial density for bacteriophage replication: Implications for significance of bacteriophages in natural ecosystems, Appl. Environ. Microbiol, vol.49, pp.19-23, 1985. ,
Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut, Proc. Natl. Acad. Sci. USA 2013, pp.20236-20241 ,
DOI : 10.1073/pnas.1206136109
Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut, Nature Microbiology, vol.35, issue.1, pp.38-46, 2018. ,
DOI : 10.1093/nar/gkm265
Gut biogeography of the bacterial microbiota, Nature Reviews Microbiology, vol.56, issue.1, pp.20-32, 2016. ,
DOI : 10.1371/journal.pone.0053957
, Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome, Nature, vol.2012, issue.486, pp.207-214
Noninvasive measurement of anatomic structure and intraluminal oxygenation in the gastrointestinal tract of living mice with spatial and spectral EPR imaging, Proc. Natl. Acad. Sci, pp.4586-4591, 1999. ,
DOI : 10.1088/0031-9155/43/7/017
Investigation of pH and Temperature Profiles in the GI Tract of Fasted Human Subjects Using the Intellicap?? System, Journal of Pharmaceutical Sciences, vol.104, issue.9, pp.2855-2863, 2015. ,
DOI : 10.1002/jps.24274
ABSTRACT, mBio, vol.8, issue.5, pp.1343-1360, 2017. ,
DOI : 10.1128/mBio.01343-17
Modulation of Shigella virulence in response to available oxygen in vivo, Nature, vol.168, issue.7296, pp.355-358, 2010. ,
DOI : 10.1007/s004240050455
URL : https://hal.archives-ouvertes.fr/pasteur-00493767
Topographical variation in metabolic signatures of human gastrointestinal biopsies revealed by high-resolution magic-angle spinning 1H NMR spectroscopy ,
, J. Proteome Res, vol.6, pp.3944-3951, 2007.
Characterization of virus-like particles associated with the human faecal and caecal microbiota, Research in Microbiology, vol.165, issue.10, pp.803-812, 2014. ,
DOI : 10.1016/j.resmic.2014.10.006
Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome, Cell Host & Microbe, vol.19, issue.3, pp.311-322, 2016. ,
DOI : 10.1016/j.chom.2016.02.011
Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease, Disease-specific alterations in the enteric virome in inflammatory bowel disease, pp.447-460, 2015. ,
DOI : 10.1016/j.cell.2015.01.002
Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children, Proc. Natl. Acad. Sci. USA 2017, pp.6166-6175 ,
DOI : 10.1038/ismej.2011.139
Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics, Frontiers in Cellular and Infection Microbiology, vol.24, issue.138, p.29, 2014. ,
DOI : 10.1177/0022034512449466
URL : https://hal.archives-ouvertes.fr/hal-01153583
Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection, Gastroenterology, vol.152, issue.4, pp.799-811, 2017. ,
DOI : 10.1053/j.gastro.2016.11.010
infection is associated with treatment outcome, Gut, vol.7, issue.(Suppl 1), pp.634-643, 2018. ,
DOI : 10.1136/gutjnl-2017-313952
Bacteriophage adhering to mucus provide a non-host-derived immunity, Proc. Natl. Acad. Sci. USA 2013, pp.10771-10776 ,
DOI : 10.1016/0022-2836(89)90464-6
Debarbieux, L. I will survive: A tale of bacteriophage-bacteria coevolution in the gut, Gut Microbes, 2018. ,
Bacterial sensing of bacteriophages in communities: the search for the Rosetta stone, Current Opinion in Microbiology, vol.20, issue.20, pp.125-130 ,
DOI : 10.1016/j.mib.2014.05.015
URL : https://hal.archives-ouvertes.fr/pasteur-01539083
M??nage ?? trois in the human gut: interactions between host, bacteria and phages, Nature Reviews Microbiology, vol.102, issue.7, pp.397-408 ,
DOI : 10.1073/pnas.0504062102
strains as a promising new treatment for Crohn's disease, Journal of Crohn's and Colitis, vol.11, pp.840-847, 2017. ,
DOI : 10.1093/ecco-jcc/jjw224
Pulmonary Bacteriophage Therapy on Pseudomonas aeruginosa Cystic Fibrosis Strains: First Steps Towards Treatment and Prevention, PLoS ONE, vol.72, issue.Pt 10, 2011. ,
DOI : 10.1371/journal.pone.0016963.t001
URL : https://hal.archives-ouvertes.fr/pasteur-01425539
Microencapsulation of Clostridium difficile specific bacteriophages using microfluidic glass capillary devices for colon delivery using pH triggered release, PLOS ONE, vol.23, issue.2, p.186239, 2017. ,
DOI : 10.1371/journal.pone.0186239.s001
Phage-Antibiotic Synergy (PAS): ??-Lactam and Quinolone Antibiotics Stimulate Virulent Phage Growth, PLoS ONE, vol.50, issue.8, p.799, 2007. ,
DOI : 10.1371/journal.pone.0000799.g005
URL : https://hal.archives-ouvertes.fr/hal-00180524
infection in endocarditis and reduces virulence, Journal of Infectious Diseases, vol.215, pp.703-712, 2017. ,
DOI : 10.1093/infdis/jiw632
A Window of Opportunity to Control the Bacterial Pathogen Pseudomonas aeruginosa Combining Antibiotics and Phages, PLoS ONE, vol.25, issue.2, p.106628 ,
DOI : 10.1371/journal.pone.0106628.g004
URL : https://hal.archives-ouvertes.fr/hal-02015241
Synergy and Order Effects of Antibiotics and Phages in Killing Pseudomonas aeruginosa Biofilms, PLOS ONE, vol.43, issue.4, p.168615, 2017. ,
DOI : 10.1371/journal.pone.0168615.s007
, FEMS Immunology & Medical Microbiology, vol.37, issue.2, pp.395-398, 2012.
DOI : 10.1016/S0022-5193(03)00262-5
Restricting ciprofloxacin-induced resistant variant formation in biofilm of Klebsiella pneumoniae B5055 by complementary bacteriophage treatment, Journal of Antimicrobial Chemotherapy, vol.49, issue.7, pp.1212-1218, 2009. ,
DOI : 10.1128/AAC.49.7.2874-2878.2005
ABSTRACT, mBio, vol.8, issue.5, pp.1341-1358, 2017. ,
DOI : 10.1128/mBio.01341-17
Synergy between the Host Immune System and Bacteriophage Is Essential for Successful Phage Therapy against an Acute Respiratory Pathogen, Cell Host & Microbe, vol.22, issue.1, pp.38-47, 2017. ,
DOI : 10.1016/j.chom.2017.06.018
URL : https://hal.archives-ouvertes.fr/pasteur-01827320