Enterotypes of the human gut microbiome, Nature, vol.473, pp.174-80, 2011. ,
URL : https://hal.archives-ouvertes.fr/cea-00903625
A human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.464, pp.59-65, 2010. ,
URL : https://hal.archives-ouvertes.fr/cea-00908974
Structure, function and diversity of the healthy human microbiome, Nature, vol.486, pp.207-221, 2013. ,
The role of the gut microbiota in nutrition and health, Nat Rev Gastroenterol Hepatol, vol.9, pp.577-89, 2012. ,
The gut microbiota and host health: a new clinical frontier, Gut, vol.65, pp.330-339, 2016. ,
Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults, PLoS One, vol.5, p.9085, 2010. ,
The gut microbiota as an environmental factor that regulates fat storage, Proc Natl Acad Sci U S A, vol.101, pp.15718-15741, 2004. ,
Succession of microbial consortia in the developing infant gut microbiome, Proc Natl Acad Sci U S A, vol.108, issue.1, pp.4578-85, 2011. ,
Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis, Cell, vol.159, pp.514-543, 2014. ,
Temporal variability is a personalized feature of the human microbiome, Genome Biol, vol.15, p.531, 2014. ,
Oral application of Escherichia coli bacteriophage: safety tests in healthy and diarrheal children from Bangladesh, Environ Microbiol, vol.19, pp.237-50, 2017. ,
Temporal and technical variability of human gut metagenomes, Genome Biol, vol.16, p.73, 2015. ,
The Human Gut Phage Community and Its Implications for Health and Disease, Viruses, vol.9, 2017. ,
Movers and shakers: influence of bacteriophages in shaping the mammalian gut microbiota, Gut Microbes, vol.4, pp.4-16, 2013. ,
Bacteriophages: an underestimated role in human and animal health?, Front Cell Infect Microbiol, vol.4, p.39, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01204359
Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut, Proc Natl Acad Sci U S A, vol.110, pp.20236-20277, 2013. ,
Classification and quantification of bacteriophage taxa in human gut metagenomes, ISME J, vol.8, pp.1391-402, 2014. ,
Virulent bacteriophages can target O104:H4 enteroaggregative Escherichia coli in the mouse intestine, Antimicrob Agents Chemother, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01538999
Bacteriophage-host interaction: from splendid isolation into a messy reality, Curr Opin Microbiol, vol.16, pp.500-506, 2013. ,
Piggyback-the-Winner in host-associated microbial communities, NPJ Biofilms Microbiomes, vol.2, p.16010, 2016. ,
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. ,
Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics, ISME J, vol.10, pp.437-486, 2016. ,
, Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev, vol.80, pp.745-63, 2016.
CRISPR provides acquired resistance against viruses in prokaryotes, Science, vol.315, pp.1709-1721, 2007. ,
An updated evolutionary classification of CRISPR-Cas systems, Nat Rev Microbiol, vol.13, pp.722-758, 2015. ,
CRP represses the CRISPR/Cas system in Escherichia coli: evidence that endogenous CRISPR spacers impede phage P1 replication, Mol Microbiol, vol.92, pp.1072-91, 2014. ,
The Escherichia coli CRISPR system protects from lambda lysogenization, lysogens, and prophage induction, J Bacteriol, vol.192, pp.6291-6295, 2010. ,
Viral Transmission Dynamics at Single-Cell Resolution Reveal Transiently Immune Subpopulations Caused by a Carrier State Association, PLoS Genet, vol.11, p.1005770, 2015. ,
Disease-specific alterations in the enteric virome in inflammatory bowel disease, Cell, vol.160, pp.447-60, 2015. ,
Characterization of the Prophage Repertoire of African Salmonella Typhimurium ST313 Reveals High Levels of Spontaneous Induction of Novel Phage BTP1, Front Microbiol, vol.8, p.235, 2017. ,
Widely distributed lysogeny in probiotic lactobacilli represents a potentially high risk for the fermentative dairy industry, Int J Food Microbiol, vol.144, pp.503-513, 2011. ,
Characterisation of three temperate phages released from the same Lactobacillus paracasei commercial strain, International Journal of Dairy Technology, vol.63, pp.396-405, 2010. ,
Evolution of temperate pathogens: the bacteriophage/bacteria paradigm, Virol J, vol.4, p.121, 2007. ,
Gut microbiota in health and disease, Physiol Rev, vol.90, pp.859-904, 2010. ,
How stable is the human gut microbiota? And why this question matters, Environ Microbiol, vol.18, pp.2779-83, 2016. ,
In vitro and in vivo bacteriolytic activities of Escherichia coli phages: implications for phage therapy, Antimicrob Agents Chemother, vol.48, pp.2558-69, 2004. ,
Spatial structure, transmission modes and the evolution of viral exploitation strategies, PLoS Pathog, vol.11, p.1004810, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02122352
Well-temperate phage: optimal bet-hedging against local environmental collapses, Sci Rep, vol.5, p.10523, 2015. ,
Phage-induced diversification improves host evolvability, BMC Evol Biol, vol.13, p.17, 2013. ,
Prophage as a genetic reservoir: Promoting diversity and driving innovation in the host community, Evolution, vol.71, pp.2080-2089, 2017. ,
The tripartite immunity system of phages P1 and P7, FEMS Microbiol Rev, vol.17, pp.121-127, 1995. ,
Isolation of ultravirulent mutants of phage lambda, Virology, vol.84, pp.547-50, 1978. ,
Comparative rates of spontaneous mutation, Nature, vol.221, p.1132, 1969. ,
Plasmid addiction genes of bacteriophage P1: doc, which causes cell death on curing of prophage, and phd, which prevents host death when prophage is retained, J Mol Biol, vol.233, pp.414-442, 1993. ,
, Références bibliographiques
Virus of Prokaryotes, 1987. ,
Integration of genomic and proteomic analyses in the classification of the Siphoviridae family, Virology, vol.477, pp.144-54, 2015. ,
Analysis of cell size and DNA content in exponentially growing and stationary-phase batch cultures of Escherichia coli, J Bacteriol, vol.177, pp.6791-6798, 1995. ,
Differential cell kinetics in the ileum and colon of germfree rats, Scand J Gastroenterol, vol.29, pp.445-51, 1994. ,
Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota, Gastroenterology, vol.147, p.8, 2014. ,
Antibiotics in feed induce prophages in swine fecal microbiomes, MBio, vol.2, 2011. ,
Comparison of induction of B45 Helicobacter pylori prophage by acid and UV radiation, Microscopy and microanalysis, vol.19, pp.27-28, 2013. ,
Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale, Appl Environ Microbiol, vol.72, pp.6371-6377, 2006. ,
Epidemiology and risk factors for IBD, Nat Rev Gastroenterol Hepatol, vol.12, pp.205-222, 2015. ,
PHASTER: a better, faster version of the PHAST phage search tool, Nucleic Acids Res, vol.44, pp.16-21, 2016. ,
PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes, Brief Bioinform Arumugam M, vol.473, pp.174-80, 2011. ,
The defective prophage pool of Escherichia coli O157: prophage-prophage interactions potentiate horizontal transfer of virulence determinants, PLoS Pathog, vol.5, p.1000408, 2009. ,
Studies on the chemical nature of the substance inducing transformation of pneumococcal serotypes: inductions of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III, The Journal of Experimental Medicine, vol.79, pp.137-57, 1944. ,
Minimal gene regulatory circuits for a lysis-lysogeny choice in the presence of noise, PLoS One, vol.5, p.15037, 2010. ,
The gut microbiota as an environmental factor that regulates fat storage, Proc Natl Acad Sci U S A, vol.101, pp.15718-15741, 2004. ,
Single-cell analysis of lambda immunity regulation, J Mol Biol, vol.334, pp.363-72, 2003. ,
Report on a pseudolysogenic mycobacterium and a review of the literature concerning pseudolysogeny, Acta Pathol Microbiol Scand B Microbiol Immunol, vol.79, pp.428-462, 1971. ,
A novel disrupted mcr-1 gene and a lysogenized phage P1-like sequence detected from a large conjugative plasmid, cultured from a human atypical enteropathogenic Escherichia coli (aEPEC) recovered in China, J Antimicrob Chemother, vol.72, pp.1531-1564, 2017. ,
Isolation of ultravirulent mutants of phage lambda, Virology, vol.84, pp.547-50, 1978. ,
Correlation between UV dose requirement for lambda bacteriophage induction and lambda repressor concentration, J Virol, vol.26, pp.595-602, 1978. ,
Prophage induction and expression of prophage-encoded virulence factors in group A Streptococcus serotype M3 strain MGAS315, Infect Immun, vol.71, pp.7079-86, 2003. ,
CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in Crohn disease, J Clin Invest, vol.117, pp.1566-74, 2007. ,
bor gene of phage lambda, involved in serum resistance, encodes a widely conserved outer membrane lipoprotein, J Bacteriol, vol.177, pp.1247-53, 1995. ,
A bacteriophages journey through the human body, Immunological Reviews, vol.279, pp.106-128, 2017. ,
Bacteriophage adhering to mucus provide a non-host-derived immunity, Proc Natl Acad Sci U S A, vol.110, pp.10771-10777, 2013. ,
Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters, Proc Natl Acad Sci U S A, vol.112, pp.13675-80, 2015. ,
CRISPR provides acquired resistance against viruses in prokaryotes, Science, vol.315, pp.1709-1721, 2007. ,
The roles of the lambda c3 gene and the Escherichia coli catabolite gene activation system in the establishment of lysogeny by bacteriophage lambda, Proc Natl Acad Sci U S A, vol.71, pp.779-82, 1974. ,
, New Insights into the Diversity of the Genus Faecalibacterium. Front Microbiol, vol.8, p.1790, 2017.
Proteins PblA and PblB of Streptococcus mitis, which promote binding to human platelets, are encoded within a lysogenic bacteriophage, Infect Immun, vol.69, pp.6186-92, 2001. ,
Impact of Cigarette Smoking on the Gastrointestinal Tract Inflammation: Opposing Effects in Crohn's Disease and Ulcerative Colitis, Front Immunol, vol.9, p.74, 2018. ,
Host controlled variation in bacterial viruses, J Bacteriol, vol.65, pp.113-134, 1953. ,
The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients, J Med Microbiol, vol.55, pp.1141-1150, 2006. ,
Characterization of a P1-like bacteriophage carrying an SHV-2 extended-spectrum beta-lactamase from an Escherichia coli strain, Antimicrob Agents Chemother, vol.58, pp.6550-6557, 2014. ,
A virulence-associated filamentous bacteriophage of Neisseria meningitidis increases host-cell colonisation, PLoS Pathog, vol.13, p.1006495, 2017. ,
The adaptation of temperate bacteriophages to their host genomes, Mol Biol Evol, vol.30, pp.737-51, 2013. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374945
Pervasive domestication of defective prophages by bacteria, Proc Natl Acad Sci U S A, vol.111, pp.12127-12159, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374961
Effect of resource enrichment on a chemostat community of bacteria and bacteriophage, Ecology society of america, vol.78, pp.2303-2318, 1997. ,
Antibiotics, birth mode, and diet shape microbiome maturation during early life, Sci Transl Med, vol.8, pp.343-82, 2016. ,
Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin, Microbiology, vol.151, pp.2551-61, 2005. ,
Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system, Nature, vol.493, pp.429-461, 2013. ,
When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness, J Microbiol, vol.52, pp.235-277, 2014. ,
Tubules and donuts: a type VI secretion story, Mol Microbiol, vol.76, pp.815-836, 2010. ,
Prophage contribution to bacterial population dynamics, J Bacteriol, vol.185, pp.6467-71, 2003. ,
Invasive ability of an Escherichia coli strain isolated from the ileal mucosa of a patient with Crohn's disease, Infect Immun, vol.67, pp.4499-509, 1999. ,
Key role of selective viral-induced mortality in determining marine bacterial community composition, Environ Microbiol, vol.9, pp.287-97, 2007. ,
Bacteriophage-encoded bacterial virulence factors and phage-pathogenicity island interactions, Adv Virus Res, vol.82, pp.91-118, 2012. ,
Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?, BMC Genomics, vol.10, p.104, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00377407
Viral diversity and dynamics in an infant gut, Res Microbiol, vol.159, pp.367-73, 2008. ,
Here a virus, there a virus, everywhere the same virus?, Trends Microbiol, vol.13, pp.278-84, 2005. ,
, Gut Commensal E. coli Proteins Activate Host Satiety Pathways following Nutrient-Induced Bacterial Growth. Cell Metab, vol.23, pp.324-358, 2016.
Experimental coevolution with bacteria and phage. The Pseudomonas fluorescens--Phi2 model system, Infect Genet Evol, vol.7, pp.547-52, 2007. ,
The effect of spatial heterogeneity and parasites on the evolution of host diversity, Proc Biol Sci, vol.271, pp.107-118, 2004. ,
Long-term changes of bacterial and viral compositions in the intestine of a recovered Clostridium difficile patient after fecal microbiota transplantation, Cold Spring Harb Mol Case Stud, vol.2, p.448, 2016. ,
Analysis of the intestinal microbiome of a recovered Clostridium difficile patient after fecal transplantation, Digestion, vol.88, pp.243-51, 2013. ,
Stable core virome despite variable microbiome after fecal transfer, Gut Microbes, vol.8, pp.214-234, 2017. ,
Integrationdependent bacteriophage immunity provides insights into the evolution of genetic switches, Mol Cell, vol.49, pp.237-285, 2013. ,
Ecology of microbial invasions: amplification allows virus carriers to invade more rapidly when rare, Curr Biol, vol.16, pp.2048-52, 2006. ,
Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics, ISME J, vol.10, pp.437-486, 2016. ,
Bacteriophage-host interaction: from splendid isolation into a messy reality, Curr Opin Microbiol, vol.16, pp.500-506, 2013. ,
How stable is the human gut microbiota? And why this question matters, Environ Microbiol, vol.18, pp.2779-83, 2016. ,
Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion, Microbiol Mol Biol Rev, vol.68, pp.45-54, 2004. ,
Antagonistic coevolution between a bacterium and a bacteriophage, Proc Biol Sci, vol.269, pp.931-937, 2002. ,
Lateral DNA transfer: mechanisms and consequences. Cold spring Harbor, 2002. ,
The impact of prophages on bacterial chromosomes, Mol Microbiol, vol.53, pp.9-18, 2004. ,
Prophage spontaneous activation promotes DNA release enhancing biofilm formation in Streptococcus pneumoniae, PLoS One, vol.5, p.15678, 2010. ,
Crohn's disease adherentinvasive Escherichia coli colonize and induce strong gut inflammation in transgenic mice expressing human CEACAM, J Exp Med, vol.206, pp.2179-89, 2009. ,
Prophages and bacterial genomics: what have we learned so far?, Mol Microbiol, vol.49, pp.277-300, 2003. ,
Bacteriophages and the bacterial genome, pp.39-53, 2005. ,
Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut, vol.3, p.64, 2015. ,
Fusobacterium prausnitzii (Hauduroy et al.) Moore and Holdeman: Emended Description and Designation of, Neotype Strain International Journal of Systematic Bacteriology, vol.24, pp.225-254, 1974. ,
Viral Transmission Dynamics at Single-Cell Resolution Reveal Transiently Immune Subpopulations Caused by a Carrier State Association, PLoS Genet, vol.11, p.1005770, 2015. ,
Expression of a novel P22 ORFan gene reveals the phage carrier state in Salmonella typhimurium, PLoS Genet, vol.9, p.1003269, 2013. ,
Pyrosequencing-based molecular monitoring of the intestinal bacterial colonization in preterm infants, J Pediatr Gastroenterol Nutr, vol.53, pp.512-521, 2011. ,
Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation, MBio, vol.7, p.322, 2016. ,
Dietary fibre-based SCFA mixtures promote both protection and repair of intestinal epithelial barrier function in a Caco-2 cell model, Food Funct, vol.8, pp.1166-73, 2017. ,
Microbiota matures colonic epithelium through a coordinated induction of cell cycle-related proteins in gnotobiotic rat, Am J Physiol Gastrointest Liver Physiol, vol.299, pp.348-57, 2010. ,
In vitro and in vivo bacteriolytic activities of Escherichia coli phages: implications for phage therapy, Antimicrob Agents Chemother, vol.48, pp.2558-69, 2004. ,
Various physico-chemical stress factors cause prophage induction in Nitrosospira multiformis 25196--an ammonia oxidizing bacteria, Water Res, vol.44, pp.4550-4558, 2010. ,
Analysis of six prophages in Lactococcus lactis IL1403: different genetic structure of temperate and virulent phage populations, Nucleic Acids Res, vol.29, pp.644-51, 2001. ,
Phage abortive infection in lactococci: variations on a theme, Curr Opin Microbiol, vol.8, pp.473-482, 2005. ,
Interactions between satellite bacteriophage P4 and its helpers, Annu Rev Genet, vol.24, pp.465-90, 1990. ,
Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease, Science, vol.352, pp.1116-1136, 2016. ,
A Mobile Element in mutS Drives Hypermutation in a Marine Vibrio, MBio, vol.8, 2017. ,
Superinfection exclusion reveals heteroimmunity between Pseudomonas aeruginosa temperate phages, J Microbiol, vol.52, pp.515-535, 2014. ,
A phage protein that inhibits the bacterial ATPase required for type IV pilus assembly, Proc Natl Acad Sci U S A, vol.111, pp.11503-11511, 2014. ,
Gut microbiota composition correlates with diet and health in the elderly, Nature, vol.488, pp.178-84, 2012. ,
Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine, PLoS One, vol.4, p.6669, 2009. ,
, Phages in nature. Bacteriophage, vol.1, pp.31-45, 2011.
Viruses as Winners in the Game of Life, Annu Rev Virol, vol.3, pp.197-214, 2016. ,
Bacteriophage-tail-like particles associated with intra-species killing of Proteus vulgaris, J Gen Virol, vol.2, pp.29-36, 1968. ,
Clinicopathologic study of dextran sulfate sodium experimental murine colitis, Laboratory investigation, vol.69, pp.238-287, 1999. ,
Vitamin B12 Uptake by the Gut Commensal Bacteria Bacteroides thetaiotaomicron Limits the Production of Shiga Toxin by Enterohemorrhagic Escherichia coli, Toxins, 2016. ,
Positive and negative regulation by the cII and cIII gene products of bacteriophage lambda, Virology, vol.63, pp.484-91, 1975. ,
Coevolution of a virus-alga system, Appl Microbiol, vol.29, pp.234-243, 1975. ,
Ruminococcin C, a new anti-Clostridium perfringens bacteriocin produced in the gut by the commensal bacterium Ruminococcus gnavus E1, Biochimie, vol.93, pp.1487-94, 2011. ,
On an invisible microbe antagonistic toward dysenteric bacilli: brief note by Mr. F. D'Herelle, presented by Mr. Roux, Res Microbiol, vol.158, pp.553-557, 1917. ,
High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease, Gastroenterology, vol.127, pp.412-433, 2004. ,
Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease, Gastroenterology, vol.115, pp.1405-1418, 1998. ,
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proc Natl Acad Sci U S A, vol.97, pp.6640-6645, 2000. ,
The role of temperate bacteriophages in bacterial infection, FEMS Microbiol Lett, vol.363, p.15, 2016. ,
Origins and evolution of antibiotic resistance, Microbiol Mol Biol Rev, vol.74, pp.417-450, 2010. ,
Arms races between and within species, Proc R Soc Lond B Biol Sci, vol.205, pp.489-511, 1979. ,
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa, Proc Natl Acad Sci U S A, vol.107, pp.14691-14697, 2010. ,
Temperate phages acquire DNA from defective prophages by relaxed homologous recombination: the role of Rad52-like recombinases, PLoS Genet, vol.10, p.1004181, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01134590
Bacteriophages: an underestimated role in human and animal health?, Front Cell Infect Microbiol, vol.4, p.39, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01204359
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. ,
The Gut Microbiota Facilitates Drifts in the Genetic Diversity and Infectivity of Bacterial Viruses, Cell Host Microbe, vol.22, p.3, 2017. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01827316
Phagonaute: A web-based interface for phage synteny browsing and protein function prediction, Virology, vol.496, pp.42-50, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01357336
What Can Phages Tell Us about Host-Pathogen Coevolution?, Int J Evol Biol, vol.2012, p.396165, 2012. ,
A Eukaryotic-like Serine/Threonine Kinase Protects Staphylococci against Phages, Cell Host Microbe, vol.20, pp.471-81, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01402430
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing, PLoS Biol, vol.6, p.280, 2008. ,
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation, Proc Natl Acad Sci U S A, vol.108, issue.1, pp.4554-61, 2011. ,
Inflammation boosts bacteriophage transfer between Salmonella spp, Science, vol.355, pp.1211-1226, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01607431
Revisited gene regulation in bacteriophage lambda, Curr Opin Genet Dev, vol.15, pp.145-52, 2005. ,
Cooperativity in long-range gene regulation by the lambda CI repressor, Genes Dev, vol.18, pp.344-54, 2004. ,
Gut microbiota utilize immunoglobulin A for mucosal colonization, Science, vol.360, pp.795-800, 2018. ,
Gut biogeography of the bacterial microbiota, Nat Rev Microbiol, vol.14, pp.20-32, 2016. ,
Systematic discovery of antiphage defense systems in the microbial pangenome, Science, vol.359, 2018. ,
Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements, Nature, vol.431, pp.476-81, 2004. ,
A constant rate of spontaneous mutation in DNA-based microbes, Proc Natl Acad Sci U S A, vol.88, pp.7160-7164, 1991. ,
Control of the LexA regulon by pH: evidence for a reversible inactivation of the LexA repressor during the growth cycle of Escherichia coli, Mol Microbiol, vol.12, pp.621-630, 1994. ,
A composite bacteriophage alters colonization by an intestinal commensal bacterium, Proc Natl Acad Sci U S A, vol.109, pp.17621-17627, 2012. ,
Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces, Int J Syst Evol Microbiol, vol.56, pp.2437-2478, 2006. ,
Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces, Int J Syst Evol Microbiol, vol.52, pp.1615-1635, 2002. ,
Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov, Int J Syst Evol Microbiol, vol.52, pp.2141-2147, 2002. ,
The role of pH in determining the species composition of the human colonic microbiota, Environ Microbiol, vol.11, pp.2112-2134, 2009. ,
, , 2010.
, Gastroenterol Clin Biol, vol.34, pp.23-31
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes, Nat Commun, vol.5, p.4498, 2014. ,
Bad Phages in Good Bacteria: Role of the Mysterious orf63 of lambda and Shiga Toxin-Converting Phi24B Bacteriophages, Front Microbiol, vol.8, p.1618, 2017. ,
Diversity of the human intestinal microbial flora, Science, vol.308, pp.1635-1643, 2005. ,
Computational approaches to predict bacteriophage-host relationships, FEMS Microbiol Rev, vol.40, pp.258-72, 2016. ,
Molecular evidence for a new bacteriophage of Borrelia burgdorferi, J Bacteriol, vol.181, pp.7308-7321, 1999. ,
Real-time DNA sequencing from single polymerase molecules, Science, vol.323, pp.133-141, 2009. ,
Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses, ISME J, vol.11, pp.237-284, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01557484
The effects of ageing on the colonic bacterial microflora in adults, Z Gastroenterol, vol.47, pp.653-661, 2009. ,
High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments, ISME J, vol.8, pp.1503-1512, 2014. ,
Communication between viruses guides lysis-lysogeny decisions, Nature, vol.541, pp.488-93, 2017. ,
Complete Genome Sequence of Phage-Like Plasmid pECOH89, Encoding CTX-M-15, Genome Announc, vol.2, 2014. ,
Population-level analysis of gut microbiome variation, Science, vol.352, pp.560-564, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01518384
Induction of Shiga Toxin-Encoding Prophage by Abiotic Environmental Stress in Food, Appl Environ Microbiol, vol.83, 2017. ,
A new perspective on lysogeny: prophages as active regulatory switches of bacteria, Nat Rev Microbiol, vol.13, pp.641-50, 2015. ,
Human Intestinal Microflora in Health and Disease, Normal Indigenous Intestinal Flora, p.3, 1983. ,
In vivo acquisition of prophage in Streptococcus pyogenes, Trends Microbiol, vol.15, pp.297-300, 2007. ,
Microbiology: Antibiotics and adiposity, Nature, vol.488, pp.601-603, 2012. ,
Statistical structure of host-phage interactions, Proc Natl Acad Sci U S A, vol.108, pp.288-97, 2011. ,
Multi-scale structure and geographic drivers of crossinfection within marine bacteria and phages, ISME J, vol.7, pp.520-552, 2013. ,
The essential role of the cro gene in lytic development by bacteriophage lambda, Virology, vol.81, pp.352-62, 1977. ,
Genome structure of mycobacteriophage D29: implications for phage evolution, J Mol Biol, vol.279, pp.143-64, 1998. ,
Effect of antibiotic treatment on bacteriophage production by a cystic fibrosis epidemic strain of Pseudomonas aeruginosa, Antimicrob Agents Chemother, vol.55, pp.426-434, 2011. ,
Transcription antitermination: the lambda paradigm updated, Mol Microbiol, vol.18, pp.191-200, 1995. ,
Marine viruses and their biogeochemical and ecological effects, Nature, vol.399, pp.541-549, 1999. ,
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs, Bioinformatics, vol.33, pp.3113-3127, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01982199
Temperate bacterial viruses as double-edged swords in bacterial warfare, PLoS One, vol.8, p.59043, 2013. ,
Host-parasite coevolution and patterns of adaptation across time and space, J Evol Biol, vol.21, pp.1861-1867, 2008. ,
Gut microbiota as a source of novel antimicrobials, Gut Microbes, pp.1-57, 2018. ,
Novel high-molecularweight, R-type bacteriocins of Clostridium difficile, J Bacteriol, vol.194, pp.6240-6247, 2012. ,
Cloning of a chromosomal gene required for phage infection of Lactococcus lactis subsp. lactis C2, J Bacteriol, vol.175, pp.5510-5519, 1993. ,
Formation of hybrids between coliphage lambda and Salmonella phage P22 with a Salmonella typhimurium hybrid sensitive to these phages, Proc Natl Acad Sci U S A, vol.69, pp.3110-3114, 1972. ,
Interleukin 8 secretion by colonic crypt cells in vitro: response to injury suppressed by butyrate and enhanced in inflammatory bowel disease, Gut, vol.37, pp.536-579, 1995. ,
The genome sequence of Escherichia coli tailed phage D6 and the diversity of Enterobacteriales circular plasmid prophages, Virology, vol.515, pp.203-217, 2018. ,
Phage-induced lysis enhances biofilm formation in Shewanella oneidensis MR-1, ISME J, vol.5, pp.613-639, 2011. ,
Ciprofloxacin and trimethoprim cause phage induction and virulence modulation in Staphylococcus aureus, Antimicrob Agents Chemother, vol.50, pp.171-178, 2006. ,
Induction of the SOS response by hydrogen peroxide in various Escherichia coli mutants with altered protection against oxidative DNA damage, J Bacteriol, vol.171, pp.6141-6148, 1989. ,
Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting, Nature, vol.514, pp.633-640, 2014. ,
Incomplete prophage tolerance by type III-A CRISPR-Cas systems reduces the fitness of lysogenic hosts, Nat Commun, vol.9, p.61, 2018. ,
BREX is a novel phage resistance system widespread in microbial genomes, EMBO J, vol.34, pp.169-83, 2015. ,
The diversity of coliphages and coliforms in horse feces reveals a complex pattern of ecological interactions, Appl Environ Microbiol, vol.73, pp.5975-81, 2007. ,
Human genetics shape the gut microbiome, Cell, vol.159, pp.789-99, 2014. ,
Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis, J Clin Microbiol, vol.44, pp.4136-4177, 2006. ,
Effect of normal microbial flora on intestinal surface area, Am J Physiol, vol.201, pp.175-183, 1961. ,
Diversity-generating retroelement homing regenerates target sequences for repeated rounds of codon rewriting and protein diversification, Mol Cell, vol.31, pp.813-836, 2008. ,
Effects of microbial contamination on the cecum enlargement of germfree rats, Scand J Gastroenterol, vol.5, pp.309-323, 1970. ,
Bacterial viruses enable their host to acquire antibiotic resistance genes from neighbouring cells, Nat Commun, vol.7, p.13333, 2016. ,
Bacteria-phage coevolution and the emergence of generalist pathogens, Am Nat, vol.177, pp.44-53, 2011. ,
Host-parasite coevolutionary arms races give way to fluctuating selection, Ecol Lett, vol.14, pp.635-677, 2011. ,
The genetical evolution of social behaviour. I, J Theor Biol, vol.7, pp.1-16, 1964. ,
The genetical evolution of social behaviour. II, J Theor Biol, vol.7, pp.17-52, 1964. ,
A representative of the dominant human colonic Firmicutes, Roseburia faecis M72/1, forms a novel bacteriocin-like substance, Anaerobe, vol.23, pp.5-8, 2013. ,
The tripartite immunity system of phages P1 and P7, FEMS Microbiol Rev, vol.17, pp.121-127, 1995. ,
Lambda II. Cold spring Harbor, 1983. ,
Significance of bacteriophages for controlling bacterioplankton growth in a mesotrophic lake, Appl Environ Microbiol, vol.61, pp.333-373, 1995. ,
The HflB protease of Escherichia coli degrades its inhibitor lambda cIII, J Bacteriol, vol.179, pp.358-63, 1997. ,
Independent functions of viral protein and nucleic acid in growth of bacteriophage, J Gen Physiol, vol.36, pp.39-56, 1952. ,
Diversity of phage infection types and associated terminology: the problem with 'Lytic or lysogenic, FEMS Microbiol Lett, vol.363, 2016. ,
Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice, ISME J, vol.10, pp.460-77, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01303788
Pyrosequencing-based analysis of the mucosal microbiota in healthy individuals reveals ubiquitous bacterial groups and microheterogeneity, PLoS One, vol.6, p.25042, 2011. ,
A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem, Proc Natl Acad Sci U S A, vol.96, pp.9833-9841, 1999. ,
Characterisation of intestinal bacteria in infant stools using real-time PCR and northern hybridisation analyses, FEMS Microbiol Ecol, vol.54, pp.77-85, 2005. ,
Multiple mechanisms drive phage infection efficiency in nearly identical hosts, Molecular biology of bacteriophage mu, vol.190, pp.624-656, 1975. ,
Characterization of viruslike particles associated with the human faecal and caecal microbiota, Res Microbiol, vol.165, pp.803-815, 2014. ,
Sak4 of Phage HK620 Is a RecA Remote Homolog With Single-Strand Annealing Activity Stimulated by Its Cognate SSB Protein, Front Microbiol, vol.9, p.743, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02179070
Genetic regulatory mechanisms in the synthesis of proteins, J Mol Biol, vol.3, pp.318-56, 1961. ,
Characterization of a new virulent phage infecting the lactic acid bacterium Oenococcus oeni, Food Microbiology, vol.54, pp.167-77, 2016. ,
Composition and temporal stability of the gut microbiota in older persons, ISME J, vol.10, pp.170-82, 2016. ,
Seasonal and diel abundance of viruses and occurrence of lysogeny/bacteriocinogeny in the marine environment, Marine Ecology Progress Series, vol.104, pp.163-72, 1994. ,
The abundance of lysogenic bacteria in marine microbial communities as determined by prophage induction, Marine Ecology Progress Series, vol.142, pp.27-38, 1996. ,
Bacteria penetrate the inner mucus layer before inflammation in the dextran sulfate colitis model, PLoS One, vol.5, p.12238, 2010. ,
Bacteriophage-mediated competition in Bordetella bacteria, Proc Biol Sci, vol.273, pp.1843-1851, 2006. ,
Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives, Gut, vol.60, pp.631-638, 2011. ,
Vertical mother-neonate transfer of maternal gut bacteria via breastfeeding, Environ Microbiol, vol.16, pp.2891-904, 2014. ,
G inversion in bacteriophage Mu DNA is stimulated by a site within the invertase gene and a host factor, Cell, vol.41, pp.771-80, 1985. ,
Mutations in a temperate bacteriophage affecting its ability to lysogenize Escherichia coli, Virology, vol.3, pp.42-61, 1957. ,
Role of the gut microbiota in immunity and inflammatory disease, Nat Rev Immunol, vol.13, pp.321-356, 2013. ,
The lit gene product which blocks bacteriophage T4 late gene expression is a membrane protein encoded by a cryptic DNA element, e14, J Bacteriol, vol.170, pp.2056-62, 1988. ,
A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria, Nature, vol.554, pp.118-140, 2018. ,
The Phyre2 web portal for protein modeling, prediction and analysis, Nat Protoc, vol.10, pp.845-58, 2015. ,
Antibiotic therapy in inflammatory bowel disease: a systematic review and meta-analysis, Am J Gastroenterol, vol.106, pp.661-73, 2011. ,
Spatial disturbances in altered mucosal and luminal gut viromes of dietinduced obese mice, Environ Microbiol, vol.18, pp.1498-510, 2016. ,
Lysogeny is prevalent and widely distributed in the murine gut microbiota, ISME J, vol.12, pp.1127-1168, 2018. ,
Inhibition of Escherichia coli O157:H7 attachment by interactions between lactic acid bacteria and intestinal epithelial cells, J Microbiol Biotechnol, vol.18, pp.1278-85, 2008. ,
Lytic to temperate switching of viral communities, Nature, vol.531, pp.466-70, 2016. ,
The phage lambda CII transcriptional activator carries a C-terminal domain signaling for rapid proteolysis, Proc Natl Acad Sci U S A, vol.99, pp.14964-14973, 2002. ,
Quantitative kinetic analysis of the bacteriophage lambda genetic network, Proc Natl Acad Sci U S A, vol.102, pp.4470-4475, 2005. ,
Phage lambda CIII: a protease inhibitor regulating the lysis-lysogeny decision, PLoS One, vol.2, p.363, 2007. ,
Succession of microbial consortia in the developing infant gut microbiome, Proc Natl Acad Sci U S A, vol.108, issue.1, pp.4578-85, 2011. ,
Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities, FEMS Microbiol Rev, vol.38, pp.916-947, 2014. ,
High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease, Gut, vol.56, pp.669-75, 2007. ,
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
The extinction dynamics of bacterial pseudogenes, PLoS Genet, vol.6, 2010. ,
Re-establishing a place for phage therapy in western medicine, Future Microbiol, vol.10, pp.685-693, 2015. ,
Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton, ISME J, vol.9, pp.2386-99, 2015. ,
Bacteriophage resistance mechanisms, Nat Rev Microbiol, vol.8, pp.317-344, 2010. ,
Exercise training modifies gut microbiota in normal and diabetic mice, Appl Physiol Nutr Metab, vol.40, pp.749-52, 2015. ,
Importance of widespread gene transfer agent genes in alphaproteobacteria, Trends Microbiol, vol.15, pp.54-62, 2007. ,
Gene transfer agents: phage-like elements of genetic exchange, Nat Rev Microbiol, vol.10, pp.472-82, 2012. ,
Crohn's diseaseassociated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly, Cell Microbiol, vol.12, pp.99-113, 2010. ,
Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults, PLoS One, vol.5, p.9085, 2010. ,
Pseudolysogeny and sequential mutations build multiresistance to virulent bacteriophages in Pseudomonas aeruginosa, Microbiology, vol.162, pp.748-63, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01280758
Faecalibacterium Gut Colonization Is Accelerated by Presence of Older Siblings, 2017. ,
Classification of Myoviridae bacteriophages using protein sequence similarity, BMC Microbiol, vol.9, p.224, 2009. ,
Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools, Res Microbiol, vol.159, pp.406-420, 2008. ,
Intestinal colonization resistance, Immunology, vol.138, pp.1-11, 2013. ,
Displacement of bacterial pathogens from mucus and Caco-2 cell surface by lactobacilli, J Med Microbiol, vol.52, pp.925-955, 2003. ,
On the structure of the glucosylated hydroxymethylcytosine nucleotides of coliphages T2, T4, and T6, J Biol Chem, vol.235, pp.3254-3263, 1960. ,
Plasmid addiction genes of bacteriophage P1: doc, which causes cell death on curing of prophage, and phd, which prevents host death when prophage is retained, J Mol Biol, vol.233, pp.414-442, 1993. ,
Listeria phage and phage tail induction triggered by components of bacterial growth media (phosphate, LiCl, nalidixic acid, and acriflavine), Appl Environ Microbiol, vol.81, pp.2117-2141, 2015. ,
Constraints on the coevolution of bacteria and virulent phage -a model, some experiments, and predictions for natural communities, Am Nat, vol.125, pp.585-602, 1985. ,
, Dysbiosis in inflammatory bowel disease: a role for bacteriophages, vol.57, pp.424-429, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00526557
Biodiversity of the mucosaassociated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD, Inflamm Bowel Dis, vol.11, pp.473-80, 2005. ,
Worlds within worlds: evolution of the vertebrate gut microbiota, Nat Rev Microbiol, vol.6, pp.776-88, 2008. ,
Microbial ecology: human gut microbes associated with obesity, Nature, vol.444, pp.1022-1025, 2006. ,
The Role of the Exo-Xis Region in Oxidative Stress-Mediated Induction of Shiga Toxin-Converting Prophages, Oxid Med Cell Longev, vol.2016, p.8453135, 2016. ,
The establishment of lysogenicity in Escherichia coli, J Bacteriol, vol.65, pp.642-51, 1953. ,
Early life dynamics of the human gut virome and bacterial microbiome in infants, Nat Med, vol.21, pp.1228-1262, 2015. ,
Bacteriophage lambda; abortive infection of bacteria lysogenic for phage P2, Proc Natl Acad Sci U S A, vol.66, pp.587-94, 1970. ,
Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage, Science, vol.295, pp.2091-2095, 2002. ,
Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study, Lancet Infect Dis, vol.16, pp.161-169, 2016. ,
Genome of bacteriophage P1, J Bacteriol, vol.186, pp.7032-68, 2004. ,
Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes: implications for phage evolution, Mol Microbiol, vol.35, pp.324-364, 2000. ,
Analytical note on certain rythmic relations in organic systems, Proc. Natl. Acad. Sci, vol.6, p.410, 1920. ,
Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs, Nucleic Acids Res, vol.38, pp.3952-62, 2010. ,
Automated classification of tailed bacteriophages according to their neck organization, BMC Genomics, vol.15, p.1027, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01204418
A role for bacteriophage T4 rI gene function in the control of phage development during pseudolysogeny and in slowly growing host cells, Res Microbiol, vol.154, pp.547-52, 2003. ,
, Pseudolysogeny. Advances in Virus Research, vol.82, pp.339-387, 2012.
Superinfection exclusion by T-even-type coliphages, Trends Microbiol, vol.2, pp.137-146, 1994. ,
Comparative genomics of Streptococcus thermophilus phage species supports a modular evolution theory, J Virol, vol.73, pp.8647-56, 1999. ,
Similarly organized lysogeny modules in temperate Siphoviridae from low GC content gram-positive bacteria, Virology, vol.263, pp.427-462, 1999. ,
Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota, Environ Microbiol, vol.18, pp.2196-213, 2016. ,
Effects of diverse environmental conditions on {phi}LC3 prophage stability in Lactococcus lactis, Appl Environ Microbiol, vol.71, pp.721-728, 2005. ,
Mutations of Bacteria from Virus Sensitivity to Virus Resistance, Genetics, vol.28, pp.491-511, 1943. ,
, Lysogeny. Bacteriol Rev, vol.17, pp.269-337, 1953.
Transmission of viruses via our microbiomes, vol.4, p.64, 2016. ,
Carbohydrate fermentation, energy transduction and gas metabolism in the human large intestine, Gastrointestinal Microbiology, pp.269-318, 1997. ,
A decrease of the butyrateproducing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis, Gut, vol.63, pp.1275-83, 2014. ,
Identification and characterization of lactococcal-prophage-carried superinfection exclusion genes, Appl Environ Microbiol, vol.74, pp.6206-6221, 2008. ,
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla, Proc Natl Acad Sci U S A, vol.106, pp.5859-64, 2009. ,
beta-lactam antibiotics induce the SOS response and horizontal transfer of virulence factors in Staphylococcus aureus, J Bacteriol, vol.188, pp.2726-2735, 2006. ,
An updated evolutionary classification of CRISPR-Cas systems, Nat Rev Microbiol, vol.13, pp.722-758, 2015. ,
Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla, Virol J, vol.12, p.164, 2015. ,
Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach, Gut, vol.55, pp.205-216, 2006. ,
Healthy human gut phageome, Proc Natl Acad Sci U S A, vol.113, pp.10400-10405, 2016. ,
The Human Gut Phage Community and Its Implications for Health and Disease, Viruses, vol.9, 2017. ,
Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay, Sci Adv, vol.3, p.1602105, 2017. ,
Generation and Analysis of Chromosomal Contact Maps of Bacteria, Methods Mol Biol, vol.1624, pp.75-84, 2017. ,
The gut microbiota and host health: a new clinical frontier, Gut, vol.65, pp.330-339, 2016. ,
Characterisation of three temperate phages released from the same Lactobacillus paracasei commercial strain, International Journal of Dairy Technology, vol.63, pp.396-405, 2010. ,
The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age, BMC Microbiol, vol.9, p.123, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00657910
Restructuring of an RNA polymerase holoenzyme elongation complex by lambdoid phage Q proteins, Proc Natl Acad Sci U S A, vol.98, pp.8972-8980, 2001. ,
CRISPR-Cas immunity in prokaryotes, Nature, vol.526, pp.55-61, 2015. ,
Rapid diversification of coevolving marine Synechococcus and a virus, Proc Natl Acad Sci U S A, vol.109, pp.4544-4553, 2012. ,
Comparative study of bacterial groups within the human cecal and fecal microbiota, Appl Environ Microbiol, vol.67, pp.4939-4981, 2001. ,
Enhanced Escherichia coli adherence and invasion in Crohn's disease and colon cancer, Gastroenterology, vol.127, pp.80-93, 2004. ,
The commensal bacterium Faecalibacterium prausnitzii is protective in DNBS-induced chronic moderate and severe colitis models, Inflamm Bowel Dis, vol.20, pp.417-447, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00931932
Molecular diversity of Escherichia coli in the human gut: new ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohn's disease, Inflamm Bowel Dis, vol.15, pp.872-82, 2009. ,
Phage-inducible islands in the Gram-positive cocci, ISME J, vol.11, pp.1029-1071, 2017. ,
The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism, PLoS Genet, vol.4, p.1000065, 2008. ,
URL : https://hal.archives-ouvertes.fr/inserm-00496049
Antagonistic coevolution of marine planktonic viruses and their hosts, Ann Rev Mar Sci, vol.6, pp.393-414, 2014. ,
Enterococcus faecalis prophage dynamics and contributions to pathogenic traits, PLoS Genet, vol.9, p.1003539, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01190746
On the interactions between virulent bacteriophages and bacteria in the gut, Bacteriophage, vol.2, pp.229-262, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01539087
Virulent bacteriophages can target O104:H4 enteroaggregative Escherichia coli in the mouse intestine, Antimicrob Agents Chemother, vol.56, pp.6235-6277, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01538999
Bacteriophage evolution differs by host, lifestyle and genome, Nat Microbiol, vol.2, p.17112, 2017. ,
Gut/brain axis and the microbiota, J Clin Invest, vol.125, pp.926-964, 2015. ,
Reciprocal interactions of the intestinal microbiota and immune system, Nature, vol.489, pp.231-272, 2012. ,
Effect of mutations in the c2 and c3 genes of bacteriophage lambda on macromolecular synthesis in infected cells, J Mol Biol, vol.49, pp.639-55, 1970. ,
Evidence of in vivo prophage induction during Clostridium difficile infection, Appl Environ Microbiol, vol.78, pp.7662-70, 2012. ,
Transcription termination controls prophage maintenance in Escherichia coli genomes, Proc Natl Acad Sci U S A, vol.110, pp.14414-14423, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00874882
Widely distributed lysogeny in probiotic lactobacilli represents a potentially high risk for the fermentative dairy industry, Int J Food Microbiol, vol.144, pp.503-513, 2011. ,
Repeatability and contingency in the evolution of a key innovation in phage lambda, Science, vol.335, pp.428-460, 2012. ,
The pyocins of Pseudomonas aeruginosa, Biochimie, vol.84, pp.499-510, 2002. ,
Effects of Bacteriophages on the Population Dynamics of Four Strains of Pelagic Marine Bacteria, Microb Ecol, vol.42, pp.395-406, 2001. ,
Bacteriophages drive strain diversification in a marine Flavobacterium: implications for phage resistance and physiological properties, Environ Microbiol, vol.11, pp.1971-82, 2009. ,
Defective site-specific integration elements are present in the genome of virulent bacteriophage LL-H of Lactobacillus delbrueckii, Appl Environ Microbiol, vol.62, pp.1847-51, 1996. ,
Movers and shakers: influence of bacteriophages in shaping the mammalian gut microbiota, Gut Microbes, vol.4, pp.4-16, 2013. ,
Using Tablet for visual exploration of second-generation sequencing data, Brief Bioinform, vol.14, pp.193-202, 2013. ,
Rapid evolution of the human gut virome, Proc Natl Acad Sci U S A, vol.110, pp.12450-12455, 2013. ,
Hypervariable loci in the human gut virome, Proc Natl Acad Sci U S A, vol.109, pp.3962-3968, 2012. ,
The human gut virome: inter-individual variation and dynamic response to diet, Genome Res, vol.21, pp.1616-1641, 2011. ,
Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82, PLoS One, vol.5, 2010. ,
Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain, Proc Natl Acad Sci U S A, vol.96, pp.9845-50, 1999. ,
Menage a trois in the human gut: interactions between host, bacteria and phages, Nat Rev Microbiol, vol.15, pp.397-408, 2017. ,
Mechanism of cell surface expression of the Streptococcus mitis platelet binding proteins PblA and PblB, Mol Microbiol, vol.64, pp.844-57, 2007. ,
Coevolution of bacteriophage PP01 and Escherichia coli O157:H7 in continuous culture, Appl Environ Microbiol, vol.69, pp.170-176, 2003. ,
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome, Nature, vol.499, pp.219-241, 2013. ,
Bacteriophage sensitivity patterns among bacteria isolated from marine waters, HELGOLÄNDER MEERESUNTERSUCHUNGEN, vol.34, pp.375-85, 1981. ,
Host-parasite interactions: recent developments in the genetics of abortive phage infections, New Biol, vol.3, pp.230-236, 1991. ,
Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery, Gut, vol.65, pp.954-62, 2016. ,
Strain-resolved community genomic analysis of gut microbial colonization in a premature infant, Proc Natl Acad Sci U S A, vol.108, pp.1128-1161, 2011. ,
Intestinal microflora of human infants and current trends for its nutritional modulation, Br J Nutr, vol.87, pp.405-425, 2002. ,
Identification of a phage-encoded Igbinding protein from invasive Neisseria meningitidis, J Immunol, vol.191, pp.3287-96, 2013. ,
Analysis of SOSinduced spontaneous prophage induction in Corynebacterium glutamicum at the singlecell level, J Bacteriol, vol.196, pp.180-188, 2014. ,
Impact of spontaneous prophage induction on the fitness of bacterial populations and host-microbe interactions, J Bacteriol, vol.197, pp.410-419, 2015. ,
Functional and genetic analysis of regulatory regions of coliphage H-19B: location of shiga-like toxin and lysis genes suggest a role for phage functions in toxin release, Mol Microbiol, vol.28, pp.1255-67, 1998. ,
Gut microbiota and IBD: causation or correlation?, Nat Rev Gastroenterol Hepatol, vol.14, pp.573-84, 2017. ,
Influence of intestinal bacterial flora on cytokine (IL-1, IL-6 and TNF-alpha) production by mouse peritoneal macrophages, Eur Cytokine Netw, vol.4, pp.133-141, 1993. ,
Protein-protein and protein-DNA interactions of sigma70 region 4 involved in transcription activation by lambdacI, J Mol Biol, vol.324, pp.17-34, 2002. ,
Disease-specific alterations in the enteric virome in inflammatory bowel disease, Cell, vol.160, pp.447-60, 2015. ,
Stability of CII is a key element in the cold stress response of bacteriophage lambda infection, J Bacteriol, vol.179, pp.5987-91, 1997. ,
DISARM is a widespread bacterial defence system with broad anti-phage activities, Nat Microbiol, vol.3, pp.90-98, 2018. ,
Contemporary Phage Biology: From Classic Models to New Insights, Cell, vol.172, pp.1260-70, 2018. ,
Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences, Nat Commun, vol.4, p.2420, 2013. ,
The human gut virome: a multifaceted majority, Front Microbiol, vol.6, p.918, 2015. ,
The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts, Nucleic Acids Res, vol.42, pp.10618-10649, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374960
Switches in bacteriophage lambda development, Annu Rev Genet, vol.39, pp.409-438, 2005. ,
Induction of phage formation in the lysogenic Escherichia coli K-12 by mitomycin C, Nature, vol.184, pp.1079-80, 1959. ,
Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease, Gut, vol.53, pp.685-93, 2004. ,
Characterization of the Prophage Repertoire of African Salmonella Typhimurium ST313 Reveals High Levels of Spontaneous Induction of Novel Phage BTP1, Front Microbiol, vol.8, p.235, 2017. ,
Uncovering Earth's virome, Nature, vol.536, pp.425-455, 2016. ,
Coevolution with viruses drives the evolution of bacterial mutation rates, Nature, vol.450, pp.1079-81, 2007. ,
Development of the human infant intestinal microbiota, PLoS Biol, vol.5, p.177, 2007. ,
Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea, ISME J, vol.6, pp.273-84, 2012. ,
Human Gut Symbiont Roseburia hominis Promotes and Regulates Innate Immunity, Front Immunol, vol.8, p.1166, 2017. ,
Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?, ISME J, vol.2, pp.579-89, 2008. ,
Induction of vaginal Lactobacillus phages by the cigarette smoke chemical benzo[a]pyrene diol epoxide, Mutat Res, vol.466, pp.57-62, 2000. ,
A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa, MBio, vol.5, p.896, 2014. ,
Anti-CRISPR: discovery, mechanism and function, Nat Rev Microbiol, vol.16, pp.12-17, 2018. ,
Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species, Nat Microbiol, vol.1, p.16085, 2016. ,
, Dynamics of coliphage infections. Fermentation Advances, pp.323-359, 1969.
The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site, Cell, vol.112, pp.131-171, 2003. ,
Bacteriophage-mediated spread of bacterial virulence genes, Curr Opin Microbiol, vol.23, pp.171-179, 2015. ,
The Phage-Inducible Chromosomal Islands: A Family of Highly Evolved Molecular Parasites, Annu Rev Virol, vol.2, pp.181-201, 2015. ,
Factors influencing the composition of the intestinal microbiota in early infancy, Pediatrics, vol.118, pp.511-532, 2006. ,
Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers, J Nutr, vol.139, pp.1619-1644, 2009. ,
Molecular evolution of a pathogenicity island from enterohemorrhagic Escherichia coli O157:H7, Infect Immun, vol.66, pp.3810-3817, 1998. ,
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7, Nature, vol.409, pp.529-562, 2001. ,
Silencing of cryptic prophages in Corynebacterium glutamicum, Nucleic Acids Res, vol.44, pp.10117-10148, 2016. ,
The purification and concentration of viruses by aqueous polymerphase systems, Virology, vol.11, pp.553-71, 1960. ,
Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity, Nat Ecol Evol, vol.2, pp.359-66, 2018. ,
The structure of natural microbial enemy-victim networks, Ecol Process, vol.2, pp.1-9, 2013. ,
The evolution of specificity in evolving and coevolving antagonistic interactions between a bacteria and its phage, Evolution, vol.62, pp.1-11, 2008. ,
Genomewide screens for Escherichia coli genes affecting growth of T7 bacteriophage, Proc Natl Acad Sci U S A, vol.103, pp.19039-19083, 2006. ,
A human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.464, pp.59-65, 2010. ,
URL : https://hal.archives-ouvertes.fr/cea-00908974
A metagenome-wide association study of gut microbiota in type 2 diabetes, Nature, vol.490, pp.55-60, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01204262
Identification of an antiinflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease, Gut, vol.65, pp.415-440, 2016. ,
The presence of the antiinflammatory protein MAM, from Faecalibacterium prausnitzii, in the intestinal ecosystem, Gut, vol.65, p.882, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01301613
Prophage excision activates Listeria competence genes that promote phagosomal escape and virulence, Cell, vol.150, pp.792-802, 2012. ,
Genome analysis of E. coli isolated from Crohn's disease patients, BMC Genomics, vol.18, p.544, 2017. ,
Filamentous bacteriophage: biology, phage display and nanotechnology applications, Curr Issues Mol Biol, vol.13, pp.51-76, 2011. ,
Inhibition of CRISPR-Cas9 with Bacteriophage Proteins, Cell, vol.168, p.10, 2017. ,
N15: the linear phage-plasmid, Plasmid, vol.65, pp.102-111, 2011. ,
Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut, Elife, vol.7, 2018. ,
Suppression of Clostridium difficile in the gastrointestinal tracts of germfree mice inoculated with a murine isolate from the family Lachnospiraceae, Infect Immun, vol.80, pp.3786-94, 2012. ,
Within-host competition determines reproductive success of temperate bacteriophages, ISME J, vol.5, pp.1451-60, 2011. ,
Real-time quantitative PCR to discriminate and quantify lambdoid bacteriophages of Escherichia coli K-12, Bacteriophage, vol.2, pp.98-104, 2012. ,
Effects of probiotics and commensals on intestinal epithelial physiology: implications for nutrient handling, J Physiol, vol.587, pp.4169-74, 2009. ,
Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances, Curr Biol, vol.9, pp.151-155, 1999. ,
Gut DNA viromes of Malawian twins discordant for severe acute malnutrition, Proc Natl Acad Sci U S A, vol.112, pp.11941-11947, 2015. ,
Viruses in the faecal microbiota of monozygotic twins and their mothers, Nature, vol.466, pp.334-342, 2010. ,
Gnotobiotic mouse model of phagebacterial host dynamics in the human gut, Proc Natl Acad Sci U S A, vol.110, pp.20236-20277, 2013. ,
The biofilm life cycle and virulence of Pseudomonas aeruginosa are dependent on a filamentous prophage, ISME J, vol.3, pp.271-82, 2009. ,
Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis, ISME J, vol.7, pp.1256-61, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01003298
The role of pseudolysogeny in bacteriophage-host interactions in a natural freshwater environment, Microbiology, vol.143, pp.2065-70, 1997. ,
Dynamics of the pseudolysogenic response in slowly growing cells of Pseudomonas aeruginosa, Microbiology, vol.144, pp.2225-2257, 1998. ,
Activity of the Escherichia coli recA-gene product, Cold Spring Harb Symp Quant Biol, vol.43, pp.917-937, 1979. ,
Association between living environment and human oral viral ecology, ISME J, vol.7, pp.1710-1734, 2013. ,
Viral and microbial community dynamics in four aquatic environments, ISME J, vol.4, pp.739-51, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-02008659
Global phage diversity, Cell, vol.113, p.141, 2003. ,
OmpC and the sigma(E) regulatory pathway are involved in adhesion and invasion of the Crohn's disease-associated Escherichia coli strain LF82, Mol Microbiol, vol.63, pp.1684-700, 2007. ,
Gut microbiota, metabolites and host immunity, Nat Rev Immunol, vol.16, pp.341-52, 2016. ,
Formation, induction, and curing of bacteriophage P1 lysogens, Virology, vol.48, pp.679-89, 1972. ,
More Is Better: Selecting for Broad Host Range Bacteriophages, Front Microbiol, vol.7, p.1352, 2016. ,
Environment dominates over host genetics in shaping human gut microbiota, Nature, vol.555, pp.210-225, 2018. ,
VirSorter: mining viral signal from microbial genomic data, PeerJ, vol.3, p.985, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01557667
RecA-independent pathways of lambdoid prophage induction in Escherichia coli, J Bacteriol, vol.180, pp.6306-6321, 1998. ,
Die Sichtbarmachung der bakteriophagen Lyse im Uebermikroskop, Naturewissenschaften, vol.28, pp.45-46, 1940. ,
A century of the phage: past, present and future, Nat Rev Microbiol, vol.13, pp.777-86, 2015. ,
Flagellar determinants of bacterial sensitivity to chi-phage, Proc Natl Acad Sci U S A, vol.96, pp.9863-9869, 1999. ,
Non-Monotonic Survival of Staphylococcus aureus with Respect to Ciprofloxacin Concentration Arises from ProphageDependent Killing of Persisters, Pharmaceuticals (Basel), vol.8, pp.778-92, 2015. ,
Viral mutation rates, J Virol, vol.84, pp.9733-9781, 2010. ,
Chemostat culture systems support diverse bacteriophage communities from human feces, vol.3, p.58, 2015. ,
Bacillus subtilis operon encoding a membrane receptor for bacteriophage SPP1, J Bacteriol, vol.186, pp.8337-8383, 2004. ,
Microbial influences in inflammatory bowel diseases, Gastroenterology, vol.134, pp.577-94, 2008. ,
Invasive Escherichia coli are a feature of Crohn's disease, Lab Invest, vol.87, pp.1042-54, 2007. ,
Functional expression of the cre-lox site-specific recombination system in the yeast Saccharomyces cerevisiae, Mol Cell Biol, vol.7, pp.2087-96, 1987. ,
Transit time of epithelial cells in the small intestines of germfree mice and ex-germfree mice associated with indigenous microorganisms, Appl Environ Microbiol, vol.42, pp.996-1001, 1981. ,
Coevolution with bacteriophages drives genome-wide host evolution and constrains the acquisition of abiotic-beneficial mutations, Mol Biol Evol, vol.32, pp.1425-1460, 2015. ,
The low incidence of diversity-generating retroelements in sequenced genomes, Mob Genet Elements, vol.2, pp.287-91, 2012. ,
Host-Parasite Coexistence: The Role of Spatial Refuges in Stabilizing Bacteria-Phage Interactions, The american Naturalist, vol.148, pp.348-77, 1996. ,
Detailed genomic analysis of the Wbeta and gamma phages infecting Bacillus anthracis: implications for evolution of environmental fitness and antibiotic resistance, J Bacteriol, vol.188, pp.3037-51, 2006. ,
Induction of SOS functions by alkaline intracellular pH in Escherichia coli, J Bacteriol, vol.168, pp.936-945, 1986. ,
Phage-Like Streptococcus pyogenes Chromosomal Islands (SpyCI) and Mutator Phenotypes: Control by Growth State and Rescue by a SpyCI-Encoded Promoter, Front Microbiol, vol.3, p.317, 2012. ,
Phage-associated mutator phenotype in group A streptococcus, J Bacteriol, vol.190, pp.6290-301, 2008. ,
Evolutionary consequences of intrapatient phage predation on microbial populations, vol.3, p.3497, 2014. ,
Butyrate inhibits inflammatory responses through NFkappaB inhibition: implications for Crohn's disease, Gut, vol.47, pp.397-403, 2000. ,
Gut microbiota in health and disease, Physiol Rev, vol.90, pp.859-904, 2010. ,
Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease, Aliment Pharmacol Ther, vol.24, pp.11-19, 2006. ,
Killing niche competitors by remote-control bacteriophage induction, Proc Natl Acad Sci U S A, vol.106, pp.1234-1242, 2009. ,
Adaptation of adherent-invasive E. coli to gut environment: Impact on flagellum expression and bacterial colonization ability, Gut Microbes, pp.1-17, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02196749
Lysis-lysogeny coexistence: prophage integration during lytic development, 2017. ,
Rat intestinal mucosal responses to a microbial flora and different diets, Gut, vol.36, pp.209-223, 1995. ,
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization, Genome Res, vol.23, pp.111-131, 2013. ,
Molecular evolution of bacteriophages: evidence of selection against the recognition sites of host restriction enzymes, Mol Biol Evol, vol.3, pp.75-83, 1986. ,
Insertion of bacteriophage phiFSW into the chromosome of Lactobacillus casei strain Shirota (S-1): characterization of the attachment sites and the integrase gene, Gene, vol.249, pp.127-161, 2000. ,
Effect of plasmids harbouring blaCTX-M on the virulence and fitness of Escherichia coli ST131 isolates, Int J Antimicrob Agents, vol.46, pp.214-222, 2015. ,
?CrAss001, a member of the most abundant bacteriophage family in the human gut, 2018. ,
Alternative bacteriophage life cycles: the carrier state of Campylobacter jejuni, Open Biol, vol.4, p.130200, 2014. ,
Bacteriophage P4: a satellite virus depending on a helper such as prophage P2, Virology, vol.51, pp.327-371, 1973. ,
Regulation of bacteriophage lambda development by guanosine 5'-diphosphate-3'-diphosphate, Virology, vol.262, pp.431-472, 1999. ,
Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface, Science, vol.228, pp.1315-1322, 1985. ,
Phage-exclusion enzymes: a bonanza of biochemical and cell biology reagents?, Mol Microbiol, vol.15, pp.415-435, 1995. ,
Analysis of bacterial bowel communities of IBD patients: what has it revealed?, Inflamm Bowel Dis, vol.14, pp.858-67, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00652970
Low counts of Faecalibacterium prausnitzii in colitis microbiota, Inflamm Bowel Dis, vol.15, pp.1183-1192, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00657435
Specificities of the fecal microbiota in inflammatory bowel disease, Inflamm Bowel Dis, vol.12, pp.106-117, 2006. ,
Short-chain fatty acids regulate the enteric neurons and control gastrointestinal motility in rats, Gastroenterology, vol.138, pp.1772-82, 2010. ,
Determination of cell fate selection during phage lambda infection, Proc Natl Acad Sci U S A, vol.105, pp.20705-20715, 2008. ,
Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells, Proc Natl Acad Sci U S A, vol.99, pp.15451-15456, 2002. ,
Self-targeting by CRISPR: gene regulation or autoimmunity?, Trends Genet, vol.26, pp.335-375, 2010. ,
CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome, Genome Res, vol.22, pp.1985-94, 2012. ,
The phage-host arms race: shaping the evolution of microbes, Bioessays, vol.33, pp.43-51, 2011. ,
The population biology of bacterial viruses: why be temperate, Theor Popul Biol, vol.26, pp.93-117, 1984. ,
Maturation of the gut microbiome and risk of asthma in childhood, Nat Commun, vol.9, p.141, 2018. ,
Characterization of enterocoliticin, a phage tail-like bacteriocin, and its effect on pathogenic Yersinia enterocolitica strains, Appl Environ Microbiol, vol.67, pp.5634-5676, 2001. ,
Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes, J Mol Biol, vol.189, pp.113-143, 1986. ,
MsmE, a lipoprotein involved in sugar transport in Streptococcus mutans, J Bacteriol, vol.175, pp.1853-1858, 1993. ,
Mechanisms and rates of decay of marine viruses in seawater, Appl Environ Microbiol, vol.58, pp.3721-3730, 1992. ,
Roseburia spp.: a marker of health, Future Microbiol, vol.12, pp.157-70, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01451661
Towards the human intestinal microbiota phylogenetic core, Environ Microbiol, vol.11, pp.2574-84, 2009. ,
Motility as a Factor in Bowel Colonization by Roseburia cecicola, an Obligately Anaerobic Bacterium from the Mouse Caecum, Microbiology, vol.130, pp.173-83, 1984. ,
Viral abundance, production, decay rates and life strategies (lysogeny versus lysis) in Lake Bourget (France), Environ Microbiol, vol.13, pp.616-646, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00820093
Genetic transformation in Staphylococcus aureus: demonstration of a competence-conferring factor of bacteriophage origin in bacteriophage 80 alpha lysates, J Bacteriol, vol.148, pp.294-300, 1981. ,
The biology of restriction and anti-restriction, Curr Opin Microbiol, vol.8, pp.466-72, 2005. ,
Genetic and life-history traits associated with the distribution of prophages in bacteria, ISME J, vol.10, pp.2744-54, 2016. ,
Getting to the core of the gut microbiome, Nat Biotechnol, vol.27, pp.344-350, 2009. ,
C-terminal extension of truncated recombinant proteins in Escherichia coli with a 10Sa RNA decapeptide, J Biol Chem, vol.270, pp.9322-9328, 1995. ,
A core gut microbiome in obese and lean twins, Nature, vol.457, pp.480-484, 2009. ,
An investigation on the nature of ultra-microscopic viruses, The Lancet, pp.1241-1284, 1915. ,
The operator and early promoter region of the Shiga toxin type 2-encoding bacteriophage 933W and control of toxin expression, J Bacteriol, vol.186, pp.7670-7679, 2004. ,
Butyrateproducing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model, ISME J, vol.7, pp.949-61, 2013. ,
The host selects mucosal and luminal associations of coevolved gut microorganisms: a novel concept, FEMS Microbiol Rev, vol.35, pp.681-704, 2011. ,
Phase variation: how to create and coordinate population diversity, Curr Opin Microbiol, vol.14, pp.205-216, 2011. ,
, Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev, vol.80, pp.745-63, 2016.
The diversity-generating benefits of a prokaryotic adaptive immune system, Nature, vol.532, pp.385-393, 2016. ,
A new evolutionary law, Evol. Theory, pp.1-30, 1973. ,
Quantitative microbiome profiling links gut community variation to microbial load, Nature, vol.551, pp.507-518, 2017. ,
Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers, FEMS Microbiol Ecol, vol.48, pp.437-483, 2004. ,
Colonisation by Faecalibacterium prausnitzii and maintenance of clinical remission in patients with ulcerative colitis, Aliment Pharmacol Ther, vol.38, pp.151-61, 2013. ,
Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands, PLoS Genet, vol.9, p.1003454, 2013. ,
Classification of inflammatory bowel disease: the old and the new, Curr Opin Gastroenterol, vol.28, pp.321-327, 2012. ,
Decreased colonization of fecal Clostridium coccoides/Eubacterium rectale species from ulcerative colitis patients in an in vitro dynamic gut model with mucin environment, FEMS Microbiol Ecol, vol.79, pp.685-96, 2012. ,
The lom gene of bacteriophage lambda is involved in Escherichia coli K12 adhesion to human buccal epithelial cells, FEMS Microbiol Lett, vol.156, pp.129-161, 1997. ,
HostPhinder: A Phage Host Prediction Tool, Viruses, vol.8, 2016. ,
Variations and fluctuations of the numbers of individuals in coexsting animal populations, Mem. R. Comitato talassogr. ital, p.131, 1927. ,
Proteins responsible for lysogenic conversion caused by coliphages N15 and phi80 are highly homologous, J Bacteriol, vol.178, pp.1484-1490, 1996. ,
Lysogenic conversion by a filamentous phage encoding cholera toxin, Science, vol.272, pp.1910-1914, 1996. ,
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease, BMC Microbiol, vol.11, p.7, 2011. ,
Meta-analysis of broad-spectrum antibiotic therapy in patients with active inflammatory bowel disease, Exp Ther Med, vol.4, pp.1051-56, 2012. ,
Cryptic prophages help bacteria cope with adverse environments, Nat Commun, vol.1, p.147, 2010. ,
Cell death in Pseudomonas aeruginosa biofilm development, J Bacteriol, vol.185, pp.4585-92, 2003. ,
The population and evolutionary dynamics of Vibrio cholerae and its bacteriophage: conditions for maintaining phage-limited communities, Am Nat, vol.178, pp.715-740, 2011. ,
An experimental study of the population and evolutionary dynamics of Vibrio cholerae O1 and the bacteriophage JSF4, Proc Biol Sci, vol.277, pp.3247-54, 2010. ,
Ecology of prokaryotic viruses, FEMS Microbiol Rev, vol.28, pp.127-81, 2004. ,
Synergistic and antagonistic effects of viral lysis and protistan grazing on bacterial biomass, production and diversity, Environ Microbiol, vol.9, pp.777-88, 2007. ,
In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli, Virology, vol.393, pp.16-23, 2009. ,
Immune loss as a driver of coexistence during host-phage coevolution, ISME J, vol.12, pp.585-97, 2018. ,
Phagebacteria infection networks, Trends Microbiol, vol.21, pp.82-91, 2013. ,
Minimum bacterial density for bacteriophage replication: implications for significance of bacteriophages in natural ecosystems, Appl Environ Microbiol, vol.49, pp.19-23, 1985. ,
Estimates of viral abundance in soils are strongly influenced by extraction and enumeration methods, Biol Fertil Soils, vol.49, pp.857-69, 2013. ,
A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes, Gastroenterology, vol.139, p.1, 2010. ,
Restriction and modification systems, Annu Rev Genet, vol.25, pp.585-627, 1991. ,
Biological and biomedical implications of the co-evolution of pathogens and their hosts, Nat Genet, vol.32, pp.569-77, 2002. ,
Advancement and applications of peptide phage display technology in biomedical science, J Biomed Sci, vol.23, p.8, 2016. ,
Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey, Nucleic Acids Res, vol.46, pp.11-24, 2018. ,
Complete Sequence of pCY-CTX, a Plasmid Carrying a Phage-Like Region and an ISEcp1-Mediated Tn2 Element from Enterobacter cloacae, Microb Drug Resist, vol.24, pp.307-320, 2018. ,
Characterization of a P1-like bacteriophage carrying CTX-M-27 in Salmonella spp. resistant to third generation cephalosporins isolated from pork in China, Sci Rep, vol.7, p.40710, 2017. ,
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability, Sci Transl Med, vol.8, pp.343-81, 2016. ,
Human gut microbiome viewed across age and geography, Nature, vol.486, pp.222-229, 2012. ,
Identification of diversity-generating retroelements in human microbiomes, Int J Mol Sci, vol.15, pp.14234-14280, 2014. ,
Comparative multi-omics systems analysis of Escherichia coli strains B and K-12, Genome Biol, vol.13, p.37, 2012. ,
Cold adaptation regulated by cryptic prophage excision in Shewanella oneidensis, ISME J, vol.10, pp.2787-800, 2016. ,
Genetic modifications to temperate Enterococcus faecalis phage Ef11 that abolish the establishment of lysogeny and sensitivity to repressor, and increase host range and productivity of lytic infection, Microbiology, vol.159, pp.1023-1058, 2013. ,
Quinolone antibiotics induce Shiga toxin-encoding bacteriophages, toxin production, and death in mice, J Infect Dis, vol.181, pp.664-70, 2000. ,
Genetic exchange in Salmonella, J Bacteriol, vol.64, pp.679-99, 1952. ,
Characterization of cryptic prophages (monocins) in Listeria and sequence analysis of a holin/endolysin gene, Microbiology, vol.141, pp.2577-84, 1995. ,
Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces, Appl Environ Microbiol, vol.68, pp.3401-3408, 2002. ,
, 5'-GTCTATTGTTCGAGCAATTC Jekyll JC 58: 5'-AAAGAAAGCCGACATTGTTG JC 59: 5'-CCGGTTATTGTAATGATTATTTCTC Prophage 1 JC 32: 5'-ACTGAAGTGCATAACTATGG JC 35: 5'-GACTTGATTGATCGTGATAC Prophage