Characterization of a T7-like lytic bacteriophage (phiSG-JL2) of Salmonella enterica serovar gallinarum biovar gallinarum

Isolation and characterization of multidrug-resistant Salmonella-specific bacteriophages and their antibacterial efficiency in chicken breast

The use of phages as biocontrol agents against antibiotic-resistant strains of Salmonella spp. is gaining attention. This study aimed to isolate lytic bacteriophages specific for multidrug-resistant Salmonella enterica serovars Typhimurium; it also evaluated the bactericidal effect of isolated phages (STP-1, STP-2, STP-3, and STP-4) from sewage sample against S. Typhimurium as host strains. Moreover, a current study evaluated the efficacy of a bacteriophage cocktail against S. Typhimurium cocktail in chicken breast meat. The 4 phages were classified under the Caudoviricetes class by morphology characterization. On host range testing, they exhibited lytic activities against S. Typhimurium, S. Enteritidis, and S. Thompson. In the stability test, the phages exhibited resistance to heat (above 70°C for 1 h) and pH (strongly alkaline for 24 h). Additionally, the phages had comparable adsorption rates (approximately 80% adsorption in under 5 min). Additionally, the latent periods ranged from 30 to 50 min, with respective burst sizes of 31, 218, 197, and 218 PFU/CFU. In vitro, bacterial challenge demonstrated that at a multiplicity of infection (MOI) of 10, each phage consistently inhibited S. Typhimurium growth at 37°C for 24 h. In the food test, the phage cocktail (MOI = 1,000) reduced S. Typhimurium in artificially contaminated chicken breast meat stored at 4°C by 0.9 and 1.2 log CFU/g after 1 and 7 d, respectively. The results point toward a promising avenue for addressing the challenge of multidrug-resistant S. Typhimurium in the food industry through the use of recently discovered phages. Notably, the exploration of phage cocktails holds significant potential for combating S. Typhimurium in chicken breast products in the times ahead.

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

Bacteriophages (phages) within the genus Przondovirus are T7-like podoviruses belonging to the subfamily Studiervirinae, within the family Autographiviridae, and have a highly conserved genome organisation. The genomes of these phages range from 37 to 42 kb in size, encode 50-60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targeting Klebsiella spp. We describe HYPPA, a HYbrid and Poly-polish Phage Assembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our assembly workflow utilised Oxford Nanopore Technologies for long-read sequencing for its accessibility, making it the more relevant long-read sequencing technology at this time, and Illumina DNA Prep for short-read sequencing, representing the most commonly used technologies globally. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics.

SGP-C: A Broad Host Range Temperate Bacteriophage; Against Salmonella gallinarum

Salmonella gallinarum is a poultry restricted-pathogen causing fowl-typhoid disease in adult birds with mortality rates up-to 80% and exhibit resistance against commonly used antibiotics. In this current study, a temperate broad host range bacteriophage SGP-C was isolated against S. gallinarum from poultry digesta. It showed infection ability in all the 15 tested field strains of S. gallinarum. The SGP-C phage produced circular, turbid plaques with alternate rings. Its optimum activity was observed at pH 7.0 and 37-42°C, with a latent period of 45 min and burst size of 187 virions/bacterial cell. The SGP-C lysogens, SGPC-L5 and SGPC-L6 exhibited super-infection immunity against the same phage, an already reported feature of lysogens. A virulence index of 0.5 and 0.001 as MV50 of SGP-C suggests its moderate virulence. The genome of SGP-C found circular double stranded DNA of 42 Kbp with 50.04% GC content, which encodes 63 ORFs. The presence of repressor gene at ORF49, and absence of tRNA sequence in SGP-C genome indicates its lysogenic nature. Furthermore, from NGS analysis of lysogens we propose that SGP-C genome might exist either as an episome, or both as integrated and temporary episome in the host cell and warrants further studies. Phylogenetic analysis revealed its similarity with Salmonella temperate phages belonging to family Siphoviridae. The encoded proteins by SGP-C genome have not showed homology with any known toxin and virulence factor. Although plenty of lytic bacteriophages against this pathogen are already reported, to our knowledge SGP-C is the first lysogenic phage against S. gallinarum reported so far.

Physiological properties of indigenous lytic bacteriophages as monophage suspension and cocktail against poultry-adapted typhoidal Salmonella variants

The emergence and spread of multidrug resistance among pathogens of the agro-food sector is increasing at an alarming rate, which has directed attention to the search for alternative to antibiotic therapy. The present work studied the physiological and population dynamics of lytic bacteriophages against avian-adapted Salmonella. Out of 28 positive samples, four bacteriophage isolates (SalØ-ABF37, SalØ-RCMPF12, SalØ-MCOH26, SalØ-DNLS42) were selected based on their ability to clearly lyse bacterial test strains. The isolates propagated were active against closely related D1 serotypes, i.e., S. Enteritidis and S. Typhimurium, with no heterologous activity against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 23235. Each of the monophage suspension and cocktail efficiently suppressed the bacterial count from exponential increase in comparison to the untreated bacterial control. The bacterial turbidity was recorded as 0.244 at λ₆₀₀ during 400 min of co-incubation, in contrast to bacterial control showing λ₆₀₀ = 0.669. The latent period was recorded to be 25, 35, 25 and 30 for SalØ-ABF37, SalØ-RCMPF12, SalØ-MCOH26 and SalØ-DNLS42, with 73.00, 97.00, 132 and 75.00 PFU cell^-1, respectively. The highest lytic activity was seen at 37.00 ˚C - 42.00 ˚C, with phage particle count being fairly stable at pH 3.00 - 9.00. Each of the isolates possessed dsDNA by being resistant to RNase A. The current study concludes that lytic phages are promising alternative to combat multidrug resistant superbugs. The physiological characterization and bacterial growth inhibition are important parameters in standardization of phage therapy.

Tackling Intrinsic Antibiotic Resistance in Serratia Marcescens with A Combination of Ampicillin/Sulbactam and Phage SALSA

During the antibiotic crisis, bacteriophages (briefly phages) are increasingly considered as potential antimicrobial pillars for the treatment of infectious diseases. Apart from acquired drug resistance, treatment options are additionally hampered by intrinsic, chromosomal-encoded resistance. For instance, the chromosomal ampC gene encoding for the AmpC-type β-lactamases is typically present in a number of nosocomial pathogens, including S. marcescens. In this study, phage SALSA (vB_SmaP-SALSA), with lytic activity against clinical isolates of S. marcescens, was isolated from effluent. Besides phage characterization, the aim of this study was to evaluate whether a synergistic effect between the antibiotic ampicillin/sulbactam (SAM) and phage can be achieved despite intrinsic drug resistance. Phage SALSA belongs to the Podoviridae family and genome-wide treeing analysis groups this phage within the phylogenetic radiation of T7-like viruses. The genome of Phage SALSA consists of 39,933 bp, which encode for 49 open reading frames. Phage SALSA was able to productively lyse 5 out of 20 clinical isolates (25%). A bacterial challenge with phage alone in liquid medium revealed that an initial strong bacterial decline was followed by bacterial re-growth, indicating the emergence of phage resistance. In contrast, the combination of SAM and phage, together at various concentrations, caused a complete bacterial eradication, confirmed by absorbance measurements and the absence of colony forming units after plating. The data show that it is principally possible to tackle the axiomatic condition of intrinsic drug resistance with a dual antimicrobial approach, which could be extended to other clinically relevant bacteria.

Broad-host-range Salmonella bacteriophage STP4-a and its potential application evaluation in poultry industry

Salmonella is regarded as the predominant cause of foodborne illnesses worldwide, and the increase of these antimicrobial-resistant strains makes it more difficult to prevent. On this occasion, bacteriophages (phages) stand out as an alternative biocontrol agent with high efficiency and low mutation rates. Salmonella phages have confronted challenges to counteract with more than 2,500 serovars of Salmonella spp. and overcome the universality of antibiotics to different species, and thus, broad-host-range phages infecting Salmonella spp. are urgently required to realize precise poultry treatment or clinical therapy. First, phage STP4-a was screened to have a broad host range through bioinformatics analysis, and then the host range assay proved that phage STP4-a could inhibit 88 out of 91 Salmonella strains. Then, in silico analysis excluded the possibility of phage STP4-a possessing any known lysogeny factors, toxins, pathogen-related genes, or foodborne allergens, and oral toxicity studies further ensured the safety of unknown factors or suspected risks. In addition, strong inhibition effects of phage STP4-a were seen on both single Salmonella strain and multiple Salmonella strains in vitro, reducing 3-5 log in 30 min. Phage STP4-a could survive and keep more than 50% activity in simulated stomach or intestine environments in vitro. In terms of antimicrobial activities in chickens, pretreatment with phage STP4-a was the most efficient approach to Salmonella biocontrol, non-detectable in feces during the 14-day experimental period. Therefore, phage STP4-a was an extremely broad-host-range and safe biocontrol agent, performing its potential as a food additive or therapeutic drug in poultry industry.

Isolation, characterization, and application of a novel specific Salmonella bacteriophage in different food matrices

Application of bacteriophages to eliminate foodborne pathogens in food matrices is an emerging research field. In this study, a promising phage candidate specific for Salmonella strains was screened and its ability to decrease Salmonella counts in some food, such as milk, sausage, and lettuce, was investigated. A total of 58 Salmonella phages were isolated from a wastewater treatment plant, sewage near a river, farm ditch near a lake, and poultry house. Among them, phages LPST10, LPST18, and LPST23 were highly efficient in infecting Salmonella Typhimurium ATCC 14028. In particular, phage LPST10 could infect all the tested Salmonella Typhimurium and Salmonella Enteritidis strains with high efficiency. Bacterial challenge tests revealed that phage LPST10 and its combination with phages LPST18 and LPST23 could consistently inhibit the growth of multiple strains. Phage LPST10 presented a lysis time of about 50 min with a burst size of 101 PFU/CFU, exhibited two distinct phases in the one-step growth curve, and was stable at a pH range of 3-13 that corresponds to the pH of most of the foods (pH 3.5-7.5) and at temperatures between 30 °C and 60 °C. Transmission electron microscopy demonstrated that phage LPST10 belongs to the Siphoviridae family, with an icosahedral head with a diameter of 83.26 nm and tail length and width of approximately 144.89 nm and 10.9 nm, respectively. A significant decrease in the bacterial counts (0.92-5.12 log10 CFU/sample) and an increase in phage titers (0-2.96 log10 PFU/sample) were observed in different food matrices tested. These results demonstrated that phage LPST10 is a promising candidate for controlling Salmonella contamination in foods owing to its safety and effectiveness.

Characterisation data of simple sequence repeats of phages closely related to T7M

Coliphages T7M and T3, Yersinia phage ϕYeO3-12, and Salmonella phage ϕSG-JL2 share high homology in genomic sequences. Simple sequence repeats (SSRs) are found in their genomes and variations of SSRs among these phages are observed. Analyses on regions of sequences in T7M and T3 genomes that are likely derived from phage recombination, as well as the counterparts in ϕYeO3-12 and ϕSG-JL2, have been discussed by Lin in “Simple sequence repeat variations expedite phage divergence: mechanisms of indels and gene mutations” [1]. These regions are referred to as recombinant regions. The focus here is on SSRs in the whole genome and regions of sequences outside the recombinant regions, referred to as non-recombinant regions. This article provides SSR counts, relative abundance, relative density, and GC contents in the complete genome and non-recombinant regions of these phages. SSR period sizes and motifs in the non-recombinant regions of phage genomes are plotted. Genomic sequence changes between T7M and T3 due to insertions, deletions, and substitutions are also illustrated. SSRs and nearby sequences of T7M in the non-recombinant regions are compared to the sequences of ϕYeO3-12 and ϕSG-JL2 in the corresponding positions. The sequence variations of SSRs due to vertical evolution are classified into four categories and tabulated: (1) insertion/deletion of SSR units, (2) expansion/contraction of SSRs without alteration of genome length, (3) changes of repeat motifs, and (4) generation/loss of repeats.

Characterization of Five Podoviridae Phages Infecting Citrobacter freundii

Citrobacter freundii causes opportunistic infections in humans and animals, which are becoming difficult to treat due to increased antibiotic resistance. The aim of this study was to explore phages as potential antimicrobial agents against this opportunistic pathogen. We isolated and characterized five new virulent phages, SH1, SH2, SH3, SH4, and SH5 from sewage samples in Tunisia. Morphological and genomic analyses revealed that the five C. freundii phages belong to the Caudovirales order, Podoviridae family, and Autographivirinae subfamily. Their linear double-stranded DNA genomes range from 39,158 to 39,832 bp and are terminally redundant with direct repeats between 183 and 242 bp. The five genomes share the same organization as coliphage T7. Based on genomic comparisons and on the phylogeny of the DNA polymerases, we assigned the five phages to the T7virus genus but separated them into two different groups. Phages SH1 and SH2 are very similar to previously characterized phages phiYeO3-12 and phiSG-JL2, infecting, respectively, Yersinia enterocolitica and Salmonella enterica, as well as sharing more than 80% identity with most genes of coliphage T7. Phages SH3, SH4, and SH5 are very similar to phages K1F and Dev2, infecting, respectively, Escherichia coli and Cronobacter turicensis. Several structural proteins of phages SH1, SH3, and SH4 were detected by mass spectrometry. The five phages were also stable from pH 5 to 10. No genes coding for known virulence factors or integrases were found, suggesting that the five isolated phages could be good candidates for therapeutic applications to prevent or treat C. freundii infections. In addition, this study increases our knowledge about the evolutionary relationships within the T7virus genus.

Simple sequence repeat variations expedite phage divergence: Mechanisms of indels and gene mutations

Phages are the most abundant biological entities and influence prokaryotic communities on Earth. Comparing closely related genomes sheds light on molecular events shaping phage evolution. Simple sequence repeat (SSR) variations impart over half of the genomic changes between T7M and T3, indicating an important role of SSRs in accelerating phage genetic divergence. Differences in coding and noncoding regions of phages infecting different hosts, coliphages T7M and T3, Yersinia phage ϕYeO3-12, and Salmonella phage ϕSG-JL2, frequently arise from SSR variations. Such variations modify noncoding and coding regions; the latter efficiently changes multiple amino acids, thereby hastening protein evolution. Four classes of events are found to drive SSR variations: insertion/deletion of SSR units, expansion/contraction of SSRs without alteration of genome length, changes of repeat motifs, and generation/loss of repeats. The categorization demonstrates the ways SSRs mutate in genomes during phage evolution. Indels are common constituents of genome variations and human diseases, yet, how they occur without preexisting repeat sequence is less understood. Non-repeat-unit-based misalignment-elongation (NRUBME) is proposed to be one mechanism for indels without adjacent repeats. NRUBME or consecutive NRUBME may also change repeat motifs or generate new repeats. NRUBME invoking a non-Watson-Crick base pair explains insertions that initiate mononucleotide repeats. Furthermore, NRUBME successfully interprets many inexplicable human di- to tetranucleotide repeat generations. This study provides the first evidence of SSR variations expediting phage divergence, and enables insights into the events and mechanisms of genome evolution. NRUBME allows us to emulate natural evolution to design indels for various applications.

Characterization of phiCFP-1, a virulent bacteriophage specific for Citrobacter freundii

Citrobacter freundii, a Gram-negative bacterium, causes many opportunistic infections. Bacteriophage phiCFP-1 was isolated and characterized by its ability to lyse the multidrug-resistant clinical C. freundii strain P10159. Transmission electron microscopy showed that the phage has an icosahedral head and a short tail, making it a Podoviridae family member. In a single-step growth experiment, phiCFP-1 exhibited an eclipse period of 20 min and a burst size of 100 particles per cell. Its genome assembled as a circular molecule when genomic sequencing was completed. However, based on genome content and organization, it was categorized as a classic T7-related phage, and such phages are known to have linear genomes with direct terminal repeats. With the quick and simple method established herein, the 38,625-bp linear double-stranded DNA with 229-bp direct terminal repeats was accurately identified. The genome contained 43 putative open reading frames and no tRNA genes. Using a proteomics-based approach, seven viral and two host proteins from purified phiCFP-1 particles were identified. Comparative genomics and recombination analyzes revealed close genetic relatedness among phiCFP-1, phiYeO3-12/vB_YenP_AP5 (from Yersinia enterocolitica O3), and phiSG-JL2 (from Salmonella enterica).

Salmonella phages and prophages: genomics, taxonomy, and applied aspects

Since this book was originally published in 2007 there has been a significant increase in the number of Salmonella bacteriophages, particularly lytic virus, and Salmonella strains which have been fully sequenced. In addition, new insights into phage taxonomy have resulted in new phage genera, some of which have been recognized by the International Committee of Taxonomy of Viruses (ICTV). The properties of each of these genera are discussed, along with the role of phage as agents of genetic exchange, as therapeutic agents, and their involvement in phage typing.

Genomic investigation of lysogen formation and host lysis systems of the Salmonella temperate bacteriophage SPN9CC

To understand phage infection and host cell lysis mechanisms in pathogenic Salmonella, a novel Salmonella enterica serovar Typhimurium-targeting bacteriophage, SPN9CC, belonging to the Podoviridae family was isolated and characterized. The phage infects S. Typhimurium via the O antigen of lipopolysaccharide (LPS) and forms clear plaques with cloudy centers due to lysogen formation. Phylogenetic analysis of phage major capsid proteins revealed that this phage is a member of the lysogen-forming P22-like phage group. However, comparative genomic analysis of SPN9CC with P22-like phages indicated that their lysogeny control regions and host cell lysis gene clusters show very low levels of identity, suggesting that lysogen formation and host cell lysis mechanisms may be diverse among phages in this group. Analysis of the expression of SPN9CC host cell lysis genes encoding holin, endolysin, and Rz/Rz1-like proteins individually or in combinations in S. Typhimurium and Escherichia coli hosts revealed that collaboration of these lysis proteins is important for the lysis of both hosts and that holin is a key protein. To further investigate the role of the lysogeny control region in phage SPN9CC, a ΔcI mutant (SPN9CCM) of phage SPN9CC was constructed. The mutant does not produce a cloudy center in the plaques, suggesting that this mutant phage is virulent and no longer temperate. Subsequent comparative one-step growth analysis and challenge assays revealed that SPN9CCM has shorter eclipse/latency periods and a larger burst size, as well as higher host cell lysis activity, than SPN9CC. The present work indicates the possibility of engineering temperate phages as promising biocontrol agents similar to virulent phages.

Complete genome sequence of IME15, the first T7-like bacteriophage lytic to pan-antibiotic-resistant Stenotrophomonas maltophilia

T7-like bacteriophages are a class of virulent bacteriophages which have a clearer genetic background and smaller genomes than other phages. In addition, it grows faster and is easier to culture than other phages. At present, the numbers of available T7-like bacteriophage genomes and Stenotrophomonas maltophilia genomes are small, and IME15 is the first T7-like virulent Stenotrophomonas phage whose sequence has been reported. It shows effective lysis of S. maltophilia. Here we announce its complete genome, and major findings from its annotation are described.

Bacteriophage T7 protein kinase: Site of inhibitory autophosphorylation, and use of dephosphorylated enzyme for efficient modification of protein in vitro

Bacteriophage T7 encodes a serine/threonine-specific protein kinase that phosphorylates multiple cellular proteins during infection of Escherichia coli. Recombinant T7 protein kinase (T7PK), normally purified in phosphorylated form, exhibits a modest level of phosphotransferase activity. A procedure is described that provides dephosphorylated T7PK with an enhanced ability to phosphorylate protein substrates, including translation initiation factor IF1 and the nuclease domain of ribonuclease III. Mass spectrometric analysis identified Thr12 as the site of IF1 phosphorylation in vitro. T7PK undergoes Mg(2+)-dependent autophosphorylation on Ser216 in vitro, which also is modified in vivo. The inability to isolate the presumptive autophosphorylation-resistant T7PK Ser216Ala mutant indicates a toxicity of the phosphotransferase activity and suggests a role for Ser216 modification in limiting T7PK activity during infection.

Significance of the bacteriophage treatment schedule in reducing Salmonella colonization of poultry

Salmonella remains the major cause of food-borne diseases worldwide, with chickens known to be the main reservoir for this zoonotic pathogen. Among the many approaches to reducing Salmonella colonization of broilers, bacteriophage offers several advantages. In this study, three bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) obtained from our collection that exhibited a broad host range against Salmonella enterica serovar Enteritidis and Salmonella enterica serovar Typhimurium were characterized with respect to morphology, genome size, and restriction patterns. A cocktail composed of the three bacteriophages was more effective in promoting the lysis of S. Enteritidis and S. Typhimurium cultures than any of the three bacteriophages alone. In addition, the cocktail was able to lyse the Salmonella enterica serovars Virchow, Hadar, and Infantis. The effectiveness of the bacteriophage cocktail in reducing the concentration of S. Typhimurium was tested in two animal models using different treatment schedules. In the mouse model, 50% survival was obtained when the cocktail was administered simultaneously with bacterial infection and again at 6, 24, and 30 h postinfection. Likewise, in the White Leghorn chicken specific-pathogen-free (SPF) model, the best results, defined as a reduction of Salmonella concentration in the chicken cecum, were obtained when the bacteriophage cocktail was administered 1 day before or just after bacterial infection and then again on different days postinfection. Our results show that frequent treatment of the chickens with bacteriophage, and especially prior to colonization of the intestinal tract by Salmonella, is required to achieve effective bacterial reduction over time.

Isolation and characterization of phi AB2: a novel bacteriophage of Acinetobacter baumannii

Multidrug-resistant strains of Acinetobacter baumannii (MDRAB) are increasingly being reported worldwide. Bacteriophage therapy is a potential alternative treatment for MDR bacterial infections. Although A. baumannii infection has been experimentally treated with phages, no MDRAB-specific phage has been characterized. In this study, 10 phages with differing host ranges and lysis efficacy for MDRAB were isolated; one of these, phi AB2, was further studied. Electron microscopy revealed phi AB2 to have an isometric head (60 nm), a short tail (diameter, 9 nm; length, 11 nm) and a double-stranded DNA genome--which was resistant to digestion with several restriction endonucleases--estimated to be 40 kb by pulsed-field gel electrophoresis. Partial genome sequencing of a 2.1 kb region gave sequences resembling the tubular proteins A and B of Pseudomonas aeruginosa phage LKA1. These data suggest that phi AB2 resembles phi KMV-like phages and is a new member of the Podoviridae family. It exhibited rapid adsorption (>99% adsorbed in 8 min), a short latent period (<10 min) and a large burst size (ca. 200); moreover, it was capable of infecting a wide spectrum of A. baumannii strains, causing virtually complete lysis, indicating that phi AB2 may be a good candidate as a therapeutic/disinfectant agent to control nosocomial infections caused by MDRAB.

Complete genomic sequence of bacteriophage felix o1

Bacteriophage O1 is a Myoviridae A1 group member used historically for identifying Salmonella. Sequencing revealed a single, linear, 86,155-base-pair genome with 39% average G+C content, 131 open reading frames, and 22 tRNAs. Closest protein homologs occur in Erwinia amylovora phage φEa21-4 and Escherichia coli phage wV8. Proteomic analysis indentified structural proteins: Gp23, Gp36 (major tail protein), Gp49, Gp53, Gp54, Gp55, Gp57, Gp58 (major capsid protein), Gp59, Gp63, Gp64, Gp67, Gp68, Gp69, Gp73, Gp74 and Gp77 (tail fiber). Based on phage-host codon differences, 7 tRNAs could affect translation rate during infection. Introns, holin-lysin cassettes, bacterial toxin homologs and host RNA polymerase-modifying genes were absent.

In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli

The gut transit of T4 phages was studied in axenic mice mono-colonized with the non-pathogenic Escherichia coli strain K-12. Thirty minutes, 1 and 2 h after phage feeding, T4 phage had reached the jejunum, ileum and cecum, respectively. Phage was found in the lumen and was also associated with the mucosa. One day later no phage was detected in the feces. Compared to germ-free control animals, oral T4 phage led to a 300-fold higher fecal phage titer in mice mono-colonized with E. coli strain WG-5. The in vivo T4 phage replication was transient and reached peak fecal titers about 8 h after oral phage application followed by a rapid titer decrease over two days. Similar data were obtained in mice colonized with E. coli strain Nissle. In contrast, orally applied T7 phage experienced a massive and sustained in vivo replication in mice mono-colonized with E. coli strain WG-5 irrespective whether phage or E. coli host was applied first. T7 phage replication occurred mainly in the large intestine. High titers of T7 phage and high E. coli cell counts coexisted in the feces. The observation of only 20% T7 phage-resistant fecal E. coli colonies suggests a refuge model where phage-sensitive E. coli cells are physically or physiologically protected from phage infection in the gut. The difference between T7 and T4 with respect to gut replication might partly reflect their distinct in vitro capacity to replicate on slowly growing cells.