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PubMed1975

Prophage-dependent plasmid integration in Staphylococcus aureus.

A study has been done of reversion to thermostability of thermosensitive, replication-defective (TSR) mutant penicillinase plasmids. All three of the expected classes of reversions were encountered: back mutation, suppression, and integration. The latter class was examined in some detail and it was found that the presence of the phi 11 phophage enhance the frequency of reversion by integration some 103-fold. Prophage-dependent integration resulted in inactivation of plasmid-linked arsenate and arsenite resistance; these revertant strains gave rise to high frequency tranducing lysates where the plasmid was restored upon transduction to its original TSR state including recovery of these resistances. The integrated plasmid-prophage complexes were stable at high temperatures (43 C) but slow growing and unstable at low (32 C); loss of either plasmid or prophage restored normal growth and stability. Sometimes restoration of the plasmid to its autonomous TSR state was observed and molecular studies showed that in most cases the plasmid was essentially the same size as before integration. In some cases an excision complex was recovered that was more than twice the size of the plasmid and could have been a plasmid-phage co-integrate. Integration also took place in the absence of the ł 11 prophage. These integrations retained all plasmid-linked resistances, were stable at all temperatures, and gave rise to low frequency transducing lysates in which the integrated state was retained upon transduction. On the basis of these results it is suggested that the prophage promotes integration at or near its attachment site.

Arsenates↗
PubMed2025

Diverse defense systems and prophages in human-associated Bifidobacterium species reveal coevolutionary "arms race" dynamics.

Bacteria of the genus Bifidobacterium are pivotal for human health, especially in early life, where they dominate the gut microbiome in healthy infants. Bacteriophages, as drivers of gut bacterial composition, can affect bifidobacterial abundance. Here, we use a bioinformatics approach to explore direct interactions between human-associated Bifidobacterium spp. and prophages, as evidenced by their genomes. Analysis of 1,086 bifidobacterial genomes reveals the presence of complex systems that prevent viral invasion, with 34 defense systems and 56 subtypes detected, including several different CRISPR-Cas systems. CRISPR spacers target almost three-quarters of bifidobacteria-derived prophages, indicating dynamic interactions. At least one prophage is present in ∼67% of strains, with phages exhibiting high genomic diversity and evidence of historical recombination. These prophages encode various defense and anti-defense systems, such as anti-CRISPR genes and restriction-modification mechanisms. Overall, this investigation reveals that coevolutionary "arms race" dynamics drive genomic diversity in both bifidobacteria and their phages.

Prophages↗
PubMed2026

Prophage Activation as an Overlooked Mechanism Underlying the Biocidal Effect of Free Nitrous Acid in Sewers.

Biogenic hydrogen sulfide produced in sewer systems causes odor nuisance and concrete corrosion, necessitating effective biocidal control. Free nitrous acid (FNA) has emerged as a promising biocide, but its unclear mechanisms complicate dosage optimization and risk assessment. Here, using Desulfovibrio vulgaris as a model lysogenic bacterium, we demonstrate that low-dose FNA (0.2-4.0 mg N/L) induces bacterial inactivation via prophage activation-associated lysis in addition to chemical oxidation. Reactive nitrogen species (RNS) scavenging tests revealed that RNS-mediated oxidative stress was closely associated with prophage activation. Activated phages further infected new hosts, reducing the viability of freshly cultured D. vulgaris cells by 25.7% and increasing total phage production 15.2-fold. The phenomenon was further validated in real sewage biofilms, where increased phage production and decreased bacterial viability were observed at a low FNA dose of 0.2 mg N/L, below the dose required for cell destruction by chemical oxidation. Furthermore, metagenomic analysis of 896 sewage samples worldwide revealed that 71.9% of recovered sewage-derived microbial genomes harbor prophages, indicating a widespread genomic basis for prophage activation-mediated bacterial inactivation. Overall, this study expands current understanding of the biocidal mechanisms of FNA and contributes to the development of environmentally sustainable biocidal strategies.

Nitrous Acid↗
PubMed2026

Pan genome clustering identifies a novel mosaic prophage specific to Salmonella Enteritidis lineage associated with the invasive disease in India.

Salmonella enterica serovar Enteritidis is a leading cause of invasive non-typhoidal Salmonella (iNTS) disease globally, particularly in sub-Saharan Africa. In contrast, the epidemiology and population structure of invasive S. Enteritidis in South Asia remain poorly characterized. This study investigates the clinical presentation, phylogenetic relationships and genomic characteristics of S. Enteritidis bloodstream infections (BSIs) in India. Clinical data were collected from 101 patients with S. Enteritidis BSI between 2012 and 2022. Whole-genome sequencing was performed on representative bloodstream isolates together with isolates from non-blood clinical specimens and poultry sources. Comparative genomic analyses included phylogenetic reconstruction, invasiveness index prediction, and prophage characterization. Infants and immunosuppressed individuals were disproportionately affected by iNTS disease. Phylogenetic analysis identified four major lineages of S. Enteritidis. Most BSI isolates clustered in a previously unrecognized lineage, designated the Global Intermediate Clade, which occupied a phylogenetic position between the Global outlier and Global epidemic clades. Bayesian inference dated its most recent common ancestor to around 1789 AD (95% HPD: 1692-1941), with global circulation confirmed by European and Asian isolates. The Global Intermediate clade exhibited the second-highest invasiveness index (median 0.221, SD 0.013) after the West African clade; however, this index reflects genomic signatures associated with invasiveness and should not be interpreted as a direct measure of virulence. Poultry isolates clustered separately from the dominant bloodstream-associated lineage. Pan-genome analysis identified a lineage-specific mosaic prophage composed of modules homologous to prophages found in diverse Enterobacterales. This study provides the first detailed genomic insight into invasive S. Enteritidis in India and identifies a previously unrecognized Global Intermediate Clade associated with bloodstream infection. The distinct phylogenetic placement and genomic features of this lineage, including a lineage-specific mosaic prophage, warrant further investigation and support the need for expanded One Health genomic surveillance.

Humans↗
PubMed1978

Regional replication of the bacterial chromosome induced by derepression of prophage lambda. IV. Escape synthesis of gal operon in phage 82.

Derepression of prophage lambda in E. coli strain K12 results in constitutive synthesis of the enzymes directed by the nearby bacterial operon, gal (escape synthesis). Phage 82 fails to cause escape synthesis despite that it lysogenizes the strain K12 at the site identical to that of lambda on the host chromosome. The reason for the observed difference between 82 and lambda is studied in the light of the recent finding that escape synthesis in lambda-lysogen is closely associated to phage-promoted replication of bacterial chromosome contiguous to the prophage including gal operon (escape replication). Excision-defective mutants from 82, 82int or 82xis, do initiate escape synthesis, suggest that the prophage 82 is normally excised too quickly after induction to allow sufficient escape replication. In support of this, much more DNA hybridizable to bacterial DNA contained in lambdagal accumulates after induction if 82int than after induction of 82. Studies with various hybrid phages between 82 and lambda have suggested: 1. The occurrence of gal escape synthesis depends on the nature of the region between b2 and N in the lambda map. 2. Regions of the 82 genome on both sides of the attachment site contribute independently to prevent gal escape synthesis. Implications of these results are discussed with regard to the factors involved in the prophage excision.

Chromosomes, Bacterial↗
PubMed1978

Transfection of Escherichia coli spheroplasts: infectious lambda prophage DNA.

High mol. wt. DNA was extracted from Escherichia coli lambda lysogens and was shown to be infectious. Its infectivity was due to prophage DNA integrated into the host chromosome rather than to DNA released from mature phage particles, as established by the following criteria: the titre of infectious DNA exceeded by 100-fold the titre of infectious units present before DNA extraction; mild shear selectively reduced prophage DNA infectivity to 2% of the unsheared DNA while lambda phage DNA infectivity retained 50% of its infectivity; DNA extracted from an E. coli (lambda c857 tsxisam6) lysogen yielded 200 times as many plaques on sup+ than on sup- spheroplasts. Thus lambda prophage DNA infectivity depends on expression of the excision gene while the infectivity of non-integrated forms of lambda does not. About 10(4) genome equivalents of E. coli DNA yielded one infectious centre unit in this assay system; this high infectivity should make prophage DNA a useful marker in genetic transformation experiments.

Coliphages↗
PubMed1975

Transformation and transfection in lysogenic strains of Bacillus subtilis: evidence for selective induction of prophage in competent cells.

Lysogenic strains of Bacillus subtilis 168 were reduced in their level of transformation as compared to non-lysogenic strains. The level of transformation decreased even further if the competent lysogenic cells were allowed to incubate in growth media prior to selection on minimal agar. This reduction in the frequency of transformation was attributable to the selective elimination of transformed lysogenic cells from the competent population. Concurrent with the decrease in the number of transformants from a lysogenic competent population was the release of bacteriophage by these cells. The lysogenic bacteria demonstrated this dramatic release of bacteriophage only if the cells were grown to competence. Both the selective elimination of transformed lysogens and the induction of prophage was prevented by the inhibition of protein synthesis. Additionally, competent lysogenic cells released significantly higher amounts of exogenous donor transforming deoxyribonucleic acid than did competent non-lysogenic cells or competent lysogenic cells incubated with erythromycin. These data establish that the induction of the prophage from the competent lysogenic cells was responsible for the selective elmination of the lysogenic transformants. A model is presented that accounts for the induction of the prophage from competent lysogenic bacteria via the induction of a repair system. It is postulated that a repair system is induced or derepressed by the accumulation of gaps in the chromosomes of competent bacteria. This hypothetical enzyme(s) is ultimately responsible for the induction of the prophage and the selective elimination of transformants.

Azo Compounds↗
PubMed1975

[The influence of several prophages on the genetic behavior of Flexner dysentery bacteria].

In conjugation experiments of Escherichia coli K-12 Hfr strains and converted clones of Shigella flexneri var. y(-:3,4) that had acquired the capacity to synthesize type of antigens IV or V it is confirmed that the locus linked to lac-pro region in Sh. flexneri chromosome called Tp locus is a site of an attachment of prophages responsible for certain type specific antigens. Lac+ hybrids of the clone converted by phage IV lost the type specific antigen IV with the frequency comparable with the loss of the aforementioned antigen by wild strains of Sh. flexneri ser 4 in similar experiments carried out previously (90,8% and 97% respectively). Lac+ hybrids of the clones converted by phage V did not lose the type antigen that corresponded to the behaviour of wild strains of serotype 5b (V: 7,8) with double lysogenicity. It was shown that the clones converted by the aforementioned phage V had acquired an immunity not only to phage V, but to phage 7,8 as well. An independent segregation of immunity to phages V and 7,8 in lac+ hybrids of the converted clone was observed. It indicates that donor strain NTCC 595/52 carries two prophages, V and "defect" 7,8 (not expressing factor 7,8). A maintenance of antigen V observed in lac+ hybrids of the converted clone in this case confirms previous suggestions that an attachment of prophage 7,8 creates a state of some inhomology in this region disturbing the recombination process. The converting phage V isolated from the strain NTCC 595/52 is probably recombinant. An analysis of the hybrid classes allows to suggest the following approximate order of markers of the prophage on the chromosome of the converted clone: aV--imm V--imm 7,8--lac.

Bacteriophages↗
PubMed1978

Control of lambda repressor prophage and establishment transcription by the product of gene tof.

Control of expression of the bacteriophage lambda (lambda) repressor was studied by measuring repressor transcription in noninduced and derepressed lambda lysogens. Three distinct modes of leftward transcription were observed from cI and the adjacent genes associated with the control of repressor synthesis: The prophage or maintenance mode Prm-cI-rex-ti repressor transcript occurs from repressed lysogens; the oop (Po-oop-to) transcript, and the lit (lit-ti) RNA, from the distal half of gene rex, both occur from induced tof+ prophage; the repressor establishment mode of transcription is observed throughout the rex-cI-tof-y-cII-oop interval between Po and ti from induced tof- prophage. The overall level of establishment mRNA synthesis is partially template dependent. However, the actual initiation step for repressor establishment transcription requires the participation of the lambda cIII, cII products, and also either requires the activity of Escherichia coli replication proteins, or is triggered by a replication initiation event. The cII cIII products do not positively stimulate de novo initiation of establishment transcription, but rather act after an initial replication-dependent step. Initiation of the establishment mode of repressor transcription is totally inhibited by more than 125-fold, in an all or none fashion, by the lambda antirepressor (Tof), the product of gene tof (cro). Since Tof only reduces the in vivo rightward transcription of cII from Pr by about 2-fold, we suggest that Tof inhibits repressor establishment transcription by either uncoupling the replication and cII-cIII dependent events, or by inhibiting the activity rather than the expression of the cIII, cII products. Our results do not fully support either of the present hypotheses that establishment transcription is initiated from the hypothetical Pre promoter in the y-interval, or arises through antitermination of the oop RNA. Since the initiation and control of the establishment mode of repressor transcription parallels the control of lit RNA synthesis, we propose a common mechanism underlies the initiation of these transcripts.

Coliphages↗
PubMed1977

Prophage induction in Escherichia coli K12 cells deficient in DNA polymerase I.

The induction of prophage lambda by ultraviolet light has been measured in E. coli K12 lysogenic cells deficient in DNA polymerase I. The efficiency of the induction process was greater in polA1 polC(dnaE) double mutants incubated at the temperature that blocks DNA replication than in polA+ polC single mutants. Similarly, the polA1 mutation sensitized tif-promoted lysogenic induction in a polA1 tif strain at 42 degrees. In strains bearing the polA12 mutation, which growth normally at 30 degrees, induction of the prophage occurred after the shift to 42 degrees. It is concluded that dissapearance of the DNA polymerase I activity leads to changes in DNA replication that are able, per se, trigger the prophage induction process.

Coliphages↗
PubMed1976

Prophage lambda induction of Escherichia coli K12 envA uvrB: a highly sensitive test for potential carcinogens.

A simple, inexpensive, and sensitive test for potential carcinogens based upon the property of carcinogens to induce prophage lambda is described. By using chemicals activated with microsomal enzymes and E. coli K12 permeable (envA) tester bacteria also deficient in DNA repair (uvrB), the range of carcinogens detected in a lysogenic induction test (inductest) has been extended. We have provided the evidence that, after activation, carcinogenic polycyclic hydrocarbons such as benzo[a5pyrene and 7,12-dimethylbenz[a]anthracene induce prophage lambda. Three variants of the test have been developed (inductests I, II, and III), which are as sensitive as the mutagenicity test of Ames et al. [Ames, B. N., McCann, J. and Yamasaki, E. (1975) Mutat. Res. 31, 347-364]. Inductests II and III provide a quantitative estimation of the inducing activity of a carcinogen. With the latter test, one can determine: (i) the cellular toxic effect of a carcinogen and (ii) the kinetics of appearance and disappearance of active metabolites. For two series of chemicals, aflatoxins and benz[a]anthracenes, there is a good correlation between their carcinogenic activity in rodents and their prophage inducing activity in bacteria. The fact that the majority of the cell population is induced makes it possible to test the inducing activity of carcinogens at the biochemical level, e.g., by measuring lambda repressor inactivation.

Biotransformation↗
PubMed1977

Heat sensitivity of Haemophilus influenzae containing defective prophage.

Strains of Haemophilus influenzae that carry a defective prophage are more sensitive to heat than is a strain that does not, even in the presence of a rec-1 mutation, which normally renders prophage noninducible. The prophage of HP1c1, a nondefective phage, does not affect the heat sensitivity.

Bacteriophages↗
PubMed1978

Plasmid cointegrates of Flac and lambda prophage.

Fifteen cointegrates of the plasmid Flac and prophage lambda that had suffered no detectable change in plasmid phenotype were isolated and characterized. The locations of the prophage insertions were determined by genetic analysis of deletion mutants obtained from each cointegrate as survivors of growth at 42 degrees C. In 11 cointegrates, the prophage was inserted between traI and lac, although probably in more than one location; in 3 others, it was on one side or the other of lac; and in 1 it was between lac and pif. Deletions covering all or part of the transfer region, as well as of lac and of pif, were obtained in the course of this analysis. Deletion mutants that had lost all known transfer genes were also oriT, but they retained the capacity to recircularize after transfer. Attempts were made to isolate lambda transducing phages for nearby plasmid genes from the cointegrates, and lambdaptraGD, lambdaptraD, lambdaptraI, and lambdadtraDI phages were obtained.

Coliphages↗
PubMed1976

Specialized transduction by bacteriophage P22 in Salmonella typhimurium: genetic and physical structure of the transducing genomes and the prophage attachment site.

P22pro-1 and P22pro-3 are specialized transducing derivatives of phage P22 that carry the proA and proB genes of Salmonella typhimurium. These genes lie immediately adjacent to the prophage attachment site on the bacterial chromosome. By examining DNA heteroduplexes in the electron microscope, we found that DNA molecules from P22pro-1 and P22pro-3 each contain a substitution which adds length to the composite genome making the intracellular replicated genome too long to fit into a single phage particle. In this respect, and in many of their biological properties, the proline-transducing phages resemble P22Tc-10, another specialized transducing phage with an oversize, intracellular replicated genome which carries a tetracycline-resistance determinant from an R-factor.--Unlike P22Tc-10, however, P22pro-1 and P22pro-3 fail to integrate normally during lysogenizing infections, even when provided with all known integration functions. These results suggest that the proline substitutions have created a defect in the phage attachment site and suggest that the Campbell model for the formation of specialized transducing phages is applicable to phage P22 with the additional feature that oversize genomes can be produced and propagated.--A physical and genetic map of the P22 genome near the prophage attachment site was constructed which shows that the insertion from the R-factor in P22Tc-10 is not at the attachment site: it is therefore unlikely that P22Tc-10 was formed in an abnormal prophage excision event as envisioned in the Campbell model, but was instead the result of a direct translocation from the R-plasmid to P22.

Chromosome Mapping↗
PubMed2026

A host-encoded prophage targets a Candidate Phyla Radiation bacterium and shapes episymbiotic interactions.

The Patescibacteriota, also known as the Candidate Phyla Radiation (CPR), represent a large lineage of ultrasmall bacteria with highly reduced genomes and obligate dependence on bacterial hosts. Although genomic analyses have revealed CRISPR-Cas and restriction-modification systems in many CPR genomes, no cognate bacteriophages (phages) have been isolated, leaving CPR-phage interactions unexplored. Nanosynbacter lyticus TM7x, the first cultivated CPR bacterium, grows episymbiotically on its host, Schaalia odontolytica XH001, in the human oral microbiome. Here, we identify Xhp1, an inducible prophage of XH001 that is preferentially activated during episymbiosis with TM7x. Released Xhp1 particles infect prophage-free XH001 via distinct strategies determined by host growth mode, establishing lysogeny under planktonic conditions but driving lytic infection during surface-associated growth. Xhp1 also binds efficiently to TM7x and exhibits limited infection under the conditions tested, indicating direct phage-CPR interactions. Importantly, TM7x modulates Xhp1 availability in a spatially dependent manner. In planktonic culture, free-floating TM7x reduces lysogenic conversion of XH001ΔXhp1, consistent with TM7x acting as a phage sink that lowers effective phage concentration. In contrast, during surface-associated growth, TM7x increases XH001ΔXhp1 susceptibility to lytic infection, likely by locally concentrating phage particles within a constrained niche. These results demonstrate that CPR bacteria can regulate viral encounter rates through spatial organization. In spatially structured environments such as oral biofilms, such modulation may shape infection dynamics and community structure. Together, this work characterizes the first CPR-targeting phage and reveals a an important role for phages in CPR-host bacteria interactions.

Prophages↗
PubMed2025

PDP-Miner: an AI/ML tool to detect prophage tail proteins with depolymerase domains across thousands of bacterial genomes.

MOTIVATION: Antibiotic resistance is predicted to become the leading cause of human mortality by 2050. Despite this, no other major antibiotic class has been approved for medical use since 1987. Nevertheless, phage tail proteins offer a promising alternative, given their depolymerase activity toward outer membrane polysaccharides. Several pathogenic bacteria harbor prophages, thus making these prophages' molecular target already known. RESULTS: We therefore developed a wrapper for an existing machine learning-based phage depolymerase prediction tool (Depolymerase-Predictor), called PDP-Miner, which annotates phage tail proteins ab initio, detects depolymerase activity within this candidate protein subset, and then performs post-hoc validation by annotating protein domains thereby allowing the user to investigate for protein domains indicative of depolymerase activity. This tool allowed identification of 10 high confidence phage depolymerase gene candidates across all 1294 Pseudomonas genomes available on the International Pseudomonas Consortium Database while also accurately reporting depolymerases in known phage genomes, similarly to other software like PhageDPO or DepoScope. AVAILABILITY AND IMPLEMENTATION: Source code, test datasets and documentation are freely available for download at http:///www.github.com/jeffgauthier/pdpminer. This software is free and open source under the GNU General Public License v3.0.

Prophages↗
PubMed2026

LAMBDA: a prophage detection benchmark for genomic language models.

Transformer-based genomic sequence models represent an emerging frontier in computational biology. Yet, their embeddings have not yet shown the same level of predictive power as natural and protein language models, highlighting a gap between current implementations and theoretical promise. Existing benchmarks for DNA language models primarily focus on classifying regulatory elements in eukaryotic genomes, leaving open the fundamental question of whether these models learn sequence-level features across whole genomes. We introduce LAMBDA, a benchmark designed to rigorously evaluate genome language model embeddings through phage-bacteria sequence discrimination across four categories of increasing complexity: probing tasks, fine-tuning assessments, diagnostic tests, and genome-wide prophage detection. Our comprehensive analysis of current genomic language models provides insight into the importance of training data selection relative to model size, the need for domain-specific training, and the capabilities and limitations of genomic language models for detecting prophage sequences. This benchmark represents a challenging genomic annotation task in the bacterial domain and addresses a key computational problem with direct relevance to microbiology and medicine.

Prophages↗
PubMed2026

LAMBDA: A Prophage Detection Benchmark for Genomic Language Models.

Transformer-based genomic sequence models represent an emerging frontier in computational biology. Yet, their embeddings have not yet shown the same level of predictive power as natural and protein language models, indicating a gap between current implementations and theoretical promise. Existing benchmarks for DNA language models primarily focus on classifying regulatory elements in eukaryotic genomes, leaving open the fundamental question of whether these models learn sequence-level features across whole genomes. We introduce LAMBDA, a benchmark designed to rigorously evaluate genome language model embeddings through phage-bacteria sequence discrimination across four categories of increasing complexity: probing tasks, fine-tuning assessments, diagnostic tests, and genome-wide prophage detection. Our comprehensive analysis of current genomic language models provides novel insights into the importance of training data quality relative to model size, the need for domain-specific training, and the application of genomic language models for detecting prophage sequences. This benchmark represents a challenging genomic annotation task in the bacterial domain and addresses a key computational problem with direct relevance to microbiology and medicine.

DNA language model↗