Aim: This study was carried out in order to evaluate the potential of bacteriophages in controlling tomato bacterial wilt disease caused by Ralstonia solanacearum. Study design: A purposive sampling technique was used...Aim: This study was carried out in order to evaluate the potential of bacteriophages in controlling tomato bacterial wilt disease caused by Ralstonia solanacearum. Study design: A purposive sampling technique was used to collect samples from bacterial wilt hot spot tomato growing areas in Kenya. Place and duration of study: The research work was done at Jomo Kenyatta University of Agriculture and Technology, between June 2020 and July 2021. Methodology: Thirty diseased plants and corresponding soil were collected from five counties, Nyeri, Kajiado, Nyandarua, Kiambu and Taita Taveta. Bacteria were isolated and characterized, and then used as hosts to propagate the phages. Tests done were gram stain, oxidation test, potassium hydroxide solubility test, H2S production test catalase test, NaCl test and sugar fermentation test. Molecular analysis and phenotyping were also done in order to identify the bacteria. The bacteriophages were then isolated through a double overlay method using R. solanacearum as the host. They were characterized and assayed in a greenhouse setting to determine their effectiveness in controlling bacterial wilt. Results: Six host bacteria were isolated and all belonged to biovar II. Four phages were observed based on morphology. Upon characterization the phages were stable at 30˚C, PH range between 6 - 7 and tolerance of more than an hour under UV light. In the greenhouse experiment, treatment of plants with bacteriophage prevented wilting after subsequent inoculation with the pathogen. A bacteriophage mix of SN1 and WT1 were used for efficacy tests due to their efficiency in plating and infection. Phage SN1 and WT1 exhibited high lytic activity and relatively high thermotolerance and acid tolerance, thereby showing great potential in the biocontrol of bacterial wilt infection across a variety of conditions. Conclusion: The results obtained in this research show that bacteriophages offer potential for the biocontrol of bacterial wilt.展开更多
Recognizing essential proteins within bacteriophages is fundamental to uncovering their replication and survival mechanisms and contributes to advances in phage-based antibacterial therapies.Despite notable progress,e...Recognizing essential proteins within bacteriophages is fundamental to uncovering their replication and survival mechanisms and contributes to advances in phage-based antibacterial therapies.Despite notable progress,existing computational techniques struggle to represent the interplay between sequence-derived and structuredependent protein features.To overcome this limitation,we introduce GLM-EP,a unified framework that fuses protein language models with equivariant graph neural networks.Bymerging semantic embeddings extracted from amino acid sequences with geometry-aware graph representations,GLM-EP enables an in-depth depiction of phage proteins and enhances essential protein identification.Evaluation on diverse benchmark datasets confirms that GLM-EP surpasses conventional sequence-based and independent deep-learning methods,yielding higher F1 and AUROC outcomes.Component-wise analysis demonstrates that GCNII,EGNN,and the gated multi-head attention mechanism function in a complementary manner to encode complex molecular attributes.In summary,GLM-EP serves as a robust and efficient tool for bacteriophage genomic analysis and provides valuable methodological perspectives for the discovery of antibiotic-resistance therapeutic targets.The corresponding code repository is available at:https://github.com/MiJia-ID/GLM-EP(accessed on 01 November 2025).展开更多
To formulate the optimal strategy of combatting bacterial biofilms,in this review we update current knowledge on the growing problem of biofilm formation and its resistance to antibiotics which has spurred the search ...To formulate the optimal strategy of combatting bacterial biofilms,in this review we update current knowledge on the growing problem of biofilm formation and its resistance to antibiotics which has spurred the search for new strategies to deal with this complication.Based on recent findings,the role of bacteriophages in the prevention and elimination of biofilm-related infections has been emphasized.In vitro,ex vivo and in vivo biofilm treatment models with single bacteriophages or phage cocktails have been compared.A combined use of bacteriophages with antibiotics in vitro or in vivo confirms earlier reports of the synergistic effect of these agents in improving biofilm removal.Furthermore,studies on the application of phage-derived lysins in vitro,ex vivo or in vivo against biofilm-related infections are encouraging.The strategy of combined use of phage and antibiotics seems to be different from using lysins and antibiotics.These findings suggest that phages and lysins alone or in combination with antibiotics may be an efficient weapon against biofilm formation in vivo and ex vivo,which could be useful in formulating novel strategies to combat bacterial infections.Those findings proved to be relevant in the prevention and destruction of biofilms occurring during urinary tract infections,orthopedic implant-related infections,periodontal and peri-implant infections.In conclusion,it appears that most efficient strategy of eliminating biofilms involves phages or lysins in combination with antibiotics,but the optimal scheme of their administration requires further studies.展开更多
The year 2015 marks 100 years since Dr.Frederick Twort discovered the"filterable lytic factor",which was later independently discovered and named "bacteriophage" by Dr.Felix d’Herelle.On this memo...The year 2015 marks 100 years since Dr.Frederick Twort discovered the"filterable lytic factor",which was later independently discovered and named "bacteriophage" by Dr.Felix d’Herelle.On this memorable centennial,it is exciting to see a special issue published by Virologica Sinica on Phages and Therapy.In this issue,readers will not only fi nd that bacteriophage research is a展开更多
Acinetobacter baumannii causes serious infections especially in immunocompromised and/or hospitalized patients.Several A.baumannii strains are multidrug resistant and infect wounds,bones,and the respiratory tract.Curr...Acinetobacter baumannii causes serious infections especially in immunocompromised and/or hospitalized patients.Several A.baumannii strains are multidrug resistant and infect wounds,bones,and the respiratory tract.Current studies are focused on finding new effective agents against A.baumannii.Phage therapy is a promising means to fight this bacterium and many studies on procuring and applying new phages against A.baumannii are currently being conducted.As shown in animal models,phages against multidrug-resistant A.baumannii may control bacterial infections caused by this pathogen and may be a real hope to solve this dangerous health problem.展开更多
Soft rot is an economically significant disease in potato and one of the major threats to sustainable potato production.This study aimed at isolating lytic bacteriophages and evaluating methods for and the efficacy of...Soft rot is an economically significant disease in potato and one of the major threats to sustainable potato production.This study aimed at isolating lytic bacteriophages and evaluating methods for and the efficacy of applying phages to control potato soft rot caused by Pectobacterium carotovorum.Eleven bacteriophages isolated from soil and water samples collected in Wuhan,China,were used to infect P.carotovorum host strains isolated from potato tubers showing soft rot symptoms in Nakuru county,Kenya.The efficacy of the phages in controlling soft rot disease was evaluated by applying individual phage strains or a phage cocktail on potato slices and tubers at different time points before or after inoculation with a P.carotovorum strain.The phages could lyse 20 strains of P.carotovorum,but not Pseudomonas fluorescens control strains.Among the 11 phages,Pectobacterium phage Wc5r,interestingly showed cross-activity against Pectobacterium atrosepticum and two phage-resistant P.carotovorum strains.Potato slice assays showed that the phage concentration and timing of application are crucial factors for effective soft rot control.Phage cocktail applied at a concentration of 1×10^9 plaque-forming units per milliliter before or within an hour after bacterial inoculation on potato slices,resulted in>90%reduction of soft rot symptoms.This study provides a basis for the development and application of phages to reduce the impact of potato soft rot disease.展开更多
Laban jameed is a dried salty dairy product obtained by fermentation of milk using a complex population of lactic acid bacteria. Jameed is considered a traditional food product in most eastern Mediterranean countries ...Laban jameed is a dried salty dairy product obtained by fermentation of milk using a complex population of lactic acid bacteria. Jameed is considered a traditional food product in most eastern Mediterranean countries and is usually made from sheep or cow milk. The aim of this study was to assess phage contamination of jameed dairy product. Two phages were isolated: one from sheep milk jameed (PPUDV) and the other from cow milk jameed (PPURV). Each of the two bacteriophages was partially characterized. The PPUDV phage was identified as a single stranded DNA virus with an approximately 20 kb genome that was resistant to RNase, whereas PPURV phage possessed a double stranded RNA genome of approximately 20 kb and was resistant to DNase. The phage bacterial strain hosts were identified as Lactobacillus helveticus and Bacillus amyloliquefaciens for PPUDV and PPURV, respectively. One step growth curve using a double layer plaque assay test was carried out to monitor the phage life cycle after host infection. PPUDV showed a latent period of about 36 h, burst period of 70 h and a burst size of about 600 Plaque Forming Units (PFU) per infected cell. PPURV phage showed a latent period of about 24 h, burst period of 47 h and a burst size of about 700 PFU per infected cell. SDS-PAGE analysis of total viral proteins showed at least three major bands (27, 40, and 45 kDa) for PPUDV. This is the first study to report the isolation of both DNA and RNA bacteriophages from laban jameed. This study adds new insights into the complexity of dairy contamination and fermentation microbiology of the jameed revealing the existence of two viral genomes in this highly dried and salty dairy product.展开更多
The continuous battle between humans and the multitude of pathogenic microorganisms in the environment has sought relief in the form of antimicrobials. But the counter attack by pathogenic organisms in the form of mul...The continuous battle between humans and the multitude of pathogenic microorganisms in the environment has sought relief in the form of antimicrobials. But the counter attack by pathogenic organisms in the form of multidrug resistance, acquired by various mechanisms such as transformation, transposition, conjugation and transduction is a major reason for concern. Bacteriophages have contributed in a significant way to dissemination of genes encoding antimicrobial resistance, heavy metal resistance and virulence factors through the phenomenon of transduction. This review aims at compiling information about the different mechanisms by which bacteriophages aid in transferring genes involved in antimicrobial resistance to Escherischia coli in various environments.展开更多
Hepatitis B virus(HBV) infection is a major global health challenge leading to serious disorders such as cirrhosis and hepatocellular carcinoma. Currently, there exist various diagnostic and therapeutic approaches for...Hepatitis B virus(HBV) infection is a major global health challenge leading to serious disorders such as cirrhosis and hepatocellular carcinoma. Currently, there exist various diagnostic and therapeutic approaches for HBV infection. However, prevalence and hazardous effects of chronic viral infection heighten the need to develop novel methodologies for the detection and treatment of this infection. Bacteriophages, viruses that specifically infect bacterial cells, with a long-established tradition in molecular biology and biotechnology have recently been introduced as novel tools for the prevention, diagnosis and treatment of HBV infection. Bacteriophages, due to tremendous genetic flexibility, represent potential to undergo a huge variety of surface modifications. This property has been the rationale behind introduction of phage display concept. This powerful approach, together with combinatorial chemistry, has shaped the concept of phage display libraries with diverse applications for the detection and therapy of HBV infection. This review aims to offer an insightful overview of the potential of bacteriophages in the development of helpful prophylactic(vaccine design), diagnostic and therapeutic strategies for HBV infection thereby providing new perspec-tives to the growing field of bacteriophage researches directing towards HBV infection.展开更多
In recent years, the development of antibiotic resistant bacteria has become a global concern which has prompted research into the development of alternative disease control strategies for the swine industry. Bacterio...In recent years, the development of antibiotic resistant bacteria has become a global concern which has prompted research into the development of alternative disease control strategies for the swine industry. Bacteriophages （viruses that infect bacteria） offer the prospect of a sustainable alternative approach against bacterial pathogens with the flexibility of being applied therapeutically or for biological control purposes. This paper reviews the use of phages as an antimicrobial strategy for controlling critical pathogens including Salmonella and Eschefich[a coli with an emphasis on the application of phages for improving performance and nutrient digestibility in swine operations as well as in controlling zoonotic human diseases by reducing the bacterial load spread from pork products to humans through the meat,展开更多
In the post-antibiotic era,the overuse of antimicrobials has led to a massive increase in antimicrobial resistance,leaving medical doctors few or no treatment options to fight infections caused by superbugs.The use of...In the post-antibiotic era,the overuse of antimicrobials has led to a massive increase in antimicrobial resistance,leaving medical doctors few or no treatment options to fight infections caused by superbugs.The use of bacteriophages is a promising alternative to treat infections,supplementing or possibly even replacing antibiotics.Using phages for therapy is possible,since these bacterial viruses can kill bacteria specifically,causing no harm to the normal flora.However,bacteria have developed a multitude of sophisticated and complex ways to resist infection by phages,including abortive infection and the clustered regularly interspersed short palindromic repeats(CRISPR)/CRISPR-associated(Cas)system.Phages also can evolve and acquire new anti-defense strategies to continue predation.An in-depth exploration of both defense and anti-defense mechanisms would contribute to optimizing phage therapy,while we would also gain novel insights into the microbial world.In this paper,we summarize recent research on bacterial phage resistance and phage anti-defense mechanisms,as well as collaborative win-win systems involving both virus and host.展开更多
Bacteriophages represent a rich and unique resource of anti-infectives to counter the global problem of antibiotic resis- tance. In this work, we assessed the bactericidal activity of two virulent staphylococcal phage...Bacteriophages represent a rich and unique resource of anti-infectives to counter the global problem of antibiotic resis- tance. In this work, we assessed the bactericidal activity of two virulent staphylococcal phages, K and 44AHJD, against S. aureus isolates of clinical significance, and tested their efficacy in vivo. The phage cocktail lysed >85% of the clinical isolates tested. Both the phages were purified by ion-exchange column chromatography following propagation in bioreactors. The purity profiles of the ion-exchange purified phages were compared with those of phages purified using cesium chloride density gradient ultracentrifugation, and infectiousness of the purified phages was confirmed by plaque forming assay. The in vivo efficacy of a phage cocktail was evaluated in an experimental murine nasal colonization model, which showed that the phage cocktail was efficacious. To our knowledge, this is the first report of phage use in an in vivo model of nasal carriage.展开更多
Environmental mycobacteria are capable of forming biofilms in low-nutrient environments, and these biofilms may act as reservoirs for opportunistic infections. The purpose of this study was to determine if bacteriopha...Environmental mycobacteria are capable of forming biofilms in low-nutrient environments, and these biofilms may act as reservoirs for opportunistic infections. The purpose of this study was to determine if bacteriophages could disrupt existing biofilms of acid-fast staining Mycobacterium smegmatis. Using the MBEC 96-well plastic peg assay system, M. smegmatis biofilms were created and then tested for their stability in the presence of mycobacteriophages isolated from a Minnesota sphagnum peat bog. All phages tested were lytic and were observed to have weak, intermediate, and strong abilities to disrupt M. smegmatis biofilms. The formation of biofilms was severely impaired in the presence of mycobacteriophages. Phage treatment was also shown to augment?M. smegmatis biofilm disruption by mechanical forces of sonication or water flow. Our study shows that, as with biofilms of Gram-positive and Gram-negative bacteria, mycobacterial biofilms are also susceptible to destruction by bacteriophages.展开更多
The minimum inhibitory concentration (MIC) is the concentration at which an antibacterial agent experiences the complete inhibition of organism growth. Bacteriophages represent a rich and unique resource of anti-infec...The minimum inhibitory concentration (MIC) is the concentration at which an antibacterial agent experiences the complete inhibition of organism growth. Bacteriophages represent a rich and unique resource of anti-infectives to counter the growing world-wide problem of antibiotic resistance. In this study, we compared the host range of lytic bacteriophages and temperate phagesbelonging to various genera, namely Staphylococcus, E. coli and Salmonella, with a range of clinical isolates using two methods: the classical agar overlay method and a newly developed MIC method. MIC was only observed with isolates that were susceptible to phage infection, which correlated with the agar overlay assay, whereas no MIC was detected with isolates that were resistant to phage infection. The simple MIC method was useful in determining phage adsorption and host range, and detecting possible prophage contamination in phage preparations. Interestingly, this method was also applicable to strain differentiation through phage susceptibility testing using a 96-well, high throughput format that proved to be easy, cost-effective, fast and reliable.展开更多
As our understanding of the role of the gut microbiome in human diseases deepens,precision engineering of the gut microbiome using bacteriophages has gained significant attention.Herein,we review the recent advances i...As our understanding of the role of the gut microbiome in human diseases deepens,precision engineering of the gut microbiome using bacteriophages has gained significant attention.Herein,we review the recent advances in bacteriophage-mediated modulation of the gut microbiome,discuss approaches at the ecological and genetic levels,and summarize the challenges and strategies pertinent to each level of intervention.Drawing on the structural attributes of bacteriophages in the context of precision engineering,we examined the latest developments in the field of phage administration.Gaining a nuanced understanding of microbiome manipulation will yield tailored strategies and technologies.This could revolutionize the prevention and treatment of diseases linked to gut pathogens and offer new avenues for the therapeutic use of bacteriophages.展开更多
Traditional fluorescence immunoassays are often hindered by false negatives or quantification inaccuracies,especially at high target concentrations,due to the aggregation-caused quenching effect of fluorescent indicat...Traditional fluorescence immunoassays are often hindered by false negatives or quantification inaccuracies,especially at high target concentrations,due to the aggregation-caused quenching effect of fluorescent indicators.This study introduces a novel fluorescence immunoassay strategy that leverages the spontaneous amino-yne click reaction to covalently assemble activated alkyne-based luminogens with aggregation-induced emission characteristics(AIEgens)onto the surface of bifunctional M13 bacteriophages,thereby facilitating efficient“lighting-up”fluorescence signal output in conjunction with magnetic-mediated immunorecognition.To further enhance the load of activated alkyne-based AIEgens and improve the fluorescence“lighting-up”efficiency,M13 bacteriophages were engineered to display varying numbers of surface-exposed lysine residues.This was achieved by inserting different quantities of lysines between the signal peptide and the amino acid sequence of the pVIII protein via a point mutation strategy.Benefiting from the synergy of AIEgen stacking-enhanced fluorescence output and M13 bacteriophagedriven signal amplification,the developed“lighting-up”immunoassay enabled highly sensitive and rapid detection of targets,from smallmolecules to pathogenic microorganisms.This work provides valuable insights into the design of“lighting-up”AIEgens for enhancing fluorescence immunoassays.Moreover,the proposed strategy offers great versatility,allowing it to be readily adapted to detect other targets simply by pairing the target with the M13 bacteriophages.展开更多
Background： The therapeutic potential of bacteriophages has been debated since their first isolation and characterisation in the early 20th century. However, a lack of consistency in application and observed efficacy...Background： The therapeutic potential of bacteriophages has been debated since their first isolation and characterisation in the early 20th century. However, a lack of consistency in application and observed efficacy during their early use meant that upon the discovery of antibiotic compounds research in the field of phage therapy quickly slowed. The rise of antibiotic resistance in bacteria and improvements in our abilities to modify and manipulate DNA, especially in the context of small viral genomes, has led to a recent resurgence of interest in utilising phage as antimicrobial therapeutics. Results： In this article a number of results from the literature that have aimed to address key issues regarding the utility and efficacy of phage as antimicrobial therapeutics utilising molecular biology and synthetic biology approaches will be introduced and discussed, giving a general view of the recent progress in the field. Conclusions： Advances in molecular biology and synthetic biology have enabled rapid progress in the field of phage engineering, with this article highlighting a number of promising strategies developed to optimise phages for the treatment of bacterial disease. Whilst many of the same issues that have historically limited the use of phages as therapeutics still exist, these modifications, or combinations thereof, may form a basis upon which future advances can be built. A focus on rigorous in vivo testing and investment in clinical trials for promising candidate phages may be required for the field to truly mature, but there is renewed hope that the potential benefits of phage therapy may finally be realised.展开更多
Vibrio harveyi is a Gram-negative,rod-shaped,polar flagellate,facultatively anaerobic,halophilic,bioluminescent marine bacteria that belongs to the family of Vibrionaceae,class,Gammaproteobacteria.This pathogenic orga...Vibrio harveyi is a Gram-negative,rod-shaped,polar flagellate,facultatively anaerobic,halophilic,bioluminescent marine bacteria that belongs to the family of Vibrionaceae,class,Gammaproteobacteria.This pathogenic organism is responsible for various diseases of vertebrates and invertebrates in marine habitats,including shrimp aquaculture.Various symptoms like lesions,gastroenteritis,skin ulcers,eye lesions,and tail rot have been observed due to V.harveyi infection.The pathogenic-ity mechanism of V.harveyi involves endotoxin lipopolysaccharide,extracellular proteases,and bacteriophage interaction.Hemolysin genes encoded extracellular hemolysin-like phospholipase B toxin could inactivate fish species via the caspase inactivation pathway,ultimately leading to apoptosis.In addition,VBNC(viable but nonculturable)cells are another basis of vibriosis outbreaks in the shrimp aquaculture sector.The extensive amount of antibiotic use promotes the generation of multidrug-resistant strains.Therefore,as an alternative strategy to combat V.harveyi infection,bacteriophages are utilized as a biocontrol agent.However,there is a lack of research on the immobilization and development of encapsulation strategies of V.harveyi-infecting bacteriophages which need to be studied further.In conclusion,the pathogenicity of V.harveyi and its biocontrol by bacteriophages has been documented in this review.展开更多
The bacteriophage clones which can bind with shiga toxin B subunit (StxB) and inhibit cytotoxicity of shiga toxin were obtained by using antibody capturing method from a 15-mer random peptide library displayed on the ...The bacteriophage clones which can bind with shiga toxin B subunit (StxB) and inhibit cytotoxicity of shiga toxin were obtained by using antibody capturing method from a 15-mer random peptide library displayed on the surface of bacteriophage fd. Among them, one peptide encoded by the random DNA region of a selected bacteriophage (A12) was synthesized and tested in vitro and in vivo, where the peptide competed with the receptor of shiga toxin to bind StxB, and inhibited the cytotoxicity and enterotoxicity of shiga toxin. The peptide can also block other apparently unrelated StxB binding bacteriophage (A3), which suggests that there are overlapping StxB interaction sites for those ligands with different sequences. The results provide a demonstration of bacteriophage display to screen peptide ligands for a small and/or unable biotinylated molecule by antibodies-capturing strategy, and take the lead for the development of receptor antagonists for shiga toxin.展开更多
Sustainability is a leading trend in the context of food production.Additionally,consumers increasingly demand safer and less-processed products.Among the different technologies used to maintain the quality and extend...Sustainability is a leading trend in the context of food production.Additionally,consumers increasingly demand safer and less-processed products.Among the different technologies used to maintain the quality and extend the shelf-life of fresh and minimally-processed food,natural antimicrobial agents offer a promising strategy to replace conventional compounds.In this regard,phage lytic proteins or lysins,such as endolysins and virion-associated peptidoglycan hydrolases(VAPGHs),have been proposed as a viable option for the avoidance and elimination of undesirable bacteria within the food production chain.Even when applied exogenously,these proteins can degrade the bacterial cell wall maintaining their lytic activity.This feature,alongside their modular structure,which can be exploited for bioengineering,provides significant biotechnological potential.However,despite the promising properties of lysins,the main obstacle for their commercialization is the limited legal information regulating their use.This challenge underscores the need to navigate complex regulatory pathways.The primary objective of this review is to address this crucial gap and summarize the many prospective applications of endolysins during the different stages of food production.By doing so,we aim to provide clarity and insight into the regulatory challenges that must be overcome for the successful utilization of lysins.展开更多
文摘Aim: This study was carried out in order to evaluate the potential of bacteriophages in controlling tomato bacterial wilt disease caused by Ralstonia solanacearum. Study design: A purposive sampling technique was used to collect samples from bacterial wilt hot spot tomato growing areas in Kenya. Place and duration of study: The research work was done at Jomo Kenyatta University of Agriculture and Technology, between June 2020 and July 2021. Methodology: Thirty diseased plants and corresponding soil were collected from five counties, Nyeri, Kajiado, Nyandarua, Kiambu and Taita Taveta. Bacteria were isolated and characterized, and then used as hosts to propagate the phages. Tests done were gram stain, oxidation test, potassium hydroxide solubility test, H2S production test catalase test, NaCl test and sugar fermentation test. Molecular analysis and phenotyping were also done in order to identify the bacteria. The bacteriophages were then isolated through a double overlay method using R. solanacearum as the host. They were characterized and assayed in a greenhouse setting to determine their effectiveness in controlling bacterial wilt. Results: Six host bacteria were isolated and all belonged to biovar II. Four phages were observed based on morphology. Upon characterization the phages were stable at 30˚C, PH range between 6 - 7 and tolerance of more than an hour under UV light. In the greenhouse experiment, treatment of plants with bacteriophage prevented wilting after subsequent inoculation with the pathogen. A bacteriophage mix of SN1 and WT1 were used for efficacy tests due to their efficiency in plating and infection. Phage SN1 and WT1 exhibited high lytic activity and relatively high thermotolerance and acid tolerance, thereby showing great potential in the biocontrol of bacterial wilt infection across a variety of conditions. Conclusion: The results obtained in this research show that bacteriophages offer potential for the biocontrol of bacterial wilt.
基金supported in part by funds from the Ministry of Science and Technology(2022FY101104).
文摘Recognizing essential proteins within bacteriophages is fundamental to uncovering their replication and survival mechanisms and contributes to advances in phage-based antibacterial therapies.Despite notable progress,existing computational techniques struggle to represent the interplay between sequence-derived and structuredependent protein features.To overcome this limitation,we introduce GLM-EP,a unified framework that fuses protein language models with equivariant graph neural networks.Bymerging semantic embeddings extracted from amino acid sequences with geometry-aware graph representations,GLM-EP enables an in-depth depiction of phage proteins and enhances essential protein identification.Evaluation on diverse benchmark datasets confirms that GLM-EP surpasses conventional sequence-based and independent deep-learning methods,yielding higher F1 and AUROC outcomes.Component-wise analysis demonstrates that GCNII,EGNN,and the gated multi-head attention mechanism function in a complementary manner to encode complex molecular attributes.In summary,GLM-EP serves as a robust and efficient tool for bacteriophage genomic analysis and provides valuable methodological perspectives for the discovery of antibiotic-resistance therapeutic targets.The corresponding code repository is available at:https://github.com/MiJia-ID/GLM-EP(accessed on 01 November 2025).
文摘To formulate the optimal strategy of combatting bacterial biofilms,in this review we update current knowledge on the growing problem of biofilm formation and its resistance to antibiotics which has spurred the search for new strategies to deal with this complication.Based on recent findings,the role of bacteriophages in the prevention and elimination of biofilm-related infections has been emphasized.In vitro,ex vivo and in vivo biofilm treatment models with single bacteriophages or phage cocktails have been compared.A combined use of bacteriophages with antibiotics in vitro or in vivo confirms earlier reports of the synergistic effect of these agents in improving biofilm removal.Furthermore,studies on the application of phage-derived lysins in vitro,ex vivo or in vivo against biofilm-related infections are encouraging.The strategy of combined use of phage and antibiotics seems to be different from using lysins and antibiotics.These findings suggest that phages and lysins alone or in combination with antibiotics may be an efficient weapon against biofilm formation in vivo and ex vivo,which could be useful in formulating novel strategies to combat bacterial infections.Those findings proved to be relevant in the prevention and destruction of biofilms occurring during urinary tract infections,orthopedic implant-related infections,periodontal and peri-implant infections.In conclusion,it appears that most efficient strategy of eliminating biofilms involves phages or lysins in combination with antibiotics,but the optimal scheme of their administration requires further studies.
基金supported by the Basic Research Program of the Ministry of Science and Technology of China(2012CB721102)the Chinese Academy of Sciences(grant No:KJZD-EW-L02)the Key Laboratory on Emerging Infectious Diseases and Biosafety in Wuhan
文摘The year 2015 marks 100 years since Dr.Frederick Twort discovered the"filterable lytic factor",which was later independently discovered and named "bacteriophage" by Dr.Felix d’Herelle.On this memorable centennial,it is exciting to see a special issue published by Virologica Sinica on Phages and Therapy.In this issue,readers will not only fi nd that bacteriophage research is a
基金supported by the statutory funds from the Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences
文摘Acinetobacter baumannii causes serious infections especially in immunocompromised and/or hospitalized patients.Several A.baumannii strains are multidrug resistant and infect wounds,bones,and the respiratory tract.Current studies are focused on finding new effective agents against A.baumannii.Phage therapy is a promising means to fight this bacterium and many studies on procuring and applying new phages against A.baumannii are currently being conducted.As shown in animal models,phages against multidrug-resistant A.baumannii may control bacterial infections caused by this pathogen and may be a real hope to solve this dangerous health problem.
基金supported financially by the Sino-Africa Joint Research Centre (SAJC201605)the Chinese Academy of Sciences (ZDRW-ZS-2016-4)
文摘Soft rot is an economically significant disease in potato and one of the major threats to sustainable potato production.This study aimed at isolating lytic bacteriophages and evaluating methods for and the efficacy of applying phages to control potato soft rot caused by Pectobacterium carotovorum.Eleven bacteriophages isolated from soil and water samples collected in Wuhan,China,were used to infect P.carotovorum host strains isolated from potato tubers showing soft rot symptoms in Nakuru county,Kenya.The efficacy of the phages in controlling soft rot disease was evaluated by applying individual phage strains or a phage cocktail on potato slices and tubers at different time points before or after inoculation with a P.carotovorum strain.The phages could lyse 20 strains of P.carotovorum,but not Pseudomonas fluorescens control strains.Among the 11 phages,Pectobacterium phage Wc5r,interestingly showed cross-activity against Pectobacterium atrosepticum and two phage-resistant P.carotovorum strains.Potato slice assays showed that the phage concentration and timing of application are crucial factors for effective soft rot control.Phage cocktail applied at a concentration of 1×10^9 plaque-forming units per milliliter before or within an hour after bacterial inoculation on potato slices,resulted in>90%reduction of soft rot symptoms.This study provides a basis for the development and application of phages to reduce the impact of potato soft rot disease.
文摘Laban jameed is a dried salty dairy product obtained by fermentation of milk using a complex population of lactic acid bacteria. Jameed is considered a traditional food product in most eastern Mediterranean countries and is usually made from sheep or cow milk. The aim of this study was to assess phage contamination of jameed dairy product. Two phages were isolated: one from sheep milk jameed (PPUDV) and the other from cow milk jameed (PPURV). Each of the two bacteriophages was partially characterized. The PPUDV phage was identified as a single stranded DNA virus with an approximately 20 kb genome that was resistant to RNase, whereas PPURV phage possessed a double stranded RNA genome of approximately 20 kb and was resistant to DNase. The phage bacterial strain hosts were identified as Lactobacillus helveticus and Bacillus amyloliquefaciens for PPUDV and PPURV, respectively. One step growth curve using a double layer plaque assay test was carried out to monitor the phage life cycle after host infection. PPUDV showed a latent period of about 36 h, burst period of 70 h and a burst size of about 600 Plaque Forming Units (PFU) per infected cell. PPURV phage showed a latent period of about 24 h, burst period of 47 h and a burst size of about 700 PFU per infected cell. SDS-PAGE analysis of total viral proteins showed at least three major bands (27, 40, and 45 kDa) for PPUDV. This is the first study to report the isolation of both DNA and RNA bacteriophages from laban jameed. This study adds new insights into the complexity of dairy contamination and fermentation microbiology of the jameed revealing the existence of two viral genomes in this highly dried and salty dairy product.
文摘The continuous battle between humans and the multitude of pathogenic microorganisms in the environment has sought relief in the form of antimicrobials. But the counter attack by pathogenic organisms in the form of multidrug resistance, acquired by various mechanisms such as transformation, transposition, conjugation and transduction is a major reason for concern. Bacteriophages have contributed in a significant way to dissemination of genes encoding antimicrobial resistance, heavy metal resistance and virulence factors through the phenomenon of transduction. This review aims at compiling information about the different mechanisms by which bacteriophages aid in transferring genes involved in antimicrobial resistance to Escherischia coli in various environments.
文摘Hepatitis B virus(HBV) infection is a major global health challenge leading to serious disorders such as cirrhosis and hepatocellular carcinoma. Currently, there exist various diagnostic and therapeutic approaches for HBV infection. However, prevalence and hazardous effects of chronic viral infection heighten the need to develop novel methodologies for the detection and treatment of this infection. Bacteriophages, viruses that specifically infect bacterial cells, with a long-established tradition in molecular biology and biotechnology have recently been introduced as novel tools for the prevention, diagnosis and treatment of HBV infection. Bacteriophages, due to tremendous genetic flexibility, represent potential to undergo a huge variety of surface modifications. This property has been the rationale behind introduction of phage display concept. This powerful approach, together with combinatorial chemistry, has shaped the concept of phage display libraries with diverse applications for the detection and therapy of HBV infection. This review aims to offer an insightful overview of the potential of bacteriophages in the development of helpful prophylactic(vaccine design), diagnostic and therapeutic strategies for HBV infection thereby providing new perspec-tives to the growing field of bacteriophage researches directing towards HBV infection.
基金the National Public Science and Technology Research Funds Projects of Ocean(Grant No.201405003-3)
文摘In recent years, the development of antibiotic resistant bacteria has become a global concern which has prompted research into the development of alternative disease control strategies for the swine industry. Bacteriophages （viruses that infect bacteria） offer the prospect of a sustainable alternative approach against bacterial pathogens with the flexibility of being applied therapeutically or for biological control purposes. This paper reviews the use of phages as an antimicrobial strategy for controlling critical pathogens including Salmonella and Eschefich[a coli with an emphasis on the application of phages for improving performance and nutrient digestibility in swine operations as well as in controlling zoonotic human diseases by reducing the bacterial load spread from pork products to humans through the meat,
基金This work was supported by the Western Medicine Program of the Zhejiang Provincial Health Commission(No.2024KY592)the Fundamental Research Funds for Central Universities of the Central South University(No.2-2050205-19-361),China.
文摘In the post-antibiotic era,the overuse of antimicrobials has led to a massive increase in antimicrobial resistance,leaving medical doctors few or no treatment options to fight infections caused by superbugs.The use of bacteriophages is a promising alternative to treat infections,supplementing or possibly even replacing antibiotics.Using phages for therapy is possible,since these bacterial viruses can kill bacteria specifically,causing no harm to the normal flora.However,bacteria have developed a multitude of sophisticated and complex ways to resist infection by phages,including abortive infection and the clustered regularly interspersed short palindromic repeats(CRISPR)/CRISPR-associated(Cas)system.Phages also can evolve and acquire new anti-defense strategies to continue predation.An in-depth exploration of both defense and anti-defense mechanisms would contribute to optimizing phage therapy,while we would also gain novel insights into the microbial world.In this paper,we summarize recent research on bacterial phage resistance and phage anti-defense mechanisms,as well as collaborative win-win systems involving both virus and host.
文摘Bacteriophages represent a rich and unique resource of anti-infectives to counter the global problem of antibiotic resis- tance. In this work, we assessed the bactericidal activity of two virulent staphylococcal phages, K and 44AHJD, against S. aureus isolates of clinical significance, and tested their efficacy in vivo. The phage cocktail lysed >85% of the clinical isolates tested. Both the phages were purified by ion-exchange column chromatography following propagation in bioreactors. The purity profiles of the ion-exchange purified phages were compared with those of phages purified using cesium chloride density gradient ultracentrifugation, and infectiousness of the purified phages was confirmed by plaque forming assay. The in vivo efficacy of a phage cocktail was evaluated in an experimental murine nasal colonization model, which showed that the phage cocktail was efficacious. To our knowledge, this is the first report of phage use in an in vivo model of nasal carriage.
文摘Environmental mycobacteria are capable of forming biofilms in low-nutrient environments, and these biofilms may act as reservoirs for opportunistic infections. The purpose of this study was to determine if bacteriophages could disrupt existing biofilms of acid-fast staining Mycobacterium smegmatis. Using the MBEC 96-well plastic peg assay system, M. smegmatis biofilms were created and then tested for their stability in the presence of mycobacteriophages isolated from a Minnesota sphagnum peat bog. All phages tested were lytic and were observed to have weak, intermediate, and strong abilities to disrupt M. smegmatis biofilms. The formation of biofilms was severely impaired in the presence of mycobacteriophages. Phage treatment was also shown to augment?M. smegmatis biofilm disruption by mechanical forces of sonication or water flow. Our study shows that, as with biofilms of Gram-positive and Gram-negative bacteria, mycobacterial biofilms are also susceptible to destruction by bacteriophages.
文摘The minimum inhibitory concentration (MIC) is the concentration at which an antibacterial agent experiences the complete inhibition of organism growth. Bacteriophages represent a rich and unique resource of anti-infectives to counter the growing world-wide problem of antibiotic resistance. In this study, we compared the host range of lytic bacteriophages and temperate phagesbelonging to various genera, namely Staphylococcus, E. coli and Salmonella, with a range of clinical isolates using two methods: the classical agar overlay method and a newly developed MIC method. MIC was only observed with isolates that were susceptible to phage infection, which correlated with the agar overlay assay, whereas no MIC was detected with isolates that were resistant to phage infection. The simple MIC method was useful in determining phage adsorption and host range, and detecting possible prophage contamination in phage preparations. Interestingly, this method was also applicable to strain differentiation through phage susceptibility testing using a 96-well, high throughput format that proved to be easy, cost-effective, fast and reliable.
基金funded by the Guangdong Basic and Applied Basic Research Foundation(2024A1515011872)the National Key R&D Program of China(2019YFA0906700).
文摘As our understanding of the role of the gut microbiome in human diseases deepens,precision engineering of the gut microbiome using bacteriophages has gained significant attention.Herein,we review the recent advances in bacteriophage-mediated modulation of the gut microbiome,discuss approaches at the ecological and genetic levels,and summarize the challenges and strategies pertinent to each level of intervention.Drawing on the structural attributes of bacteriophages in the context of precision engineering,we examined the latest developments in the field of phage administration.Gaining a nuanced understanding of microbiome manipulation will yield tailored strategies and technologies.This could revolutionize the prevention and treatment of diseases linked to gut pathogens and offer new avenues for the therapeutic use of bacteriophages.
基金funded by the Natural Science Foundation of China(32172296,52333007)Key Research and Development Program of Jiangxi Province(20243BBH81007,20232BBG70030,20232BCD44004)+3 种基金National Key Research and Development Program of China(2023YFB3810001)Key-Area Research and Development Program of Guangdong Province(2024B0101040001)Shenzhen Key Laboratory of Functional Aggregate Materials(ZDSYS20211021111400001)Science Technology Innovation Commission of Shenzhen Municipality(KQTD20210811090142053).
文摘Traditional fluorescence immunoassays are often hindered by false negatives or quantification inaccuracies,especially at high target concentrations,due to the aggregation-caused quenching effect of fluorescent indicators.This study introduces a novel fluorescence immunoassay strategy that leverages the spontaneous amino-yne click reaction to covalently assemble activated alkyne-based luminogens with aggregation-induced emission characteristics(AIEgens)onto the surface of bifunctional M13 bacteriophages,thereby facilitating efficient“lighting-up”fluorescence signal output in conjunction with magnetic-mediated immunorecognition.To further enhance the load of activated alkyne-based AIEgens and improve the fluorescence“lighting-up”efficiency,M13 bacteriophages were engineered to display varying numbers of surface-exposed lysine residues.This was achieved by inserting different quantities of lysines between the signal peptide and the amino acid sequence of the pVIII protein via a point mutation strategy.Benefiting from the synergy of AIEgen stacking-enhanced fluorescence output and M13 bacteriophagedriven signal amplification,the developed“lighting-up”immunoassay enabled highly sensitive and rapid detection of targets,from smallmolecules to pathogenic microorganisms.This work provides valuable insights into the design of“lighting-up”AIEgens for enhancing fluorescence immunoassays.Moreover,the proposed strategy offers great versatility,allowing it to be readily adapted to detect other targets simply by pairing the target with the M13 bacteriophages.
文摘Background： The therapeutic potential of bacteriophages has been debated since their first isolation and characterisation in the early 20th century. However, a lack of consistency in application and observed efficacy during their early use meant that upon the discovery of antibiotic compounds research in the field of phage therapy quickly slowed. The rise of antibiotic resistance in bacteria and improvements in our abilities to modify and manipulate DNA, especially in the context of small viral genomes, has led to a recent resurgence of interest in utilising phage as antimicrobial therapeutics. Results： In this article a number of results from the literature that have aimed to address key issues regarding the utility and efficacy of phage as antimicrobial therapeutics utilising molecular biology and synthetic biology approaches will be introduced and discussed, giving a general view of the recent progress in the field. Conclusions： Advances in molecular biology and synthetic biology have enabled rapid progress in the field of phage engineering, with this article highlighting a number of promising strategies developed to optimise phages for the treatment of bacterial disease. Whilst many of the same issues that have historically limited the use of phages as therapeutics still exist, these modifications, or combinations thereof, may form a basis upon which future advances can be built. A focus on rigorous in vivo testing and investment in clinical trials for promising candidate phages may be required for the field to truly mature, but there is renewed hope that the potential benefits of phage therapy may finally be realised.
基金The authors are grateful to Science and Engineering Research Board(SERB),a statutory body of the Department of Science&Technology,Govt.of India(Sanction Order No.CRG/2019/001750 dated 14th January,2020)for financial assistance.
文摘Vibrio harveyi is a Gram-negative,rod-shaped,polar flagellate,facultatively anaerobic,halophilic,bioluminescent marine bacteria that belongs to the family of Vibrionaceae,class,Gammaproteobacteria.This pathogenic organism is responsible for various diseases of vertebrates and invertebrates in marine habitats,including shrimp aquaculture.Various symptoms like lesions,gastroenteritis,skin ulcers,eye lesions,and tail rot have been observed due to V.harveyi infection.The pathogenic-ity mechanism of V.harveyi involves endotoxin lipopolysaccharide,extracellular proteases,and bacteriophage interaction.Hemolysin genes encoded extracellular hemolysin-like phospholipase B toxin could inactivate fish species via the caspase inactivation pathway,ultimately leading to apoptosis.In addition,VBNC(viable but nonculturable)cells are another basis of vibriosis outbreaks in the shrimp aquaculture sector.The extensive amount of antibiotic use promotes the generation of multidrug-resistant strains.Therefore,as an alternative strategy to combat V.harveyi infection,bacteriophages are utilized as a biocontrol agent.However,there is a lack of research on the immobilization and development of encapsulation strategies of V.harveyi-infecting bacteriophages which need to be studied further.In conclusion,the pathogenicity of V.harveyi and its biocontrol by bacteriophages has been documented in this review.
文摘The bacteriophage clones which can bind with shiga toxin B subunit (StxB) and inhibit cytotoxicity of shiga toxin were obtained by using antibody capturing method from a 15-mer random peptide library displayed on the surface of bacteriophage fd. Among them, one peptide encoded by the random DNA region of a selected bacteriophage (A12) was synthesized and tested in vitro and in vivo, where the peptide competed with the receptor of shiga toxin to bind StxB, and inhibited the cytotoxicity and enterotoxicity of shiga toxin. The peptide can also block other apparently unrelated StxB binding bacteriophage (A3), which suggests that there are overlapping StxB interaction sites for those ligands with different sequences. The results provide a demonstration of bacteriophage display to screen peptide ligands for a small and/or unable biotinylated molecule by antibodies-capturing strategy, and take the lead for the development of receptor antagonists for shiga toxin.
基金funded by grants PID2019-105311RB-I00(MICIU/AEI/FEDER,UE,Spain)to P.García and A.RodríguezAYUD/2021/52120(Program of Science,Technology and Innovation 2021-2023 and FEDER EU,Principado de Asturias,Spain)。
文摘Sustainability is a leading trend in the context of food production.Additionally,consumers increasingly demand safer and less-processed products.Among the different technologies used to maintain the quality and extend the shelf-life of fresh and minimally-processed food,natural antimicrobial agents offer a promising strategy to replace conventional compounds.In this regard,phage lytic proteins or lysins,such as endolysins and virion-associated peptidoglycan hydrolases(VAPGHs),have been proposed as a viable option for the avoidance and elimination of undesirable bacteria within the food production chain.Even when applied exogenously,these proteins can degrade the bacterial cell wall maintaining their lytic activity.This feature,alongside their modular structure,which can be exploited for bioengineering,provides significant biotechnological potential.However,despite the promising properties of lysins,the main obstacle for their commercialization is the limited legal information regulating their use.This challenge underscores the need to navigate complex regulatory pathways.The primary objective of this review is to address this crucial gap and summarize the many prospective applications of endolysins during the different stages of food production.By doing so,we aim to provide clarity and insight into the regulatory challenges that must be overcome for the successful utilization of lysins.
