bims-fagtap 2025-05-18 papers

bims-fagtap

Biomed News

on Phage therapies and applications

Issue of 2025–05–18
eighteen papers selected by
Luca Bolliger, lxBio

Characterization and purification of Pseudomonas aeruginosa phages for the treatment of canine infections.
Phage Therapy for Urinary Tract Infections: Progress and Challenges Ahead.
Adjunctive phage therapy improves antibiotic treatment of ventilator-associated-pneumonia with Pseudomonas aeruginosa.
Phage therapy: a promising approach for Staphylococcus aureus diabetic foot infections.
Six Novel Pseudomonas aeruginosa Phages: Genomic Insights and Therapeutic Potential.
WGS of a lytic phage targeting biofilm-forming carbapenem-resistant Klebsiella pneumoniae prevalent in a tertiary healthcare setup.
Phage diversity in human breast milk: a systematic review.
[Cost aspects and reimbursement requirements of phage therapy].
Can bacteriophage be stabilised by lipid encapsulation when nebulised for inhalation delivery against Pseudomonas aeruginosa?
In silico and in vitro comparative analysis of 79 Acinetobacter baumannii clinical isolates.
taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level.
Virome drift in ulcerative colitis patients: faecal microbiota transplantation results in minimal phage engraftment dominated by microviruses.
HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences.
Alternative treatment candidates to antibiotic therapy for bovine mastitis in the post-antibiotic era: a comprehensive review.
Innovative strategies targeting oral microbial dysbiosis: unraveling mechanisms and advancing therapies for periodontitis.
Exploring deep learning in phage discovery and characterization.
Harnessing advances in mechanisms, detection, and strategies to combat antimicrobial resistance.
Validation of a Cystic Fibrosis Co-Culture Model for the Identification of Dual Acting Compounds with Antibiotic and Antibiotic Adjuvant Properties.

BMC Microbiol. 2025 May 14. 25(1): 289

Characterization and purification of Pseudomonas aeruginosa phages for the treatment of canine infections.

Anne Dalponte, Viviane Filor, Antina Lübke-Becker, Marcus Fulde, Thomas Alter, Mathias Müsken, Wolfgang Bäumer.

   BACKGROUND: Pseudomonas aeruginosa is an opportunistic pathogen that causes infections in both human and veterinary medicine, presenting significant challenges in treatment because of biofilm production and its intrinsic resistance. This problem is exacerbated by the increase in acquired antimicrobial resistance. Bacteriophage (phage) therapy has emerged as a promising alternative for treating infection classically treated with antibiotics, offering a targeted approach to combat this infection. This study aimed to evaluate the therapeutic potential of 7 phages, focusing on their suitability for treating canine infections, as well as their purification and safety analysis for therapeutic use.
RESULTS: Two self-isolated phages and five provided phages were analysed. All tested phages reduced bacterial load in vitro; however, their efficacy varied across different concentrations. The host range analysis revealed a spectrum between 9.8 and 68.6% of canine clinical P. aeruginosa isolates. In our in vitro tests 3 out of 7 phages were able to significantly reduce the biofilm biomass, achieving reductions up to 93.38%. The sequence analysis did not discover known virulence factors and genes connected to antimicrobial resistance mechanisms. The self-isolated phages were classified as lysogenic, whereas the other phages had a lytic infection cycle. Through the purification of the phages, high-titre phage preparations (> 1011 PFU/ml) were generated with high stability for at least 1.5 years. The tested endotoxin units are below the regulatory limits.
CONCLUSION: Investigating phages as alternative treatment option seems promising with lytic phages covering a broad host range and a genomic potential for biofilm degradation. These findings support the development of phage cocktails as a targeted alternative for treating canine P. aeruginosa infections, particularly in cases of antibiotic resistance, and highlight the importance of selecting well-characterized lytic phages for therapeutic efficacy and safety.

Keywords:   Pseudomonas aeruginosa ; Phage therapy

DOI:  https://doi.org/10.1186/s12866-025-04005-4
Int Urogynecol J. 2025 May 13.

Phage Therapy for Urinary Tract Infections: Progress and Challenges Ahead.

Chase J Morgan, Haley Atkins, Alan J Wolfe, Linda Brubaker, Saima Aslam, Catherine Putonti, Michael B Doud, Lindsey A Burnett.

   INTRODUCTION AND HYPOTHESIS: Urinary tract infection (UTI) treatment is a growing public health concern owing to increasing antimicrobial resistance. Phage therapy, an alternative or adjunctive treatment to antibiotics, has the potential to address this challenge. However, clinical use of phage therapy is hindered by knowledge gaps and inconsistent reporting. The objective was to review the current state of phage therapy for UTIs and highlight research priorities that can optimize phage clinical efficacy.
METHODS: Current literature on UTI phage therapy was examined, focusing on the lack of standardized phage susceptibility testing, phage characterization, and microbiological assessments during and after treatment.
RESULTS: Critical areas requiring further investigation include appropriate phage dosing, optimal routes of administration, and the dynamics of phage-host and phage-patient interactions. The influence of the urinary microbiome, including endogenous phages, on treatment outcomes also needs to be better understood. Suggested data collection and reporting standards should be developed and implemented to improve clinical impact of studies examining phage therapy for UTI. Randomized clinical trials are needed to establish efficacy and determine the best practices for clinical use.
CONCLUSION: Phage therapy is a promising alternative to antibiotics for managing UTIs, especially in the face of rising antimicrobial resistance. To fully realize its potential, however, future research must focus on standardized protocols, dosing strategies, and the role of the urinary microbiome, with an emphasis on rigorously conducted clinical trials. These steps are essential for integrating phage therapy into mainstream UTI treatment regimens.

Keywords:  Phage therapy; Urinary phage; Urinary tract infection; Urinary virome

DOI:  https://doi.org/10.1007/s00192-025-06136-8
Nat Commun. 2025 May 15. 16(1): 4500

Adjunctive phage therapy improves antibiotic treatment of ventilator-associated-pneumonia with Pseudomonas aeruginosa.

Chantal Weissfuss, Jingjing Li, Ulrike Behrendt, Karen Hoffmann, Magdalena Bürkle, Chunjiang Tan, Gopinath Krishnamoorthy, Imke H E Korf, Christine Rohde, Baptiste Gaborieau, Laurent Debarbieux, Jean-Damien Ricard, Martin Witzenrath, Matthias Felten, Geraldine Nouailles.

Bacterial multidrug resistance poses an urgent challenge for the treatment of critically ill patients developing ventilator-associated pneumonia (VAP). Phage therapy, a potential alternative when conventional antibiotics fail, has been unsuccessful in first clinical trials when used alone. Whether combining antibiotics with phages may enhance effectiveness remains to be tested in experimental models. Here, we use a murine model of Pseudomonas-induced VAP to compare the efficacy of adjunctive phage cocktail for antibiotic therapy to either meropenem or phages alone. Combined treatment in murine VAP results in faster clinical improvement and prevents lung epithelial cell damage. Using human primary epithelial cells to dissect these synergistic effects, we find that adjunctive phage therapy reduces the minimum effective concentration of meropenem and prevents resistance development against both treatments. These findings suggest adjunctive phage therapy represents a promising treatment for MDR-induced VAP, enhancing the effectiveness of both antibiotics and phages while reducing adverse effects.

DOI: https://doi.org/10.1038/s41467-025-59806-y
J Virol. 2025 May 14. e0045825

Phage therapy: a promising approach for Staphylococcus aureus diabetic foot infections.

Lucile Plumet, Chloé Magnan, Denis Costechareyre, Albert Sotto, Jean-Philippe Lavigne, Virginie Molle.

  Diabetic foot infections (DFIs), predominantly caused by Staphylococcus aureus, pose a significant healthcare challenge with severe consequences, including amputation. Phage therapy, which utilizes bacteriophages to specifically target bacterial pathogens, has emerged as a promising alternative to conventional antibiotic treatments. This review evaluates the efficacy of phage therapy as a complementary treatment for DFIs caused by S. aureus, synthesizing evidence from preclinical and clinical studies while addressing the limitations and challenges associated with current research. The analysis highlights promising results from diabetic animal models, demonstrating effective bacterial load reduction and improved wound healing. Clinical case reports and series further underline significant improvements in infection management and ulcer healing, with no major adverse effects reported. Ongoing clinical trials are also discussed, offering insights into the study parameters evaluating phage therapy potential efficacy and safety for S. aureus-related DFIs. While the collected data highlight the potential of phage therapy as a valuable complement to traditional antibiotic treatments, particularly in managing antibiotic-resistant infections, further research is essential to address existing limitations, including gaps in long-term efficacy data and challenges in standardization. With continued investigation, phage therapy holds significant potential to alleviate the healthcare burden of DFIs and improve patient outcomes.

Keywords:  Staphylococcus aureus; animal models; bacteriophages; clinical cases; clinical trials; diabetic foot infections; phage therapy

DOI:  https://doi.org/10.1128/jvi.00458-25
Phage (New Rochelle). 2025 Mar;6(1): 32-40

Six Novel Pseudomonas aeruginosa Phages: Genomic Insights and Therapeutic Potential.

Amit Rimon, Ortal Yerushalmy, Jonathan Belin, Sivan Alkalay-Oren, Lilach Gavish, Shunit Coppenhagen-Glazer, Ronen Hazan.

   Introduction: Pseudomonas aeruginosa is an opportunistic pathogen that causes health care-associated infections. The rise of antibiotic-resistant bacterial strains necessitates alternative treatment strategies, with bacteriophage therapy being a promising approach.
Methods: Six bacteriophages were isolated from sewage samples. Phage isolation involved centrifugation, filtration, and plaque assays. The morphology of each sample was examined using transmission electron microscopy (TEM). Genomic DNA was sequenced and compared among the isolates. The phages' lytic activities were assessed using growth curve analysis.
Results: The phages displayed distinct genomic characteristics, grouping into three genomic clusters. No known virulence or antibiotic resistance genes were detected, indicating their safety for therapeutic use. Taxonomic analysis identified the phages as belonging to the genera Pbunavirus, Nipunavirus, Abidjanvirus, and a novel genus. TEM analysis revealed their diverse morphologies. Temperate phages showed less effective lytic activities.
Conclusion: Several of the isolated bacteriophages show potential as candidates for phage therapy research and could be effective against P. aeruginosa infections.

Keywords:  Pseudomonas aeruginosa; phage genomics; phage therapy

DOI:  https://doi.org/10.1089/phage.2024.0037
Microb Pathog. 2025 May 08. pii: S0882-4010(25)00405-X. [Epub ahead of print]205 107680

WGS of a lytic phage targeting biofilm-forming carbapenem-resistant Klebsiella pneumoniae prevalent in a tertiary healthcare setup.

Sambuddha Chakraborty, I Dinakaran, Anusha Karunasagar, Wasim Ahmed, Juliet Mohan Raj, Indrani Karunasagar, Medhavi Vashisth, Ashwini Chauhan.

  Carbapenem-resistant Enterobacteriaceae (CRE) are listed as a priority-one critical pathogen category by the WHO because of their abysmal treatment outcomes owing to antibiotic inefficiency. Among CRE, Klebsiella pneumoniae is prevalent in acquiring resistance genes and withstanding the last-resort drugs. Additionally, its ability to form robust biofilms further exacerbates the treatment challenges. The escalating resistance and recalcitrance of biofilm-residing bacteria against standard antibiotic treatments demand an alternative to antibiotics. Phages, being nature-tailored, are a never-ending arsenal against the bacteria because of their capacity to lyse bacteria rapidly and co-evolve with bacteria. In our study, we isolated K. pneumoniae from patients at Madras Medical Mission Hospital (MMMH), India, and assessed their antibiogram profiles, presence of carbapenemase genes, and biofilm-forming abilities. 100 % of the strains were extended-spectrum beta-lactamase producing, multidrug-resistant (ESBL-MDR), with 95 % harbouring carbapenemase genes. Among the isolates, 65 % were strong biofilm formers, and the rest were moderate. Further, we isolated a bacteriophage, SAKp11, from the hospital sewage, which was able to lyse 62 out of 167 clinical isolates and successfully reduced 99.99 % viable bacterial cells of the 24-h-old biofilm of strong biofilm forming MDR K. pneumoniae strains. Whole genome analysis revealed that SAKp11, with a genome size of 59,338bp, belonged to the Casjensviridae family, one of the less explored bacteriophage families. Comprehensive characterization of SAKp11 indicated its suitability for therapeutic use. Our study highlights the severity of drug-resistant K. pneumoniae in Indian healthcare and the inadequacy of current antibiotics, underscoring the potential of phages as an alternative therapeutic option.

Keywords:  Alternative to antibiotics; Carbapenemase; K. pneumoniae, biofilm; Multi drug resistance; Phage therapy

DOI:  https://doi.org/10.1016/j.micpath.2025.107680
Eur J Pediatr. 2025 May 10. 184(6): 334

Phage diversity in human breast milk: a systematic review.

Yanping Guo, Ying Liu, Songzhou Xu, Ruolin Zhang, Zhangbin Yu, Wanxiang He.

  Breast milk is not sterile. The microbiome in human milk serves as a crucial source of early gut microbes for infants, directly impacting the host's health. This microbiome includes bacteria, viruses, archaea, and fungi. Bacteriophages, as key components of the virome, continually prey on bacterial hosts, thereby influencing the development of early gut microbial communities. Pertinent records from various databases, including EMBASE, Cochrane Library, PubMed, and Web of Science, were comprehensively reviewed against inclusion criteria up to March 24, 2025. A checklist was employed to assess the risk of bias in the selected studies. After screening a total of 635 records, we included 5 studies with 182 women and 251 samples. Seven families of bacteriophages were identified, primarily Herelleviridae, Myoviridae, Podoviridae, Siphoviridae, Caudoviridales, Microviridae, and Inoviridae. Their abundance varies at different stages of lactation and can be vertically transmitted through breastfeeding. However, due to the limited number of studies and methodological differences, it is not yet possible to determine which maternal and infant characteristics influence the abundance of these bacteriophages.
CONCLUSION: Human milk contains abundant bacteriophages that bind to specific bacterial hosts and are transmitted vertically from mother to infant, collectively shaping the infant's gut microbiome. Conducting more longitudinal studies on mother-infant pairs will help better determine the composition of bacteriophages in human milk and their functional impact on infant development.
WHAT IS KNOWN: • Human milk is a source of diverse microbes, including bacteriophages, that contribute to the establishment of the infant gut microbiome. • Bacteriophages can influence bacterial populations by infecting specific bacterial hosts.
WHAT IS NEW: • Human milk harbors abundant and diverse bacteriophages that are vertically transmitted from mother to infant. • Current evidence underscores the need for longitudinal studies to clarify the role of milk-derived bacteriophages in shaping infant gut microbiota and development.

Keywords:  Bacteriophages; Diversity; Human breast milk; Phages

DOI:  https://doi.org/10.1007/s00431-025-06173-x
Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2025 May 13.

[Cost aspects and reimbursement requirements of phage therapy].

Dennis Häckl, Jutta Dillschneider, Christian Elsner.

  Phage therapy is considered a promising approach for the targeted treatment of bacterial infections. It has not yet been approved as a regular form of medical therapy in Germany. This article examines the economic and reimbursement challenges of phage therapy as a targeted treatment option for bacterial infections. Two production approaches are distinguished. On the one hand, patient-independent, industrial production of standardized phage therapies could potentially lower costs through economies of scale, yet is associated with uncertainties due to fixed costs, requirements for Good Manufacturing Practice (GMP), and host-specific activity. On the other hand, individual production in (hospital) pharmacies enables patient-specific phage mixtures via magistral compounding but requires production, logistical efforts, and quality management. A significant cost factor is also the diagnostics needed for the identification of bacterial pathogens, which requires additional investments.The current situation in Germany shows that phage therapeutics are so far prescribed and reimbursed only as part of individual treatment attempts; they are neither established as regular medicinal products nor as first-line therapy. Exceptions such as the "Potential Method" (§ 137c SGB V) and emergency supply (§ 2 Abs. 1a SGB V) allow for reimbursement under certain conditions, but require justifications and generate transaction costs.This article provides recommendations for promoting phage therapy, including drawing parallels to the reimbursement of CAR-T cell therapy with additional fees for patient-specific therapeutics; for ready-to-use products, outcome-based reimbursement models and evidence-based assessments are discussed. To create economic incentives, state funding instruments are needed.

Keywords:  Antibiotics; Economic efficiency; GMP; Hospital pharmacy; Reimbursement

DOI:  https://doi.org/10.1007/s00103-025-04065-x
Int J Pharm. 2025 May 08. pii: S0378-5173(25)00507-1. [Epub ahead of print]678 125670

Can bacteriophage be stabilised by lipid encapsulation when nebulised for inhalation delivery against Pseudomonas aeruginosa?

Yue Cao, Yuncheng Wang, Mengyu Li, Dipesh Khanal, Hak-Kim Chan.

Inhaled bacteriophage (phage) therapy is emerging as a promising approach to combat multidrug-resistant (MDR) respiratory pathogens such as Pseudomonas aeruginosa. Aerosol delivery by nebulization poses challenges for maintaining phage stability, often resulting in titer losses due to mechanical stresses. This study evaluated the use of liposomal encapsulation to protect phages during nebulization. Two P. aeruginosa phages, PEV2 (short-tail) and PEV40 (long-tail), were selected for this work. Liposomes were prepared using DSPC, cholesterol, Tween 80, and cationic lipid DOTAP. Encapsulation efficiencies were 78 % for PEV2 and 90 % for PEV40, with mean particle sizes of 300 nm and 650 nm, respectively. Nebulization by jet and vibrating mesh devices showed that the liposome-encapsulated phages were able to preserve viability, with titer losses below 0.4 log10 (PEV40) and 0.07 log10 (PEV2). In contrast, non-encapsulated phages experienced titer reductions of up to 1.23 log10, especially by jet nebulization. Vibrating mesh nebulization generated slightly larger droplets (∼5.6 µm) but with better phage recovery (> 90 %) and respirable fractions (> 70 %) for both types of phages encapsulated in liposomes. These results demonstrate that the approach of lipid encapsulation effectively protects phages from mechanical damage during nebulization, maintaining bioactivity for aerosol delivery to enhance the success of inhaled phage therapy.

DOI: https://doi.org/10.1016/j.ijpharm.2025.125670
Microbiol Spectr. 2025 May 16. e0284924

In silico and in vitro comparative analysis of 79 Acinetobacter baumannii clinical isolates.

Martina Scarrone, Dann Turner, Moïra Dion, Denise Tremblay, Sylvain Moineau.

  Acinetobacter baumannii is a significant nosocomial bacterial pathogen that poses a substantial infection risk due to its high resistance to antibiotics and ability to survive in hospital environments. In this study, we performed comprehensive in silico and in vitro analyses on 79 A. baumannii clinical isolates from different geographical locations to uncover their genomic and epidemiological characteristics as well as their antibiotic and phage susceptibilities. Our findings revealed considerable genomic diversity among the isolates, as shown by average nucleotide identity (ANI) heat maps, multilocus sequence typing (MLST), and core genome MLST (cgMLST). We identified several international clones known for their high antibiotic resistance and global prevalence. Surprisingly, we also observed that the number of antimicrobial resistance genes (ARGs) was higher in isolates containing CRISPR-Cas systems. Plaque assays with 13 phages indicated that Acinetobacter phages have a narrow host range, with capsule loci (KL) serving as a good indicator of phage-bacteria interactions. The presence of CRISPR-Cas systems and other antiviral defense mechanisms in A. baumannii genomes also appears to play a key role in providing phage resistance, regardless of the phage receptors. We also found that spacers associated with subtypes I-F1 and I-F2 CRISPR-Cas systems predominantly target prophages, suggesting a role in maintaining genomic stability and contributing to phage-bacteria co-evolution. Overall, this study provides a set of highly characterized A. baumannii clinical isolates for future studies on antibiotic-phage-bacteria interactions.IMPORTANCEAcinetobacter baumannii poses a significant challenge to the healthcare system due to its antibiotic resistance and strong survival mechanisms. This study examines a diverse collection of 79 clinical isolates to deepen our understanding of A. baumannii's genetic characteristics and its defense mechanisms against both antibiotics and phages. Genomic analysis revealed globally prevalent, highly resistant clones and uncovered a complex role for CRISPR-Cas systems. Although CRISPR-Cas systems were not widespread among these isolates, they primarily targeted prophages. Additionally, the study emphasizes the importance of capsule types as indicators of phage susceptibility. Together, these findings provide insights into the pathogen's resilience and evolutionary adaptations, potentially guiding future research on infection control strategies and new therapeutic approaches to combat A. baumannii infections.

Keywords:  Acinetobacter baumannii; CRISPR-Cas; antimicrobial resistance (AMR); bacteriophages; capsule loci (KL); multilocus sequence typing (MLST); phages

DOI:  https://doi.org/10.1128/spectrum.02849-24
Phage (New Rochelle). 2025 Mar;6(1): 5-11

taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level.

Andrew Millard, Rémi Denise, Maria Lestido, Moi Taiga Thomas, Deven Webster, Dann Turner, Thomas Sicheritz-Pontén.

   Background: Bacteriophages are classified into genera and species based on genomic similarity, a process regulated by the International Committee on the Taxonomy of Viruses. With the rapid increase in phage genomic data there is a growing need for automated classification systems that can handle large-scale genome analyses and place phages into new or existing genera and species.
Materials and Methods: We developed taxMyPhage, a tool system for the rapid automated classification of dsDNA bacteriophage genomes. The system integrates a MASH database, built from ICTV-classified phage genomes to identify closely related phages, followed by BLASTn to calculate intergenomic similarity, conforming to ICTV guidelines for genus and species classification. taxMyPhage is available as a git repository at https://github.com/amillard/tax_myPHAGE, a conda package, a pip-installable tool, and a web service at https://phagecompass.ku.dk.
Results: taxMyPhage enables rapid classification of bacteriophages to the genus and species level. Benchmarking on 705 genomes pending ICTV classification showed a 96.7% accuracy at the genus level and 97.9% accuracy at the species level. The system also detected inconsistencies in current ICTV classifications, identifying cases where genera did not adhere to ICTV's 70% average nucleotide identity (ANI) threshold for genus classification or 95% ANI for species. The command line version classified 705 genomes within 48 h, demonstrating its scalability for large datasets.
Conclusions: taxMyPhage significantly enhances the speed and accuracy of bacteriophage genome classification at the genus and species levels, making it compatible with current sequencing outputs. The tool facilitates the integration of bacteriophage classification into standard workflows, thereby accelerating research and ensuring consistent taxonomy.

Keywords:  bacteriophage; phages; taxonomy

DOI:  https://doi.org/10.1089/phage.2024.0050
Gut Microbes. 2025 Dec;17(1): 2499575

Virome drift in ulcerative colitis patients: faecal microbiota transplantation results in minimal phage engraftment dominated by microviruses.

Daan Jansen, Sara Deleu, Clara Caenepeel, Tine Marcelis, Ceren Simsek, Gwen Falony, Kathleen Machiels, João Sabino, Jeroen Raes, Séverine Vermeire, Jelle Matthijnssens.

  Ulcerative colitis (UC) is an inflammatory bowel disease characterized by recurrent colonic inflammation. Standard treatments focus on controlling inflammation but remain ineffective for one-third of patients. This underscores the need for alternative approaches, such as fecal microbiota transplantation (FMT), which transfers healthy donor microbiota to patients. The role of viruses in this process, however, remains underexplored. To address this, we analyzed the gut virome using metagenomic sequencing of enriched viral particles from 320 longitudinal fecal samples of 44 patients enrolled in the RESTORE-UC FMT trial. Patients were treated with FMTs from healthy donors (allogenic, treatment) or themselves (autologous, control). We found that colonic inflammation, both its presence and location, had a greater impact on the gut virome than FMT itself. In autologous FMT patients, the virome was unstable and showed rapid divergence over time, a phenomenon we termed virome drift. In allogenic FMT patients, the virome temporarily shifted toward the healthy donor, lasting up to 5 weeks and primarily driven by microviruses. Notably, two distinct virome configurations were identified and linked to either healthy donors or patients. In conclusion, inflammation strongly affects the gut virome in UC patients, which may lead to instability and obstruct the engraftment of allogeneic FMT.

Keywords:  Ulcerative colitis; fecal microbiota transplants; virome; virome community types; virome drift

DOI:  https://doi.org/10.1080/19490976.2025.2499575
Gigascience. 2025 Jan 06. pii: giaf037. [Epub ahead of print]14

HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences.

Abdullatif Al-Najim, Sven Hauns, Van Dinh Tran, Rolf Backofen, Omer S Alkhnbashi.

   BACKGROUND: Bacteriophages are among the most abundant organisms on Earth, significantly impacting ecosystems and human society. The identification of viral sequences, especially novel ones, from mixed metagenomes is a critical first step in analyzing the viral components of host samples. This plays a key role in many downstream tasks. However, this is a challenging task due to their rapid evolution rate. The identification process typically involves two steps: distinguishing viral sequences from the host and identifying if they come from novel viral genomes. Traditional metagenomic techniques that rely on sequence similarity with known entities often fall short, especially when dealing with short or novel genomes. Meanwhile, deep learning has demonstrated its efficacy across various domains, including the bioinformatics field.
RESULTS: We have developed HVSeeker-a host/virus seeker method-based on deep learning to distinguish between bacterial and phage sequences. HVSeeker consists of two separate models: one analyzing DNA sequences and the other focusing on proteins. In addition to the robust architecture of HVSeeker, three distinct preprocessing methods were introduced to enhance the learning process: padding, contigs assembly, and sliding window. This method has shown promising results on sequences with various lengths, ranging from 200 to 1,500 base pairs. Tested on both NCBI and IMGVR databases, HVSeeker outperformed several methods from the literature such as Seeker, Rnn-VirSeeker, DeepVirFinder, and PPR-Meta. Moreover, when compared with other methods on benchmark datasets, HVSeeker has shown better performance, establishing its effectiveness in identifying unknown phage genomes.
CONCLUSIONS: These results demonstrate the exceptional structure of HVSeeker, which encompasses both the preprocessing methods and the model design. The advancements provided by HVSeeker are significant for identifying viral genomes and developing new therapeutic approaches, such as phage therapy. Therefore, HVSeeker serves as an essential tool in prokaryotic and phage taxonomy, offering a crucial first step toward analyzing the host-viral component of samples by identifying the host and viral sequences in mixed metagenomes.

Keywords:  bacteria; deep learning; genomics; metagenomic; phages

DOI:  https://doi.org/10.1093/gigascience/giaf037
Microb Pathog. 2025 May 08. pii: S0882-4010(25)00409-7. [Epub ahead of print]205 107684

Alternative treatment candidates to antibiotic therapy for bovine mastitis in the post-antibiotic era: a comprehensive review.

Sepideh Askari, Abolfazl Rafati Zomorodi, Fatemeh Aflakian.

  Mastitis, an inflammation of mammary tissue frequently associated with infection, is a prevalent disease among dairy animals. Bacterial intra-mammary infection is identified as a primary cause of bovine mastitis (BM). In dairy cattle, antimicrobials are used for mastitis treatment during the lactating phase and for dry cow therapy. Although self-curing can occur, the success of mastitis treatment depends on several factors, including the type of bacteria responsible for the infection, the effectiveness of the administered antibiotics, and the host's overall immune response. Moreover, the growing resistance of microorganisms to antibiotics has restricted the available treatment options for managing intramammary infections. In addition, the utilization of critically essential antimicrobials in animals raised for food production may elevate the risk of human infections that are challenging to treat. Therefore, it is crucial to have alternative treatments with equivalent or superior effectiveness as part of any stewardship program. These may include the application of nanotechnology, stem cell technology, photodynamic and laser radiation or the use of traditional herbal medical plants, nutraceuticals, antibacterial peptides, bacteriocins, antibodies therapy, bacteriophages, phage lysins, and probiotics as alternatives to antibiotics. This review aims to discuss the potential of vaccination as an indirect strategy, along with nanotechnology, probiotics, stem cell therapy, antimicrobial peptides, photodynamic therapy, laser irradiation, and antibody treatments as direct approaches. These approaches are examined as possible alternative therapeutic options to antibiotic treatment for BM.

Keywords:  Alternative treatments; Antibiotic resistance; Bovine mastitis; Vaccination

DOI:  https://doi.org/10.1016/j.micpath.2025.107684
Front Cell Infect Microbiol. 2025 ;15 1556688

Innovative strategies targeting oral microbial dysbiosis: unraveling mechanisms and advancing therapies for periodontitis.

Yang Li, Xinyu He, Guocheng Luo, Juanjuan Zhao, Guohui Bai, Delin Xu.

  Periodontitis, a prevalent inflammatory oral disease, is intricately linked to disruptions in the oral microbiome, a state known as microbial dysbiosis. This review explores the pivotal roles of key pathogens, including Porphyromonas gingivalis and Tannerella forsythia, in driving periodontitis and examines the underlying molecular mechanisms that disrupt microbial homeostasis. We discuss how interactions among bacterial species affect the oral ecosystem's balance and how microbial metabolites influence the host immune responses, contributing to disease progression. Leveraging these insights, we propose cutting-edge therapeutic approaches aimed at restoring microbial equilibrium. These include personalized pharmacological interventions tailored to individual microbiome profiles and innovative microbiome-targeted strategies such as probiotic formulations and bacteriophage therapy. By precisely modulating microbial communities, these strategies hold promise for enhancing treatment efficacy, preventing disease recurrence, and mitigating issues like antimicrobial resistance. Overall, this review paves the way for novel prevention and management techniques in periodontitis, offering significant improvements in oral health outcomes for patients.

Keywords:  mechanistic insights; microbial dysbiosis; oral microbiome; periodontitis; therapeutic strategies inflammatory response

DOI:  https://doi.org/10.3389/fcimb.2025.1556688
Virology. 2025 Apr 29. pii: S0042-6822(25)00172-2. [Epub ahead of print]609 110559

Exploring deep learning in phage discovery and characterization.

Monyque Karoline de Paula Silva, Vitória Yumi Uetuki Nicoleti, Barbara da Paixão Perez Rodrigues, Ademir Sergio Ferreira Araujo, Joel Henrique Ellwanger, James Moraes de Almeida, Leandro Nascimento Lemos.

  Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The discovery of novel bacteriophages using large-scale metagenomic data has been accelerated by the accessibility of deep learning (Artificial Intelligence), the increased computing power of graphical processing units (GPUs), and new bioinformatics tools. This review addresses the recent revolution in bacteriophage research, ranging from the adoption of neural network algorithms applied to metagenomic data to the use of pre-trained language models, such as BERT, which have improved the reconstruction of viral metagenome-assembled genomes (vMAGs). This article also discusses the main aspects of bacteriophage biology using deep learning, highlighting the advances and limitations of this approach. Finally, prospects of deep-learning-based metagenomic algorithms and recommendations for future investigations are described.

Keywords:  DNA sequencing; Deep learning; Machine learning; Viral ecology; bacteriophages

DOI:  https://doi.org/10.1016/j.virol.2025.110559
Sci Total Environ. 2025 May 14. pii: S0048-9697(25)01282-3. [Epub ahead of print]982 179641

Harnessing advances in mechanisms, detection, and strategies to combat antimicrobial resistance.

Ritik Kumar Thakur, Kaushal Aggarwal, Nayan Sood, Aman Kumar, Sachin Joshi, Priya Jindal, Rashmi Maurya, Preeti Patel, Balak Das Kurmi.

  Antimicrobial resistance (AMR) is a growing global health crisis, threatening the effectiveness of antibiotics and other antimicrobial agents, leading to increased morbidity, mortality, and economic burdens. This review article provides a comprehensive analysis of AMR, beginning with a timeline of antibiotics discovery and the year of first observed resistance. Main mechanisms of AMR in bacteria, fungi, viruses, and parasites are summarized, and the main mechanisms of bacteria are given in detail. Additionally, we discussed in detail methods for detecting AMR, including phenotypic, genotypic, and advanced methods, which are crucial for identifying and monitoring AMR. In addressing AMR mitigation, we explore innovative interventions such as CRISPR-Cas systems, nanotechnology, antibody therapy, artificial intelligence (AI), and the One Health approach. Moreover, we discussed both finished and ongoing clinical trials for AMR. This review emphasizes the urgent need for global action and highlights promising technologies that could shape the future of AMR surveillance and treatment. By integrating interdisciplinary research and emerging clinical insights, this study aims to guide individuals toward impactful solutions in the battle against AMR.

Keywords:  AMR mitigation; Alternative therapies; Antimicrobial resistance (AMR); Global health; Resistance timeline

DOI:  https://doi.org/10.1016/j.scitotenv.2025.179641
ACS Infect Dis. 2025 May 11.

Validation of a Cystic Fibrosis Co-Culture Model for the Identification of Dual Acting Compounds with Antibiotic and Antibiotic Adjuvant Properties.

Anne E Mattingly, Haoting Li, Roberta J Melander, Christian Melander.

  Infections in the lungs of cystic fibrosis (CF) patients are often polymicrobial in nature, typically comprising Pseudomonas aeruginosa and Staphylococcus aureus. Compounds that act as an antimicrobial agent against one of these pathogens, and as an antibiotic adjuvant against the other, could provide a valuable approach to treating such infections, however a model that mimics the unique environment found with the CF lung is required for the identification and characterization of such molecules. To address this, we employed a S. aureus/P. aeruginosa coculture screening model in synthetic sputum, and identified compounds from our in-house library that simultaneously have potent anti-S. aureus activity, and potentiate colistin against colistin-resistant P. aeruginosa. The two lead compounds, 12F1 and 12G9, control growth of both species when dosed alongside sub-inhibitory concentrations of colistin, highlighting the potential of using a single molecule as both an antibiotic and antibiotic adjuvant to target multiple species in polymicrobial infections, as well as the importance of conducting activity screens in clinically relevant media.

Keywords:  Pseudomonas aeruginosa; Staphylococcus aureus; adjuvant; antibiotic; co-culture; cystic fibrosis

DOI:  https://doi.org/10.1021/acsinfecdis.5c00226