bims-fagtap 2025-07-20 papers

Issue of 2025–07–20
four papers selected by
Luca Bolliger, lxBio

Comput Struct Biotechnol J. 2025 ;27 2924-2932

Bacteriophage-based strategies for biocontrol and treatment of infectious diseases.

Trinh Thi Trang Nhung, Swati Verma, Saravanaraman Ponne, Gautam Kumar Meghwanshi, Thomas Schön, Rajender Kumar.

Bacteriophages are viruses that infect bacteria, which are essential for controlling bacterial diversity. Among the novel aspects, phage display-based strategies are used for epitope mapping and the development of immunotherapy. A recent classification system has been developed based on the recent sequencing methods and bioinformatic tools. The unique specificity of phages is of increasing use in biocontrol, where bacteriophages are applied to target and reduce harmful bacterial populations in agriculture, food preservation and safety, offering a sustainable alternative to chemical exposure and a plausible solution to excessive misuse of antibiotics. Phage therapy has emerged as a complement to antibiotics for difficult-to-treat infectious diseases such as multi-drug resistant bacteria where other alternatives are lacking. The ability of bacteriophages to specifically target pathogenic bacteria while sparing the normal flora makes them attractive treatment options. Among the challenges are the slow uptake of phage therapy in the clinical setting, a lack of standardisation and regulatory issues. Nevertheless, phage-based strategies are likely to become a future cornerstone for biocontrol and treatment of infectious diseases.

Keywords: Antimicrobial resistance; Bacteriophage; Biocontrol; Phage therapy and antibiotic

DOI: https://doi.org/10.1016/j.csbj.2025.06.046

Microbiol Res. 2025 Jul 11. pii: S0944-5013(25)00237-X. [Epub ahead of print]300 128278

Phage engineering strategies to expand host range for controlling antibiotic-resistant pathogens.

Song Zhang, Jin-Chul Kim, Juhee Ahn.

Bacteriophages are known as a promising alternative to control rising bacterial resistance. The adsorption phase is critical for the successful infection of phages, as it determines their ability to recognize and attach to specific bacterial host cells. However, their limited host ranges due to narrow host specificity significantly limit their potential applications and overall effectiveness. Receptor-binding proteins (RBPs) are crucial in the recognition process, and modifying these proteins provides a valuable opportunity to broaden host ranges and enhance adsorption rates. Therefore, gaining a more comprehensive understanding of the interactions between phages and their bacterial hosts is essential. To overcome this challenge, various in vivo and in vitro engineering platforms have been developed, including recombineering, clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) systems, yeast-based technologies, and cell-free systems. These methods provide diverse strategies and flexibility for constructing customized phage genomes with desired characteristics, ultimately enhancing phage application efficiency. This review discusses different types of RBPs in phages and their mechanisms of adsorption, highlighting their relevance for adaptable engineering strategies. We also summarize various phage engineering platforms and explore the design of synthetic phages with expanded host ranges. Finally, we highlight the advantages and limitations of current engineering methods, providing insights to guide future research efforts.

Keywords: CRISPR-Cas system; Homologous recombination; Host range; Phage engineering; Phage reboot; Receptor binding protein

DOI: https://doi.org/10.1016/j.micres.2025.128278

Microlife. 2025 ;6 uqaf014

"French Phage Network" annual conference: ninth meeting report.

Fernando Clavijo-Coppens, Deborah M Crepin, Héloïse Croizet, Arthur Planche, Lucile Plumet, Judith Sar, Kandas Traore.

This meeting report summarizes the scientific activities of the ninth annual conference of Phages.fr, organized by the French Phages network. This year, the conference took place from 12 to 14 November 2024, in Sète, in the south of France. The conference hosted 136 participants from both the public and private sectors, representing 63 French groups and 16 international ones from Austria, Belgium, Finland, Germany, Guinea, Sweden, the UK, and the USA. The meeting brought together both young and senior scientists, offering them the opportunity to share their findings and ideas across four main topics: Ecology and Evolution, Phage-Host Interaction, Structure and Assembly, and Applications in Therapy and Biotechnology. For the first time, Phages.fr also offered a special session dedicated to the social and human sciences applied to microbiology. Over the 3 days, a total of 62 presentations were given (20 oral presentations and 42 posters), and five invited speakers delivered exceptional lectures introducing each session. The ninth annual symposium concluded with a public lecture titled "Viruses of Bacteria: New Allies in Human and Agricultural Health." The lecture aimed to raise public awareness about the therapeutic potential of phages in combating harmful bacteria that affect human and plant health, as well as their role in food safety.

Keywords: applications in therapy and biotechnologies; bacteriophage; phage ecology and evolution; phage–host interaction; social and human sciences; structure and assembly

DOI: https://doi.org/10.1093/femsml/uqaf014

J Dent. 2025 Jul 09. pii: S0300-5712(25)00404-X. [Epub ahead of print]161 105960

Bacteriophages for periodontal pathogens control: A systematic review.

Felipe Gomes Dallepiane, Malena Alejandro Coimbra Nogueira, Lucas Menezes Dos Anjos, Gilberto De Souza Melo, Bruno Henriques, Gislaine Fongaro, Ariadne Cristiane Cabral Cruz.

OBJECTIVES: Faced with the growing challenge of bacterial resistance to antibiotics, bacteriophages emerge as a promising alternative due to their specificity and ability to lyse specific bacteria. This systematic review aims to analyze the efficacy of bacteriophage therapy in controlling the growth of periodontal pathogen.
DATA SOURCES: The protocol was registered in PROSPERO (CRD42023479696). The review followed PRISMA guidelines, utilizing a PICOS framework. Studies were identified through searches in seven databases (Embase, LILACS, PubMed, SCOPUS, Web of Science, Google Scholar and ProQuest) up to November 2024.
STUDY SELECTION: In vitro studies were evaluating the use of bacteriophages for this purpose were considered eligible. References were selected through a two-phase process. RoBDEMAT was used to assess the risk of bias. The certainty of the cumulative evidence was evaluated using the GRADE criteria.
RESULTS: Eight studies were included, all demonstrating bacteriophages are effective in controlling periodontopathogenic bacteria growth. Four periodontal pathogen bacteria were analyzed, including Aggregatibacter actinomycetemcomitans (n = 3), Fusobacterium nucleatum (n = 3), Streptococcus gordonii (n = 2), and Porphyromonas gingivalis (n = 1). Eleven different types of bacteriophages were described, including: S1249 (n = 2), ΦSG005 (n = 2), JD-Fnp1 (n = 1), d-Fnp2 (n = 1), JD-Fnp3 (n = 1), JD-Fnp4 (n = 1), JD-Fnp5 (n = 1), FNU1 (n = 1), Aabφ01 (n = 1), Aabφ01-1 (n = 1), and Fnp02 (n = 1). The predominant method for evaluating bacterial growth was optical density measurement (n = 7) colony-forming unit (CFU) (n = 3).
CONCLUSION: Bacteriophage therapy effectively controls periodontal pathogenic bacteria in vitro, offering a possibility promising strategy for treating periodontitis, especially in antimicrobial-resistant cases. However, further research is needed to validate these findings in more complex models, such as multispecies biofilms and clinical settings.
CLINICAL SIGNIFICANCE: This study underscores the potential of bacteriophages as an innovative and targeted alternative for managing periodontal disease.

Keywords: Bacteria; Bacteriophage; Biofilm; Periodontal disease; Systematic review

DOI: https://doi.org/10.1016/j.jdent.2025.105960