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Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order and the families , and . Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy.
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http://dx.doi.org/10.3390/v13030506 | DOI Listing |
Biotechnol Lett
September 2025
Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
Phage contamination poses a significant threat to industrial fermentation, leading to substantial economic losses. Virulent T-even type phages (T2/T4/T6) represent particularly concerning biological hazards in fermentation systems. This paper developed a novel CRISPR/Cas12a-based system integrated with recombinase polymerase amplification (RPA), enabling ultrasensitive identification of T-even type phages.
View Article and Find Full Text PDFPhilos Trans R Soc Lond B Biol Sci
September 2025
Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Baden-Württemberg, Germany.
Phages infect bacteria and have recently re-emerged as a promising strategy to combat bacterial infections. However, there is a lack of methods to predict whether and why a particular phage can or cannot infect a bacterial strain based on their genome sequences. Understanding the complex interactions between phages and their bacterial hosts is thus of considerable interest.
View Article and Find Full Text PDFBrief Bioinform
August 2025
Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland.
The increasing interest in finding new viruses within (meta)genomic datasets has fueled the development of computational tools for virus detection and characterization from environmental samples. One key driver is phage therapy, the treatment of drug-resistant bacteria with tailored bacteriophage cocktails. Yet, keeping up with the growing number of automated virus detection and analysis tools has become increasingly difficult.
View Article and Find Full Text PDFFood Microbiol
January 2026
Food Microbiology Key Laboratory of Sichuan Province, School of Food Science and Bioengineering, Xihua University, Chengdu, 610039, China. Electronic address:
Fermented vegetables are widely favored by consumers for their distinctive flavors and nutritional value, with their quality attributes being closely associated with microbiome dynamics. Recent advances in high-throughput sequencing technologies have revealed abundant bacteriophage resources within the fermented vegetable microbiome. These viral components significantly influence fermentation processes and product characteristics by modulating microbial community structure and function.
View Article and Find Full Text PDFMicrobiome
August 2025
School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong SAR, China.
Background: There is a diverse assemblage of microbes in air in built environments (BEs), but our understanding of viruses and their interactions with hosts in BEs remains incomplete. To address this knowledge gap, this study analyzed 503 metagenomes isolated from air samples from public transit systems in six global cities, namely Denver, Hong Kong, London, New York City, Oslo, and Stockholm. Viral genomes were recovered from samples via metagenomic binning, and viruses' taxonomy, functional potential, and microbial hosts were determined.
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