The never-ending battle between lactic acid bacteria and their phages

C Philippe, JK Cornuault, AG de Melo… - FEMS Microbiology …, 2023 - academic.oup.com
Over the past few decades, the interest in lactic acid bacteria (LAB) has been steadily
growing. This is mainly due to their industrial use, their health benefits as probiotic bacteria …

Knowing and naming: phage annotation and nomenclature for phage therapy

SR Grigson, SK Giles, RA Edwards… - Clinical Infectious …, 2023 - academic.oup.com
Bacteriophages, or phages, are viruses that infect bacteria shaping microbial communities
and ecosystems. They have gained attention as potential agents against antibiotic …

Correcting modification-mediated errors in nanopore sequencing by nucleotide demodification and reference-based correction

CS Chiou, BH Chen, YW Wang, NT Kuo… - Communications …, 2023 - nature.com
Abstract The accuracy of Oxford Nanopore Technology (ONT) sequencing has significantly
improved thanks to new flowcells, sequencing kits, and basecalling algorithms. However …

A novel Queuovirinae lineage of Pseudomonas aeruginosa phages encode dPreQ0 DNA modifications with a single GA motif that provide restriction and CRISPR Cas9 …

NS Olsen, TK Nielsen, L Cui, P Dedon… - Nucleic Acids …, 2023 - academic.oup.com
Deazaguanine DNA modifications are widespread in phages, particularly in those with
pathogenic hosts. Pseudomonas phage iggy substitutes∼ 16.5% of its genomic 2 …

[HTML][HTML] Exploring the transcriptional landscape of phage–host interactions using novel high-throughput approaches

L Putzeys, L Wicke, A Brandão, M Boon… - Current Opinion in …, 2024 - Elsevier
In the last decade, powerful high-throughput sequencing approaches have emerged to
analyse microbial transcriptomes at a global scale. However, to date, applications of these …

Bacteriophages and their unique components provide limitless resources for exploitation

CM Szymanski - Frontiers in Microbiology, 2024 - frontiersin.org
Since the original discovery of bacteriophages by William Twort in 1915, and Félix d'Hérelle
in 1917, there have been numerous reports describing the use of these “filterable viruses” in …

Sensing of DNA modifications by pAgo proteins in vitro

M Beskrovnaia, A Agapov, K Makasheva, DO Zharkov… - Biochimie, 2024 - Elsevier
Many prokaryotic Argonaute (pAgo) proteins act as programmable nucleases that use small
guide DNAs for recognition and cleavage of complementary target DNA. Recent studies …

Bacmethy: A novel and convenient tool for investigating bacterial DNA methylation pattern and their transcriptional regulation effects

JH Liu, Y Zhang, N Zhou, J He, J Xu, Z Cai, L Yang… - iMeta, 2024 - Wiley Online Library
DNA methylation serves as the primary mode of epigenetic regulation in prokaryotes,
particularly through transcriptional regulation. With the rapid implementation of third …

Discovery of a pentose as a cytosine nucleobase modification in Shewanella phage Thanatos-1 genomic DNA mediating enhanced resistance towards host …

D Brandt, AK Dorrich, M Persicke, T Leonhard, M Haak… - bioRxiv, 2024 - biorxiv.org
Co-evolution of bacterial defense systems and phage counter defense mechanisms has
resulted in an intricate biological interplay between bacteriophages and their prey. To evade …

A stargate mechanism of Microviridae genome delivery unveiled by cryogenic electron tomography

P Bardy, CIW MacDonald, PC Kirchberger, HT Jenkins… - bioRxiv, 2024 - biorxiv.org
Single-stranded DNA bacteriophages of the Microviridae family are major components of the
global virosphere. Microviruses are highly abundant in aquatic ecosystems and are …