Prophages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of , a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Genome Project (GP) dataset comprises 1011 complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the prophage genomic content in the GP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29.5% (298) of the GP genomes contain prophages, of which only 32.2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in . We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages.
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http://dx.doi.org/10.1080/19490976.2024.2379440 | DOI Listing |
Extremophiles
December 2024
Laboratório de Ecologia E Biotecnologia Microbiana, Instituto de Microbiologia Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal Do Rio de Janeiro (UFRJ), Bloco I, Rio de Janeiro (RJ), Brazil.
Since prophages can play a multifaceted role in bacterial evolution, this study aims to characterize the virome of Rummeliibacillus stabekisii, a bacterium isolated from different environments, including Antarctic soil and NASA spacecraft floors. From the analyses, it was found that the Antarctic strain, PP9, had the largest number of prophages, including intact ones, indicating potential benefits for survival in adverse conditions. In contrast, other strains harbored predominantly degenerate prophages, suggesting a dynamic process of gene gain and loss during evolution.
View Article and Find Full Text PDFMicrobiol Resour Announc
December 2024
Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa, Israel.
Leptolyngbya phage Dor1 was induced by mitomycin C from a fishpond and was isolated on IU 594. The 41,522-bp genome of Leptolyngbya phage Dor1 has 93.77% intergenomic similarity with Leptolyngbya phage LPP-1; however, unlike LPP-1, Dor1 carries an HNH endonuclease in its DNA polymerase gene.
View Article and Find Full Text PDFAntimicrob Agents Chemother
December 2024
Department of Pathology, University of California, San Diego, California, USA.
Bacteriophages are an increasingly attractive option for the treatment of antibiotic-resistant infections, but their efficacy is difficult to discern due to the confounding effects of antibiotics. Phages are generally delivered in conjunction with antibiotics, and thus, when patients improve, it is unclear whether the phages, antibiotics, or both are responsible. This question is particularly relevant for enterococcus infections, as limited data suggest phages might restore antibiotic efficacy against resistant strains.
View Article and Find Full Text PDFBMC Microbiol
December 2024
College of Agriculture and Forestry, Linyi University, Linyi, Shandong, 276005, China.
Multidrug-resistant (MDR) Acinetobacter baumannii (A. baumannii) is currently recognized not only as a significant nosocomial pathogen but also is an emerging bacterial infection in food-producing animals, posing a critical threat to global health. However, this is a hindrance to detailed bioinformatic studies of MDR A.
View Article and Find Full Text PDFEvol Appl
December 2024
CIRAD UMR PVBMT Saint Pierre France.
In an era of trade globalization and climate change, crop pathogens and pests are a genuine threat to food security. The detailed characterization of emerging pathogen populations is a prerequisite for managing invasive species pathways and designing sustainable disease control strategies. Huanglongbing is the disease that causes the most damage to citrus, a crop that ranks #1 worldwide in terms of fruit production.
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