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The gastrointestinal microbiome influences physiological functions and is altered in a variety of diseases. The causality of "dysbiosis" in the pathogenesis is not always proven; association studies are often involved. Patients with IBD, bacteria, fungi, bacteriophages, and archaea show disease-typical patterns associated with metabolome disturbances.
View Article and Find Full Text PDFExploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism.
mSystems
January 2025
Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.
Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference data sets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline optimized for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%.
View Article and Find Full Text PDFsuperinfection drives Pf phage transmission within airway infections in patients with cystic fibrosis.
bioRxiv
January 2025
Center for Excellence in Pulmonary Biology, Division of Pulmonary Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA.
Pf bacteriophages, lysogenic viruses that infect , are implicated in the pathogenesis of chronic infections; phage-infected (Pf+) strains are known to predominate in people with cystic fibrosis (pwCF) who are older and have more severe disease. However, the transmission patterns of Pf underlying the progressive dominance of Pf+ strains are unclear. In particular, it is unknown whether phage transmission commonly occurs horizontally between bacteria within the airway via viral particles or if Pf+ bacteria are mostly acquired via new infections.
View Article and Find Full Text PDFPhage vB_KlebPS_265 Active Against Resistant/MDR and Hypermucoid K2 Strains of .
Viruses
January 2025
Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.
is an important opportunistic pathogen often resistant to antibiotics. Specific phages can be useful in eliminating infection caused by . phage vB_KlebPS_265 (KlebP_265) and its host strain were isolated from the sputum of a patient with infection.
View Article and Find Full Text PDFActivation and modulation of the host response to DNA damage by an integrative and conjugative element.
J Bacteriol
January 2025
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Mobile genetic elements help drive horizontal gene transfer and bacterial evolution. Conjugative elements and temperate bacteriophages can be stably maintained in host cells. They can alter host physiology and regulatory responses and typically carry genes that are beneficial to their hosts.
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