Related papers: PhageMind: Generalized Strain-level Phage Host Ran…

Motivation: Bacteriophages are viruses infecting bacteria. Being key players in microbial communities, they can regulate the composition/function of microbiome by infecting their bacterial hosts and mediating gene transfer. Recently,…

Phage therapy is an alternative treatment method for bacterial infections. It has shown particular promise in reducing bacterial load while preventing antibiotic resistance. Here, we develop a mathematical model of a bacterial infection…

Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new…

Bacteriophages (or phages), which infect bacteria, have two distinct lifestyles: virulent and temperate. Predicting the lifestyle of phages helps decipher their interactions with their bacterial hosts, aiding phages' applications in fields…

Bacteriophages, often referred to as the dark matter of the biosphere, play a critical role in regulating microbial ecosystems and in antibiotic alternatives. Thus, accurate interpretation of their genomes holds significant scientific and…

Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might…

Bacteriophages are viruses infecting bacteria and archaea. Many phage species cause infections which lead to the certain death of the infected prokaryotic host cell and the release of a large batch of phage progeny, yet they have been able…

Phages use bacterial host resources to replicate, intrinsically linking phage and host survival. To understand phage dynamics, it is essential to understand phage-host ecology. A key step in this ecology is infection of bacterial hosts.…

Motivation: There is accumulating evidence showing the important roles of bacteriophages (phages) in regulating the structure and functions of the microbiome. However, lacking an easy-to-use and integrated phage analysis software hampers…

As antibiotic resistance continues to pose a significant threat to public health, alternative treatments are urgently needed. Phage therapy, which utilizes bacteriophages to specifically target bacterial pathogens, has emerged as a…

Bacteriophages are central to microbial ecosystems for balancing bacterial populations and promoting evolution by applying strong selection pressure. Here we review some of the known aspects that modulate phage-bacteria interaction in a way…

Sequence differences between the strains of bacteria comprising host-associated and environmental microbiota may play a role in community assembly and influence the resilience of microbial communities to disturbances. Tools for…

Bacteria and their viruses ("bacteriophages") coexist in natural environments forming complex infection networks. Recent empirical findings suggest that phage-bacteria infection networks often possess a nested structure such that there is a…

Bacteria pose unique challenges for genome-wide association studies (GWAS) because of strong structuring into distinct strains and substantial linkage disequilibrium across the genome. While methods developed for human studies can correct…

Phages are one of the most present groups of organisms in the biosphere. Their identification continues and their taxonomies are divergent. However, due to their evolution mode and the complexity of their species ecosystem, their…

A fundamental challenge in microbial ecology is determining whether bacteria compete or cooperate in different environmental conditions. With recent advances in genome-scale metabolic models, we are now capable of simulating interactions…

The relationship between the design and functionality of molecular networks is now a key issue in biology. Comparison of regulatory networks performing similar tasks can give insights into how network architecture is constrained by the…

Background: Phage therapy shows promise for treating antibiotic-resistant Klebsiella infections. Identifying phage depolymerases that target Klebsiella capsular polysaccharides is crucial, as these capsules contribute to biofilm formation…

Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely…

When planktonic bacteria adhere together to a surface, they begin to form biofilms, or communities of bacteria. Biofilm formation in a host can be extremely problematic if left untreated, especially since antibiotics can be ineffective in…