Prophage Hunter: an integrative hunting tool for active prophages
Identifying active prophages is critical for studying coevolution of phage and bacteria,
investigating phage physiology and biochemistry, and engineering designer phages for …
investigating phage physiology and biochemistry, and engineering designer phages for …
vRhyme enables binning of viral genomes from metagenomes
Genome binning has been essential for characterization of bacteria, archaea, and even
eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed …
eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed …
Reversible conjugation of a CBASS nucleotide cyclase regulates bacterial immune response to phage infection
Prokaryotic antiviral defence systems are frequently toxic for host cells and stringent
regulation is required to ensure survival and fitness. These systems must be readily …
regulation is required to ensure survival and fitness. These systems must be readily …
Classifying the unclassified: a phage classification method
CM Chibani, A Farr, S Klama, S Dietrich, H Liesegang - Viruses, 2019 - mdpi.com
This work reports the method ClassiPhage to classify phage genomes using sequence
derived taxonomic features. ClassiPhage uses a set of phage specific Hidden Markov …
derived taxonomic features. ClassiPhage uses a set of phage specific Hidden Markov …
Deciphering active prophages from metagenomes
K Kieft, K Anantharaman - Msystems, 2022 - Am Soc Microbiol
Temperate phages (prophages) are ubiquitous in nature and persist as dormant
components of host cells (lysogenic stage) before activating and lysing the host (lytic stage) …
components of host cells (lysogenic stage) before activating and lysing the host (lytic stage) …
High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains
Background Temperate phages influence the density, diversity and function of bacterial
populations. Historically, they have been described as carriers of toxins. More recently, they …
populations. Historically, they have been described as carriers of toxins. More recently, they …
Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment
K Tang, W Wang, Y Sun, Y Zhou, P Wang… - Nucleic Acids …, 2021 - academic.oup.com
The life cycle of temperate phages includes a lysogenic cycle stage when the phage
integrates into the host genome and becomes a prophage. However, the identification of …
integrates into the host genome and becomes a prophage. However, the identification of …
Putative plasmid prophages of Bacillus cereus sensu lato may hold the key to undiscovered phage diversity
EG Piligrimova, OA Kazantseva, AN Kazantsev… - Scientific reports, 2021 - nature.com
Bacteriophages are bacterial viruses and the most abundant biological entities on Earth.
Temperate bacteriophages can form prophages stably maintained in the host population …
Temperate bacteriophages can form prophages stably maintained in the host population …
Genomic insights into methicillin-resistant Staphylococcus pseudintermedius isolates from dogs and humans of the same sequence types reveals diversity in …
N Phumthanakorn, S Schwendener, V Donà… - PLoS …, 2021 - journals.plos.org
Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an important opportunistic
pathogenic bacterium of dogs that also occasionally colonize and infect humans. However …
pathogenic bacterium of dogs that also occasionally colonize and infect humans. However …
Down in the pond: Isolation and characterization of a new Serratia marcescens strain (LVF3) from the surface water near frog's lettuce (Groenlandia densa)
I Friedrich, B Bodenberger, H Neubauer, R Hertel… - PLoS …, 2021 - journals.plos.org
Serratia marcescens is a species that belongs to the family of Yersiniaceae. This family
comprises taxa representing opportunistic human-and phytopathogens but also plant growth …
comprises taxa representing opportunistic human-and phytopathogens but also plant growth …