iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria
The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied
through metagenomics. While metagenomes enable high-throughput exploration of the viral …
through metagenomics. While metagenomes enable high-throughput exploration of the viral …
DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models
Bacteriophages (phages) are viruses that infect bacteria. Many of them produce specific
enzymes called depolymerases to break down external polysaccharide structures. Accurate …
enzymes called depolymerases to break down external polysaccharide structures. Accurate …
Tailless and filamentous prophages are predominant in marine Vibrio
K Steensen, J Séneca, N Bartlau, XA Yu… - The ISME …, 2024 - academic.oup.com
Although tailed bacteriophages (phages) of the class Caudoviricetes are thought to
constitute the most abundant and ecologically relevant group of phages that can integrate …
constitute the most abundant and ecologically relevant group of phages that can integrate …
Coordinated transcriptional response to environmental stress by a Synechococcus virus
B Rihtman, A Torcello-Requena, A Mikhaylina… - The ISME …, 2024 - academic.oup.com
Viruses are a major control on populations of microbes. Often, their virulence is examined in
controlled laboratory conditions. Yet, in nature, environmental conditions lead to changes in …
controlled laboratory conditions. Yet, in nature, environmental conditions lead to changes in …
Metagenomic time series reveals a Western English Channel viral community dominated by members with strong seasonal signals
LM Bolaños, M Michelsen, B Temperton - The ISME Journal, 2024 - academic.oup.com
Marine viruses are key players of ocean biogeochemistry, profoundly influencing microbial
community ecology and evolution. Despite their importance, few studies have explored …
community ecology and evolution. Despite their importance, few studies have explored …
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants
Background Phage therapy, reemerging as a promising approach to counter antimicrobial-
resistant infections, relies on a comprehensive understanding of the specificity of individual …
resistant infections, relies on a comprehensive understanding of the specificity of individual …
Protein embeddings improve phage-host interaction prediction
With the growing interest in using phages to combat antimicrobial resistance, computational
methods for predicting phage-host interactions have been explored to help shortlist …
methods for predicting phage-host interactions have been explored to help shortlist …
Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago
L Nishimura, A Tanino, M Ajimoto, T Katsumura… - Plos one, 2024 - journals.plos.org
Coprolites contain various kinds of ancient DNAs derived from gut micro-organisms, viruses,
and foods, which can help to determine the gut environment of ancient peoples. Their …
and foods, which can help to determine the gut environment of ancient peoples. Their …
Lytic bacteriophage vB_KmiS-Kmi2C disrupts biofilms formed by members of the Klebsiella oxytoca complex, and represents a novel virus family and genus
F Newberry, P Shibu, T Smith-Zaitlik… - Journal of Applied …, 2023 - academic.oup.com
Aims This study aimed to characterize the lytic phage vB_KmiS-Kmi2C, isolated from
sewage water on a GES-positive strain of Klebsiella michiganensis. Methods and Results …
sewage water on a GES-positive strain of Klebsiella michiganensis. Methods and Results …