iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

S Roux, AP Camargo, FH Coutinho, SM Dabdoub… - PLoS …, 2023 - journals.plos.org
The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied
through metagenomics. While metagenomes enable high-throughput exploration of the viral …

DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models

R Concha-Eloko, M Stock, B De Baets… - PLOS Computational …, 2024 - journals.plos.org
Bacteriophages (phages) are viruses that infect bacteria. Many of them produce specific
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 …

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 …

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 …

Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants

Y Yang, K Dufault-Thompson, W Yan, T Cai, L Xie… - …, 2024 - academic.oup.com
Background Phage therapy, reemerging as a promising approach to counter antimicrobial-
resistant infections, relies on a comprehensive understanding of the specificity of individual …

Protein embeddings improve phage-host interaction prediction

MEM Gonzales, JC Ureta, AMS Shrestha - PloS One, 2023 - journals.plos.org
With the growing interest in using phages to combat antimicrobial resistance, computational
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 …

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 …