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 …

[HTML][HTML] Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence

X Liu, Y Liu, J Liu, H Zhang, C Shan… - Neural Regeneration …, 2024 - journals.lww.com
A growing body of evidence suggests that the gut microbiota contributes to the development
of neurodegenerative diseases via the microbiota-gut-brain axis. As a contributing factor …

Digital phagograms: predicting phage infectivity through a multilayer machine learning approach

C Lood, D Boeckaerts, M Stock, B De Baets… - Current Opinion in …, 2022 - Elsevier
Machine learning has been broadly implemented to investigate biological systems. In this
regard, the field of phage biology has embraced machine learning to elucidate and predict …

A systematic analysis of marine lysogens and proviruses

Y Yi, S Liu, Y Hao, Q Sun, X Lei, Y Wang… - Nature …, 2023 - nature.com
Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we
systematically analyze existing genomic sequences of marine prokaryotes to compile a …

Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles

J Lopez-Simon, M Vila-Nistal, A Rosenova… - Nature …, 2023 - nature.com
Viruses play an important role in the marine ecosystem. However, our comprehension of
viruses inhabiting the dark ocean, and in particular, under the Antarctic Ice Shelves, remains …

Genetic determinants of host tropism in Klebsiella phages

B Beamud, N García-González, M Gómez-Ortega… - Cell reports, 2023 - cell.com
Bacteriophages play key roles in bacterial ecology and evolution and are potential
antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we …

Bacteriophages: Vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems?

X Shuai, Z Zhou, X Ba, Y Lin, Z Lin, Z Liu, X Yu, J Zhou… - Water Research, 2024 - Elsevier
Antimicrobial resistance poses a serious threat to human health and is responsible for the
death of millions of people annually. Hospital wastewater is an important hotspot for …

Phage therapy for crops: concepts, experimental and bioinformatics approaches to direct its application

JL Villalpando-Aguilar, G Matos-Pech… - International journal of …, 2022 - mdpi.com
Phage therapy consists of applying bacteriophages, whose natural function is to kill specific
bacteria. Bacteriophages are safe, evolve together with their host, and are environmentally …

Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

Y Peng, Z Lu, D Pan, LD Shi, Z Zhao, Q Liu… - The ISME …, 2023 - academic.oup.com
Deep sea cold seep sediments have been discovered to harbor novel, abundant, and
diverse bacterial and archaeal viruses. However, little is known about viral genetic features …

Knowing and naming: phage annotation and nomenclature for phage therapy

SR Grigson, SK Giles, RA Edwards… - Clinical Infectious …, 2023 - academic.oup.com
Bacteriophages, or phages, are viruses that infect bacteria shaping microbial communities
and ecosystems. They have gained attention as potential agents against antibiotic …